Table of Contents

CHAPTER 1 - INTRODUCTION .............................................................................. 22

1.1
What's in the Fledermaus Package? ................................................................. 23
1.2
How to Use the Fledermaus Package ................................................................ 25
1.3
Fledermaus Manual Conventions ...................................................................... 25
1.4
Fledermaus Software Conventions .................................................................... 26
1.4.1 Text or Entry Fields .......................................................................................... 26
1.4.2 File Selection Widget ........................................................................................ 27
1.4.3 Ranged Slider Controls ..................................................................................... 27
CHAPTER 2 - FLEDERMAUS .................................................................................. 28
2.1
Introduction ......................................................................................................... 28
2.1.1 Starting Fledermaus .......................................................................................... 29
2.1.2 Command Line Options .................................................................................... 29
2.1.3 Object Oriented Visualization........................................................................... 30
2.1.4 Multistage Interruptible Rendering ................................................................... 30
2.1.5 ShiftScapeTM Rendering Engine ....................................................................... 31
2.1.6 Fledermaus User Interface ................................................................................ 31
2.2
Main Visualization Window............................................................................... 32
2.2.1 Data Exploration Modes ................................................................................... 32
2.2.2 Profiling ............................................................................................................ 37
2.3
Geo-Referencing Info Bar .................................................................................. 38
2.4
Time Bar .............................................................................................................. 38
2.4.1 Time Display and Manipulation Area............................................................... 39
2.4.2 Time Control Area ............................................................................................ 39
2.4.3 Time Options .................................................................................................... 40
2.5
Control Panel ....................................................................................................... 41
2.5.1 Using Polygon Select Mode.............................................................................. 43
2.6
Main Menu Bar ................................................................................................... 44
2.6.1 File Menu .......................................................................................................... 44
2.6.2 Exploration Menu ............................................................................................. 50
2.6.3 Controls Menu .................................................................................................. 52
2.6.4 Rendering Menu................................................................................................ 54
2.6.5 Import Menu ..................................................................................................... 56
2.6.6 Import Gridded Data ......................................................................................... 56
2.6.7 Import Ungridded Data ..................................................................................... 56
2.6.8 Import Image ..................................................................................................... 56
2.6.9 Import Vertical Image ....................................................................................... 56
2.6.10 Import Lines ................................................................................................... 57
2.6.11 Import Points .................................................................................................. 57
2.6.12 Import PFM .................................................................................................... 61
2.6.13 Import DXF/DWG ......................................................................................... 61
2.6.14 Import ArcGIS Shape ..................................................................................... 61
2.6.15 Import Model.................................................................................................. 62

2.6.16 Import S-57 ENC ........................................................................................... 62

2.6.17 Create Menu ................................................................................................... 62
2.7
Tools Menu .......................................................................................................... 64
2.7.1 Contouring ........................................................................................................ 64
2.8
Data Object Control Region .............................................................................. 73
2.8.1 Geo-Picking ...................................................................................................... 73
2.9
Data Object List .................................................................................................. 75
CHAPTER 3 - 3DEDITOR ......................................................................................... 78
3.1
Introduction to the 3DEditor ............................................................................. 78
3.1.1 Starting the 3DEditor ........................................................................................ 79
3.1.2 3DEditor Interface ............................................................................................ 79
3.2
Main Visualization Window............................................................................... 80
3.3
Control Bar .......................................................................................................... 84
3.4
Right-Click Menu................................................................................................ 87
3.4.1 Selection Menu ................................................................................................. 87
3.4.2 Edit Menu.......................................................................................................... 88
3.4.3 Hide Menu ........................................................................................................ 89
3.4.4 OmniViewer ...................................................................................................... 89
3.5
Menus ................................................................................................................... 89
3.5.1 File Menu .......................................................................................................... 89
3.5.2 Display Menu .................................................................................................... 90
3.6
Slices Menu .......................................................................................................... 91
3.6.1 Options Menu.................................................................................................... 92
3.7
Editor Panels ....................................................................................................... 93
3.7.1 Attributes Panel ................................................................................................. 93
3.7.2 Soundings Panel ................................................................................................ 94
3.7.3 Surface Panel .................................................................................................... 96
3.7.4 Utilities Panel .................................................................................................... 97
3.8
Slice-Based Editing ............................................................................................. 98
3.9
Hotkeys................................................................................................................. 99
3.10 Customizing the 3D Editor............................................................................... 101
3.11 Editing Targets in the 3D Editor ..................................................................... 101
3.12 Format Specific Operations ............................................................................. 103
3.12.1 SHOALS Hydro/HOF .................................................................................. 103
3.13 Connectors ......................................................................................................... 104
3.14 Second Depths ................................................................................................... 105
3.15 Audit File ........................................................................................................... 105
3.16 Editing CUBE Hypotheses ............................................................................... 107
3.16.1 Viewing the CUBE Hypotheses ................................................................... 107
3.16.2 Editing Hypotheses with the Control Bar .................................................... 108
3.16.3 Right-click Menu for CUBE Editing ........................................................... 109
3.16.4 Cube Panel in the 3D Editor ......................................................................... 110
3.16.5 Creating a Custom Hypothesis ..................................................................... 111
CHAPTER 4 - SCIENTIFIC DATA TYPES .......................................................... 112

4.1
Introduction ....................................................................................................... 112
4.2
Common Object Controls ................................................................................ 113
4.2.1 Colormap......................................................................................................... 113
4.2.2 Shading ........................................................................................................... 113
4.2.3 Bounds ............................................................................................................ 115
4.2.4 Geo-Referencing ............................................................................................. 115
4.2.5 Time ................................................................................................................ 116
4.2.6 Info .................................................................................................................. 117
4.3
Root Node .......................................................................................................... 117
4.3.1 Scene Tab ........................................................................................................ 117
4.3.2 Lighting Tab.................................................................................................... 118
4.4
Digital Terrain Model (DTM) Classes ............................................................ 118
4.4.1 SonarDTM ...................................................................................................... 118
4.5
3D Geometric Classes ....................................................................................... 122
4.5.1 3D Point Class................................................................................................. 122
4.5.2 3D Line/Polygon Class ................................................................................... 124
4.5.3 3D Grid Class .................................................................................................. 127
4.5.4 Solid Model Class ........................................................................................... 129
4.6
Imagery Visualization Classes ......................................................................... 131
4.6.1 GeoImage Class .............................................................................................. 132
4.6.2 Vertical Image Class ....................................................................................... 134
4.6.3 Vertical Curtain/Seismic Class ....................................................................... 135
4.7
Simple Visualization Classes ............................................................................ 136
4.7.1 2D Grid Class .................................................................................................. 136
4.7.2 2D Plane Class ................................................................................................ 136
4.7.3 Label Class ...................................................................................................... 137
4.7.4 CUBE Class .................................................................................................... 137
4.7.5 Quadratic Class ............................................................................................... 137
4.8
PFM Class .......................................................................................................... 137
4.8.1 Coverage Control Panel .................................................................................. 138
4.8.2 Visualization Control Panel ............................................................................ 145
4.8.3 Targets Panel ................................................................................................... 146
4.8.4 Filters Panel .................................................................................................... 148
4.9
Outputting CUBE Hypotheses ......................................................................... 151
4.9.1 Recube Area .................................................................................................... 152
4.9.2 Filter Soundings .............................................................................................. 152
4.9.3 Output Surface ................................................................................................ 154
4.9.4 Cube Options .................................................................................................. 154
4.10 Vessel Class ........................................................................................................ 157
4.10.1 Vessel Tab .................................................................................................... 157
4.10.2 Vessel Distances Tab ................................................................................... 159
4.10.3 Vessel Tools Tab .......................................................................................... 161
4.10.4 Vessel Advanced Setup Dialog .................................................................... 162
4.10.5 Vessel Monitor Dialog ................................................................................. 163
4.10.6 Vessel Display Options Dialog .................................................................... 164
4.10.7 Vessel Advanced Profile Dialog .................................................................. 165

CHAPTER 5 - DMAGIC ........................................................................................... 166

5.1
Introduction ....................................................................................................... 166
5.2
Starting DMagic ................................................................................................ 166
5.3
User Interface .................................................................................................... 166
5.4
Display Region................................................................................................... 167
5.5
Source Data Region........................................................................................... 167
5.6
SD Data Region ................................................................................................. 167
5.7
Object Attributes Region ................................................................................. 168
5.8
Control Bar ........................................................................................................ 168
5.9
Menu Bar ........................................................................................................... 169
5.10 File Menu ........................................................................................................... 169
5.10.1 Create Project ............................................................................................... 169
FIGURE 5-5 - PROJECT HIERARCHY ................................................................... 170
5.10.2 Delete Project ............................................................................................... 170
5.10.3 Open Project ................................................................................................. 171
5.10.4 Edit Project ................................................................................................... 171
Figure 5-6 Edit Project Dialog ................................................................................. 171
5.10.5 Close Project ................................................................................................ 171
5.10.6 Add Source Data .......................................................................................... 171
5.10.7 Add SD File.................................................................................................. 174
5.10.8 Add PFM File ............................................................................................... 174
5.10.9 Preference ..................................................................................................... 174
5.10.10 Screen Capture ........................................................................................... 177
5.10.11 Pause .......................................................................................................... 178
5.10.12 Recent Projects .......................................................................................... 178
5.10.13 Exit............................................................................................................. 178
5.11 View Menu ......................................................................................................... 179
5.12 Rendering Menu................................................................................................ 179
5.13 Tools Menu ........................................................................................................ 180
5.13.1 Plot Ungridded Files..................................................................................... 181
5.13.2 Grid Ungridded Files .................................................................................... 182
5.13.3 Export Ungridded Files ................................................................................ 185
5.13.4 Apply Tides .................................................................................................. 187
5.13.5 Build PFM .................................................................................................... 188
5.13.6 Build Blank PFM ......................................................................................... 193
5.13.7 Unload PFM ................................................................................................. 193
5.13.8 Append PFM ................................................................................................ 193
5.13.9 Delete Line from PFM ................................................................................. 194
5.13.10 Filter PFM.................................................................................................. 194
5.13.11 Update/Verify PFM ................................................................................... 194
5.13.12 View Histogram ......................................................................................... 194
5.13.13 Convert Grid to SD .................................................................................... 195
5.13.14 Convert Image to SD ................................................................................. 196
5.13.15 Edit Image.................................................................................................. 197
5.13.16 Convert Image to SD ................................................................................. 198

5.13.17 Export Image to Google Earth ................................................................... 199

5.13.18 Convert Vector to SD ................................................................................ 199
5.13.19 Edit Coordinate System ............................................................................. 199
5.13.20 Edit Configuration ..................................................................................... 200
5.13.21 View Metadata ........................................................................................... 200
5.13.22 Clean Metadata .......................................................................................... 201
5.13.23 Remove Errors ........................................................................................... 201
5.14 Surface Sub-Menu ............................................................................................ 201
5.14.1 Extract Area.................................................................................................. 201
5.14.2 Mask Area .................................................................................................... 202
5.14.3 Export ........................................................................................................... 203
5.14.4 Calculate Slope ............................................................................................. 204
5.14.5 Calculate Rugosity ....................................................................................... 206
5.14.6 Interpolate..................................................................................................... 206
5.14.7 Resample ...................................................................................................... 207
5.14.8 Surface Statistics .......................................................................................... 208
5.15 Help Menu ......................................................................................................... 208
CHAPTER 6 - FMGEOCODER TOOLBOX ......................................................... 210
6.1
Introduction to FMGeocoder Toolbox (FMGT) ............................................ 210
6.2
FMGT Supported Data Formats ..................................................................... 211
6.3
FMGT Interface ................................................................................................ 212
6.3.1 Step 1 Create the Project .............................................................................. 214
6.3.2 Step 2 Add Source Files ............................................................................... 214
6.3.3 Step 3 Process the Data ................................................................................ 219
6.3.4 Step 4 Exporting Data .................................................................................. 226
6.4
FMGT Processing Pipeline............................................................................... 227
6.5
Preferences......................................................................................................... 229
6.6
Main Menu Bar ................................................................................................. 231
6.6.1 File Menu ........................................................................................................ 231
6.6.2 View Menu...................................................................................................... 237
6.6.3 Settings Menu ................................................................................................. 238
6.6.4 Processing Menu ............................................................................................. 248
6.6.5 Tools Menu ..................................................................................................... 249
6.6.6 Help Menu ...................................................................................................... 258
6.7
Source Files Panel ............................................................................................. 260
6.7.1 Source Files ..................................................................................................... 260
6.7.2 Visual Objects ................................................................................................. 266
6.8
Mosaic Information Panel ................................................................................ 272
6.9
Processing Panel ................................................................................................ 273
6.9.1 Automatic Processing Tab .............................................................................. 273
6.9.2 Manual Processing Tab ................................................................................... 274
6.9.3 Messages Tab .................................................................................................. 278
6.9.4 Histogram Panel .............................................................................................. 279
6.9.5 ARA Tab ......................................................................................................... 280
6.10 Status Bar .......................................................................................................... 281

6.11 Map View ........................................................................................................... 281

6.12 Tool Bar ............................................................................................................. 283
6.12.1 Camera ......................................................................................................... 283
6.12.2 Cursor Modes ............................................................................................... 283
6.12.3 Display Options ............................................................................................ 285
6.12.4 Editing Tools ................................................................................................ 286
6.12.5 Beam Tools .................................................................................................. 288
6.13 Plotting Widgets ................................................................................................ 288
CHAPTER 7 - ROUTEPLANNER .......................................................................... 291
7.1
Introduction ....................................................................................................... 291
7.2
Starting Routeplanner ...................................................................................... 291
7.3
User Interface .................................................................................................... 291
7.4
Route Display Region ....................................................................................... 292
7.4.1 Bottom Display Bar ....................................................................................... 293
7.5
Control Bar ........................................................................................................ 293
7.6
Profile Region .................................................................................................... 295
7.7
Object Region .................................................................................................... 296
7.8
Control Region .................................................................................................. 296
7.9
Menu Bar ........................................................................................................... 298
7.9.1 File Menu ........................................................................................................ 298
7.9.2 Import Menu ................................................................................................... 299
7.9.3 Export Menu ................................................................................................... 299
7.9.4 Help Menu ...................................................................................................... 301
CHAPTER 8 - CROSSCHECK ................................................................................ 302
8.1
Introduction ....................................................................................................... 302
8.2
Starting Crosscheck .......................................................................................... 302
8.3
User Interface .................................................................................................... 304
8.4
Data Sets Region ............................................................................................... 304
8.5
Surface Display.................................................................................................. 305
8.6
Histogram .......................................................................................................... 305
8.7
Data Analysis Region ........................................................................................ 305
8.8
Menu Bar ........................................................................................................... 306
8.8.1 File Menu ........................................................................................................ 306
8.9
Object Menu ...................................................................................................... 308
8.9.1 Surface Projection ........................................................................................... 308
8.9.2 Line Projection ................................................................................................ 309
8.10 Import Menu ..................................................................................................... 309
8.10.1 Import un-gridded data ................................................................................. 309
8.11 Help Menu ......................................................................................................... 310
CHAPTER 9 - VESSEL MANAGER....................................................................... 311
9.1
Vessel Manager ................................................................................................. 311

CHAPTER 10 - OMNIVIEWER .............................................................................. 322

10.1 Introduction ....................................................................................................... 322
10.2 Starting Omniviewer ........................................................................................ 322
10.3 User Interface .................................................................................................... 323
10.4 Data View ........................................................................................................... 323
10.5 Control Panel Region ........................................................................................ 324
10.6 Menu Bar ........................................................................................................... 324
10.6.1 File Menu ..................................................................................................... 324
10.6.2 Help Menu .................................................................................................... 325
CHAPTER 11 - FLEDERMAUS AND GIS ............................................................ 326
11.1 Introduction to Fledermaus ArcGIS Connectivity ..................................... 327
11.2 Bathymetry Quick Start Guide ....................................................................... 327
11.2.1 Step 1 Creating the Workspace ................................................................. 327
11.2.2 Step 2 Transferring Fledermaus Data to ArcGIS ...................................... 330
11.2.3 Step 3 Loading ArcGIS Data to a Fledermaus Scene ............................. 339
11.3 Creating ArcGIS Workspaces ......................................................................... 341
11.3.1 Folder Workspace....................................................................................... 341
11.3.2 File Workspace ........................................................................................... 342
11.3.3 Personal Workspace ................................................................................... 342
11.3.4 ArcSDE Workspace ..................................................................................... 343
11.4 Connecting to Workspaces ............................................................................ 344
11.5 Transferring Data to ArcGIS.......................................................................... 345
11.5.1 SD Points...................................................................................................... 346
11.5.2 SD Lines ....................................................................................................... 348
11.5.3 SD GeoImage ............................................................................................... 350
11.5.4 11.5.4 SD Surface ....................................................................................... 351
11.5.5 SD PFM......................................................................................................... 353
11.5.6 Interpretation ............................................................................................. 358
11.5.7 SD Scalar ...................................................................................................... 360
11.6 Scalar TransferLoading Data from ArcGIS ................................................. 362
11.6.1 Feature Loading .......................................................................................... 363
11.6.2 Raster Loading ............................................................................................ 370
11.6.3 Other Workspace Operations .................................................................... 371
CHAPTER 12 - FMMIDWATER ............................................................................ 387
12.1 Introduction to FMMidwater .......................................................................... 387
12.2 FMMidwater Supported Data Formats .......................................................... 388
12.3 FMMidwater Interface ..................................................................................... 389
12.4 Quick Start Guide ............................................................................................. 391
12.4.1 Step 1 Create the Project ........................................................................... 391
12.4.2 Step 2 Add Source Files ............................................................................ 391
12.4.3 Step 3 Converting Files ............................................................................. 395
12.4.4 Step 4 Threshold Filtering ......................................................................... 399
12.4.5 Step 5 Data Export .................................................................................... 402
12.5 Project Files ....................................................................................................... 407

12.5.1 Creating Projects .......................................................................................... 407

12.5.2 Opening Projects .......................................................................................... 408
12.6 FMMidwater Preferences ................................................................................ 409
12.7 Main Menu Bar ................................................................................................. 412
12.7.1 File Menu ..................................................................................................... 413
12.7.2 View Menu ................................................................................................... 418
12.7.3 Tools Menu .................................................................................................. 419
12.7.4 Filter Menu ................................................................................................... 427
12.7.5 Help Menu .................................................................................................... 429
12.8 Tree View ........................................................................................................... 430
12.8.1 Source Files Sensor Node ......................................................................... 430
12.8.2 Source Files Navigation Node .................................................................. 431
12.8.3 Source Files Midwater Node ..................................................................... 432
12.8.4 Visual Objects SD Files ............................................................................ 432
12.9 Water Column View ......................................................................................... 433
12.9.1 Water Column View Fan........................................................................... 433
12.9.2 Water Column View Beam ....................................................................... 434
12.9.3 Water Column View Stacked .................................................................... 435
12.10
Map View ....................................................................................................... 436
12.12
Tool Bar ......................................................................................................... 438
12.12.1 Map View Tools ........................................................................................ 438
12.12.2 Water Column View Tools ........................................................................ 439
12.13
Beam View Options....................................................................................... 442
12.14
Signal Options ............................................................................................... 443
12.15
Time Bar ........................................................................................................ 444
12.16
Status Bar ...................................................................................................... 444
12.17
Converting Source Files to GWC Format .................................................. 445
12.18
Picking Features for Export ......................................................................... 449
12.19
Plotting Widgets ............................................................................................ 450
CHAPTER 13 - INTERPRETATION...................................................................... 452
13.1 Introduction to Fledermaus Interpretation .................................................... 452
13.2 Quick Start Guide ............................................................................................. 453
13.2.1 Step 1 Adding Interpretation Objects ........................................................ 453
13.2.2 Step 2 Editing Key Names ........................................................................ 454
13.2.3 Step 3 Creating Interpretation Areas ......................................................... 456
13.2.4 Step 4 Saving, Exporting, or Transferring Interpretation.......................... 458
13.3 SD Interpretation Control Panel ..................................................................... 459
13.3.1 Display Options ............................................................................................ 459
13.3.2 Draping Options ........................................................................................... 460
13.3.3 Interpretation Information ............................................................................ 461
13.3.4 Select Actions ............................................................................................... 461
13.3.5 Tools ............................................................................................................. 467

Figure 1-1 - The Linux, Macintosh, and Windows Versions ................................................ 22

Figure 1-2 - File selection widget .................................................................................................. 27
Figure 1-3 - Color Selection Dialog ............................................................................................... 27
Figure 2-1 - Main Fledermaus Window....................................................................................... 28
Figure 2-2 - Fledermaus Main Window ...................................................................................... 32
Figure 2-3 - Predictor Navigating Over a 3D DTM .................................................................. 33
Figure 2-4 - Non-flight Exploration Interface ........................................................................... 34
Figure 2-5 - Rotation of Surface ..................................................................................................... 36
Figure 2-6 - Rotation Widget Colors ............................................................................................. 36
Figure 2-7 - Profile Dialog ................................................................................................................ 37
Figure 2-8 - Fledermaus Time Bar ................................................................................................ 38
Figure 2-9 - Time Display Area ....................................................................................................... 39
Figure 2-10 - Time Control Area .................................................................................................... 39
Figure 2-11 - Time Options Sub-Menu ........................................................................................ 40
Figure 2-12 - Fledermaus File Menu ............................................................................................ 44
Figure 2-13 - Snapshot Dialog......................................................................................................... 45
Figure 2-14 - Preferences Dialog ................................................................................................... 46
Figure 2-15 - Interaction Mode Pop-up....................................................................................... 46
Figure 2-16 - Display Mode Pop-up .............................................................................................. 46
Figure 2-17 - General Preferences ................................................................................................ 47
Figure 2-18 - Turntable Mode Preferences................................................................................ 48
Figure 2-19 - 3D Flight Mode Preferences ................................................................................. 49
Figure 2-20 - Geo-Referencing Preferences .............................................................................. 50
Figure 2-21 - Exploration Menu ..................................................................................................... 51
Figure 2-22 - Controls Menu............................................................................................................ 52
Figure 2-23 - Color Map Control Dialog ...................................................................................... 53
Figure 2-24 - View Manager Dialog .............................................................................................. 54
Figure 2-25 - Rendering Menu ........................................................................................................ 55
Figure 2-26 - Import Menu............................................................................................................... 56
Figure 2-27 - Import Lines Dialog ................................................................................................. 57
Figure 2-28 - Import Points ............................................................................................................. 58
Figure 2-29 Custom ASCII Configuration dialog .................................................................. 59
Figure 2-30 - Import Shapefile ....................................................................................................... 62
Figure 2-31 - Create Menu ................................................................................................................ 63
Figure 2-32 - Add Shape Sub-Menu .............................................................................................. 63
Figure 2-33 - Tools Menu .................................................................................................................. 64
Figure 2-34 - Contouring Dialog .................................................................................................... 65
Figure 2-35 - Surface Difference Wizard - Stage 1 .................................................................. 66
Figure 2-36 Map Sheet Creation Dialog ................................................................................... 67
Figure 2-37 - Surface Statistics Dialog ......................................................................................... 68
Figure 2-38 - Reprojection Dialog ................................................................................................. 68
Figure 2-39 - Drape Image Dialog ................................................................................................. 69
Figure 2-40 - Attach Scalar Dialog ................................................................................................. 70
Figure 2-41 - Mask Surface Dialog ................................................................................................ 70
Figure 2-42 - Extract Area Dialog .................................................................................................. 71
Figure 2-43 - Render Movie Dialog ............................................................................................... 72

Figure 2-44 - Control Region showing the Data Set Panel. .................................................. 73
Figure 2-45 - Control Region showing the Geo-Picking display ........................................ 74
Figure 2-46 - Sample SonarDTM class ......................................................................................... 75
Figure 2-47 - The Constant Controls on the Data Set Control ............................................ 75
Figure 2-48 Object List Right-Click Menu ............................................................................... 76
Figure 3-1 - Selected Area for Edit in Fledermaus .................................................................. 79
Figure 3-2 - 3DEditor Interface Overview.................................................................................. 80
Figure 3-3 - Selecting Soundings using Select Mode .............................................................. 83
Figure 3-4 - 3DEditor Control Bar ................................................................................................. 84
Figure 3-5 - Color By Menu .............................................................................................................. 86
Figure 3-6 - Select By Menu ............................................................................................................. 87
Figure 3-7 - 3DEditor Selection Menu ......................................................................................... 88
Figure 3-8 - 3D Editor Edit Menu................................................................................................... 88
Figure 3-9 - 3D Editor Hide Menu ................................................................................................. 89
Figure 3-10 - 3DEditor File Menu .................................................................................................. 90
Figure 3-11 - 3DEditor Display Menu .......................................................................................... 91
Figure 3-12 - Show/Hide Files Dialog .......................................................................................... 91
Figure 3-13 - 3DEditor Slices Menu .............................................................................................. 92
Figure 3-14 - 3D Editor Options Menu ........................................................................................ 92
Figure 3-15 - 3DEditor Preferences Dialog................................................................................ 93
Figure 3-16 - 3DEditor Attributes Control Panel .................................................................... 94
Figure 3-17 - 3DEditor Soundings Control Panel .................................................................... 94
Figure 3-18 - Selection of Sounding Shape ................................................................................ 95
Figure 3-19 - Selection of Sounding Color .................................................................................. 95
Figure 3-20 - Coloring a surface by Line ..................................................................................... 95
Figure 3-21 - Displaying a smooth surface in the 3D Editor ............................................... 96
Figure 3-22 - 3D Editor Surface Control Panel ......................................................................... 96
Figure 3-23 - Displaying a flat surface in the 3D Editor........................................................ 97
Figure 3-24 - 3D Editor Utilities Control Panel ........................................................................ 97
Figure 3-25 - Using the 3D Editor in slice mode ...................................................................... 98
Figure 3-26 - 3D Editor Shoals Menu ......................................................................................... 101
Figure 3-27 - Editing Targets ........................................................................................................ 102
Figure 3-28 - Targets Right-Click Menu .................................................................................... 102
Figure 3-29 - Showing connectors in the 3D Editor ............................................................. 104
Figure 3-30- Soundings with Second Depths .......................................................................... 105
Figure 3-31 - Using the 3D Editor to edit Cube Hypotheses ............................................. 107
Figure 3-32 - Control Bar in the 3D Editor when editing hypotheses ........................... 108
Figure 3-33 - Select Menu when editing hypotheses ........................................................... 109
Figure 3-34 - Edit Menu when editing hypotheses ............................................................... 109
Figure 3-35 - Cube Panel in the 3D Editor................................................................................ 110
Figure 3-36 - Confidence Intervals in the 3D Editor ............................................................ 111
Figure 4-1 The Colormap attribute panel ............................................................................. 113
Figure 4-2 The shading attribute panel ................................................................................. 114
Figure 4-3 The bounds attribute panel .................................................................................. 115
Figure 4-4 The copy bounds dialog ......................................................................................... 115
Figure 4-5 The georeferencing attribute panel .................................................................. 116

Figure 4-6 The time attribute panel ........................................................................................ 116

Figure 4-7 The info attribute panel ......................................................................................... 117
Figure 4-8 The scene attribute panel ...................................................................................... 117
Figure 4-9 The lighting attribute panel.................................................................................. 118
Figure 4-10 - Sample SonarDTM .................................................................................................. 119
Figure 4-11 - SonarDTM Controls ............................................................................................... 119
Figure 4-12 - Sample Surface Series ........................................................................................... 121
Figure 4-13 - Surface Series Controls......................................................................................... 121
Figure 4-14 - Sample 3D Points .................................................................................................... 122
Figure 4-15 - 3D Point Controls ................................................................................................... 123
Figure 4-16 - 3D Point Color By Options .................................................................................. 123
Figure 4-17 - 3D Point Marker Type Options.......................................................................... 123
Figure 4-18 - 3D Line Controls ..................................................................................................... 124
Figure 4-19 - 3D Line Color By Menu ......................................................................................... 124
Figure 4-20 - Setting Line Heights ............................................................................................... 125
Figure 4-21 - Resampling and Draping Lines ......................................................................... 125
Figure 4-22 - Difference between Drape and Resample and Drape ................................ 126
Figure 4-23 - 3D Grid and SonarDTM ........................................................................................ 127
Figure 4-24 - 3D Grid Controls ..................................................................................................... 128
Figure 4-25 - Sample Solid Model................................................................................................ 129
Figure 4-26 - Solid Model Controls ............................................................................................. 130
Figure 4-27 - Transform Vertices of a Solid Model ............................................................... 130
Figure 4-28 - Sample GeoImage ................................................................................................... 132
Figure 4-29- Geo-Image Controls ................................................................................................ 133
Figure 4-30 - Example of Masking a GeoImage ...................................................................... 133
Figure 4-31 - Sample Vertical Image with a DTM.................................................................. 134
Figure 4-32 - Vertical Image Controls ........................................................................................ 134
Figure 4-33 - Vertical Curtain Controls ..................................................................................... 135
Figure 4-34 - 2D Grid Controls ..................................................................................................... 136
Figure 4-35 - 2D Plane Controls ................................................................................................... 136
Figure 4-36 - Label Controls .......................................................................................................... 137
Figure 4-37 - Coverage Control Panel ........................................................................................ 138
Figure 4-38 - Extraction of PFM Data for Visualization ...................................................... 139
Figure 4-39 - Suspect Data Flag .................................................................................................... 140
Figure 4-40 - Bin Header Dialog Box .......................................................................................... 141
Figure 4-41 - Export Soundings Dialog ..................................................................................... 143
Figure 4-42 - Export Shoal Soundings Dialog ......................................................................... 144
Figure 4-43 - Bin Info Dialog Box................................................................................................. 145
Figure 4-44 - Visualization Control Panel ................................................................................ 145
Figure 4-45 - Targets Panel............................................................................................................ 146
Figure 4-46 - Adding or Moving a Target ................................................................................. 147
Figure 4-47 - Viewing a Snippet Associated with a Target ................................................ 147
Figure 4-48 - Filters Panel .............................................................................................................. 148
Figure 4-49 - Filter Options for Suspect Soundings ............................................................. 149
Figure 4-50 - Filter Options for the Plotted Soundings Algorithm ................................. 150
Figure 4-51 - Filter Options for Feature Soundings ............................................................. 150

Figure 4-52 - CUBE Tools Menu ................................................................................................... 152

Figure 4-53 - Recube Area Dialog ................................................................................................ 152
Figure 4-54 - CUBE Filter Soundings Dialog............................................................................ 153
Figure 4-55 - CUBE Output Surface Dialog............................................................................... 154
Figure 4-56 CUBE Options Dialog ............................................................................................ 155
Figure 4-57 Create Custom Hypotheses from Features Dialog .................................... 156
Figure 4-58 - Sample Vessel Screenshot ................................................................................... 157
Figure 4-59 - Vessel Controls ........................................................................................................ 158
Figure 4-60 Vessel Distances Tab ............................................................................................ 159
Figure 4-61 Vessel Tools Tab ..................................................................................................... 161
Figure 4-62 Vessel Advanced Setup Dialog .......................................................................... 162
Figure 4-63 Vessel Monitor Dialog .......................................................................................... 163
Figure 4-64 Vessel Display Options Dialog .......................................................................... 164
Figure 4-65 Vessel Advanced Profile Dialog ........................................................................ 165
Figure 5-1 - DMagic Main Window ............................................................................................. 167
Figure 5-2 - Control Bar................................................................................................................... 168
Figure 5-3 - DMagic File Menu ...................................................................................................... 169
Figure 5-4 - Create Project Dialog ............................................................................................... 169
Figure 5-5 - Project Hierarchy ...................................................................................................... 170
Figure 5-6 Edit Project Dialog ................................................................................................... 171
Figure 5-7 - Add Source Data Wizard (Stage 1) ..................................................................... 172
Figure 5-8 - Add Source Data Wizard (Stage 2) ..................................................................... 173
Figure 5-9 - Add Source Data Wizard (Stage 3) ..................................................................... 173
Figure 5-10 - DMagic Preferences - Display ............................................................................ 174
Figure 5-11 - DMagic Preferences - Georeferencing ............................................................ 175
Figure 5-12 - DMagic Preferences - Shading and Color Maps .......................................... 176
Figure 5-13 - DMagic Preferences - Source Data ................................................................... 177
Figure 5-14 - DMagic Screen Capture Dialog .......................................................................... 178
Figure 5-15 - DMagic View Menu ................................................................................................ 179
Figure 5-16 - DMagic Rendering Menu ..................................................................................... 179
Figure 5-17 - DMagic Tools Menu ............................................................................................... 180
Figure 5-18 - DMagic Plotting Toolbar ...................................................................................... 181
Figure 5-19 - DMagic Gridding Wizard (Stage 1) .................................................................. 182
Figure 5-20 - DMagic Gridding Wizard (Stage 2) .................................................................. 183
Figure 5-21 DMagic Gridding Wizard (Stage 3) ................................................................. 184
Figure 5-22 - DMagic Gridding Wizard (Stage 4) .................................................................. 185
Figure 5-23 - DMagic Export Ungridded Data Wizard (Stage 1) ..................................... 186
Figure 5-24 DMagic Export Ungridded Data Wizard (Stage 2) .................................... 186
Figure 5-25 - DMagic Export Ungridded Data Wizard (Stage 3) ..................................... 187
Figure 5-26 - DMagic Apply Tides Dialog ................................................................................. 188
Figure 5-27 - PFM Build Wizard (Stage 1) ............................................................................... 189
Figure 5-28 - PFM Build Wizard (Stage 2) ............................................................................... 190
Figure 5-29 - PFM Build Wizard (Stage 3) ............................................................................... 190
Figure 5-30 - PFM Build Wizard (Stage 4) ............................................................................... 191
Figure 5-31 - PFM Build Wizard (Stage 5) ............................................................................... 192
Figure 5-32 - PFM Build Wizard (Stage 6) ............................................................................... 193

Figure 5-33 - PFM Delete Line Dialog ........................................................................................ 194

Figure 5-34 - View Histograms Dialog ....................................................................................... 195
Figure 5-35 - Convert Grid to SD Wizard (Stage 1) .............................................................. 195
Figure 5-36 - Convert Grid to SD Wizard (Stage 2) .............................................................. 196
Figure 5-37 Convert Grid to SD Wizard (Stage 3) .............................................................. 196
Figure 5-38 - DMagic Edit Image Toolbar ................................................................................ 197
Figure 5-39 DMagic Google Earth Export ............................................................................. 199
Figure 5-40 - DMagic Edit Coordinate System Dialog.......................................................... 199
Figure 5-41 DMagic Edit Configuration Dialog ................................................................... 200
Figure 5-42 - DMagic View Metadata Dialog ........................................................................... 201
Figure 5-43 - Surface Sub-Menu................................................................................................... 201
Figure 5-44 - DMagic Extract Area Dialog ................................................................................ 202
Figure 5-45 - DMagic Mask Area Dialog .................................................................................... 203
Figure 5-46 - DMagic Export Dialog ........................................................................................... 204
Figure 5-47 - DMagic Calculate Slope Dialog .......................................................................... 205
Figure 5-48 - DMagic Calculate Rugosity Dialog .................................................................... 206
Figure 5-49 - DMagic Interpolate Dialog .................................................................................. 207
Figure 5-50 - DMagic Resample Dialog ..................................................................................... 207
Figure 5-51 - DMagic Surface Statistics Dialog....................................................................... 208
Figure 5-52 - DMagic Help Menu ................................................................................................. 208
Figure 6-1 - FMGT User Interface ................................................................................................ 212
Figure 6-2 - Create Project Dialog ............................................................................................... 214
Figure 6-3 - Add Files Wizard, Page 1 ........................................................................................ 215
Figure 6-4 - Add Files Wizard - Page 2 ...................................................................................... 215
Figure 6-5 - File Indexing ................................................................................................................ 216
Figure 6-6 - File Metadata .............................................................................................................. 217
Figure 6-7 - File Coverage............................................................................................................... 217
Figure 6-8 - Swath SD ....................................................................................................................... 218
Figure 6-9 - Files Loaded ................................................................................................................ 218
Figure 6-10 - Backscatter Processing......................................................................................... 219
Figure 6-11 - Filter Processing ..................................................................................................... 220
Figure 6-12 - Mosaic Processing .................................................................................................. 220
Figure 6-13 - Mosaic Visual Layer ............................................................................................... 221
Figure 6-14 - Mosaic Layer Zoomed ........................................................................................... 222
Figure 6-15 - Statistics Processing .............................................................................................. 223
Figure 6-16 - Statistics Layers ...................................................................................................... 224
Figure 6-17 - Transparent Statistical Layer ............................................................................ 224
Figure 6-18 - ARA Processing ....................................................................................................... 225
Figure 6-19 - ARA Visual Layer .................................................................................................... 225
Figure 6-20 - Visual Layer Export Menu ................................................................................... 226
Figure 6-21 Generic Processing Pipeline .............................................................................. 227
Figure 6-22 Parallel Stage Processing .................................................................................... 227
Figure 6-23 FMGT Processing Stages ..................................................................................... 228
Figure 6-24 Generic Processing Pipeline .............................................................................. 229
Figure 6-25 - Preferences - General Tab ................................................................................... 229
Figure 6-26 - Preferences - Coordinates Tab .......................................................................... 231

Figure 6-27 - FMGT File Menu ...................................................................................................... 231

Figure 6-28 - Add Source Files Dialog Panel 1 .................................................................... 232
Figure 6-29 - Add Files Dialog - Panel 2 .................................................................................... 233
Figure 6-30 - Bathymetry/Backscatter File Pairs Dialog - Panel 1................................. 233
Figure 6-31 - Bathymetry/Backscatter File Pairs Dialog - Panel 2................................. 234
Figure 6-32 - Bathymetry/Backscatter File Pairs Dialog - Panel 3................................. 234
Figure 6-33 - Bathymetry/Backscatter File Pairs Dialog - Panel 4................................. 235
Figure 6-34 - Reference Grid ......................................................................................................... 236
Figure 6-35 - PFM Edits ................................................................................................................... 237
Figure 6-36 - FMGT View Menu ................................................................................................... 238
Figure 6-37 - Settings Menu........................................................................................................... 238
Figure 6-38 - Processing Dialog Backscatter Options ...................................................... 239
Figure 6-39 - Processing Dialog - AVG Options ...................................................................... 240
Figure 6-40 - Processing Dialog - Statistics Options ............................................................ 241
Figure 6-41 - Processing Dialog - Navigation Options......................................................... 242
Figure 6-42 Processing Dialog - .ALL Format Options ..................................................... 243
Figure 6-43 Processing Dialog - .XTF Format Options ..................................................... 244
Figure 6-44 - Processing Dialog - Sonar Defaults .................................................................. 244
Figure 6-45 - Mosaic Options ........................................................................................................ 246
Figure 6-46 - Mosaic Style Options ............................................................................................. 246
Figure 6-47 - Sensor Configuration ............................................................................................ 247
Figure 6-48 - Project Coordinate System.................................................................................. 248
Figure 6-49 - Directory Monitoring ............................................................................................ 248
Figure 6-50 - Processing Menu ..................................................................................................... 248
Figure 6-51 - Tools Menu ................................................................................................................ 249
Figure 6-52 - Beam Pattern Correction Dialog ....................................................................... 250
Figure 6-53 - Edit Selection Tool ................................................................................................. 250
Figure 6-54 - Beam Pattern Correction - After Classification ........................................... 251
Figure 6-55 - Beam Pattern Viewer ............................................................................................ 251
Figure 6-56 - Angle vs. Range Analysis Dialog........................................................................ 252
Figure 6-57 - Backscatter Adjustment Dialog ......................................................................... 254
Figure 6-58 - Plot Roll/Pitch ......................................................................................................... 255
Figure 6-59 - Plot Heading ............................................................................................................. 255
Figure 6-60 - Plot Heave.................................................................................................................. 256
Figure 6-61 - Plot Power/Gain ..................................................................................................... 256
Figure 6-62 - Backscatter Dialog.................................................................................................. 257
Figure 6-63 - Beam Average Dialog ............................................................................................ 258
Figure 6-64 - Help Menu ................................................................................................................. 259
Figure 6-65 - FMGT About Box ..................................................................................................... 259
Figure 6-66 - Licensing Dialog ...................................................................................................... 260
Figure 6-67 - Source Files Tab ...................................................................................................... 260
Figure 6-68 - Source File Metadata ............................................................................................. 261
Figure 6-69 - Source Root Node Context Menu ...................................................................... 262
Figure 6-70 - Source File Node Context Menu ........................................................................ 263
Figure 6-71 - Source File Node - View Sub-Menu.................................................................. 264
Figure 6-72 - Source File Node - Export Sub-Menu .............................................................. 265

Figure 6-73 - Points ARA Object................................................................................................... 265

Figure 6-74 - Visual Objects Tab .................................................................................................. 266
Figure 6-75 - Statistics Layers ...................................................................................................... 266
Figure 6-76 - ARA Layers ................................................................................................................ 267
Figure 6-77 - Mosaic Context Menu ............................................................................................ 268
Figure 6-78 - Surface Export Dialog ........................................................................................... 269
Figure 6-79 - ArcGIS Export Dialog ............................................................................................. 270
Figure 6-80 - Statistics Context Menu ........................................................................................ 270
Figure 6-81 - ARA Context Menu ................................................................................................. 271
Figure 6-82 - Reference Grid Context Menu ............................................................................ 272
Figure 6-83 - Mosaic Information Panel ................................................................................... 273
Figure 6-84 - Automatic Processing Tab .................................................................................. 274
Figure 6-85 - Manual Processing Tab ........................................................................................ 275
Figure 6-86 - Clear Flags Dialog ................................................................................................... 275
Figure 6-87 - Diagonal Survey Line ............................................................................................ 276
Figure 6-88 - Tile Layout................................................................................................................. 277
Figure 6-89 - Rendered Tiles ......................................................................................................... 278
Figure 6-90 - Messages Tab ........................................................................................................... 279
Figure 6-91 - Histogram Control .................................................................................................. 279
Figure 6-92 - ARA Control .............................................................................................................. 280
Figure 6-93 - ARA Quick Modeling Tools.................................................................................. 280
Figure 6-94 - Status Bar................................................................................................................... 281
Figure 6-95 - ARA and Statistical Layer Status ....................................................................... 281
Figure 6-96 - Map View Panel ....................................................................................................... 282
Figure 6-97 - Line Selection ........................................................................................................... 282
Figure 6-98 - Tool Bar ...................................................................................................................... 283
Figure 6-99 - Select Mosaic Area.................................................................................................. 284
Figure 6-100 - Check in Area ......................................................................................................... 284
Figure 6-101 - Select Segment ...................................................................................................... 285
Figure 6-102 - Cut Segment ........................................................................................................... 286
Figure 6-103 - Add Segment .......................................................................................................... 287
Figure 6-104 - Force on Top .......................................................................................................... 287
Figure 6-105 - Fill Gaps Only ......................................................................................................... 288
Figure 6-106 - Plot Widget ............................................................................................................. 289
Figure 6-107 - Plot Widget Zooming .......................................................................................... 290
Figure 6-108 - Plot Widget Settings............................................................................................ 290
Figure 7-1 - Routeplanner Interface Overview ...................................................................... 292
Figure 7-2 - Routeplanner Bottom Display Bar ..................................................................... 293
Figure 7-3 Control Bar Command Icons ................................................................................ 293
Figure 7-4 - Profile ............................................................................................................................ 295
Figure 7-5 - Routeplanner Object Manager ............................................................................. 296
Figure 7-6 - Route Controls ............................................................................................................ 297
Figure 7-7 - Node Parameters Dialog ......................................................................................... 298
Figure 7-8 File menu ..................................................................................................................... 298
Figure 7-9 Export menu options .............................................................................................. 300
Figure 7-10 Export cross profile control dialog ................................................................. 300

Figure 8-1 Crosscheck command line .................................................................................... 303

Figure 8-2 - Crosscheck Main Window...................................................................................... 304
Figure 8-3 - Crosscheck File Menu .............................................................................................. 306
Figure 8-4 - Input File Configuration Dialog ........................................................................... 307
Figure 8-5 - Crosscheck Object Menu......................................................................................... 308
Figure 8-6 - Crosscheck Reference Surface Coordinate System Dialog ........................ 309
Figure 8-7 - Crosscheck Input Line Coordinate System Dialog ........................................ 309
Figure 9-1 - VesselManager application window .................................................................. 311
Figure 9-2 - VesselManager data flow ....................................................................................... 312
Figure 9-3 - Setting up VesselManager ...................................................................................... 313
Figure 9-4 Message Configuration Setup .............................................................................. 315
Figure 9-5 - Data output coordinate format ............................................................................ 317
Figure 9-6 Vehicle Setup .............................................................................................................. 318
Figure 9-7 Data Logging Setup .................................................................................................. 319
Figure 9-8 File Menu for VesselManager .............................................................................. 320
Figure 9-9 Raw Acquired Message Display .......................................................................... 320
Figure 9-10 Processed Navigation Message Display ........................................................ 321
Figure 10-1 - Omniviewer Main Window ................................................................................. 323
Figure 10-2 - Omniviewer File Menu ......................................................................................... 324
Figure 10-3 - Omniviewer View Header Window ................................................................ 325
Figure 11-1 Create Menu ................................................................................................................ 328
Figure 11-2 - Arc Workspace Attribute Panel ........................................................................ 328
Figure 11-3 - Workspace Creation .............................................................................................. 329
Figure 11-4 File Workspace Connection ............................................................................... 329
Figure 11-5 - PFM Attribute Panel .............................................................................................. 330
Figure 11-6 - Transfer Soundings ................................................................................................ 331
Figure 11-7 - Transfer Options ..................................................................................................... 332
Figure 11-8 - ArcGIS Transfer Complete................................................................................... 333
Figure 11-9 - ArcCatalog Soundings ........................................................................................... 334
Figure 11-10 - Survey Area Polygon........................................................................................... 335
Figure 11-11 - Bathymetry Raster .............................................................................................. 336
Figure 11-12 - Image Raster .......................................................................................................... 337
Figure 11-13 - Workspace Using Individual Transfers ....................................................... 337
Figure 11-14 PFM Transfer Wizard ........................................................................................ 338
Figure 11-15 - Image Raster .......................................................................................................... 339
Figure 11-16 Workspace Context Menu ................................................................................ 339
Figure 11-17 Load Feature to Scene Dialog ......................................................................... 340
Figure 11-18 Fledermaus Create Menu ................................................................................. 341
Figure 11-19 Folder Workspace ............................................................................................... 342
Figure 11-20 File Workspace..................................................................................................... 342
Figure 11-21 Personal Workspace .......................................................................................... 343
Figure 11-22 SDE Configuration Dialog ................................................................................. 343
Figure 11-23 SDE Workspace .................................................................................................... 344
Figure 11-24 Workspace Connection ..................................................................................... 344
Figure 11-25 Get Children........................................................................................................... 345
Figure 11-26 Get Children Complete ...................................................................................... 345

Figure 11-27 Disconnected Workspace ................................................................................. 346

Figure 11-28 Points Attribute Panel ....................................................................................... 346
Figure 11-29 Transfer SD Points .............................................................................................. 347
Figure 11-30 SD Point Transfer ................................................................................................ 348
Figure 11-31 Lines Attribute Panel ......................................................................................... 348
Figure 11-32 Lines Transferred as Lines or Polygons. .................................................... 349
Figure 11-33 GeoImage Attribute Panel ................................................................................ 350
Figure 11-34 GeoImage Transferred as 1-Band or 3-Band............................................ 351
Figure 11-35 Surface Attribute Panel ..................................................................................... 352
Figure 11-36 Surface Transfer .................................................................................................. 353
Figure 11-37 - Image Raster .......................................................................................................... 354
Figure 11-38 PFM Soundings Transfer Dialog .................................................................... 355
Figure 11-39 PFM Transfer Wizard ........................................................................................ 357
Figure 11-40 PFM Transfer ........................................................................................................ 358
Figure 11-41 Interpretation Attribute Panel ....................................................................... 359
Figure 11-42 Interpretation Transfer .................................................................................... 360
Figure 11-43 Scalar Attribute Panel........................................................................................ 361
Figure 11-44 Feature Tree .......................................................................................................... 362
Figure 11-45 Load to Scene ........................................................................................................ 363
Figure 11-46 Point Loading Options ....................................................................................... 364
Figure 11-47 Points Loaded to Scene ..................................................................................... 365
Figure 11-48 Multipoint Loading Options ............................................................................ 366
Figure 11-49 Line & Polyline Loading Options ................................................................... 367
Figure 11-50 Lines Loaded to Scene ....................................................................................... 368
Figure 11-51 Polygon Load as Interpretation ..................................................................... 369
Figure 11-52 - Interpretation Loaded to Scene...................................................................... 370
Figure 11-53 Raster Loading ..................................................................................................... 371
Figure 11-54 - Create Blank PFM................................................................................................. 372
Figure 11-55 - Create Blank PFM Wizard Page 1 ............................................................... 372
Figure 11-56 - Create Blank PFM Wizard Page 2 ............................................................... 373
Figure 11-57 - Create Blank PFM Wizard Page 3 ............................................................... 373
Figure 11-58 - Create Blank PFM Wizard Page 4 ............................................................... 374
Figure 11-59 Create Blank PFM Wizard Page 5 .............................................................. 375
Figure 11-60 Create Blank PFM Wizard Page 6 .............................................................. 375
Figure 11-61 Append to PFM ..................................................................................................... 376
Figure 11-62 Select PFM .............................................................................................................. 377
Figure 11-63 PFM Append Wizard Page 1 ........................................................................ 377
Figure 11-64 PFM Append Wizard Page 2 ........................................................................ 378
Figure 11-65 PFM Append Wizard Page 3 ........................................................................ 378
Figure 11-66 PFM Append Coverage Map ............................................................................ 379
Figure 11-67 Rename Object ..................................................................................................... 380
Figure 11-68 Delete Object ......................................................................................................... 380
Figure 11-69 Add Dataset ........................................................................................................... 381
Figure 11-70 Feature Dataset Coordinates .......................................................................... 381
Figure 11-71 Feature Dataset Transfer Destination......................................................... 382
Figure 11-72 Feature Dataset Tree View .............................................................................. 382

Figure 11-73 - Image Raster .......................................................................................................... 383

Figure 11-74 Raster Catalog Coordinates ............................................................................. 383
Figure 11-75 Raster Catalog Transfer Destination ........................................................... 384
Figure 11-76 Raster Catalog Tree View ................................................................................. 384
Figure 11-77 Add Raster to Catalog ........................................................................................ 385
Figure 11-78 Raster Catalog Entry .......................................................................................... 386
Figure 12-1 - FMMidwater User Interface ............................................................................... 389
Figure 12-2 - Create Project Dialog............................................................................................. 391
Figure 12-3 - Add Files Wizard, Page 1 ..................................................................................... 392
Figure 12-4 - Add Files Wizard - Page 2.................................................................................... 392
Figure 12-5 - File Indexing ............................................................................................................. 393
Figure 12-6 - File Metadata ............................................................................................................ 393
Figure 12-7 - File Coverage ............................................................................................................ 394
Figure 12-8 - Swath SD .................................................................................................................... 394
Figure 12-9 - Files Loaded .............................................................................................................. 395
Figure 12-10 - GWC Wizard - Page 1 .......................................................................................... 396
Figure 12-11 - GWC Wizard - Page 2 .......................................................................................... 397
Figure 12-12 - GWC Wizard - Page 3 .......................................................................................... 398
Figure 12-13 - GWC Conversion Dialog..................................................................................... 398
Figure 12-14 - GWC Files Loaded ................................................................................................ 399
Figure 12-15 - Stacked View .......................................................................................................... 400
Figure 12-16 - Composite Slider .................................................................................................. 400
Figure 12-17 - Final Stacked View .............................................................................................. 401
Figure 12-18 - SD Export Panel .................................................................................................... 403
Figure 12-19 - Beam Fan SD Object ............................................................................................ 404
Figure 12-20 - Beam View Options ............................................................................................. 404
Figure 12-21 - Beam Line SD Object ........................................................................................... 405
Figure 12-22 - Points SD Object ................................................................................................... 406
Figure 12-23 - Volume SD Object................................................................................................. 407
Figure 12-24 - Create Project Dialog .......................................................................................... 407
Figure 12-25 - Project Hierarchy ................................................................................................. 408
Figure 12-26 - Opening Other Projects ..................................................................................... 409
Figure 12-27 - Preferences Dialog General Tab.................................................................. 410
Figure 12-28 - Preferences Dialog - Coordinates Tab ......................................................... 411
Figure 12-29 - Preferences Dialog - Format Specific Tab .................................................. 412
Figure 12-30 - File Menu ................................................................................................................. 413
Figure 12-31 - Export Panel........................................................................................................... 415
Figure 12-32 - ASCII Out ................................................................................................................. 417
Figure 12-33 - Midwater Contact Dialog .................................................................................. 418
Figure 12-34 - View Menu .............................................................................................................. 419
Figure 12-35 - Tools Menu ............................................................................................................. 419
Figure 12-36 - Fish Traps - Stacked View with Thresholds Applied ............................. 420
Figure 12-37 - Map View - Selected Area ................................................................................. 420
Figure 12-38 - Map View - Plotted Water Column Data ..................................................... 421
Figure 12-39 - Nadir Detect - Step 1 ........................................................................................... 422
Figure 12-40 - Nadir Detect Step 2 .......................................................................................... 422

Figure 12-41 - Nadir Detect Step 3 .......................................................................................... 423

Figure 12-42 - Nadir Detect - Step 4 ........................................................................................... 423
Figure 12-43 - 'Blanked' Beam Line SD ..................................................................................... 424
Figure 12-44 - Vessel Reference Frame .................................................................................... 424
Figure 12-45 - Sensor Configuration Dialog ............................................................................ 425
Figure 12-46 - Plot Dialog............................................................................................................... 426
Figure 12-47 - Plot Settings ........................................................................................................... 426
Figure 12-48 - Filter Menu ............................................................................................................. 427
Figure 12-49 - Chirp Data - No AGC ............................................................................................ 428
Figure 12-50 - Chirp Data - With AGC ........................................................................................ 428
Figure 12-51 - Beam Selector Dialog .......................................................................................... 429
Figure 12-52 - Help Menu ............................................................................................................... 429
Figure 12-53 Source Files Tree View ...................................................................................... 430
Figure 12-54 - Sensor Node Context Menu .............................................................................. 431
Figure 12-55 - Navigation Node Context Menu...................................................................... 432
Figure 12-56 - Midwater Node Context Menu ........................................................................ 432
Figure 12-57 - Beam View Options ............................................................................................. 433
Figure 12-58 - Fan View Zooming ............................................................................................... 434
Figure 12-59 - Beam View Zooming ........................................................................................... 435
Figure 12-60 - Stacked View Zooming ....................................................................................... 436
Figure 12-61 - Vessel Position ...................................................................................................... 437
Figure 12-62 - Tool Bar ................................................................................................................... 438
Figure 12-63 - Area Select Tool .................................................................................................... 440
Figure 12-64 - Beam View Picking .............................................................................................. 440
Figure 12-65 - Measure Tool ......................................................................................................... 441
Figure 12-66 - Mask Tool Show/Hide ........................................................................................ 442
Figure 12-67 - Beam View Options ............................................................................................. 442
Figure 12-68 - Signal Options Panel ........................................................................................... 444
Figure 12-69 - Timeline Bar........................................................................................................... 444
Figure 12-70 - Cursor Info Dialog ................................................................................................ 445
Figure 12-71 - GWC Wizard - Page 1 .......................................................................................... 446
Figure 12-72 - GWC Wizard - Page 2 .......................................................................................... 447
Figure 12-73 - GWC Wizard - Page 3 .......................................................................................... 448
Figure 12-74 - Feature Picking ..................................................................................................... 449
Figure 12-75 - Pick Table ................................................................................................................ 449
Figure 12-76 - Plot Widget ............................................................................................................. 450
Figure 12-77 - Plot Widget Zooming .......................................................................................... 451
Figure 12-78 - Plot Widget Settings............................................................................................ 451
Figure 13-1 - Fledermaus Create Menu..................................................................................... 453
Figure 13-2 Empty Interpretation Object ............................................................................. 454
Figure 13-3 - Key Field Editor ....................................................................................................... 455
Figure 13-4 - Edited Key Fields .................................................................................................... 456
Figure 13-5 Selecting an Area .................................................................................................... 457
Figure 13-6 Add To Key ............................................................................................................... 458
Figure 13-7 SD Interpretation Control Panel ...................................................................... 459
Figure 13-8 Hole Markers ........................................................................................................... 460

Figure 13-9 Initial Area Selection ............................................................................................ 461

Figure 13-10 Add Overlapped Areas ...................................................................................... 462
Figure 13-11 Add New Overlapped ......................................................................................... 462
Figure 13-12 Removing an Area ............................................................................................... 463
Figure 13-13 Remove an Enclosed Area ............................................................................... 463
Figure 13-14 Overwrite Overlapping Area........................................................................... 464
Figure 13-15 Overwrite Enclosed Area ................................................................................. 464
Figure 13-16 Object Selection ................................................................................................... 465
Figure 13-17 Clip Before.............................................................................................................. 466
Figure 13-18 Clip After ................................................................................................................. 467
Figure 13-19 Key Field Edit Dialog .......................................................................................... 468
Figure 13-20 Tools Menu ............................................................................................................ 469
Figure 13-21 Generate Interpretation Image Dialog ........................................................ 469
Figure 13-22 GeoImage SD ......................................................................................................... 470
Figure 13-23 ArcGIS Menu.......................................................................................................... 471

Chapter 1 -

Introduction

The Fledermaus suite of software continues to provide a powerful set of interactive

3D visualization tools for data preparation, analysis and presentation. It allows one to
assemble and explore a virtual 3D world containing many object models including
surfaces, images, points, lines, and cross-sections. The software is tailored for the
display of geographic data, for example digital terrain models of the ocean floor or a
3D contour map of a mountain range; however, it is quite flexible and has been used
to visualize such diverse objects as crop growth rates, oil field development/pipelines
and chemical reactions.

Figure 1-1 - The Linux, Macintosh, and Windows Versions

Fledermaus has been designed specifically to allow near real-time, interactive display
of very large complex 3D objects at their full resolution. Fledermaus features our
ShiftScapeTM rendering engine, which automatically adjusts the amount of detail in a
scene based on the performance of your hardware. Two visualization interfaces are
provided that allow you to literally fly through the virtual 3D-exploration space. This
makes the exploration of data a simple and intuitive process. The exploration
environment is closely coupled with intuitive data analysis tools, which help delve into
the information behind the imagery.
The Fledermaus package allows the import of a wide variety of data formats and
creates richly featured 3D models. For examples: one can generate a simple 3D

surface color banded by height; or a high-resolution satellite image can be draped

over the same 3D surface producing a combined 3D model.
Many objects can be visualized in the same 3D-exploration space, such as, two 3D
surfaces show a shipping channel, one from before a dredging operation and one
after the completed operation; add a model of the channel design and you have a
complete, obvious representation of the design and the results of the dredging work
all in a single 3D scene. Additional tools provide quantitative analysis such as queries
to determine how much material was dredged.
Data files produced in Fledermaus can be distributed to anyone along with iView4D,
which provides a free interactive 3D viewer for these data sets.

1.1 What's in the Fledermaus Package?

The following is a list of applications with a graphical user interface (GUI) that are
available in both the Standard and Professional configurations:

Fledermaus - Main interactive 3D exploration application (some limitations

exist in the Standard Configuration).

DMagic - Interactive data preparation application

iView4D Free 4D exploration tool for Fledermaus prepared data

FMCommand System setup and application launching tool. Provides a

GUI for cmdop, and manages 3D input devices such as the Bat.

Omniviewer Spreadsheet like viewer for many point and Multibeam data
formats

RoutePlanner Interactive route planning tool

CrossCheck Performs interactive point vs. surface analysis

VesselManager Manages real time serial port input such as NMEA data

DMagic is the main interactive data preparation tool for DTM surfaces. Within its 2D
display, data is available for preview and analysis. It also helps build and edit color
maps to support visualization operations.
iView4D is a free application that we provide for viewing and exploring SD and scene
files produced by the Fledermaus package. It provides the same mouse based
exploration interface as Fledermaus albeit with much more limited capabilities. This
allows people to distribute work done in Fledermaus to other people who dont
currently have access to a Fledermaus license.

The cmdop program drives many command line based utilities and data processing
tools. Many of them duplicate functionality found in the main programs but in a form
that allows scripting and automation of repetitive data processing tasks. There are
also utilities that perform special functions or are late breaking additions that have not
yet been integrated into the main applications. These applets can also be combined
in scripts to facilitate batch processing of data or automate repetitive processing
tasks. Some command line programs are not available in the Standard version of
Fledermaus. See the Command Line Reference manual for more information.

1.2 How to Use the Fledermaus Package

The specific steps you use to assemble a 3D scene will depend on the object type to
be visualized. Generally, data is imported and converted into a Fledermaus object
and loaded into the visualization program (Fledermaus).
The most common objects used are the 3D surface and its variants: a 3D surface
draped with an image or a 3D surface draped with a scalar field. Fledermaus can
directory import many types of data along with producing surfaces from point data.
For more sophisticated data preparation and management you you normally start
with DMagic:

Use DMagic to import your many types of data for visualization and
processing.

Use DMagic to format and preview the surface. Usually you color it, with a
color map and shade it to highlight the relief.

Load this object into Fledermaus to visualize and explore the surface.

It is also possible to perform many data preparation operation by command line

applets. This is particularly useful when performing the exact same data preparation
steps for many datasets. Command line applets can by placed in a script, which
reduces the first three steps to a single command.
For other object types, either the GUI conversion applications listed above or related
command line applications are used to prepare your data and convert it into
Fledermaus objects.
Fledermaus also provides direct importers for a wide variety of data types from the
File > Import menu.

1.3 Fledermaus Manual Conventions

A number of notational conventions are used throughout the Fledermaus
documentation.
When the documentation makes reference to a user interface item, the feature being
discussed will be italicized, whether it is a menu bar, a pull-down menu, a list box, a
dialog box, or labels within those features. For example: Click the Process button to
initiate the action.
Application menu commands are often abbreviated with the greater than symbol. For
example File > Load Objects refers to the Load Objects command located under the
File menu. Also, if a filename is referenced in the text, it will usually be placed inside
quotes and italicized such as filename.ext.

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Commands entered directly through the command line prompt are shown in a
common format throughout the documentation. Examples of a command appear in a
fixed width font as illustrated below. Most of the commands have options. The
commands and their options are listed in a standard format as shown in the example
below:
cmdop xyztoscalar <
<
<
[
[
[
[
[

-cell <cellsize> >

-in <inputXYZfilename> >
-out <outputBaseFilename> >
-range <minZ> <maxZ> ]
-invert ]
-nogeo ]
-info ]
-h ]

The options are listed in two different kinds of brackets, angle brackets <>, and
square brackets [ ]. Options that are in <angle brackets> are required for the
command to run, while those in [square brackets] are optional. In the example above,
the cell, -in, and -out options are required while all the other options are not.
Most examples of commands appear on a single line. In some cases the command
line is too long and had to be broken in two. The example below shows the broken
command line appearing on two lines with the second line indented:
cmdop xyztoscalar -in infile.xyz
-out testfile -cell 5.0

Although it is split in two, the command should be thought of as a single continuous

command and would be entered on the command line as shown below:
cmdop xyztoscalar -in infile.xyz -out testfile -cell 5.0

All applications have an option h for help that displays information about the
applications command line arguments and how they should be used to make the
application work properly. In addition, they all support ver as an option to show the
version number of the given program.

1.4 Fledermaus Software Conventions

A number of user interface features are commonly used throughout the Fledermaus
Package and their function remains constant. However the look and feel may change
slightly from platform to platform to match the expected style of the operating system.
The following describes these conventions.

1.4.1 Text or Entry Fields

Text input fields, or text fields for short, are found throughout the application; some
present information and others request information. Normally those that require

information to be typed have a different background color (normally white on

Windows/Mac and pinkish on Unix). In all cases the Enter key must be pressed to
load / enter the text field information.

1.4.2 File Selection Widget

The file selection widget shown below appears in many places throughout the
applications when the system needs a specified file to continue.

Figure 1-2 - File selection widget

This interface element includes a text entry field for a filename to be specified, plus a
or Browse button to the right of the filename. If the full path to the file is
known, its name and path can be entered directly by typing in it and pressing the
Enter key. This will load the file and initiate whatever action is supposed to occur.
More commonly though, clicking the right hand side button is used to bring up a
standard file selection dialog from which the file can be located and opened. Thus the
file selection widget provides a quick means to enter a file name but still provides
access to the standard file open dialog for ease of use. If the files path is longer than
the display area then the start of the path name will be clipped. To see the full path,
click the mouse cursor in the text field and drag to the left or right as necessary.

1.4.3 Ranged Slider Controls

Using a slider to select from a range of values is quite commonly used in the
Fledermaus system applications. However, we often add an additional button at the
right hand edge of the slider with the label . Clicking this button brings up a dialog
which allows you to see and change the range of the slider. This is important
because in some circumstances the default range is not appropriate. In these cases
you can simply change the effective range of the slider. For sliders such as the one in
Figure 1-3 below you can also directly enter the value. Note however, only values
within the current range of the slider will be accepted.

Figure 1-3 - Color Selection Dialog

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Chapter 2 - Fledermaus

Figure 2-1 - Main Fledermaus Window

2.1 Introduction
Fledermaus is the central visualization application in the IVS system, which provides
a visual, interactive 4D data exploration and analysis environment. Fledermaus has
many different features and functions, some of which include:

the 4D data exploration system;

simultaneous representation of multiple data objects;

data management of a hierarchy of visualized objects;

robust geo-referencing system;

data analysis, quality control, editing; and

movie making

2.1.1 Starting Fledermaus

Depending on the operating system, Fledermaus can be started by double clicking
on the Fledermaus application icon, typing its name in a command line, or selecting it
from the Fledermaus program group located in the Windows Start menu. On the
Windows platform, double-clicking on a data file associated with Fledermaus such as
those with the .sd or .scene endings will start Fledermaus and load the selected
file.

2.1.2 Command Line Options

When started from a command line a number of options are available upon start up.
These are detailed below.
fledermaus

[
[
[
[
[
[
[
[
[
[
[

-data < file1.sd > [ file2.sd file3.sd ... ] ]

-scene < file.scene > ]
-image < imageFile1 [ imageFile2 ... ]> ]
-pfm < file1.pfm [ file2.pfm ... ] > ]
-flightpath < file.fph > ]
-mode < turntable | flight > ]
-device < isotrak | logitech > ]
-port < SerialPortName > ]
-global <global_scene_scale> ]
-view <cameraViewFile > ]
-h ]

When any of the optional command line arguments are specified they will override
your default preferences.
Any file names that follow the -data argument are assumed to be scientific data (.sd)
files that can be loaded into Fledermaus.
The -scene option specifies a scene file that could be loaded upon startup.
The -image option lets you directly load one or more image files of any format
supported by Fledermaus. If an image is in a format that supports georeferencing
such as a geotif, the image can be positioned and sized accordingly.
The -pfm option provides a quick method to load one or more PFM data files.
The -flightpath argument specifies a flightpath file to be loaded on startup.
The -mode option specifies which data exploration mode the system should use
upon startup.
The -device option specifies the default 3D input device to use with the system.
Normally this should be specified in the preferences.

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The -port command is used to specify the default serial port to use for communication
with the given 3D device. Again this is normally specified in the preferences.
The -view command allows loading a camera view file that specifies the location and
orientation of the camera. View files can be created through the View Manager.
The -h option will display the command line help text and exit.

2.1.3 Object Oriented Visualization

The visualization system is designed from the ground up to provide flexible objectoriented visualization. Each loaded data set in the system is considered an object.
The system supports many different types of objects, which can be categorized into
two types, either visual data objects or container objects, also called container nodes.
Visual data objects are designed to display some type of data within the system. For
example, surfaces are visualized using the SonarDTM visual object type. This object
type displays a shaded, uniformly gridded surface. When multiple objects are loaded
the scene does not merely consist of a large collection of polygons but rather a
collection of self-contained objects that work together to represent a scene.
Container objects provide data management abilities and allow the system to display
multiple objects simultaneously. The primary duty of a container node is to manage a
list of children objects. Any child object can itself be another container object with the
ability to manage a list of its children. The result is that the system is capable of
maintaining a hierarchical tree of objects.

2.1.4 Multistage Interruptible Rendering

One of the key features of Fledermaus is the ability to present and explore extremely
large data sets in near real-time. Fledermaus provides a very sophisticated rendering
engine to optimize the display of data in the most effective manner possible. The
system uses a two level rendering scheme to accomplish this goal.
Level one provides interactive rendering of the data objects using a degraded, or
lower resolution, version of the data objects. By reducing the amount of data to be
rendered (redrawn), the required update rates for smooth visualization are achieved
and the data objects can be rotated and moved in near real-time.
Normally, exploration of the data is done using this degraded model. However, as
soon as the exploration is stopped, the system immediately starts to draw the scene
at the highest possible resolution. The time it takes to complete the final level can
vary widely from a few seconds to many depending on the complexity of the scene.
The final level is usually drawn in the foreground where you see the final image as it
progressively renders over the first level rendition. The system rendering is smart,
drawing only what needs to be shown and attempts to draw from the center of the
screen outward.

2.1.5 ShiftScapeTM Rendering Engine

Fledermaus features the powerful ShiftScapeTM Rendering Engine. ShiftScapeTM
consists of a number of complex algorithms that automatically adjust the amount of
detail in the scene when exploring data. The effects of ShiftScapeTM can be seen
when zooming into a data set. As the viewpoint gets closer to a surface, more and
more detail is displayed. The detail is adjusted based on the performance of your
graphics hardware: for faster machines, more detail will be shown and for slower
machines, less detail is shown.

2.1.6 Fledermaus User Interface

The main Fledermaus application window consists of five important regions. These,
shown in Figure 2-2, are listed below and explained in detail in the following section.
Main Visualization Window in the center is the viewport into the virtual 3D world;
Geo-Referencing Info Bar just below the menu bar contains two information fields.
The first one displays information about the current rendering state, and the second
larger one displays the geographic position of the cursor when over the Main
Visualization Window;
Toolbar in the upper right hand side of the application provides dataset configuration
and interaction controls and also contains a few of the more commonly used system
functions;
Main Menu Bar that runs along the top of the application contains six menus that
provide file input and output functions, exploration and rendering options, data set
control dialogs, and options for a number of data tools; and
Data Object Control Region along the bottom of the window. All of the objects in the
3D scene can be edited using the information found here.

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Figure 2-2 - Fledermaus Main Window

2.2 Main Visualization Window

The Main Visualization Window is the viewport into the virtual 3D world. It is primarily
a display space but does contain a number of controls and interaction functions.
There are two different exploration modes that affect the visualization window and
these modes are described in the sections below. In addition to the exploration
modes, the mouse is used to perform actions such as geo-picking and surface
profiling.

2.2.1 Data Exploration Modes

Fledermaus provides two mechanisms for exploring data objects in virtual 3D data
space. Each mode allows you to position a virtual camera in the scene resulting in a
presentation of what the camera sees from its position and orientation within the
world. The exploration modes use different controls and user input to move this
camera about the scene.
The 3D flight uses a six-degree of freedom input device.
The mouse-controlled widget navigation interface, is based on a centered zoom and
rotate data manipulation technique.

Each of the exploration modes has strengths and weaknesses. The flight mode
provides for smooth navigation across both large and small datasets while the
widgets provide a fast and effective center, zoom and spin interface that quickly
focuses attention on the area of interest.
2.2.1.1 3D Flight Mode
This mode of exploration provides a powerful means to navigate around the 3D data
space with the use of a 3D input device, such as the BAT, or Space Navigator. A
supported 3D input device must be connected and turned on before starting this mode.
If using the BAT, press and hold down the trigger button on the 3D input device to
begin flying. While the button is held down, hand movements of the device are
mapped in a natural fashion to movements within the 3D scene.
For example, to move forward in the scene simply push your hand forward while
holding down the trigger. To move to the right you move your hand to the right.
Rotations are accomplished in a similar manner. To turn left you twist your hand to
the left, to turn up twist your hand upwards and so on and so forth. The speed of
movement in the 3D scene is mapped non-linearly from the hand movements of the
input device. Slow hand motions provide detailed and fine adjustments while fast
movements accelerate the exploration speed allowing you to quickly move around
the entire scene.

Figure 2-3 - Predictor Navigating Over a 3D DTM

The sample image in Figure 2-3 shows a visualization of a user flying northward,
beginning a downward turn, over a digital terrain map of eastern North America and
the Caribbean. The rectangular box, with its corresponding tails, is called the
predictor. It aids in navigation and helps prevent getting lost in the virtual world. As
you fly around the 3D data set, the predictor shows where you will be a short time in

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the future. The tails of the predictor provide a cue to velocity and a brief history of
movements. Thus it can be easily seen if you are going forward, backwards, or
turning, along with how fast you are currently moving (the longer the tail the faster).
2.2.1.2 Widget Navigation Interface
The alternate exploration mode is a mouse based widget navigation (pick and zoom)
interface that uses on screen widgets and direct interaction with the data space. The
main point to remember with this interface is that all rotations and zoom occur about
the center of the screen and picking on a new location will move that point in the
scene to the center of the display.
There are a number of different modes that affect the usage of the mouse buttons:
Explore, Select, and Polygon Select, indicated by three icons in the Mode section of
the Control Panel. A number of widgets have been included but these are not
necessary in all the modes. Figure 2-4 shows the layout of the on screen widgets.
See the Control Panel section for more information about the different modes.

Figure 2-4 - Non-flight Exploration Interface

The primary method of moving the data in the Fledermaus visualization window is via
the three buttons on the mouse. Their use depends on the mode selected. See Table
2.1 for a summary. The Explore mode is set as the default.
M o u s e
Modes

Left

B u t t o n s
Middle

Right

Explore

Click and drag Animated move to Click and drag for

surface to rotate picked
position profile
about either axis Zoom in if mouse
vertical
or moved up
horizontal
Zoom out if mouse
moved down
Note: In Explore mode, it is unnecessary to pick the surface
to obtain the position, as it is continuously updated as the
cursor is moved over the surface.

Select

Click on surface Same as Explore

for co-ordinate

Same as Explore

Polygon Select

Click on surface to Same as Explore

define points for
line or polygon
vertices
Double
click
to
close
polygon

Same as Explore

Same as Explore

Same as Explore

Click and drag on Same as Explore

surface
to
measure
distances.

Same as Explore

Area Select

Measure

Table 2.1 - Non-Flight use of Mouse Buttons

One feature of this interface is the use of the middle mouse button to pick and
zoom. Middle clicking on a point in the scene will move the center of the display to
that point. After the mouse click, if the button is held down then the view can be
zoomed in by dragging the mouse up or to the right, or zoomed out by dragging the
mouse down or to the left. This effectively allows both movements and zooming to be
accomplished with a single mouse button. Note that the pick and zoom function is
available in all modes. Any mouse equipped with a mouse wheel can now use the
wheel to zoom in or out of the scene. Rolling the wheel forward zooms in and rolling
the wheel backward zooms out.
While in Explore mode, the surface can be rotated by clicking and dragging with the
left mouse button anywhere on the Main Visualization Window. However, in the other

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modes the left mouse button serves a different purpose. The screen can be rotated in
these modes by clicking and dragging directly on the rotation widgets, as shown in
Figure 2-5. When the surface is being rotated around either axis, the corresponding
arrow bar will turn blue. Using the widget to rotate the data and then pressing the
middle mouse button while still rotating will lock the rotation at a constant velocity.
The arrowed bar on the rotation widget will change color from blue to pink to confirm
that the rotation has been locked as shown in Figure 2-6.

Figure 2-5 - Rotation of Surface

Figure 2-6 - Rotation Widget Colors

In Figure 2-6 the left image shows how the widget looks when rotating under user
control and the right image shows the widget locked in continuous rotation. Note that
the N on the rotation widgets indicates which direction is north.
The cone shaped arrowhead at the top of the vertical axes can also be grabbed and
dragged up or down to dynamically change the vertical exaggeration of the scene.
The value of vertical exaggeration will be shown in the Exag field near the bottom left
corner of the screen.
The widgets on the side of the Main Visualization Window may be used to either
zoom or translate. Translation moves the surface away from the center cursor and is

useful for viewing data away from the main surface such as a hanging sub-surface
seismic image.
The widgets have the ability to show a dynamic scale along their axis (see
Fledermaus Preferences). The scale is shown along both the vertical and horizontal
axis in units of the data set depending on the geo-referencing information. The
distances shown are from the center point of the axis. Normally geographic
coordinates are automatically projected to meters to give an easily understood
distance measurement. As you pan and zoom with the interface the scale will
dynamically adjust. The number of labels displayed is minimized so they dont
overwhelm the visualization but convey enough useful information.
In addition to the axis labeling, it is also possible to view the compass and declination
angles. A label associated with each rotation control will display. The top rotation
label displays the compass direction in degrees (0 is North, 180 is South, etc.). The
left rotation label displays the view angle to the surface. A negative number, for
example negative thirty, indicates that you are looking down on the surface at a thirtydegree angle. A positive angle would indicate that you are looking up at the surface
from below it.

2.2.2 Profiling
In the visualization window, clicking and dragging the right mouse button across the
scene produces a profile as shown in Figure 2-7. The profile is displayed in the
Profile Dialog. If this dialog is not already opened, it opens automatically when the
profile is drawn on the 3D surface.

Figure 2-7 - Profile Dialog

The colors displayed in the dialog represent the color of the surface profiled. The
axes are labeled with the height and distance along the profile. The length of the
profile, the vertical exaggeration and the profile's end points are displayed in the
Distance, V-Scale and End Points text fields, respectively. As the mouse cursor is
moved over the profile, the slope at that point is displayed in the Slope text field.
By clicking on the Profile button at the bottom left of the screen, a drop-down menu is
displayed with a number of options. Select the Save Profile menu option to save the
current profile to disk. Profiles are saved as a text file with the extension .pfl. Each

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point in the profile will be written out to the file as a distance along the profile and an
x, y, and height position. A profile that has been saved can be loaded from disk by
clicking the Open Profile menu option and selecting the profile in the file dialog box.
Click the Clear Profile menu option to erase the current profile. Click Recompute
Profile to recalculate the height of each point along the profile. This option is useful if
the scene has changed and you wish to update the profile to the current heights. The
Screen Capture menu item can be used to save an image of the current profile to
either a .Tif or .Eps file. Click the Screen Capture option and select the destination
image file and type using the file dialog box.
By default each time you drag a new profile the vertical scale automatically adjusts its
value. The Lock Scale toggle button locks the vertical exaggeration to which ever
value is entered, thus new profiles will maintain the same vertical scale. This option is
useful when trying to do comparative profiles. Click the Close button to dismiss the
Profile dialog.

2.3 Geo-Referencing Info Bar

The Geo-Referencing Info Bar sits directly at the bottom of the Fledermaus
application window and consists of two informational text fields. The right one
displays information about the rendering state of the visualization window and the left
field displays geo-referencing information for the cursors position within the
visualization window. There are 3 possible values for the rendering state: Normal,
Exploring, and Rendering Best. When the scene is fully rendered in the main window
the state will be Normal. As soon as an exploration action occurs such as flying,
using the 3D input device, or manipulating the navigation widgets, the system will
switch into Exploration mode. This mode normally renders the image in a somewhat
degraded state to make the scene motion smooth. The moment the exploration
stops, the system switches into Rendering Best mode while the application works to
fully render the data in the highest possible resolution. When the rendering is
complete the system returns to Normal mode.

2.4 Time Bar

The Time Bar is located directly below the main 3D visualization window and
contains all information and controls related to the time referencing functionality. As
shown in Figure 2-8, the time bar is divided into three major areas: the display area,
the control area, and the time options. Each area is explained in more details in the
following sections.

Figure 2-8 - Fledermaus Time Bar

2.4.1 Time Display and Manipulation Area

The Time Display Area that is located on the left side of the time bar provides both a
display of the current time, as well as the ability to interactively manipulate the current
time.

Figure 2-9 - Time Display Area

2.4.2 Time Control Area

Figure 2-10 - Time Control Area

To the right of the Time Display Area are a number of controls for adjusting both the
rate and the current mode of the time system. The default rate is 1:1, which means
that 1 second of real time equals one second of model time. This value can be
changed manually, or it can be modified using the following buttons:
Decrease the rate by a factor of 2
Increase the rate by a factor of 2
Reset the rate to 1:1
The mode controls are designed to emulate the controls on a DVD player and have
the following operations:
Jump to the beginning of time
Advance time at the current rate
Stop the advancement of time
Jump to the end of time
Start Recording Keyframes

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Figure 2-11 - Time Options Sub-Menu

2.4.3 Time Options

The Time drop down menu as illustrated in Figure 2-11, provides a number of
controls for working with the time system.
Loop - Instead of just playing to the current end of time, the system will continuously
return to the beginning of time.
Include Date - This will add a date display in the time display area.
Set Begin/End Times - This option allows you to set the beginning and ending times
for the current scene. There is also an option to rescale any existing keyframes to the
new length of time. If the keyframes are not rescaled, they will remain at the exact
same point in time as the original time frame.
Attach Camera to Main View - This command will attach the currently active camera
to the main Fledermaus display area.
Attach Camera to New View - This command will attach the current active camera to
the New View display area.
Auto Record Keyframes - When recording a movie, Fledermaus automatically
records keyframes as the camera moves around the scene. Editing other objects in
the scene is possible while the movie is being played and the Auto Keyframe
Spacing will be used when recording the keyframes as well. For example if
transparency is being animated, it is possible to drag the transparency slider during a
movie and Fledermaus will automatically generate keyframes for the transparency
using the Auto Keyframe Spacing.
Set Auto Keyframe Spacing - The Auto Keyframe Spacing indicates how often
Fledermaus generates keyframes. Note that this value is in real-world seconds, not in
the rate of the scene playback. The default Auto Keyframe Spacing is 1.0, meaning

that a keyframe is generated every second. Smaller values will generate more
keyframes and will be closer to the exact path traced by the camera. Longer values
will generate fewer keyframes which often makes a smoother animation path and
paths with fewer keyframes are easier to edit.
Clear Flightpath - To clear all keyframes for the currently active camera object, the
Clear Flightpath command can be used.

2.5 Control Panel

The Control Panel is located to the right of the Main Visualization Window and
contains a number of commonly used buttons that are discussed in turn here.
Camera Group
Clicking on the Reset Camera button returns to the default camera position. The
default camera view is normally looking down at the data at about 45 degrees;
however, this can be changed in the General Preferences if an alternate view is
desired. If the data objects are lost from view in the 3D scene simply click this button
to return to the default viewpoint.
Zoom to object (Z-key) button will move the camera so that you are viewing the
currently active data object.
Mode Group
The next set of buttons on this panel are the mode toggles. The three options
presented here control the effects of the three mouse buttons when used in the Main
Visualization Window. The five possible modes include:

Explore

Select, and

Polygon Select, and

Area Select, and

Measure

The default mode is Explore and optimizes the mouse buttons functionality to aid in
quickly and effectively navigating around the 3D visualized world.

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The Select mode is used for explicit geo-picking and is often used to support special
actions for the various loaded data objects. The actual actions depend on the data
type loaded and are described in detail in the chapter on data object types. Usually
when a surface is geo-picked, a cross appears at the pick point and the coordinates
of the point will appear in the Geo-Referencing Info Bar.
The Polygon Select mode is used to draw polygon structures or lines by picking
points on the visualized data. These polygons are used in conjunction with tools like
the Surface Query Tool and can also be saved into other data objects for
representing things like track lines, polygonal areas of interest, features on data, etc.
To aid in moving quickly between the picking modes with minimum mouse
movements, change of modes can be achieved by pressing the following shortcut
keys:

Space Bar Explore

S Select

P Polygon Select

A - Area Select

M - Measure Tool

Edit Group

Translate: This control is used to translate the current object in the X,

Y, or Z direction. These translations will directly modify the georeferencing
bounds for the object.

Rotate: The rotate control is used to rotate the current object around
the current rotation point.

Scale: The overall scale of any object can be adjusted using the
Scale control. The scale can be adjusted in one dimension at a time, or by
selecting the center of the control, all dimensions at the same time.

Change Rotation Point: To modify the point which the rotate control is
centered on, the Change Rotation Point control is used.

Display Group

The Color Map button will show or hide the currently loaded color
map in the Main Visualization Window. See the Controls > Color Map

Display menu for details on how to load a color map for display. If no color
map is currently loaded, toggling this option on has no effect.

The Bounding Coords button will show or hide the Root Node's
bounding box and associated coordinate labels. Note that coordinate
labels only appear after data has been loaded.

The Widgets button will show or hide the interaction widgets in the
Main Visualization Window. The shortcut key H can also be used to
accomplish the same task

The Object Selection button is used to toggle the selection widgets

that are displayed for the currently selected object. The button is on by
default.

2.5.1 Using Polygon Select Mode

To add a line, change to the Polygon Select mode and then pick the required points
on the surface. To save the line, select Data > Add 3D Lines, and then press the Add
Polygon Selection button in the 3D Line attribute panel.
Picking new points and pressing the Add Polygon Selection button again will add
another line. To create a closed polygon, double click on the last point entered.
Once the required lines are loaded they can be saved using the Save Object function
under the File menu. The lines can also be exported as an ASCII XYZ file by
pressing the Export XYZ button on the 3D Lines attribute panel and entering the
desired file name.
The polygon selection can also be used with the Geo-Picking Tab. See Section 2.8.1
for more information.

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2.6 Main Menu Bar

2.6.1 File Menu

Figure 2-12 - Fledermaus File Menu

2.6.1.1 Open Data Object/Scene

Prepared data is loaded into Fledermaus using the Open Data Object/Scene
command. The standard file dialog box allows the loading of one or more SD objects
or one Scene file. When a file is loaded, it will be added to the object list in the Data
Object Control region.
2.6.1.2 Save Object
The Save Object menu option is used to save the currently selected object to disk.
The currently selected object will be highlighted in the Data Set Control list located at
the bottom left corner of the Fledermaus window.
2.6.1.3 Save Scene
This option is used to save a scene file containing all currently loaded data objects,
their transformation settings, and any other visualization parameters.
2.6.1.4 Clear Scene
The Clear Scene option will remove all currently loaded SD files from Fledermaus.
2.6.1.5 Screen Capture
This option is used to save an image in the current visualization window to a file for
printing or publication. Selecting this option brings up the Snapshot dialog box.

Figure 2-13 - Snapshot Dialog

The image can be saved as either a tiff image or as an encapsulated postscript (eps)
file. Choose the image format from the Image Type pop-up. The entry field at the top
displays the name of the image file to be saved. The Image Size entry field gives the
output size (width x height) of the generated image both in pixels and in Megabytes.
The image size is based on the actual dimensions of the visualization window and
the magnification factor specified by the Magnification slider bar.
The magnification factor will be multiplied with the dimensions of the visualization
window to give the final image size. For example in Figure 2-13 the final image size
will be 4563 by 2265 pixels, the file will be 39.4 Megabytes in size and the
magnification factor is 3. With a magnification factor of 1 the image size will match the
visualization window exactly. Note that the amount of memory required for an image
increases by the square of the image dimensions. The memory requirements
indicate how much RAM will be required to save the image and may not reflect the
actual size of the resulting image file due to compression. When magnifying the
image ensure that enough memory is available in your machine to hold the image
before it is written to the file.
2.6.1.6 Preferences
Select the File > Preferences menu to open the Preferences dialog box shown in
Figure 2-14. Preferences are used to save personal settings for a number of options
that effect how Fledermaus runs.
Fledermaus offers an extensive number of settings that can be configured through
the Preferences dialog, for examples: system start-up settings, system colors, and
settings for the 3D flight exploration mode.

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Figure 2-14 - Preferences Dialog

The Preference Groups list box on the left-hand side of the dialog shows the
available preference groups. Selecting a preference group will display its controls on
the right hand side of the dialog. There are also a number of buttons along the
bottom of the dialog. The OK button applies all of the changed preferences and hides
the dialog from view. The Cancel button dismisses the dialog without saving any
changes. The Apply button sets all changed preferences without hiding the dialog
box. The Reset button will reset the preferences to their default (starting) values.
2.6.1.6.1

Startup

The Startup preferences determine how Fledermaus will run when started. You can
set the starting exploration mode and the default display mode. There are two
settings in this group, each configured through a pop-up menu. The two pop-up
menus are shown in Figure 2-15 and Figure 2-16.

Figure 2-15 - Interaction

Mode Pop-up

Figure 2-16 - Display Mode

Pop-up

The Interaction Mode pop-up lets you select the default exploration mode. See the
Exploration menu section for more details about these modes. The Display Mode
pop-up lets you select the default display mode. See the description of these modes

in the Rendering menu section. Note that changes to the Startup options will have no
effect until Fledermaus restarts.
2.6.1.6.2

General

The General preference group is a miscellaneous collection of settings that do not fit
in any other group. This dialog is shown in Figure 2-17. To return all docking panels
to their original positions when Fledermaus was started, click the Reset Dock
Windows button.
The Fledermaus background and foreground colors are displayed in colored boxes
to the right of each label in the Colors group. The background color gives the screen
color for the Main Visualization Window. The foreground color is used for things like
the bounding box and the color map outline. Clicking on either button beside the
color will allow a new color to be selected using the standard color selection dialog
(see the Color Selection Dialog section in Chapter 1 for more information).
To configure the Clipping Planes, the Global Scene Scaling Factor, or Push Back
Scale text fields type in a new value. For more information about the clipping planes
and the global scale refer to documentation for the Controls > Projection dialog box.

Figure 2-17 - General Preferences

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Turntable

Figure 2-18 - Turntable Mode Preferences

The Turntable Mode Preferences group contains options for the display of the
turntable widget interface in the center of the screen that consists of two axes and
two rotation scrollbars. The Show Widgets toggle controls whether these widgets will
be visible upon start up. If visible, the Show Rotation Scrollbars toggle controls if the
rotation scrollbars are visible. If set to invisible, a small circle will be drawn in their
place. When geo-referenced, a set of rulers will be drawn along the axis, consisting
of a number of tick marks and labels indicating the distance along the axis. The rulers
can be turned on or off using the Show Rulers toggle. If the Show Angles toggle is
enabled, the compass direction angle will be displayed by the top widget and the
angle of declination will be displayed by the left widget.
2.6.1.6.4

3D Flying

The 3D Flying preferences group controls the 3D flight exploration mode. Refer to the
Main Visualization Window section for more details about this particular exploration
mode. This preferences group is shown in Figure 2-19.

Figure 2-19 - 3D Flight Mode Preferences

The device toggle buttons on the left-hand side let you select the type of 3D device
you are connecting. Please check the picture to make sure the device you are
selecting corresponds to the device that is attached to the computer. The serial port
for the device can be chosen through the Device Port drop-down list.
The Predictor On/Off toggle lets you turn the displayed predictor on or off. Normally
the predictor is not displayed when you pause your flight. If you want to keep the
predictor displayed even when you are not moving, check the Retain Predictor check
box. If you do not want to see a predictor at any time during your exploration,
uncheck the Predictor On/Off check box.
There are four input fields that allow control of the sensitivity of the 3D flight
algorithm. Control values are changed by entering a new value in the appropriate text
field. The Move Threshold is the distance, in centimetres you must move the 3D
device before flying will begin. The Velocity Scale affects the speed with which you
travel through the 3D world. Similarly, the Turn Rate Scale affects the speed with
which you turn in the 3D world. For these scale factors an increase in the number
increases your speed or turn rate. The Alpha Scale affects the increase in turn rate
with increases in speed. Generally you will not need to change this last parameter.
2.6.1.6.5

Geo-Reference

The Geo-Referencing group preferences control the default settings for the georeferencing system. This group is shown in Figure 2-20.

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Figure 2-20 - Geo-Referencing Preferences

When the Always Show Bounding Coordinates toggle is set, the bounding box and
associated labels are shown for each data set by default.
2.6.1.7 Recent Objects
The File > Recent Objects sub-menu displays a continually updated list of recently
loaded sd object files. Clicking on any of the displayed files will load the
corresponding sd file. This option can be very useful when working with a group of
files that are constantly being reloaded time after time.
2.6.1.8 Recent Scenes
This sub-menu serves the same purpose as the recent objects menu but lists scene
files that have been recently loaded.
2.6.1.9 Exit
The Exit menu command is used to stop running Fledermaus. It will bring up a
message dialog that asks you to confirm the quit operation.

2.6.2 Exploration Menu

The Exploration menu controls how you interact with your data in the virtual 3D
world. This menu lists the available exploration methods including: a 3D Flight mode
which uses a six degree of freedom input device and a Turntable mode which uses a
set of direct manipulation widgets to explore your data. These modes are all
described in more detail in the Data Exploration Modes section.

Figure 2-21 - Exploration Menu

2.6.2.1 Plan View

The plan view is a special 2D display mode which can be used to display your scene
without any perspective modifications that occur with a 3D display.
2.6.2.2 3D Flight
Selecting the 3D Flight command changes the system interaction mode to the flight
based exploration mode using a 3D input device. If the input device has already been
activated the mode switch will occur instantaneously but if the device needs to be
initialized a warning dialog will appear and the system will start the device before
switching into the flight mode. For detailed information about how to operate in the
3D flight mode see the details in Section 2.2.1.1.
2.6.2.3 Turntable
Selecting the Turntable command changes the system interaction mode to the
widget based navigation interface. For detailed information about how to use this
mode see Section 2.2.1.2.
2.6.2.4 Stereo Mode
If the appropriate hardware is installed, the Stereo Mode option can change the Main
Visualization Window to display the data in stereo to be used in conjunction with a
pair of 3D stereo glasses. If the proper hardware is not installed, the current screen
settings will not support stereo, or if the stereo configuration file indicates that stereo
is not available, then this menu option will be disabled. Select this menu option to
activate or de-activate stereo mode. Stereo lets you interactively fly through data
space with the enhanced 3D sensation provided by stereo viewing. Liquid crystal
shutter glasses are required to work in this mode. See the section on Stereo
Hardware Setup in the installation manual for more information.

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2.6.2.5 Split Screen Stereo

Click the Split Screen Stereo menu option to enter split screen stereo mode. In this
mode, the Main Visualization Window splits into two parts: the left side displays what
the left eye would see and the right side displays what the right eye would see in a
3D scene. Using special hardware, these two images can be sent to two different
projectors and using polarized light, can be combined into a high-quality stereo
image. Click the Split Screen Stereo option again to leave split screen stereo mode.

2.6.3 Controls Menu

Figure 2-22 - Controls Menu

The Controls menu contains a variety of functions for controlling the interaction and
display of your data. The first section of this menu is used to show or hide the
different dock able windows in the Fledermaus display. This option is especially
useful on a dual headed system where some dialogs can be moved to the secondary
monitor allowing for a much larger visualization display area.
The second group of commands are described in the following sections.
2.6.3.1 Color Map Position
Selecting this option opens the Color Map Position dialog. This dialog is used to
setup the display of a labeled color map in the Visualization Window. In this way you
can provide a simple legend for any data set you have loaded.

Figure 2-23 - Color Map Control Dialog

The number of labels on the color map is specified using the Num Labels entry.
Changing any of these entry fields and hitting the Enter key causes the color map,
displayed in the Main Visualization Window, to be updated to reflect the changes.
The approximate position of the color map in the Main Visualization Window is
controlled using the rectangle in the lower right hand corner of the dialog. This
rectangle represents the Main Visualization Window with the small white box
representing the location the color map will be displayed. Clicking in the rectangular
boxed area will move the small white color map outline to a new location, placing the
color map to the same relative position in the Main Visualization Window.
2.6.3.2 View Manager
The View Manager button opens the View Manager Dialog shown in Figure 2-24.
This dialog allows the loading and/or saving of a particular camera position and time
to a file. The saved view is not linked to any data objects; it is merely a position,
orientation and time in the virtual 3D world.

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Figure 2-24 - View Manager Dialog

To save a viewpoint, click on the Record View button. The description for the view
can be changed by clicking on the default name that is first provided. To return to the
viewpoint that is stored in one of these files simply single click on the file name in the
View Manager list box.
2.6.3.3 New View
The New View menu option opens up a new 3D display window that can be explored
separately from the Main Visualization Window. This allows for multiple simultaneous
views of the visualized data. The secondary view is also used with some of the object
classes like the Vessel class to provide a view of the data from the perspective of the
Vessel.

2.6.4 Rendering Menu

The Rendering menu is used to configure the multistage rendering in Fledermaus.
Specifically, it determines how the high-resolution image is drawn when you pause in
your exploration; this is one of the important steps in the multi-stage interruptible
rendering algorithm. For more details about this, see the description of this feature in
the Main Visualization Window section. The Rendering menu is somewhat different
from the other menus; it contains four choices of which only one is active at any given
time. The rendering mode is determined by which menu command you select and
the current mode will be checked in the menu. For example, in Figure 2-25 the
Overlay with Hi-Res rendering mode is currently active.

Figure 2-25 - Rendering Menu

Rendering > Interactive In this mode the system continually redraws the scene
regardless of any user activity. The scene is drawn in the lower-resolution exploration
mode. This mode is used for dynamic scenes such as one having a real time Vessel
moving around in the scene.
Rendering > Replace with Hi-Res - Renders the high-resolution image in the
background, then it clears the low-resolution image and replaces it with the highresolution image. This provides an accurately rendered image but does not provide
any visual feedback while rendering the high-res imagery.
Rendering > Overlay with Hi-Res - Redraws the high-resolution image over top of the
low-resolution image. This is the most frequently used mode as one sees the high
resolution rendering as it progresses and can easily choose when to interrupt it.
Rendering > Overlay and Replace - Combines the previous two choices to provide
the best of both worlds: redraws the high resolution image both over the top of the
low resolution image and in the background, and clears the mixed low/high resolution
image and replaces it with the high resolution only.
2.6.4.1 Timed Redraw
This is a special rendering mode similar to Interactive, however rather than
continuously rendering the scene, it will automatically update based on a specific
time interval.

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2.6.5 Import Menu

Figure 2-26 - Import Menu

2.6.6 Import Gridded Data

The Import Gridded Data option will launch the gridded data import wizard. For
details of this wizard, see the DMagic chapter.

2.6.7 Import Ungridded Data

The Import Ungridded Data option will launch the data gridding wizard. For details of
this wizard, see the DMagic chapter.

2.6.8 Import Image

The Import Image menu option allows an image to be loaded directly into
Fledermaus. Select the file using the File Selection Dialog to begin the loading
process. Images will display as flat images in the scene.

2.6.9 Import Vertical Image

The Import Vertical Image option works similar to the Import Image option. Select
one of the supported image types using the standard file dialog box. This option
creates an image that is vertical in the scene. Seismic profiles or vertical pictures can
be imported using this function.

2.6.10

Import Lines

Fledermaus provides a convenient dialog for importing 2D/3D line and polygon data
into the system. The dialog box shown in Figure 2-27 facilitates this process.

Figure 2-27 - Import Lines Dialog

An ordering of YXZ would interpret the 1st coordinate as Y, the 2nd as X, and so on.
The 2D orderings, XY, and YX would look for only two values per line and would
default the Z coordinate to zero. These mappings can be changed using the Change
Mappings button.
The Sentinel text field is a special value which, when read from the input file,
indicates that the next point read will belong to a new line. As the application reads
the input file, each vertex of a line will be read. When the application reads the
sentinel value this triggers the start of a new line. For example:
1000
2000
2501
9999
1500
3000
3500

0
10
20
9999
30
40
50

-50.5
-58.2
-82.0
9999
-32.5
-74.0
-80.3

If the sentinel value is 9999 then this example represents two separate lines, each
with 3 vertices and the two lines are separated by the sentinel line 9999 9999 9999.

2.6.11

Import Points

The Import Points dialog shown in Figure 2-28 is used to produce a 3D Point data
object from an ascii data file. By default the system will assume an ascii file with
columns of data. This dialog can be used to select which columns are treated as x, y,
and z. In addition up to two fields can be selected to represent associated data along
with a label and action field. The label will treat the data as a label to be shown and

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the action expect the data to represent a command that the operating system can
run. This can be used to trigger external actions (like play a movie, lauch a web
brower to a specific page, etc.) when points are clicked. Data fields surrounded by
double quotes are treated as text field and can only be used for labels or actions. For
example, the following input file could have the labels One, Two, and Three
beside the three points:
333350.05
333385.22
333613.48

6251655.64
6252322.64
6252715.10

-14.24
-13.12
-14.42

"One"
"Two"
"Three"

By default the system will assume the data columns are ordered x, y, and z.

Figure 2-28 - Import Points

If you want to change the mappings, say you have y, x, z data click the Change
Mappings button to select the desired fields. The Custom ASCII Configuration
button brings up a sophisticated interface for importing more complex ASCII files.
This interferce shown in Figure 2-29, lets you perform actions such as skipping
header lines and setting the column separator if necessary. The system attempts to
analyze your input file and guess the number of data columns but if it is incorrect you
can adjust it. You then have the ability to configure each column. By default the
system tries to treat it as a number or if in quotes a string field. For dates and times,
which are often complex, there is the ability to configure how the fields are combined
together to represent and data and time. After configuring your ASCII file you will
probably need to use the Change Mappings button to select which fields are used
for what.

Figure 2-29 Custom ASCII Configuration dialog

In the ASCII configuration dialog, the gui elements include:

1. Header lines to skip: If there are lines at the beginning of the file that should be
ignored, enter the number of lines here.
2. Column Separator: The character used to separate columns. By default
("automatic"), both commas and spaces/tabs will be treated as column separators.
You can enter a comma if you don't want to accept whitespace-separated columns.
Whitespace after a column separator is always ignored.
3. Number of Columns: The number of columns or fields on each line of the input file.
Below these, a number of widgets are displayed; each line of widgets corresponding
to a column in the output file. The following widgets are displayed:
1. A color box: the field will ve highlighted this color in the preview if the file is being
read correctly.
2. The field number
3. A drop-down box for selecting the field type. The following options are available:
a) Integer Field: Can contain positive or negative whole numbers. For example: 1, 23,
-45, 0.

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b) Numeric Field: Any decimal number. For example: 0, 16, 128.2398, -12.3. Also
accepts trailing N, S, E or W, where S and W make th number negative, i.e.: 123.4N
= 123.4, 123.4S = -123.4, 123.4E = 123.4, 123.4W = -123.4.
c) Delimited String Field: A string that begins and ends with the specified character, '"'
by default. When this option is selected, a new box will appear where you can specify
the delimiter. For example, putting "'" in the box will cause the reader to except
single-quoted strings: 'A string' rather than "A string".
d) Fixed-Width String Field: A string column that always contains the same number of
characters but has no delimiter. (e.g. no quotes). When this option is selected, a new
widget will appear allowing you to enter the number of characters in the string.
e) Date-Time Field: When this option is selected, a box will appear allowing you to
enter a template for reading in a time value. The following characters have special
meaning; any other characters will be treated as a separator:
y

Year

Month

Day

hour

minute

second

ap or AP "AM" or "PM". If the template contains 'h' but not 'ap', then the hour will be
assumed to be 0-24.
z

millisecond

Examples:
Template

Valid Input Example

yyyy-MM-dd h:mm:ss.ss

"1990-03-12 18:23:37.35"

dd-MM-yyyy h:mm:ss ap

"12-03-1990 6:23:37 pm"

dd/MM/yyyy/hh/mm/ss/zzzz

"12/03/1990/18/23/37/3523"

hh:mm:ss.ssss

"18:23:37.3523"

hh:mm:ss.zzzz

"18:23:37.3523"

At the bottom of the dialog a preview window displays the first few lines of the input
file. When the reader is set up correctly, each column will be highlighted with thge
corresponding color in the preview.
In the example of Figure 2-29 the first field is a date and time and you can see the
configuration used to parse it properly. You can edit the configuration to import fairly
complex ascii files. This custom ASCII configuration dialog is also available in other
areas of the software where ascii point files are used for example as a source for
gridding.

2.6.12

Import PFM

One of the ways PFM files can be imported in Fledermaus is by using the Import
PFM menu option. Select a .pfm file with the File Selection Dialog to load the file.

2.6.13

Import DXF/DWG

The Import DXF/DWG command supports the direct importation of AutoCAD

DXF/DWG files into Fledermaus.

2.6.14

Import ArcGIS Shape

The Import ArcGIS Shape dialog allows for the reading of ESRI ArcGIS shapefiles
containing points, lines, polygons, or polylines.
Once a file is selected using the standard file dialog box, the dialog shown in Figure
2-30 will be displayed. Information about the selected object is shown in the File
Information area. For example, shapefiles will show the type of data (point, line,
polygon, etc.) and any detailed information on the data stored. If a database file
associated with a shape file is found, the imported data can be colored by one of the
fields of the database by selecting the field name from the Color by Attribute Field
popup. The database can also be viewed in a table by clicking on the Attribute Table
button. Click the Ok button to load and convert the ArcView file into a new
Fledermaus object.

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Figure 2-30 - Import Shapefile

2.6.15

Import Model

The Import Model menu option allows a solid model, consisting of a number of
polygons, to be loaded directly into Fledermaus. Choose a solid model with the File
Selection Dialog to begin the loading process.

2.6.16

Import S-57 ENC

The Import S-57 menu option allows an S-57 chart format, consisting of a number of
layers, to be loaded directly into Fledermaus. Choose a solid model with the File
Selection Dialog to begin the loading process. The mapping of S-57 attributes to
Fledermaus is done automatically.

2.6.17

Create Menu

The commands in the Create menu, as shown in Figure 2-31, make it easy to insert
a number of different data types directly into Fledermaus. Each of these data types
are fully documented in Chapter 3 on Fledermaus Scientific Data Types.

Figure 2-31 - Create Menu

The data objects that can be added include:

Plane - Adds a simple 2D plane whose z-height can be specified.

Grid - Adds a simple 2D grid object to the 3D scene.

3D Grid - Inserts a grid that can be draped on the 3D surface.

Label - Inserts a 2D textual label into the scene.

Figure 2-32 - Add Shape Sub-Menu

Shape - Adds a shape such as a box, sphere, cylinder, or cone.

Lines - Inserts an object that can visualize 2D or 3D line segments.

Vessel - Adds a vehicle object into the scene that can be linked to a realtime navigation system to have the object dynamically move in the scene.

Camera - Adds a new camera object that can be used for creating movies.

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Parent - Adds a new parent node to the scene. This object does not have
visualize any data directly, but is instead allows common objects to be
grouped and manipulated together.

2.7 Tools Menu

The Tools menu contains a number of operations that can be performed on data in
the 3D scene.

Figure 2-33 - Tools Menu

2.7.1 Contouring
Selecting the Contouring menu option will open the contouring dialog as shown in
Figure 2-34. It is necessary to specify which elevations will be contoured. The easiest
way to generate intervals is to click the Quick Intervals button. Clicking this button will
add a number of intervals in the Elevation Values in Range list box. To generate
contours at regular intervals specify the minimum starting elevation and the elevation
step amount in the Starting Elevation and Elevation Step fields. Once these values
are specified, clicking on the Generate Elevation Intervals will automatically add the
appropriate elevations to the list. Note that only intervals that fall within the range of
the selected data object will be added. Specific intervals can also be added directly
by typing the value in the Single Elevation entry field and clicking the Add button. The
new interval will then be added to the list. Intervals can be removed by highlighting
them and clicking the Delete Selected Values button. The Delete All Values will clear
all the entries in the list.

Figure 2-34 - Contouring Dialog

Labels can be generated for the contours by enabling the Label Contours toggle. If
the Label Contours toggle is turned on, enter the size of the labels to be generated in
the Label Size field. The size entered is approximately the height of the letters in units
of the data.
Once the desired contour intervals have been specified, clicking the Apply button
generates the contours and makes them appear in the 3D scene. The Cancel button
simply closes the dialog without performing the contouring operation.
2.7.1.1 Surface Difference
The Surface Difference command, which brings up the dialog box shown in Figure
2-35. It is used to initiate several kinds of surface-surface and surface-plane queries.
Object types that can be queried are selectable through the Surface #1 and #2 list
boxes, and the type of query to be applied is selected via the Query Type radio
buttons.
The selected query is applied to the specified data objects, and the scope of the
query is specified via the Query Polygon options. By default, the query is applied to
the common or intersection area of both input surfaces. However, a polygon can be
used to constrain the query scope to within a certain area. A polygon can be loaded
from the current polygon selection in the Main Visualization Window by clicking the
Load Vertices from Polygon Selection button. Alternately, a polygon can be loaded

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from an XY text file by clicking the Load Vertices from File button. Click the Clear
Loaded Vertices button to remove all vertices.

Figure 2-35 - Surface Difference Wizard - Stage 1

Clicking the Apply button initiates the query and the system computes the resulting
surface adding it to the list of available objects. The Query Results section of the
dialog displays information about the area and volume of the surface resulting from a
query.

2.7.1.2 Create Map Sheet

Figure 2-36 Map Sheet Creation Dialog

This menu item opens the Map Sheet Dialog, which is used to create and save a top
down, plan view of the current 3D scene as an image. There are two types of map
sheets that can be created: a Basic Map Sheet which displays only a top down view
of the data, and an Annotated Map Sheet which displays the map plus a title, scale,
and borders (Annotated Map Sheets must be saved in encapsulated postscript
format).
The Map Sheet dialog as shown in Figure 2-36 gives control over the map scale and
output image size for the map sheet. First, enter the final scale for this image in the
Map Scale text field. This defines the map scale to the real world scale. In the
example dialog, a map scale of 1:2400 means 1 unit on the map is 2400 units in the
real world. When this value is entered the width and height text fields just below the
map scale are updated. These values reflect the width and height (in inches) that the
map must be printed to accurately reflect the scale specified. The annotated width
and height (in inches) will reflect the exact size of the map if saved as an annotated
encapsulated postscript file.
In this dialog, specify the output file name using the File name field and specify the
image format in the Image Type pop-up. If saving the image as an encapsulate
postscript, then further options are given to either save the image as a Basic Map or
as an Annotated map. If the image is saved as an Annotated Map then the title of the
map image can be specified and the map image will automatically be saved as an
annotated map as described earlier. You also have the option to display a North
Arrow on the map using the toggle to the right of the Title area. To increase the
resolution of the output, specify a magnification factor in the Resolution slider. Click
on the Save button to save the image. Clicking on the Cancel button will dismiss the
dialog and take no action.

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2.7.1.3 Surface Statistics

Figure 2-37 - Surface Statistics Dialog

Surface statistics of the loaded surface can be viewed using the Tools > Surface
Statistics menu option. The Surface Statistics dialog box, shown in , will appear.
Properties of the current data set will be shown in the left text box, while the Surface
Statistics Information text box is populated with statistics about the data set.
2.7.1.4 Reproject
The Reproject tool can be used to convert an SD surface object from one coordinate
system to another. The dialog is shown in Figure X and will display both the current
(input) coordinate system and the output coordinate system, however only the output
coordinate system can be changed.

Figure 2-38 - Reprojection Dialog

2.7.1.5 Drape Image on Surface

Use the Drape Image on Surface menu option to import an image and drape it over a
SonarDTM surface. Click the Browse button to specify the path and name of the
image file using the standard file selection dialog, or select from the list of available
objects.
When importing an image, the software first cuts out regions from both the image and
the DTM that overlap. In order to match areas of the DTM and image, georeferencing
must be given for the image in the Georeferencing for image fields. Note that if an
image is opened that contains georeferencing (e.g. a geo-tiff), the values will
automatically be filled into the fields.

Figure 2-39 - Drape Image Dialog

Next, if the image has a higher resolution than the DTM, the DTM is rescaled to
match the image; however, if the DTM has a higher resolution than the image then
the image will be rescaled to match the DTM.
2.7.1.6 Attach Scalar to Surface
Any standalone scalar SD files can be attached to a surface SD file using the Attach
Scalar to Surface tool. Once attached, the scalar file can be used to shade the
surface and the scalar data will be displayed during any geo-picking operation on the
SD surface. The dialog for attaching a scalar is shown in Figure 2-40.

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Figure 2-40 - Attach Scalar Dialog

2.7.1.7 Mask Surface

Any surface can be masked using the Mask Surface tool. The surface file to be
masked will be the currently active data set and it will be displayed in the Apply Mask
To text field at the top of the dialog.
The Mask Source can be either an SD object or a supported geo-referenced image
file. The Mask Source will knock a hole in the loaded data component files whenever
data from the Mask Source is found intersecting any of the loaded data component
files. If the Mask Source is a geo-referenced image file, than the Ignore Transparent
Pixels checkbox will be activated. This gives the option to either ignore any
transparent pixels when masking the surface or not.

Figure 2-41 - Mask Surface Dialog

2.7.1.8 Extract Area

It is possible to export a region of the currently selected surface by selecting Extract
Area from the Tools menu. This menu option brings up the Bounds Entry dialog box,
where a rectangular sub-region of the surface may be extracted from the currently
selected surface or scalar object (see Figure 2-42).
A region to cut may be specified in one of three ways:
Custom Min and Max: specify a rectangular sub-section of the data by giving the
lower left and upper right coordinates of the box
Center and Radius: specify a rectangular sub-section of the data by giving the center
point, x radius, and y radius of the box
Corner and Size: specify a rectangular sub-section of the data by giving the lower left
corner plus the width and height

Figure 2-42 - Extract Area Dialog

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2.7.1.9 Render Movie

Figure 2-43 - Render Movie Dialog

The Fledermaus package contains tools that support the creation of standalone
digital videos from flight paths produced within the visualization system. These videos
can be viewed by most computer video players (such as QuickTime or Windows
Media Player) and display the data at its full resolution, not the reduced exploring
mode resolution used when animating in Fledermaus.
The first part of the Render Movie dialog is the Save movie as...section. This will
determine the root name for all movie frames that are generated. Your filename will
have a four-digit number and a file extension added to it: If, for example, your movie
contains 300 frames, you select JPEG as the image format and D:\foo\bar as the
base file name, the files generated will be stored in D:\foo\ and named bar.0001.jpg,
bar.0002.jpg, bar.0003.jpg, . . . bar.0300.jpg.
In the Output Format field, you must select the file format to save the images as
TIFF or JPEG. JPEG images are slightly lower quality than TIFFs but use
considerably less hard disk space.
The final option in the Render Movie dialog is Antialiasing, Antialiasing works by
rendering each frame at a higher resolution and then scaling them down to the
resolution of the output movie. This results in a higher quality image but causes
rendering to take quite a bit longer. The antialiasing factor is the size difference
between the rendered frame and the output moviean antialiasing factor of three will
mean that the render window will by three times as wide and high as the final movie.
In order for rendering to work properly the entire Render Window must be visible on
the screen with no other windows in front of it. (The exception to this is on Macintosh
computers; on these machines rendering will still work properly even if other windows
are in front of the Render Window.) Since the render window will be as big as the
output movie frames (larger if antialiasing is used), it may not always be possible to
render an entire frame at one time.

After you have adjusted all the parameters, position the Render Window so that the
entire window fits on the screen and is not covered up by any other windows. Dont
worry about the Data Sets window or Render Movie dialog as these will both
disappear once rendering starts. You must also ensure that there is no screen saver
active on your machine since it would obscure the Render Window when it activates.
Please see your operating system manual or IT support personnel for instructions on
disabling your screen saver if you dont know how. Once you are ready to proceed,
click the OK button to begin rendering. Rendering will probably take several minutes
to complete, during which time the Render Window must remain unobstructed.

2.8 Data Object Control Region

The Data Object Control Region provides information and controls for the data
objects actively loaded into Fledermaus. This section provides details that are
common to all data object types. Specific information about the attribute controls of
the wide variety of Fledermaus data types is found in Chapter 3 (SD Objects) of the
manual. This resizable region, show in Figure 2-44, is located along the bottom of the
Main Visualization Window. The vertical size of this region can be changed by
clicking and dragging on the horizontal bar that runs along the top of this region.
When the cursor is over the resize bar it changes from the standard left pointing
arrow to a light crosshair cursor. Reducing the size of this region makes the Main
Visualization Window larger and vice-versa.

Figure 2-44 - Control Region showing the Data Set Panel.

The Control Region has two different panels, the Data Set Control and the GeoPicking panel that are activated by clicking on their respective tabs located on the
bottom left. Clicking on the tab will bring that panel to the front. These panels are
described below.

2.8.1 Geo-Picking
The geo-picking panel, shown in Figure 2-45, has two sets of controls on the right
hand side of the display.
The first set consists of the Current Point text fields that display the actively picked
point along with additional text fields that allow a coordinate to be located in the 3D
visualization window. Clicking the left mouse button with the cursor in the 3D display

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while in Selection mode places a 3D crosshair at the picked point and fills in the X, Y,
and Z coordinates in the Current Point text fields.
The second set of controls allows you to locate a coordinate location in the 3D
display. After entering the X and Y coordinates in the text fields below the Locate
Point button and clicking the Locate Point button, a long vertical line will be drawn
through this X and Y location in the 3D scene. Clicking on the Clear Point button will
clear both text fields and remove the vertical line from the 3D display.

Figure 2-45 - Control Region showing the Geo-Picking display

A table on the left side of the panel is used to store a number of points. When
Fledermaus is in Select mode and the Auto Add Points toggle is enabled, a point will
be added to the table every time a point is clicked in the Main Visualization Window
with the mouse. The table lists the X, Y, Z positions for the point and a Scalar value if
it exists. Any of the values in the table can be edited by double-clicking on a table
cell. A label can be assigned to a point by double-clicking on a Label field and
entering a value. Click the Clear button along the bottom of the table to remove all
points. To import points from an XYZ file, click the Import button and select a file, or
to export points from the table, click the Export button. A 3D Point object can be
created from the selected points by clicking the Table Action button and selecting
Create 3D Point Object. Similarly, a 3D Line object can be created by clicking the
Table Action button and selecting Create 3D Line Object.
2.8.1.1 Object Attribute Controls
Shown to the right of the loaded object list is the attribute control area, which takes up
the bulk of the display space for the Data Object Control Region. The display will
change depending on the type of object currently selected in the list. These controls
provide the ability to manipulate data type specific information related to the selected
object. This includes things such as how the information is presented and what
actions can be performed on the selected data set. Each data type in Fledermaus
has its own set of controls. These can range from a few controls to a highly
sophisticated system, such as the PFM sounding class, which is a substantial data
processing system wrapped up into an object. The following sample screen shots
illustrate attribute displays for several common object types including the SonarDTM,
3D Line, and PFM object types.

Figure 2-46 - Sample SonarDTM class

Refer to Chapter 3 on Data Types, which describes in detail the function and controls
of the many object types available in Fledermaus.

2.9 Data Object List

The data set control provides the ability to manage data objects actively loaded into
the application. In addition, it provides access to data set specific control functions for
the selected object. The control is shown in Figure 2-47. The only controls on the
panel that are constantly displayed are found on the left hand side of the display. The
rest of the data set control will change depending on what kind of data object is
selected.
2.9.1.1 Object List

Figure 2-47 - The Constant Controls on the Data Set Control

The list-box in the center of these controls displays the names of all currently loaded
data objects. If there are more objects than can fit in the list box a scroll bar appears
so you can scroll up and down the list. Selecting an object's name makes it the active
object that the rest of the controls manipulate. The object names are indented to
show the hierarchical relationship between the objects. All objects are considered
children of the root node, which is why the seven loaded objects in the example are
indented from the root node. However, some of the children may themselves have

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children. These second-generation children are further indented from their parent to
show this relationship. Any transformation performed on the parent of a group of
children objects will also affect all the children as well. For example, if the Z scale of
the root node is increased by a factor of two, every object's Z axis will appear to be
scaled by a factor of two. If a data object has no descendants then transformations
performed on it will affect only it. The same relationship applies when showing or
hiding objects. Hiding the root node automatically hides all of its children, which hides
every data object in the system. To show or hide a data object, click on the checkbox
to the left of the object name.
To close a data object file, removing it from the 3D scene, select its name in the data
list and press the Delete key. Note that this only removes it from the active 3D scene
it does not affect the sd file on disk in any way. Objects can also be deleted from the
Right-Click Menu.
2.9.1.2 Object List Right-Click Menu

Figure 2-48 Object List Right-Click Menu

To access the Right-Click Menu as shown in Figure 2-48, click the right mouse
button on an object in the list.
Rename Object will allow a new name to be assigned to the selected object. Enter a
new name in the Name field and click OK to apply the change, or Cancel to dismiss
the dialog.
Zoom to Object will move the camera so that the currently selected object is
displayed in the main display area.
Clicking the Save Object menu option will save the selected object to disk.
Remove Object will remove the object from the current scene.
Clear Scene will remove all currently loaded objects from Fledermaus.
2.9.1.3 Exaggeration Field
The Exaggeration text field stores the current vertical exaggeration factor for the root
node, which corresponds to the vertical exaggeration factor for the entire scene. To
change this value, enter a new number in the text field and press the Enter key. A
value of 1.0 results in no vertical exaggeration, while a value of 2.0 results in the

heights being stretched twice as high as they should be, and so on. The
exaggeration can also be adjusted by clicking and dragging the cone on top of the
central widget in the turntable interface mode.
2.9.1.4 Tool Options

The tool options button will display a dialog containing any options related to the
currently active tool. The following tools have options:
- Translate Tool: Options for manually entering translation values.
- Measure Tool: Options for changing the measurement algorithm.
- Selection Tools: Option for clearing the current selection.
2.9.1.5 Undo

The Undo command is used to undo one or more changes that were made using any
of the manipulation tools, which includes translation, scaling, or rotation.
2.9.1.6 Object Lock

The Object Lock button will prevent any of the manipulation tools from operating on
the selected data object. By default, all surface objects have the lock enabled.

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Chapter 3 - 3DEditor

3.1 Introduction to the 3DEditor

The 3DEditor is the main application used to perform area based editing on a PFM
file. This application provides the functionality to examine and edit many of the flags
contained within the PFM. As well, numerous options exist to visualize the data in
useful ways, including drawing the surface associated with a set of soundings, or
drawing lines connecting the swaths in a multi-beam file. The 3DEditor is usually
used to edit soundings but can also be used to edit CUBE Hypotheses or Targets as
well. For editing Targets see Section 3.11 and for editing CUBE Hypotheses see
Section 3.16. The rest of this document assumes that soundings are being edited.
Editing is usually performed by first selecting a set of soundings, and then rejecting,
un-rejecting, setting, or clearing a flag for those soundings. While using the 3DEditor,
the mouse is used for navigating through the scene and also selecting and
deselecting soundings. The right-click menu also contains many options for editing
and can be accessed by right clicking on the main window.

3.1.1 Starting the 3DEditor

Currently the 3DEditor can only be started from Fledermaus when a PFM file is
loaded and an area is extracted. To load an area in the 3D Editor, make a selection
on a PFM file using Select mode, as shown in Figure 3-1, and click the Launch 3D
Editor button in the Surface Control Panel. As a shortcut, the 3D Editor can also be
started by pressing the 3 key when the Main Visualization Window is selected.
Alternately, a polygon can be picked on the surface using Polygon Select mode in
Fledermaus. Then, when the 3DEditor is loaded, only the area inside of the polygon
will be displayed. Figure 3-2 shows a surface resulting soundings loaded in the 3D
Editor. If the selected area contains more than 150000 points, a dialog asking for
confirmation will be displayed before the points are loaded in the editor.

Figure 3-1 - Selected Area for Edit in Fledermaus

3.1.2 3DEditor Interface

The general layout of the 3DEditor is similar to the main Fledermaus functionality and
contains the following components (shown in Figure 3-2):
Main Visualization Window
Control Bar
Editor Panels

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Figure 3-2 - 3DEditor Interface Overview

Each component of the interface is discusses in the sections below.

3.2 Main Visualization Window

The Main Visualization Window of the 3DEditor displays the soundings from the PFM
file that are being edited. The unedited soundings will be displayed as a set of small
cubes that are colored by height. To navigate around the display, the same widgetbased interface as Fledermaus is used.
Outside of the soundings shown in the Main Visualization Window is a green, 3dimensional grid that represents the bounds of the loaded data. In UTM, the Eastings
and Northings are displayed along the bottom of the data and in Geographic
coordinates, the longitude and latitude are shown. The grid spacing along the bottom
of the grid indicates the cell spacing of the file. Determining which soundings
contribute to which cell can be examined by looking straight down (plan view). The
different height values are shown in meters along the vertical axis.

When the mouse is moved, the sounding located closest to the mouse cursor
becomes highlighted and information pertaining to it is displayed at the top of the
window. The displayed information includes the record, sub-record, line, file, UTM
coordinate, and Geographic coordinate. As well, the number of selected soundings is
displayed at the top left of the interface. To prevent the sounding information from
being constantly updated as the mouse is moving, double-click the left mouse button
to lock the currently highlighted sounding. Double-clicking a second time will unlock
the sounding.
The 3DEditor contains five modes: Explore, Select, Area Select, Record Select, and
Measure. Each one of these modes can be activated from the Control Bar (see
Section 3.3). Switching into Select or Area Select mode, and then clicking the left
mouse button selects points. Once selected, a white cross will appear over a
sounding to indicate that it has been selected. Note that the title bar displays the total
number of points being viewed, and the box at the top left of the screen displays the
number of selected soundings. Record Select mode allows selecting and deselecting
whole records at a time (i.e. one entire ping). To deselect a set of points, hold down
the Shift key while clicking or dragging with the left mouse button. Table 3.1
describes the usage of the three mouse buttons in the available modes. The Explore
mode is set as the default. Figure 3-3 shows a selected set of soundings after
dragging in Select mode.
To measure the distance between two soundings, switch into Measure mode and
click the left mouse button on the first sounding to measure from. Moving the mouse
to another sounding in the display will cause a line to be drawn between the
soundings in the Main Visualization Area and the distance in meters will be displayed
in the upper left corner of the interface. The compass angle and the angle of
declination between the soundings will also be displayed in the upper left corner.
Click the left mouse button again to start another measurement.

Left

Mouse Buttons
Shift + Left
Middle

Right

Modes
Explore

Pick and drag

surface to rotate
about
either
horizontal
or
vertical axis.

Animated move to Show rightselected position, click menu

and zoom in if
mouse moved up,
or zoom out if
mouse
moved
down.

Select

Single click to Single click to Same as Explore

select
the deselect
the
highlighted point; highlighted

Same
Explore

as

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drag to select a point; drag to

box shaped area. deselect a box
shaped area.
Area
Select

Single click to
select
the
highlighted point;
drag to select an
irregular area.

Single click to Same as Explore

deselect
the
highlighted
point; drag to
deselect
an
irregular area.

Same
Explore

as

Record
Select

Single click to
select the record
(swath) that the
highlighted point
is a part of; drag
to
select
all
records
that
contain a point in
the box.

Single click to Same as Explore

deselect
the
record (swath)
that
the
highlighted point
is a part of; drag
to deselect all
records
that
contain a point
in the box.

Same
Explore

as

Measure

Single click to
start
measurement.
Single click again
to
stop
measurement.

Same as Explore

Same
Explore

as

Table 3.1 - Mouse Buttons in the 3D Editor

Figure 3-3 - Selecting Soundings using Select Mode

Depending upon the flags set for a sounding, it will appear as a different symbol in
the Main Visualization Window. How the different soundings appear can be
controlled using the Soundings Panel in the Editor Panels or the Control Bar. Table
3.2 lists all sounding classes in order of priority and lists the default display attributes.
See Section 3.7.2 for more information about changing the sounding display.
Sounding Type

Default Display Attributes

Deleted

Red Diamond

Feature

White Cylinder

Plotted

Outlined box colored by depth

Suspect

Yellow Diamond

Normal

Box colored by depth

Table 3.2 - Types of soundings in the 3D editor

Note that some formats now support NBR (i.e. no bottom return) soundings. These
soundings have an X and Y position, but no depth. If the PFM contains a custom flag
named NBR, soundings with that flag set will be drawn as an outline shape (usually
an outline red diamond) at the base of the 3DEditor.

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3.3 Control Bar

The Control Bar on the right side of the interface as shown in Figure 3-4, is used for
controlling the view, editing mode, sounding display, and for simple editing.

Figure 3-4 - 3DEditor Control Bar

The buttons located at the top of the Control Bar allow control of the Camera:
The Reset button will return the viewpoint to the initial position.
The Plan button locates the viewpoint directly above the data.

The North button will allow viewing of the data towards the north.
The East button will moves the camera so it is looking east.
Clicking the Slope button will try to orient the view so that it is looking along the
slope of the data. This option is useful if the data is roughly planar, as the outliers will
typically lie above or below the slope of the data.
The Editing Mode area indicates whether the 3D Editor is editing soundings, CUBE
Hypotheses, or Targets. The interface changes depending upon which editing mode
is selected. When in either CUBE Editing or Target Editing mode, the color of the 3D
grid and the color of the status panels will change to indicate that the editor is in a
different mode. See Section 3.16 for information on CUBE Editing and see Section
3.11 for information on Target Editing.
The different cursor modes are described in the previous section on the Main
Visualization Window. The four modes available modes, including their shortcut keys
in brackets, are as follows:
Explore Mode (Space)
Select Mode (S)
Area Select Mode (A)
Record Select Mode (R)
Measure Mode (M)
The Display group controls which items are visible in the Main Visualization Window.
If the Soundings toggle is enabled, all non-rejected soundings are displayed on the
screen. If the Rejected toggle is set, all soundings that have been rejected are drawn
(these soundings are usually drawn as red diamonds). The surface generated from
the unrejected soundings can be displayed by clicking the Surface toggle, or lines
connecting all soundings in a single record can be drawn by enabling the Connectors
toggle. If the Targets toggle is enabled, any targets in the current area are displayed
and if the Hypotheses toggle is enabled, any loaded CUBE Hypotheses are shown.

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The Soundings group allows configuration of various properties of the displayed

soundings in the Main Visualization Window. Use the Color By menu to control how
non-rejected soundings are displayed on the screen (see Figure 3-5).

Figure 3-5 - Color By Menu

If any custom flags or attributes exist in the PFM, they will also be available in the
menu. For more information on coloring soundings see Section 3.7.2. The Highlight
By menu allows drawing all soundings that match a certain flag as a lighter color. Any
available custom flags will also appear in this menu. If a dataset has a custom
attribute, second depths can be drawn using the Sec. Depths menu (see Section
3.13 for more information). The Size slider controls how large the points are drawn
on the screen.
The current selection can be cleared by clicking the Clear button. To invert the
selection (deselect all selected points and select all previously unselected points),
click the Invert button. Some extra options for selecting soundings can be accessed
by clicking the Select By button, which will display the menu in Figure 3-6. Selecting
any of the menu options that correspond to flags (i.e. Modified, Suspect, Plotted,
etc.), will select all soundings in the editor that have that flag set. Clicking the
Manually Rejected option will select all soundings that have been rejected by an
operator, and clicking the Filter Rejected option will select all soundings that have
been rejected by an automated filter. The Rejected menu option will select both
manual and filter rejected soundings at the same time. See Section 3.7.4 for more
information on the Shoal, Deep, or Outliers options.

Figure 3-6 - Select By Menu

Once a selection has been made with the mouse, the selected points can be marked
as invalid by clicking the Reject button. Note that the rejected points are not actually
removed from the file but a flag is set. To view the rejected points, click the Rejected
toggle in the Mode group. The rejected soundings can then be selected with the
mouse and undeleted by pressing the Unreject button.

3.4 Right-Click Menu

The right-click menu can be accessed by right-clicking on the Main Visualization
Window. The Control Bar can be used for simple rejecting and unrejecting of data,
but to set other flags (suspect, plotted, feature, etc.), the right-click menu must be
used.

3.4.1 Selection Menu

The Selection > Select Sounding and Selection > Deselect Sounding menu options,
accessed using the right mouse button, are used to select or deselect the highlighted
point (see Figure 3-7). Clicking the Select Record option will select the whole record
that contains the highlighted point and Deselect Record will deselect the whole
record that contains the highlighted point. The Select Line, and Select File options
work the same way: they select all soundings that have the same line or file as the
highlighted sounding. The Clear and Invert options are identical to the buttons on the
Control Bar and are only located here for convenience. Note that some operations
have shortcut keys that are listed to the right of the menu item.

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Figure 3-7 - 3DEditor Selection Menu

3.4.2 Edit Menu

The Edit Menu (see Figure 3-8) is the main method of setting flags in the 3D Editor.
The Reject and Unreject menu options are identical to the buttons on the Control Bar.
The other flags, Suspect, Plotted, and Feature can be edited using the Set or Clear
menu options. Note that if any custom flags exist in the PFM file, they will appear in
the Set or Clear menu options (some files may have Class1 and Class2, other files
may have other flags). The typical use of the Edit menu is to make a selection and
then select one of the options from the menu. However, if no soundings are selected
when one of the Edit options is selected, the operation will be applied to the
highlighted sounding. For example, to simply reject one bad point, make sure no
points are selected, highlight the point by moving the mouse over it, right click, and
select Edit > Reject.

Figure 3-8 - 3D Editor Edit Menu

3.4.3 Hide Menu

Figure 3-9 shows the Hide menu, which can be used to temporarily hide some of the
soundings in the display so that other soundings can be viewed more easily. For
example, an operator may wish to view just one line or one file at a time. Hiding a
sounding makes no changes to the actual file and soundings will remain hidden only
as long as the current editor session is open. To hide a set of soundings, first select
them using the mouse and then click Hide > Hide Selected. The Hide > Hide
Unselected will hide all of those soundings that are not selected. To unhide
soundings, click the Hide > Unhide All menu option. To view one line at a time,
highlight a sounding that is part of that line, click Selection > Select Line, and then
Hide > Hide Unselected.

Figure 3-9 - 3D Editor Hide Menu

3.4.4 OmniViewer
Clicking the OmniViewer menu option will open the OmniViewer application (see the
Additional Data Tools chapter for more information). The OmniViewer will display
information from the original data files for the selected sounding. Note that the
OmniViewer will only work if the original sources files are in the correct place on disk
(the files should match the file= statement in the status bar of the 3D editor).

3.5 Menus
3.5.1 File Menu
The File menu (see Figure 3-10) is used to save changes, close the 3D Editor, or
move the visible area. After changes have been made, the File > Save menu option
must be clicked to write the changes to the disk. Optionally, the File > Save & Exit
command saves any changes and then closes the editor. The Exit button will close
the editor and any unsaved changes will be lost. Clicking on the Save or Save & Exit
button will also update the surface being displayed in the main Fledermaus window.
If auditing is turned on, any changes written to the PFM file are also written to an
audit file. See Section 3.13 for more information.

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Figure 3-10 - 3DEditor File Menu

Click the Set Checked Area option to mark the bins in the current area as checked or
click the Reset Checked Area option to clear the checked flag from all bins in the
area. The Move North, Move South, Move East, and Move West options can be
used to shift the whole loaded area by 50% in the given direction. These options can
be used to systematically scan through the data. The Expand Area option loads in a
larger area around the current area (zooms out), and the Shrink Area option loads a
smaller area (zooms in). To prevent the z range from changing while scanning
through data, see the Lock Z Range option on the Options menu.

3.5.2 Display Menu

The Display menu, shown in Figure 3-11, controls what items are displayed in the
Main Visualization Window. The Show Grid option controls whether the green grid is
displayed around the data points. Turn off the Show 3D Grid control to just show the
base of the grid. Show Stalks draws a line from each point to the base and is most
useful for datasets containing only a few number of points. The Show Coordinates
option controls whether the X, Y, and Z labels are shown along the edges of the grid.
The interaction widgets can be shown or hidden using the Show Widgets menu
option. If the widgets are visible, then the Show Rulers and Show Angles options
determine whether the axes labels or direction angles are shown respectively. The
Show Second Depth Stalks toggle is used when displaying second depths (see
Section 3.13).

Figure 3-11 - 3DEditor Display Menu

The Show/Hide Lines or Show/Hide Files displays a dialog box similar to Figure 3-12.
This dialog shows a list of all files or lines that have soundings loaded in the editor.
Check or uncheck the box beside each item to show or hide that item. The Apply
button performs the operation without closing the dialog. The OK button applies the
operation and closes the dialog and the Close button cancels the operation.

Figure 3-12 - Show/Hide Files Dialog

3.6 Slices Menu

The Slices Menu allows viewing just a portion of the points that are loaded in the 3D
Editor. Click Start Slice to enter slice-editing mode or End Slice to leave slice-editing
mode. While in slice-editing mode, use Next Slice to advance to the next slice or
Previous Slice to return to the last slice. See Section 3.8 for more information about
slice-based editing.

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Figure 3-13 - 3DEditor Slices Menu

3.6.1 Options Menu

Figure 3-14 shows the Options Menu, which can be used to control the current
interface. The Options > Save Current Interface option writes the current state of the
interface to a preference file. The next time the 3DEditor is loaded, the interface will
be configured the same as when saved. Included in the current state of the interface
is the shape and color of each type of sounding, all display options, background
color, and current color map. For example, if you wish the interface to draw
soundings with spheres, make the change and select Options > Save Current
Interface. Then, every time the editor is loaded, the soundings will be drawn using the
desired shapes.

Figure 3-14 - 3D Editor Options Menu

The Options > Reset Interface returns the interface to the original set of options.
Save Current Interface must be selected again to make the changes permanent. The
Preferences menu option displays the Preferences dialog as shown in Figure 3-15.

Figure 3-15 - 3DEditor Preferences Dialog

By clicking the Set Background Color button, a new background color can be
selected for the editor using a Standard Color Picker. Enter a color map to use when
coloring soundings in the Color map field, or select one using a file dialog box by
pressing the Browse button. Colors for the connectors can also be chosen by clicking
on the Set Left Color or Set Right Color buttons (the default is green and red). Adjust
the width of connector lines by entering a new value in the Connector Line Width text
field. Press Apply to set the selected preferences or OK to apply the preferences and
close the dialog. Clicking Cancel will dismiss the dialog without making changes.
When the Lock Z Range toggle is enabled on the Options menu, the 3D Editor will
not automatically adjust the displayed z range depending upon the data range.
Actually, the displayed range may increase if data is loaded outside of the range, but
the range will not decrease. This option is useful for comparing different areas in the
3D Editor. When used with the Move North/South/East/West options on the File
menu, the z range will not jump to fit the data. Click the Lock Z Range toggle to turn
this option on or off.
Note that the Control Bar or Editor Panels can be shown or hidden by clicking on the
Control Bar and Editor Panels menu options respectively.

3.7 Editor Panels

The Editor Panels are a set of tabs along the bottom of the screen. These tabs are
only for advanced editing as most of the editor functionality is contained in the
Control Bar and the Right-Click Menu.

3.7.1 Attributes Panel

The Attributes Panel displays a table of all currently selected soundings. This table
includes all of the information stored in the PFM file for each sounding. When a
sounding is selected in the table, it is displayed in a highlighted color and is also
highlighted in the Main Visualization Window. The Attributes Panel is shown in Figure
3-16. To sort the table in ascending or descending order, the headings of the different
columns can be clicked with the mouse. Note that to prevent the selected soundings

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in the Main Visualization Window from changing as the mouse moves, the window
can be double-clicked to lock the selection.

Figure 3-16 - 3DEditor Attributes Control Panel

3.7.2 Soundings Panel

The Soundings panel, shown in Figure 3-17, allows control of how different
soundings are displayed. The Gap text field indicates the point gap used when
exploring the surface and the Auto toggle informs the ShiftScapeTM rendering engine
to automatically adjust the gap. There are two main sounding classes: rejected and
normal (not rejected), as well as three selected sounding classes: suspect, plotted,
and feature.

Figure 3-17 - 3DEditor Soundings Control Panel

The shape, color, and visibility of each sounding class can be controlled separately.
Each sounding can either be displayed as a box, point, sphere, diamond, cylinder, or
outlined box. For large data sets, displaying soundings as points may be faster than
the other shapes. A variety of coloring methods also exist including coloring by depth,
solid color, record, sub-record, line, file, modified, or checked. Note that if the PFM
file contains any additional attributes or flags, they will also appear in this menu and
can be used for coloring the surface. Figure 3-18 and Figure 3-19 show the pull down
menu selections for Shape and Color By. Coloring a surface by line or record makes
visualizing which soundings are related much easier. For an example of coloring a
surface by line, see Figure 3-20. The Color By menu in this tab is similar to the Color
By menu used in the Control Bar.
If any selected sounding type is marked as invisible, then all points of this type are
displayed as normal soundings. To view only those soundings that are marked with a
certain flag, turn off the Visible toggle for Normal soundings, and turn on the Visible
toggle for whichever selecting soundings you wish to view.

Figure 3-18 - Selection of Sounding Shape

Figure 3-19 - Selection of Sounding Color

Figure 3-20 - Coloring a surface by Line

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3.7.3 Surface Panel

Figure 3-21 - Displaying a smooth surface in the 3D Editor

The 3D Editor is now capable of displaying the surface or DTM that result from a set
of soundings as shown in Figure 3-21. The Surface Panel (Figure 3-22) controls how
the surface is displayed. To show the surface, select the Visible toggle or click the
Surface toggle in the Control Bar. If the Surface Stalks toggle is enabled, a stalk is
drawn from each sounding to the created surface. By default, each surface is drawn
via interpolation and thus might not match exactly what is expected. To draw each
cell at the exact calculated height, enable the Flat toggle (shown in Figure 3-23).
Also, shading is usually applied to the generated surface. At times the shadows can
be distracting and can be turned off using the Shade toggle.

Figure 3-22 - 3D Editor Surface Control Panel

The Surface, Color By, Transparency, Mesh Gap, and Auto controls are similar to the
Surface Control tab in the main Fledermaus window. See Section 4.8.2 for more
information. One additional option on this tab is to display an Outlined Surface, which
is a regular DTM with a white grid laid on top.

Figure 3-23 - Displaying a flat surface in the 3D Editor

3.7.4 Utilities Panel

The Utilities Panel, shown in Figure 3-24, contains a number of utilities for selecting
soundings in the editor. Clicking the Shoal button will select the shoalest sounding in
the whole area and clicking the Deep button will select the deepest sounding in the
whole area. The Outliers button will select all soundings in a bin that are more than
Dist meters away from the average bin height.

Figure 3-24 - 3D Editor Utilities Control Panel

The four buttons on the right side are used to select a set of soundings that have a
certain flag set. Clicking the Suspect flag will select all soundings in the editor that
have the suspect flag set. The Plotted, Features, and Rejected buttons work similarly

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for their respective flags. These buttons can be used for a search-and-replace type
operation. For example, to change all flags in the display from plotted to feature, click
the Plotted button and then on the right-click menu select Edit > Set Feature and then
Edit > Clear Plotted.

3.8 Slice-Based Editing

Figure 3-25 - Using the 3D Editor in slice mode

Slice-Based Editing allows loading a large number of soundings into the 3D Editor
and then viewing cross sections of the data in a systematic way to inspect all of the
data points. Enter slice-based editing mode by clicking the Slices > Start Slice menu
option, or the Start button in the Slices section of the Control Bar. The 3D Editor will
show a cross-section of the data containing a certain percentage of the whole range
of the data. Yellow lines will be drawn on the base plane to indicate the bounds of the
slice (see Figure 3-25). Note that the orientation of the slices is chosen based on the
current view direction when slice-mode is started.
Change the percentage of data to be shown by entering a value in the Slice Size field
in the Control Bar and pressing Enter (the default is 5 percent). To view the next slice
in the data, click the Slices > Next Slice menu option, press F10, or click the right
arrow on the scroll bar that appears in the Slices section of the Control Bar. To go
back to the previous slice, click Slices > Previous Slice, press F9, or click the left

arrow on the slices scroll bar. Note that the central thumb in the slices scroll bar can
be dragged to any position to move the slice through the whole range of data.
End slice-ending mode by clicking Slices > End Slice, or press the Stop button in the
Slices section. Note that slice-mode also works with a polygon selection and with
Cube hypotheses.

3.9 Hotkeys
For convenience, a number of short-key or hotkeys are provided in the editor. The
following table lists the hotkeys available in the 3D Editor.
Operation

Hotkey

Modes
Explore

Space Bar

Select

Area Select

Record Select

Measure

Selection
Clear

Invert

Select Sounding

Select Line

Deselect Sounding

Shift + T

Deselect Line

Shift + L

Editing
Reject

Undelete

Set Suspect Flag

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Set Plotted Flag

Set Feature Flag

Clear Suspect Flag

Shift + E

Clear Plotted Flag

Shift + P

Clear Feature Flag

Shift + F

File
Save

Ctrl + S

Save & Exit

Ctrl + Shift + S

Exit

Ctrl + X

Display
Show Widgets

Hide
Hide Selected

Hide Unselected

Shift + V

Unhide All

Ctrl + Shift + V

Interface
Show/Hide
Panels

Editor Ctrl + 1

Slices
Start Slice

Ctrl + I

End Slice

Shift + Ctrl + I

Next Slice

F10

Previous Slice

F9

Shoals
Hide/Display

Neighbors
Targets
Edit Targets

Cube
Show/Hide
Nodes

Cube K
Table 3.3 - 3D Editor Hotkeys

3.10

Customizing the 3D Editor

The 3D Editor can be customized depending upon the type of data that is loaded.
Customized commands can be added to the right-click menu and will appear under a
menu indicating the current type of the data. For example, Figure 3-26 shows three
custom menu items for the Shoals Hydro format. If the data were in GSF or HTF
format, a different menu could be shown. A number of options exist for creating rightclick commands. For more information, see the 3DEditorOptions file, located in the
/ivs/configurations directory where Fledermaus was installed.

Figure 3-26 - 3D Editor Shoals Menu

3.11

Editing Targets in the 3D Editor

The 3D Editor can also be used to edit targets (see Section 4.8.3 for an introduction
to working with targets). To enter Target editing mode, click the Target Editing toggle
or press the G key. Note that when in target editing mode, the interface will act
differently than when editing soundings. As an added indicator that the editor is in
target editing mode, the grid and status panels will both be displayed as blue (see
Figure 3-27).

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Figure 3-27 - Editing Targets

Targets are displayed as large yellow spheres in the scene. To select a target, enter
Select mode and click on a target or right-click on a target and click Select Target.
Selected targets will be displayed with a white cross on them. Note that only one
target may be selected at a time. Most editing on targets is performed using the rightclick menu as shown in Figure 3-28.

Figure 3-28 - Targets Right-Click Menu

To unselect all targets, right-click and select the Clear Target Selection option. To
add a new target, right-click on a sounding in the editor, and then select the Add
Target at Highlighted Sounding. To delete a target, select a target and then click the
Delete Target menu option.

To move a target, first select the Target you wish to modify using Select mode or the
Select Target menu option. To move a target to a specific sounding, right-click on the
sounding and select Move Target to Highlighted Sounding. Note that a target does
not have a stored height value, so only the longitude and latitude of the target will be
modified to match the sounding. To enter a specific longitude and latitude for a target,
right-click and select Edit Target Position and edit the position with the dialog that is
displayed.
Note that all target editing operations are instantaneous and do not need to be
saved.

3.12
3.12.1

Format Specific Operations

SHOALS Hydro/HOF

The 3D Editor contains some additional functionality for PFM files built from the
SHOALS Hydro/HOF file type. If the highlighted sounding is from a SHOALS file, the
right click menu will have an extra Shoals Hydro menu, as shown in Figure 3-26. This
menu may be different, depending upon which options are installed on your machine.
Clicking the Shoals > IVS Waveditor menu option will display the waveditor program,
(for more information, see the Addition Data Tools chapter).
When the waveditor program is run, the 3D Editor will display the 8 neighbors around
the highlighted sounding that are displayed in the nine-up view of the waveditor. To
toggle the neighbors display, press the N key. Double-clicking the display will lock
the highlighted sounding as usual, but will also allow highlighting the individual
neighbors. When a neighbor is highlighted, it will be draw with a lighter background in
the waveditor display.

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Connectors

Figure 3-29 - Showing connectors in the 3D Editor

Connectors in the 3D Editor are a series of line segments joining the soundings in a
record and are shown in Figure 3-29. This is useful for multi-beam files to visualize
which soundings belong to an individual swath. To display connectors, select the
Connectors toggle from the Control Bar. By default, those soundings on the left hand
side of the track line are displayed as red and those on the right hand side of the
track line are displayed as green. To change these colors, use the Options >
Preferences menu option to open the Preferences dialog (see Section 3.6.1). The
width of the connector lines can also be controlled through the same dialog.

3.14

Second Depths

Figure 3-30- Soundings with Second Depths

The Second Depths area is used for soundings that have an attached attribute that
stores an additional depth. This depth may be a second depth, as from a Shoals
system, or a non-tide corrected depth, etc. Choose the attribute that represents the
second depth from the Sec Depths menu in the Control Bar. Each second depth is
shown as a wire-frame box or symbol, as shown in Figure 3-30. If the Display >
Show Second Depth Stalks toggle is enabled, a line is drawn between the original
and the second depth.

3.15

Audit File

When any changes are written to disk using the 3D editor, each changed sounding
can be written to an audit file. Also, when areas are checked or unchecked in
Fledermaus, that information can be written to the file. The audit file has the same
name and location as the PFM file except it has the extension .audit instead of
.pfm. The audit file is an ASCII text file consisting of the date and time each
sounding was edited, the username of the person running the editor, and all
sounding information in the attributes table. This text file can then be loaded into a
spreadsheet for further analysis. To control when information is written to the audit
file, edit the /configurations/PFMOptions file where Fledermaus was installed. By
default, auditing is turned off for sounding edits, but is enabled when areas are
checked or unchecked.
USER

DATE

PING

BEAM FILE EASTING

NORTHING

LON

LAT

DEPTH SELECT SUSPECT DELETED FEATURE

mpaton 2001/05/23 9:14

476075 0

599064.2 8830325.5

141'54"19.9

-10'34"47.7

-8.60

False

False

True

False

mpaton 2001/05/23 9:15

310143 0

599068.1 8830323.0

141'54"20.0

-10'34"47.8

-8.70

False

False

True

False

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Table 3.4 - Example of Audit File from Editing

3.16
3.16.1

Editing CUBE Hypotheses

Viewing the CUBE Hypotheses

After a CUBE PFM has been created with DMagic, the PFM file can be opened in
Fledermaus using the regular method. In the PFM Attribute Panel, the CUBE surface
in the PFM can be displayed by selecting Cube Flt. Surface from the Surface dropdown menu.
Select an area on the PFM surface and load the 3D Editor (see Section 3.1.1 for
more information).

Figure 3-31 - Using the 3D Editor to edit Cube Hypotheses

To view the Cube hypotheses in the 3D Editor, click the Cube Editing toggle, located
on the upper right of the Control Bar (Figure 3-31). When the Cube Editing toggle is
activated, the interface of the 3D Editor will change. To indicate the editor is in a
different mode, the color of the grid and the color of the status panels will change to
yellow. To show the Cube hypotheses without entering Cube editing mode, click the
Hypotheses toggle in the Display group.
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Each Cube hypothesis is represented as a flat plate, indicating the height of the
hypotheses. The currently selected hypothesis is displayed as a large plate, and the
alternate hypotheses are displayed as smaller plates. All of the plates in a single bin
are joined by a line through their centers. To hide the soundings in the editor, disable
the Soundings toggle. Clicking the Surface toggle will show the interpolated surface
formed from the Cube hypotheses.
When the Cube Editing toggle is enabled, the interface changes to work on
hypotheses instead of soundings (note that the k key can be used to turn on or off
Cube editing mode). When moving the mouse over the screen, the closest
hypothesis will be highlighted and information about that hypothesis will be displaying
in the status bar.
Selecting hypotheses works similar to selecting soundings. Enter any of the selection
modes and single click to select a hypothesis, or click and drag to select multiple
hypotheses. A hypothesis that is selected will be drawn with a solid white outline.
Note that in each bin, at most one hypothesis can be selected at a time.

3.16.2

Editing Hypotheses with the Control Bar

The Control Bar on the right hand side changes slightly when the Cube toggle is
enabled. Click the Clear or Invert buttons to modify the selected hypotheses. Clicking
the Reject button will delete the hypotheses in the currently selected bins. The
Unreject button will undelete hypotheses that have been deleted (click the Show
Rejected toggle in the Cube Panel to view deleted hypotheses).

Figure 3-32 - Control Bar in the 3D Editor when editing hypotheses

The process of marking an alternate hypothesis as the selected hypothesis is called

overriding and can be accomplished by selecting alternate hypotheses and clicking
the Override button. The selected hypotheses can be reset to the original hypothesis
chosen by the Cube algorithm by clicking the Reset button. Overriding is usually the
main editing operation when working with Cube surfaces.

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3.16.3

Right-click Menu for CUBE Editing

Figure 3-33 - Select Menu when editing hypotheses

The right-click menu also changes when the Cube toggle is enabled. The Select
menu (Figure 3-33) allows hypotheses to be selected, deselected, cleared, and
inverted, similar to the Control Bar. The Select Connected menu option starts at the
currently highlighted hypotheses and spreads out, selecting any neighboring
hypotheses that are close enough in depth to their neighbors. Use the Select
Connect option to select hypotheses that lie along a flat surface.
When the Move Selection Up menu option is clicked, any bins that have a hypothesis
selected will have the next highest hypothesis in the bin selected. Similarly, the Move
Selection Down menu option causes the next lowest hypothesis in the bin to be
selected. These commands allow all of the shoal or deep hypotheses to be selected
easily. For example, press C then I to select all hypotheses, press ] repeatedly
until the topmost hypotheses are all selected, and then press O to override all the
hypotheses.

Figure 3-34 - Edit Menu when editing hypotheses

The Edit menu on the right-click menu contains options similar to the Control Bar.
Use the Override Hypotheses and Reset Hypotheses to select other hypotheses
from a bin. The Delete Hypotheses and Undelete Hypotheses commands reject or
unreject hypotheses. Note that if a selection is made, these commands apply to all of
the selected hypotheses, otherwise the command is applied to the currently
highlighted hypotheses.
The Hide menu is similar to the menu for editing soundings. This menu allows hiding
of the selected hypotheses with Hide Selected, or hiding of the unselected
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hypotheses with Hide Unselected. To unhide soundings, use the Unhide All menu
option.
The Recube menu option re-runs the Cube algorithm on the current area being
edited. Instead of editing hypotheses, an operator may delete a set of soundings (for
example, from a burst failure), and re-run the Cube algorithm to generate better
quality hypotheses. The Recube algorithm can also be run from the Tools menu in
the Fledermaus PFM Panel.

3.16.4

Cube Panel in the 3D Editor

Figure 3-35 - Cube Panel in the 3D Editor

A number of additional options for editing hypotheses are included on the Cube panel
at the bottom of the screen. If the Cube panel is not visible, click the Options > Editor
Panels menu option. The first toggle, Cube Editing Mode, is identical to the Cube
Editing toggle on the upper-right area of the Control Bar. Enabling this toggle
switches the interface into hypothesis-editing mode. When the Cube Editing Mode
toggle is enable, the Show Cube Hypotheses is automatically enabled as well.
However, the Show Cube Hypotheses toggle may be turned on by itself to just view
Cube hypotheses without entering hypothesis-editing mode. This option is useful to
view Cube hypotheses, but edit the soundings.
The Cube hypotheses can be colored by a number of different methods using the
Color By drop-down menu. The Confidence, Num. Soundings, and Hyp. Strength
options are read from the extra attributes of the bin). The Overridden option marks all
bins as yellow that are set to one of the alternate hypotheses. The Color option
allows coloring of the hypotheses by a solid color and the Custom option colors any
bins yellow that contain a custom hypothesis (see Section 3.16.5).
By default, a line is drawn connecting all hypotheses in a bin. To hide this line,
deselect the Connect Hypotheses toggle. If the Show Conf. Intervals toggle is
enabled, a line representing the 95% confidence interval is displayed about each
hypothesis (see Figure 3-36). Enabling the Show Rejected toggle will display all
hypotheses that have been rejected. This toggle is necessary to unreject hypotheses.

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Figure 3-36 - Confidence Intervals in the 3D Editor

The last three sliders in the Cube panel control how the selected and alternate
hypotheses are displayed on the screen. The Hyp. Transparency slider controls the
transparency of the selected hypotheses and the Alt. Hyp. Transparency slider
controls the transparency of the alternate hypotheses. The sliders range from fully
transparent on the far left to fully opaque on the far right. The Alt. Hyp. Size slider
controls how large the alternate hypotheses are drawn. The slider value ranges from
full size on the far right to hidden on the far left.

3.16.5

Creating a Custom Hypothesis

Sometimes an operator may wish to identify a sounding as the chosen height of the
surface (this sounding is sometimes called a feature sounding or golden sounding).
To accomplish this task, turn off the Cube toggle and turn on the Soundings toggle in
the Control Bar. To view the Cube hypotheses at the same time as editing
soundings, click the Show Cube Hypotheses toggle in the Cube Panel. While editing
soundings, right-click on a sounding and select the Set Custom Hypothesis option
from the menu. This action will generate a new hypothesis and place it at the same
height as the sounding. The confidence interval for the created hypotheses will be
the same as the confidence interval for the sounding. A custom flag called Custom
Hypo. Flag will be set for the sounding. To remove the custom hypothesis, override
one of the other hypotheses in the bin. Note that only one sounding in a bin can be
marked as a custom hypothesis at a time.

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Chapter 4 - Scientific Data Types

4.1 Introduction
One of the primary features of Fledermaus is its ability to load a variety of data types
at different resolutions and explore and analyze them together in a 3D scene. Each
object type supported by Fledermaus is called a scientific data class or SD class for
short. Any file that is prepared for loading into Fledermaus is given the filename
extension sd, as in mysurface.sd.
Each SD class contains a user interface component, which is displayed in the Data
Object Control Region of Fledermaus or DMagic. Interaction with the objects is
normally performed through this graphical interface; however, controls for general
exploration in the Main Visualization Window remain basically the same for any
object.
This chapter describes each SD class supported by Fledermaus and provides details
on:
what data it represents,
how its data is displayed in the 3D virtual world,
the graphical user interface used to interact with the object, and
some notes on how data in the class is prepared for the visualization process.
A summary of the SD classes described in this chapter are as follows:
Digital terrain model (DTM) - SonarDTM, Surface Series
3D geometric points, lines, polygons, grids, and solid models.
Imagery visualization geo-image, vertical image, and imagery curtain.
Simple visualization grid, plane, cube, label, and quadratic.
Geo-Spatial quality control PFM.
Vessel real-time Vessel or ROV monitoring.
Volume - object for interacting and rendering volume objects.

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4.2 Common Object Controls

There are a number of controls that are shared across multiple different object types.
These common controls will be explained in the following sections, before getting into
the object specific controls.

4.2.1 Colormap
The Colormap tab can be used to display both the current color map and a histogram
of depth values.

Figure 4-1 The Colormap attribute panel

Data Range: The original full range of the data set.

User Range: The currently applied range of data.
Reset Button: Resets the range to the original data range.
Apply Button: Applies the current user range to the surface.
Change Colormap... Button: Allows the user to select an alternative colormap. .Once
selected, the surface will be re-shaded using the new colormap.
Tools Menu
Edit CMap: This will launch the color map editing and manipulation dialog.
Save as Image: This will save the current color map display area as an image file.
Import: This command can be used to import color maps from other packages for
use in Fledermaus.
Export to ASCII: Any colormap can be exported to an ASCII text file using this
command.

4.2.2 Shading
There are six parameters of the illumination model that can be adjusted to customize
your shaded image as shown in Figure 4-2. These parameters are: the light position
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and direction, the amount of ambient light, the specular component, the shadow
softness, and the vertical exaggeration of the heights. Pressing the button
located to the right of each of the light parameters displays a dialog box where the
parameter values can be entered directly.

Figure 4-2 The shading attribute panel

Shadow Direction: The arrow in this box represents the sun direction, which can be
rotated to any azimuth from 0 to 360 degrees by clicking and dragging the left mouse
button inside the box. The actual angle is displayed in red text near the center of the
box. The sphere in the middle of the diagram displays the current direction and
length of the cast shadows. Dragging the slider located on the right side of the
Shadow Direction box adjusts the length of the shadows (thus sets the height of the
sun). In the example shown in the figure the light is coming from the North West
(upper left). At the bottom of the area the Effective Sun Angle is listed. This value lists
the approximate sun elevation in degrees, where 0 degrees indicates the sun would
be at the horizon and 90 degrees would indicate the sun would be directly overhead.
The rest of the parameters are controlled via the following slider controls.
Ambient: This slider controls the amount of ambient or background light in the lighting
model. It primarily affects the amount of light that appears in cast shadows. High
ambient light makes the entire image brighter and the shadows less distinct.
Specular: This slider controls the amount of glossy highlight that appears. High
specular makes the surface appear to be very glossy. Low specular will provide a
matte finish.
Soft Shadows: This slider controls how sharp or soft the shadow edges are.
Vertical Scale: The height of the surface can be artificially increased or decreased to
change the shadow length. Occasionally this is useful to enhance a low relief surface
or reduce a very high relief surface. It is usually better to use the Shadow
Direction/Length box to configure and adjust the shadow length.
All of the sliders work in a standard way. To change the position of the slider select
and drag it using the left mouse button. To go directly to a specific part of the slider
bar click the middle mouse button.
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4.2.3 Bounds
Every object displayed in Fledermaus has a set of X,Y and Z bounds that locate the
object is geo-spatial space. The bounds for each object are displayed and modified
using the Bounds tab, as shown in Figure 4-3.

Figure 4-3 The bounds attribute panel

Figure 4-4 The copy bounds dialog

4.2.4 Geo-Referencing
In addition to the bounds tab, every object also has a Geo-Referencing tab that
defines the coordinate system for that object. The coordinate system can be changed
by using the combo box when selecting common coordinate systems or the Select
button can be used to launch the advanced coordinate systems dialog.
Some object types (such as SonarDTM) can be reprojected to the coordinate system
of the scene by using the Reproject Now button. If the data object type does not
support reprojecting, this option will not be available.

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Time Figure 4-5 The georeferencing attribute panel

4.2.5 Time
The Time tab is the central location for viewing and editing the keyframes for each
Fledermaus data object.
There are five groups of keyframes:
Position/Orientation
Scale
Transparency
Visible
Frame
Add Key: Add a new keyframe at the current time and attribute state.
Delete Key: Delete the currently selected keyframe.
Previous Key: Move back to the previous keyframe.
Next Key: Advance to the next keyframe.

Figure 4-6 The time attribute panel

Clear Keyframes for Current Group: This option will clear any recorded keyframes
that are part of the currently selected group.
Clear Keyframes for All Groups: Instead of just clearing keyframes for one group, this
option will clear all recorded key frames.
Import Keyframes: This command allows keyframes stored in the FAN format to be
imported into the current object.
Export Keyframes: Keyframes can be exported from the current object using the FAN
format. The exported file can be loaded into any other Fledermaus object.
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Show Path Toggle: This toggle with turn on a graphical path in the 3D visualization
window for the current object.
Range: This command is used to specify what range of the path data will be
displayed.
Shape: Theses options will affect how the path is displayed in the visualization
window.
Width: The width parameter is used to adjust the size of the data objects path.

4.2.6 Info
The Info tab is used to display key/value pairs of information relevant to the object.

Figure 4-7 The info attribute panel

4.3 Root Node

The root node of a scene has its own special set of tabs, which will be described in the
following section.

Figure 4-8 The scene attribute panel

4.3.1 Scene Tab

Horizontal Coordinate System / Vertical Datum: This option is used to specify the
coordinate system for the overall scene and display area.

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Geographic Unit Display: Coordinates that are in geographic units will be displayed
using this format.
Projected Unit Display: The display of project units will use the format specified by
this option.
Display Mode: Used to specify if the main display will be flat, or spherical.
Background Color: Specifies the background color of the main display area.
Foreground Color: Specifies the foreground color used in the main display area.
Swap Colors: Swaps the current foreground and background colors.

4.3.2 Lighting Tab

The lighting tab on the root node is used to set the global lighting direction. This is not
used for shading surfaces, but does apply to 3D Models and Shape objects.

Figure 4-9 The lighting attribute panel

4.4 Digital Terrain Model (DTM) Classes

In Fledermaus, a DTM is a uniformly gridded surface that represents the discrete
sampled function z = f(x, y). X and Y are sampled on the uniform grid and Z is the height
(or depth) at the specified X and Y coordinates.

4.4.1 SonarDTM

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Figure 4-10 - Sample SonarDTM

The SonarDTM class allows for the possibility of data holes (called holidays). This is
where some of the cells of a uniformly sampled surface are unknown and therefore
should not be rendered in the display. The controls for the SonarDTM class are
shown in Figure 4-11.

Figure 4-11 - SonarDTM Controls

These control how the SonarDTM object is displayed in the Main Visualization
Window. The value in the Mesh Gap textfield determines how much the DTM is
degraded while moving in an exploration mode. For example, a value of 1 will result
in all points being used, and a value of 2 results in every second point being used.
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The Auto toggle enables the ShiftScapeTM rendering engine to automatically adjust
how much the DTM is degraded based on the performance of your computer.
To adjust the Mesh Gap by hand, disable the Auto toggle and enter a value in the
Mesh Gap textfield. A lower Mesh Gap means more data is drawn so the screen may
redraw slower. A higher Mesh Gap means less data is drawn so the screen can
redraw faster. When working with large data sets and the screen is rendering slowly,
increase the Mesh Gap and you will be able to move much more easily through the
data.
The Transparency slider controls the current transparency value. Dragging the slider
right or left will make the DTM more or less transparent, where the right position
corresponds to completely transparent and the left position corresponds to
completely solid.
When using transparency, note that transparent objects work best when they are
drawn last. That is, the transparent object needs to be loaded so that it is the last in
the object list. Objects can be re-ordered by dragging and dropping them within the
Fledermaus object list. (left-click and drag the object up or down.)
The two toggle buttons change the DTM from a wire frame display to a solid shaded
surface Surface Series

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Figure 4-12 - Sample Surface Series

The surface series class is based on the SonarDTM class but adds the ability to store
and visualization a set or series of SonarDTMs within a single object. The resulting
surfaces can then be animated in time to explore time dependent changes in the
surface model. To create a surface series object the SonarDTM objects are
generated in the normal fashion. A command line applet called mksurfseries is used
to combine multiple SonarDTM objects into a surface series.

Figure 4-13 - Surface Series Controls

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The attribute controls shown in Figure 4-13 are similar to those of the SonarDTM
class with the following exceptions. The Animation Mode popup menu contains two
options either Animated Series, or Selected Slice. When Animated Series is selected
the visualization will automatically step through the slices one at a time each time the
scene is redrawn. Once the last slice is drawn the process repeats from the
beginning. When the mode is Selected Slice, the Select Slice slider bar makes it
easy to select a given time slice. The Time Step Delay slider controls the speed of
the animation. When the slider is at the far left the image will change each frame but
as you move it to the right the switch will require more time steps before it changes to
the next available image. If the object was assembled with a time reference then a
large label will be shown indicating the time step of the displayed image.

4.5 3D Geometric Classes

4.5.1 3D Point Class

Figure 4-14 - Sample 3D Points

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The 3D Point class is capable of visualizing 2D and 3D point data with optional labels
attached. This class serves a variety of purposes, from labeling points of interest in a
3D scene, to displaying a large point surface. Sometimes looking at the individual
measurements is more useful than viewing a gridded surface of these points. The
much more complex classes such as the PFM processing class also make use of
points to display their information; however, they provide much more associated
functionality including editing and on the fly surface generation.
3D points can be imported into Fledermaus using the File > Import > Import Points
menu command or the mkpoint3d command line program.

Figure 4-15 - 3D Point Controls

Figure 4-16 - 3D Point Color By Options

Figure 4-17 - 3D Point Marker Type Options

The controls for a 3D Point object are shown in Figure 4-15. The Gap textfield is
used to decrease the number of points drawn when exploring the data. For example,
when using a gap value of 2, every second point is displayed. If the Auto toggle is
enabled, the ShiftScapeTM rendering engine will automatically choose the best point
gap based on the speed of your hardware. The Drape Points button is used to drop
points vertically until they lie on the surface below. The color-coding of the points can
be selected from the Color By menu, shown in Figure 4-16. Options include coloring
by a Solid Color, the Z coordinate of the points (Point Height), or an additional
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Attribute. Thus the color information of a point can provide an additional dimension of
information. When Solid Color is selected from the list, the color can be selected
using the Standard Color Picker Dialog. The Marker Type pop-up menu, shown in
Figure 4-17, allows a different symbol to be displayed for the points. The choices
currently include squares, circles, crosshairs, cubes, diamonds, cylinders, spheres,
and points.
Three sliders located on the right side of the panel also control how the points are
drawn. The size of the points can be adjusted by dragging the Point Radius slider. All
points can be offset vertically a small amount by adjusting the Point Offset slider.
Some point files have labels attached to particular points and the size of these labels
can be controlled using the Label Size slider. An exact value can be entered by
typing a value in the textfield to the left of each slider. Also, by clicking the button
to the right of the slider, the starting value, current value, and ending value for the
slider can be specified.

4.5.2 3D Line/Polygon Class

The 3D Line class is used to represent information that has been broken down into
2D and 3D lines. Lines of this class are actually polylines and can consist of any
number of line segments. Polygons can also be represented in this SD class by
marking the polylines as closed. Thus lines, polylines, and polygons can all be
represented in the same object.
Many of the converters such as those that read ArcView shape files or DXF files will
tend to produce this type of visual object. Line objects can also be created using the
File > Import > Import Lines menu command or the mklines command line applet.

Figure 4-18 - 3D Line Controls

Figure 4-19 - 3D Line Color By Menu

Figure 4-18 shows the available controls for the 3D Line class. The thickness of the
lines is specified by entering a value in the Line Width textfield and pressing Enter.
The Gap textfield is similar to the gap for the points class and controls how much the
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line class is degraded. The ShiftScapeTM rendering engine will automatically set the
gap if the Auto toggle is enabled. There are three options for coloring a 3D line file, as
shown in Figure 4-19. Selecting Solid Color will display all lines as a single color. The
color can be choosing by clicking the Change Color button and selecting a color
using the Standard Color Picker Dialog. The Line Height option will color a line based
on its height. If an attribute is attached to the file, the lines can be colored by attribute
by selecting the Attribute option. The Interpret Closed Polygons as Filled toggle
draws the lines as filled polygons. Note this toggle only has an effect if the original SD
file was built using the -poly flag in mklines or a polygon ESRI shape file was
imported.
The controls in the Line Height box allow the z values of the points in the lines to be
controlled. The Offset slider can be used to move the lines slightly above the surface
and is useful if lines are lying directly on a surface. The Drape Lines button will drop
all vertices of the lines until they lay on the surface below. The Set Heights button will
display a dialog as shown in Figure 4-20. Enter a value in the dialog and press OK to
set all lines in the object to a specific height.

Figure 4-20 - Setting Line Heights

One limitation of the Drape command is that it only drapes the vertices of the line on
the surface. Therefore, if the line does not contain many vertices, it will only be
partially touching the surface. The solution is to resample the line before draping
using the Resample and Drape button. This command will display a dialog as shown
in Figure 4-21 that is used to input the resampling interval. New vertices will be
added to the line based on this interval. For example, a value of 5 means that a new
vertex will be added every 5 meters along the line. The result of the Drape command
and the Resample and Drape command for the same line can be seen in Figure
4-22(a) and Figure 4-22(b) respectively. Note the units of this dialog are based on the
units of the current data. If the object is using geographic coordinates, than an
interval of decimal degrees should be specified.

Figure 4-21 - Resampling and Draping Lines

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(b)
Figure 4-22 - Difference between Drape and Resample and Drape

The current line object can be dynamically edited using the options in the Edit box.
Clicking the Add Polygon Selection button adds the current polygon selection to the
line object. See the Polygon Selection Mode section in Fledermaus for more
information. The Delete Last button removes the last line that was added. All lines
can be deleted by clicking the Clear All button. The current line object can be
exported to an ASCII XYZ file by clicking the Export XYZ button and selecting an
output file in the resulting file selection dialog.

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4.5.3 3D Grid Class

Figure 4-23 - 3D Grid and SonarDTM

The 3D Grid class allows for a variable sized 3D grid to be added to a Fledermaus
scene. To do this, Add 3D Grid is selected from the Data menu and this will add an
Internal 3D Grid object to the current scene (see Figure 4-23). The default bounds of
the 3D grid are based on the root node bounds and 100 meter spacing. The following
parameters can be changed for any 3D Grid object:

X and Y minimum value,

X and Y range,

Grid size, and

Grid color,

Once the size of the grid has been defined, click the Drape Grid button to
drape the grid onto the surface. If the surface is very rough, the grid may
not match the landscape exactly. For a better approximation, the grid can
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be subdivided by adjusting the Interp Factor and clicking the Interpolate

Grid button. The higher the interpolation factor, the better the grid will
match the surface. Even when interpolated, the lines may not be drawn
correctly since both the lines and the surface lie at the same height. To
raise the lines slightly above the surface, use the Transform dialog
accessed by clicking the Transform button. Figure 4-23 shows a
SonarDTM with a 3D grid loaded and draped on the surface with 50 meter
spacing. The 3D Grid controls are shown in Figure 4-24.

Figure 4-24 - 3D Grid Controls

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4.5.4 Solid Model Class

Figure 4-25 - Sample Solid Model

A Solid Model is a three dimensional object in a scene consisting of a number of

polygons. Solid Models might represent ships, drilling platforms, bridges, etc.
Currently Solid Models can be loaded in Fledermaus using the File > Import > Import
Model menu option or through the mksolid command line program. Both 3DS and
Wavefront OBJ files are supported. Figure 4-25 shows the results after the addition
of a model and Figure 4-26 shows the Solid Model controls.
When enabled, the Auto Adjust Detail toggle notifies the ShiftScapeTM rendering
engine to automatically adjust the number of polygons drawn depending upon your
graphics hardware. When the Ignore Vert. Exaggeration toggle is enabled, the model
is drawn the same height regardless of the exaggeration of the scene. This option is
useful for ships, subs, or other objects in the scene that should not be stretched when
the vertical exaggeration is changed.
The color of the model can be controlled by clicking the Set Color button and
selecting a color using the Standard Color Picker. Note that if a model originally
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contained many colors, all colors will be overwritten with the indicated color. Some
programs may output polygons with vertices in the wrong order, which will result in
the lighting calculations on the model being incorrect. Clicking the Flip Normals
button will attempt to correct this problem and clicking the Flip Normals button again
will undo the operation. The transparency of the model can be controlled by dragging
the Transparency slider. Note that the lighting direction can be changed by selecting
the Controls > Light Sources menu option.

Figure 4-26 - Solid Model Controls

To change the position of a model after it has been added to the scene, alter the georeferencing coordinates by clicking on the Transform button or the Controls > GeoReferencing menu option. Alternately, the model can be transformed by clicking the
Transform Vertices button, which displays the Transform Vertices dialog as shown in
Figure 4-27.

Figure 4-27 - Transform Vertices of a Solid Model

The Transform Vertices dialog can be used to rotate, translate, or scale the vertices
of a solid model. Note that this operation is different than using the Transform button
in the Data Set Controls because this transformation permanently modifies the
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vertices. The model can be rotated around the X, Y, or Z axes using the Rotate text
fields, moved to a new location using the Translate text fields, or resized using the
Scale text fields. Click the Transform button to apply the changes and close the
dialog, or the Apply button to transform the vertices without closing the dialog. Click
the Cancel button to close the dialog without making any changes, or the Reset
button to return all of the fields to their original values. Note that any rotations will take
place before any translations and any translations will take place before any scaling.
In general, it is easier to use this dialog to only apply either a rotation, translation, or
scale at a time. In this case, make sure the Reset button is pressed after each
transformation is performed.

4.6 Imagery Visualization Classes

This small family of data types involves those that deal with the visualization of 2D
imagery data and the variety of methods that they can be visualized and represented
in the 3D virtual world of Fledermaus. The class types include the GeoImage, Vertical
Image (VImage), and Vertical Curtain (VCurtain) classes.

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4.6.1 GeoImage Class

Figure 4-28 - Sample GeoImage

Imagery has many uses within the Fledermaus visualization system and is commonly
draped on related surfaces. It is often very useful to be able to bring 2D imagery into
the 3D scene to complement the 3D data currently loaded. For example, one might
have a bathymetric map showing the depths of a lake or river channel and want to
bring in a satellite image of the region. The 2D image can be added to the scene as a
geo-image object and properly geo-referenced within the scene (see Figure 4-28). To
add the image, select the Import > Import Image File menu option and select an
image file with the standard file selection dialog box.

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Figure 4-29- Geo-Image Controls

GeoImage objects can also dynamically interact with the scene via the controls in
Figure 4-29. The Image Visualization Options control what is displayed for the
GeoImage when in explore mode. If Low Resolution Texture is selected, a lowresolution version of the image is displayed and the High Resolution Texture option
causes the actual pixels from the image to be displayed at all times. If the Auto Select
Resolution toggle is enabled, the ShiftScapeTM rendering engine will automatically
decide when to use high-resolution or low-resolution textures.
By default, 2D images are assigned a height of 0.0 (sea level) but the height can be
interactively controlled by entering a value in the Height textfield and selecting the
Use Geo. Height toggle.
One method of combining DTMs and GeoImages into a single scene is to mask the
image. This is done by using surfaces in the scene to knock holes in the imagery
over the location where its data resides, allowing one to see through the imagery to
the surface of the underlying data. To perform this operation, click the Compute Mask
button and select the Mask Out Areas toggle. An example of a masked image is
given in Figure 4-30.

Figure 4-30 - Example of Masking a GeoImage

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4.6.2 Vertical Image Class

Figure 4-31 - Sample Vertical Image with a DTM

The Vertical Image (VImage) class is a close sibling of the GeoImage class. It
provides many of the same features with the exception that this surface is
perpendicular to the XY plane. As an example this could be an image of a parameter
in the water column, or a seismic profile of the sub-surface (see Figure 4-31). The
input required is the image in a format supported by the application (such as a tiff
image), the coordinates of the left and right-hand edge of the image, and the Z range
of the image.

Figure 4-32 - Vertical Image Controls

The procedure for adding a vertical image to the scene is similar to that for the
GeoImage. Click the File > Import > Import Vertical Image menu option and select an
image file with the standard file selector dialog box to add a VImage to the loaded scene.
Enter the co-ordinates of the left and right hand edges in the Start X, Start Y, End X,
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and End Y textfields, and the Z range in the MinZ and Max Z textfields, all shown in
Figure 4-32. When moved, the Vimage must be geo-referenced to properly place it in the
3D scene (i.e. the Geo-Reference button must be clicked). Vertical Images can also be
created with the mkvimage command line program. Click the Rotate button to rotate the
vertical image clockwise by 90 degrees.
The Use Low Resolution Texture, Use High Resolution Texture, and Auto toggles are
similar to those controls in the GeoImage class. The Mask Out Area toggle is also
similar to the GeoImage class but requires that the source image file contains an
alpha channel with white in the areas to mask out.

4.6.3 Vertical Curtain/Seismic Class

The Vertical Curtain (VCurtain) class is similar to the vertical image class with one
key difference. In the Vertical Image class the resulting image is still flat, a plane
arbitrary orientated perpendicular to the XY plane. In this class the vertical (Z) range
of the data is held constant but a geographic location of each column of pixels in the
image is specified. Thus the imagery can weave in and out according to the points
specified. A good example where this type of class is very useful is in the
visualization of processed seismic imagery where the image follows the track of the
ship that collected the imagery. Vertical Curtains can be generated through the
mkvcurtain command line program.

Figure 4-33 - Vertical Curtain Controls

The controls for the VCurtain class are shown in Figure 4-33. The Mesh Gap textfield
can be used to display a coarser curtain while exploring and the Auto toggles notifies
the ShiftScapeTM rendering engine to automatically adjust the mesh gap. The Use
Low/High Resolution option will display a low-resolution image while exploring and a
high-resolution image when the scene is full drawn. The Use Low Resolution option
will always display the low-resolution image and the Use High Resolution option will
always display the high-resolution image. With the Auto Select Resolution option
enabled, ShiftScapeTM chooses whether to use high or low-resolution textures.
To mask out the black areas of the curtain, click the Compute Mask button and select
the Mask Out Areas check box. Note that some VCurtains are generated with a
mask so it will not have to be calculated.

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4.7 Simple Visualization Classes

4.7.1 2D Grid Class
The 2D Grid class adds a simple 2D grid into the 3D scene. The controls for a grid
are shown in Figure 4-34. The number of rows and columns can be controlled with
the # Rows and # Cols textfields. When a grid is added to the current scene, it will
cover the entire geo-referenced area. By default, the grid will display in the middle of
the depth range, but can be moved to the top or bottom of the depth range using the
Top and Bottom toggle buttons. The Grid Color button is used to control the display
color of the grid.

Figure 4-34 - 2D Grid Controls

4.7.2 2D Plane Class

The 2D Plane class adds a simple 2D colored plane (rectangle) into the 3D scene.
For example, a transparent blue plane could be added to a scene to represent the
sea surface. This class is very useful in applications such as dredging where you
have a DTM and want to make sure the channel is deeper than a specified depth.
Adding a plane at the depth makes it obvious to see any parts of the DTM that are
higher than the plane. This type of object is often used with the Fledermaus surface
query command. For example, queries between a plane and a surface are common
to find out how much material must be dredged as in the example above.

Figure 4-35 - 2D Plane Controls

The geographic height of the plane is controlled by the user by entering a value in the
Height textfield and selecting the Use Geo. Height toggle, located on the 2D Plane
control panel shown in Figure 4-35. To change the color or transparency of the plane,
click the Set Color or adjust the Transparency slider respectively.
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4.7.3 Label Class

The Label class provides a simple way to add a textual label into the 3D scene and
arbitrarily position it.

Figure 4-36 - Label Controls

The text used for the label can be controlled with the Label textfield, as shown in
Figure 4-36. Also, the line width and color can be controlled with the Line Width
textfield and Label Color button respectively.

4.7.4 CUBE Class

This rudimentary class adds a simple solid cube into the scene. This object is
occasionally used to mark areas of interest in the 3D scene but has limited
usefulness beyond that.

4.7.5 Quadratic Class

The quadratic class provides for the visualization of a sphere, disk, or cone object.
These objects are sometimes useful to have to act as markers of other solid entities
within the 3D scene. Controls provide options for the quality, color, and construction
of the desired quadratic shape.

4.8 PFM Class

All PFM viewing and manipulation is done through the main Fledermaus interface.
The following section describes the capabilities of viewing and editing PFM files
within Fledermaus.
The data in the PFM bins are used to build regularly gridded surfaces that describe
the shape of the terrain and can be explored using normal exploration methods. The
individual records and their attributes can also be displayed for selected regions in
the 3D Editor. Some features of the PFM objects data controls are:

Switch between six DTM's: filtered and unfiltered surfaces of shallowest,

average and deepest sounding in each bin.

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Color-code the DTM by depth, standard deviation, sounding density,

various flags, or by attribute.

Highlight suspect, plotted, or feature soundings in the data set.

Display the DTM semi-transparent or as wire frame.

Select and view soundings and their attributes in the 3D editor.

Create and export the DTM to a separate SonarDTM object at any time.

When a PFM data object is selected in the data set control you will be presented with
the controls shown in Figure 4-37.

4.8.1 Coverage Control Panel

Once a PFM file has been loaded as described in Figure 4-37, the Coverage Control
Panel will be shown by default when the object is selected from the Data Set Control.
Bins that contain data that have been checked will appear light grey and those not
checked will be red.

Figure 4-37 - Coverage Control Panel

A surface object is created for visualization by highlighting a region on the coverage

map by holding down the left mouse button and dragging the mouse until the desired
region is enclosed in the selection rectangle. After selecting the area press the right
mouse button and select Extract Selected Region. To load the whole surface from
the PFM press down the right mouse button and select Extract Entire Area (see
Figure 4-38). The dimensions of the selected area (in meters) are shown in the Area
text field.

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Figure 4-38 - Extraction of PFM Data for Visualization

In addition, the PFM Coverage Control panel has specific tools for working with the
surface. The first option is the Surface pull-down menu, which provides a choice
between displaying the unfiltered shallow, average or deep surfaces, along with the
filtered shallow, average or deep surfaces. The unfiltered surface shows a surface
from all available soundings in the PFM file while the filtered surface does not include
soundings marked as deleted. The Color pull-down menu directly below the Surface
selection menu provides a choice of the attribute used to color the surface:
Standard deviation;
Height;
Sounding density;
Deleted flag;
Modified flag;
Checked flag;
Suspect flag;
Plotted flag;
Feature flag;
File number;
Line number; and,
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Custom Flags or Attributes (if they exist).

The Highlight menu allows areas of the PFM that have a certain flag set to be
highlighted in the main display (highlighted areas will appear lighter than the
surrounding areas). Select one of the available flags from the Highlight menu to
enable this option. Using highlighting, it is possible to visualize more than one
variable at a time (e.g. the surface could be colored by depth and the areas that are
checked could be highlighted).
There is also an option to directly display what bins contain either selected, plotted, or
feature soundings. This can be controlled using the Flags pull down. When either of
the flags is selected, markers will appear on the surface indicating which bins contain
soundings with the given flag (see Figure 4-39). This option is independent from the
set color of the surface. The setting of the flags will be from either the functions on
the Filters Panel or from manual edits in the 3D Editor.

Figure 4-39 - Suspect Data Flag

As the processing continues, the Check button allows the users to set areas that
have already been processed and approved. This can then be shown on the
visualized surface and also in the overview on the Coverage Control panel, as shown
in Figure 4-37. The checked areas will be displayed as grey on the Coverage Map
when the Show Checked Areas toggle is enabled. The Check button sets all bins in
an area as checked and the Uncheck button undoes this process. The area that is
set or reset depends upon the value of the Scope drop-down list. When the scope is
Loaded Area, the extracted area is modified; when the scope is Selection, only the
area chosen using the Select Mode is modified; when the scope is Entire PFM File,
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the whole file is modified. Setting or resetting checked areas is recorded in the Audit
file.
The remaining controls on the Coverage Control panel are related to the analysis and
editing of the underlying sounding data. Some of these options require a selection on
the surface that can be accomplished by entering the Select mode on the top right of
the application and clicking and dragging on the surface. The available options in the
Edit Control box are outlined as follows:
Launch 3D Editor runs the Fledermaus 3D Editor on the selected area. Also can be
started by pressing the 3 key. See Section 3.1 for a full description.
Bin Header Displays summary information about the PFM file, as shown in Figure
4-40.

Figure 4-40 - Bin Header Dialog Box

The Tools menu button has the following options:

Launch Area Editor runs the NAVO editor tool on the selected area. This option
only works under Linux and the PFM_EDIT environment variable must point to the
editor path.
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Create Surface Object creates a SonarDTM of the currently extracted area. The
new surface will appear in the Data Set Control list.
Export Soundings writes all soundings in a specific area to a variety of formats
including ASCII XYZ, ASCII XYZ + Attributes, and NAVO/Caris ascii files. The area
to extract can be chosen using the Export Soundings dialog as shown in Figure 4-41.
Choose the Selection toggle to output all soundings in the selection box on the
surface, choose Loaded Area to output all soundings in the extracted area, or export
all soundings in the file by choosing the Entire PFM File toggle. The set of soundings
to export can be chosen using a combination of the Base Sounding Selection On
area, and the Refine Selection Based On Sounding Flags area. Use the Base
Soundings Selection On area to choose whether just accepted soundings, rejected
soundings, or both are output to the file. If any of the checkboxes in the Refine
Selection Based On Sounding Flags area are turned on, then only the soundings that
have one of those flags set are output to the file. Turning on the Automatically
Unproject Soundings if Necessary toggle when the data is in the UTM projection
causes the soundings to be converted to geographic coordinates before exporting.
The data can be output as ASCII XYZ by selecting Ascii XYZ Only from the Select
Output Format drop-down list. Selecting Ascii XYZ + Attributes exports any available
PFM attributes as well as the x, y, and z locations, and finally the soundings can be
exported in a special ASCII format used by NAVO and Caris by selecting
NAVO/Caris Ascii from the list.

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Figure 4-41 - Export Soundings Dialog

Export Shoal Soundings outputs a text file that contains a set of XYZ points
representing the shoalest sounding in each bin of the selected area (see Figure
4-42). The selected area can either be Selection (use the select tool to highlight an
area), Loaded Area (the entire area that has been extracted), or Entire PFM File (the
whole file). If the Automatically Unproject Soundings if Necessary toggle is set and
the data is in UTM projection, the soundings will be converted to geographic
coordinates before they are output. The output format can be specified with the
Select Output Format drop-down list and can either be Ascii XYZ Only, Ascii XYZ +
Attributes, or NAVO/Caris Ascii.

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Figure 4-42 - Export Shoal Soundings Dialog

Export Survey Lines this option writes a list of all survey lines that intersect the
indicated area to an ASCII file. The area to check can either be Selection to output
lines just in the selection box, Loaded Area to output lines in the extracted area, or
Entire PFM File to output all lines in the PFM file.
Export Survey Files this option writes a list of all survey data files that intersect the
indicated area to an ASCII file. The area can either be set to the selection box by
choosing the Selection toggle, the extracted area by selecting the Loaded Area
toggle, or the entire PFM by selecting the Entire PFM File toggle.
Bin Info - displays a dialog box, shown in Figure 4-43, with a number of fields that
contain information in each bin. Once the dialog box is shown, move the cursor over
the surface in the Explore mode and the fields will display the data for the bin closest
to the cursor position.
Cube contains a submenu with a number of options for working the Cube PFMs.
See Chapter 6 for more information.

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Figure 4-43 - Bin Info Dialog Box

4.8.2 Visualization Control Panel

The Visualization Control panel is used to adjust the display options for the extracted
PFM bin file. The extracted surface can be manipulated with many of the same
Fledermaus tools available for SonarDTMs. These include geo-picking coordinates,
profiling, contouring, and re-shading.

Figure 4-44 - Visualization Control Panel

The Transparency, Mesh Gap, Auto, Wireframe, and Shaded Surface controls are
used to control the appearance of the DTM. These controls are similar to those for a
regular SonarDTM (see Chapter 3 in the Fledermaus Reference Manual).

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4.8.3 Targets Panel

A target, sometimes called a contact, is a special point of interest with a number of
attached attributes and possibly an attached snippet image file. Targets are stored in
a separate XML file using the standard NAVO target format and the file name of the
XML file is stored within the PFM file. When a PFM file is loaded containing a valid
targets file, the targets will automatically be displayed and can be editing using the
Targets panel shown in Figure 4-45. Note that targets have only a latitude and
longitude position and no depth value is stored (targets are usually displayed as lying
on a surface if one is available at the location of the target).

Figure 4-45 - Targets Panel

Targets are displayed as spheres in a scene and can be hidden or shown using the
Show Targets toggle. The current target file is displayed in the text field at the top of
the panel. If a target file exists but is not associated with the current PFM, click the
Set Target File button and select the XML file using the standard file dialog box. To
create a new targets file, click the Create Target File button and select a new file to
create.
If multiple targets exist in the scene the targets will be displayed as yellow. To select
a target, enter Select mode and then click near a target. The target will change color
to white, indicating that the target is selected and information about the target will be
displayed in the Geographic and Projection Position fields. As well, information from
the XML file will be displayed in the text area to the right of the fields. To move the
target to a new position, click the Edit Positioning button and enter the geographic
position of the target in the dialog that is displayed.

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Figure 4-46 - Adding or Moving a Target

To add a target, click the Add Target button and enter the geographic position of the
target in the dialog that is displayed (see Figure 4-46). Note that if a point is picked on
the surface of a DTM while in Select mode (a white cross will appear on the surface),
then the position of the last picked point will be displayed in the Enter Target Position
dialog. To delete a target, click on the target while in Select mode and click the
Delete Target button.
Some targets have an associated snippet image. If a snippet exists for the target,
click the View Snippet button and the image will be loaded in displayed in a separate
dialog (see Figure 4-47). To associate a snippet image with a target, select the
target, click the Add/Update Snippet button, and select a valid image file.

Figure 4-47 - Viewing a Snippet Associated with a Target

Targets can also be added, deleted, and moved using the 3D Editor. See Section
3.11 for more information.

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4.8.4 Filters Panel

The Filters Panel allows filters to be run on the current PFM file and is shown in
Figure 4-48. All operations in this panel depend on the setting of the Scope pull down
menu. The different options for the scope are as follows:
Selection area selected by dragging with the mouse in Select mode;
Loaded Area (default) currently extracted area; or,
Entire PFM File all soundings in the PFM file.

Figure 4-48 - Filters Panel

Three types of operations exist in the Filters panel: Select, Clear, and Export. Each
operation can be run on the Suspect, Plotted, or Feature flags and the buttons for
each flag are located to the right of the flag label. The Select button will run a filter on
all soundings in the selection scope to automatically set flags of a certain type. The
Clear button will remove the given flag from all soundings in the given selection
scope. To save all soundings in the selection scope that have a certain flag, click the
Export button.
4.8.4.1 Selecting Suspect Soundings
The suspect soundings selection filter assists the user in identifying soundings that
may be incorrect. Clicking the Select button beside the Suspect Soundings label will
display the Suspect Filter Options dialog, shown in Figure 4-49. The filter will select
all soundings with depths that are more than a certain threshold away from the
average depth in a bin. Enter a threshold in the Depth Threshold Difference text field
and click the Filter button.

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Figure 4-49 - Filter Options for Suspect Soundings

Bins that contain suspect soundings can be shown by setting the Color popup menu
to Suspect or the Flags menu to Suspect on the Surface Control panel.
4.8.4.2 Selecting Plotted Soundings
Automatically selecting soundings for plotting can be accomplished through the
Select button to the right of the Plotted Soundings label. This operation is used to run
a sounding selection algorithm and will display the dialog box as shown in Figure
4-50. Normally the chart scale is specified to determine the default distance between
selected soundings that are entered in the Chart Scale text field. For example a value
of 20000 implies a chart scale of 1:20000. This gives the default minimum distance
between soundings and is based on assuming 5mm text for the resulting chart. You
can directly enter the minimum distance, overriding the suggested default for the
given chart scale, by typing a new value in the Minimum Distance text field. The
Selection Factor that defaults to four is used in algorithm and generally should be left
alone. A smaller number improves the quality of the selection but increases running
time (the default has been found to be a good balance). The Parameter Status field
shows the criterion for running the algorithm. You cannot select soundings if you
select an unreasonable chart scale for the bin size of the PFM. The dialog box will
display a message just below the parameter status to indicate if the selected
parameters are acceptable or not. If they are not you must increase the chart scale
(or minimum distance).

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Figure 4-50 - Filter Options for the Plotted Soundings Algorithm

If advanced filters are to be used with the selection algorithm, enable the Use Filter
Parameters toggle. Before being selected by the filter, the sounding must pass three
criteria: it must be in a bin with more than a certain number of soundings, its height
must be far enough away from the average bin height, and the standard deviation of
the sounding must be above a certain level. Enter values in the Minimum Beams,
Difference from Average Surface (0.25 = 25%), and Standard Deviations for accept
text fields respectively to control these options. If Use Filter Parameters is off, the
bottom three text fields are ignored. Click the Filter button to run the filter on the
selection scope.
Setting the Color popup menu to Plotted or the Flags menu to Plotted on the Surface
Control panel will display which bins contain the plotted flag.
4.8.4.3 Selecting Feature Soundings

Figure 4-51 - Filter Options for Feature Soundings

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Selecting feature soundings is performed by clicking the Select button to the right of
the Feature Soundings label. This will display the dialog as shown in Figure 4-51.
Specify the minimum distance apart of shoals in the horizontal plane (Selection
Interval), and specify the depth range for consideration in the Z Range Minimum and
Z Range Maximum text fields. Click the Filter button to begin the algorithm.
The actual algorithm is a two-step process. In the first step, the process searches
through all the data based on the defined cell size and finds the shallowest sounding
that is not flagged as deleted and is within the selected depth range. In addition, the
entry of the minimum and maximum values allows the user to restrict the process to
only those soundings within the selected depth range. The second step prunes the
list of selected shoal soundings based on the range interval entered. In this step, the
selected soundings are first sorted in descending order. The shallowest is selected
and then any sounding that lies within the entered range is deleted. The next
shallowest sounding is selected and any soundings that lie within the entered range
to it are deleted.
Soundings with the feature flag set can be shown by setting the Color popup menu to
Feature; or the Flags menu to Feature on the Surface Control panel. Also, a list of
feature soundings can be shown by clicking the Table button to the right of the
Feature Soundings label.
4.8.4.4 Feature Soundings Table
The Feature Soundings Table is used for both the displaying and working with the
data records that have been flagged as features. The selected sounding in the table
will be highlighted and will also be highlighted by a red stalk in the Fledermaus
window. If further details of the data point are required, the details can be examined
in the same manner to the 3D Editor table (Figure 3-16). On completion the table
can be saved as an ASCII file for use elsewhere by right clicking on the table and
selecting Save PFM Table As.

4.9 Outputting CUBE Hypotheses

Most options for outputting CUBE PFMs are located on the Tools drop-down menu in
the PFM Attributes Panel in Fledermaus (see Figure 4-52). The three available
options are discussed in the next sections.

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Figure 4-52 - CUBE Tools Menu

4.9.1 Recube Area

Clicking the Tools > Cube > Recube Area will re-run the CUBE hypothesis
generation algorithm on the chosen area. This command is useful if soundings that
should not contribute to CUBE hypotheses have been deleted and the hypotheses
should be re-generated (this option is also available on the right-click menu of the 3D
Editor when editing CUBE hypotheses).

Figure 4-53 - Recube Area Dialog

The Recube algorithm can be run on the current selection box, the extracted area, or
the entire PFM file. Choose either the Selection, Loaded Area, or Entire PFM File
toggle respectively to select the desired area (see Figure 4-53). Click the OK button
to rerun the algorithm or click Cancel to close the dialog. When the CUBE PFM is
generated through PFMDirect, the Cube algorithm is automatically run on the entire
file.

4.9.2 Filter Soundings

The Cube Filter Soundings dialog as shown in Figure 4-54, is used to apply a filter to
a set of soundings in the PFM file based on the Cube surface. This option can be
used in conjunction with the Tools > Export Soundings option to write out a set of
soundings that match the Cube surface within a certain tolerance.

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Figure 4-54 - CUBE Filter Soundings Dialog

The filter is applied to all soundings outside of a certain range from the Cube surface.
Enter a scale factor in the Filter Parameters box to control how many standard
deviations away from the surface the filter is applied. The filter can be run on all
soundings inside the current selection box by selecting the Selection toggle, or all
soundings in the extracted area by selecting the Loaded Area toggle. Alternately, the
filter can be applied to all soundings using the Entire PFM File toggle.
There are four possible outcomes for the filter depending upon which Filter Action is
chosen:
Set Rejected Flag set the filter rejected flag for all soundings that match the filter.
Set Suspect Flag set the suspect flag for all soundings that match the filter.
Clear Rejected Flag clear the filter rejected flag for all soundings that match the
filter. This operation is the reverse of the Set Rejected Flag filter and should not
unreject any soundings rejected manually through the 3DEditor.
Clear Suspect Flag clear the suspect flag for all soundings that match the filter. This
operation is the reverse of the Set Suspect Flag filter.
The filter can be instructed to not modify soundings around a set of targets by
enabling the Dont Filter Soundings Near Targets/Contacts toggle and entering a file
in the Filename field. Click the Browse button to select a file using a standard file
select dialog box. The target file can either be an XML or ascii file. If an XML file (with
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a .xml extension) is specified than it will be assumed to be a NAVO formatted XML

target file and will be processed accordingly. The filter will extract the target positions
from the file and project them as necessary according to the projection information
from the CUBE based PFM file. Currently a maximum of 256 targets are supported
from an XML target file. If a file does not have the .xml extension then it will be
processed as an ASCII file which simply reads the x and y positions from each line of
the file. The first two fields of any line must be in the order of x then y. Any extra fields
are simply ignored. The program attempts to detect and project geographic
coordinates into the UTM space of the PFM (If it is indeed a UTM PFM.) Projected
coordinates can be directly supplied in the file as well. In performing the filtering,
soundings that are less than the distance specified in the Target Radius field away
from a target are not modified. Input the distance in meters.

4.9.3 Output Surface

The current CUBE surface can be output to an ASCII file using the Tools > Cube >
Output Surface menu option. For each bin of the PFM that contains a valid CUBE
hypothesis, an ASCII XYZ point is outputted representing the center of the bin
followed by a value representing the uncertainty of the chosen hypothesis.
The area of the PFM to output can be chosen using the CUBE Output Surface Dialog
(see Figure 4-55). Select the Selection toggle to output the area inside the selection
box or select the Loaded Area toggle to output the entire extracted area. If the Entire
PFM File toggle is selected, all bins in the file are written.

Figure 4-55 - CUBE Output Surface Dialog

4.9.4 Cube Options

Different options for the CUBE surface can be controlled with the Tools > Cube > Cube
Options menu option, which displays the Cube Options dialog (see Figure 4-56). Both
the Hypothesis Resolution Algorithm and Capture Distance options affect how the
Recube algorithm is run using Tools > Cube > Recube Area.

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Figure 4-56 CUBE Options Dialog

When running the CUBE algorithm, sometimes multiple hypotheses are generated.
The algorithm must make a best guess on which hypothesis is correct using a
Hypothesis Resolution Algorithm. The following algorithms are supported:
Num. Samples The hypothesis containing the most soundings will be chosen.
Neighborhood The algorithm searches all the neighbors of the cell looking for a cell
with only one hypothesis. If a cell is found with one hypothesis, this cell is used as a
guide in choosing a hypothesis; otherwise the Num. Samples algorithm is used.
Num. Samples + Neighborhood A combination of the two previous algorithms.
Predicted Surface The algorithm computes the median surface of the input
soundings as uses that surface as a guide in choosing the hypothesis.
Usually the Predicted Surface algorithm performs the best and is the default,
although other algorithms may perform well depending upon the type of data.
Internally, the CUBE algorithm has no concept of cells. A sounding may contribute to
many different hypotheses depending on how far away the sounding is away from
the hypothesis center in the XY plane. The Capture Distance option controls how far
the sounding can be to contribute to a hypothesis and the algorithm assumes that
deeper soundings will be less accurate. If the distance from the hypothesis center to
the sounding is less than the sounding height multiplied by the Capture Distance
percentage, the sounding will be included in the hypothesis. Smaller Capture
Distance values result in less soundings contributing to a hypothesis and larger
values result in more soundings contributing to a hypothesis. If the Capture Distance
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is too small, holes may appear in the data. The default value is 5 percent. In some
cases, this Capture Distance does not make sense so to turn the algorithm off, enter
100 as the Capture Distance value.
The CUBE options menu also allows you to turn any soundings that have been
flagged as features, either in the original source files or from within Fledermaus in
custom hypothesis. This means that for any feature soundings the final CUBE
surface will have a depth at exactly the same location. Figure 4-57 displays the dialog
for setting custom hypothesis from features. The only option is what scope you would
like the operation to affect.

Figure 4-57 Create Custom Hypotheses from Features Dialog

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4.10

Vessel Class

Figure 4-58 - Sample Vessel Screenshot

The Vessel Operations Class allows real-time visualization of a Vessel in a 3D

scene. A vessel may be a ship, ROV, AUV, oil platform, or any other vehicle. Vessel
data can be read through the serial port, or played back from a pre-recorded file. The
VesselManager application, discussed in Chapter 6: Additional Data Tools, must be
run at the same time as Fledermaus and is used to process the incoming Vessel
information. To add a Vessel to the current scene, select the Data > Add Vessel
menu option. In the Data Set Control area, the Vessel interface will appear as shown
in Figure 4-59. Initially, a yellow cross will be drawn in the scene signifying that a
Vessel is present, but not activated.

4.10.1

Vessel Tab

To activate the Vessel, enter the id number of the object (found from the
VesselManager) in the Vessel ID text field and press the Activate button. The Status
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text field should change from Not Initialized to Active if VesselManager is running
correctly. To view the VesselManager at any time, click the Show VesselManager
button on the right side of the interface. Once activated, the Vessel will appear as a
small, white vehicle shown in Figure 4-58.
As data is read by the VesselManager, the position and orientation of the Vessel will
change in real-time. By default, the Fledermaus Main Visualization Window does not
continually update so that even though the Vessel is moving, the results will not be
shown on the screen. To force the display to continually update, select the Rendering
> Interactive menu option. To stop updating the screen, select another option from
the Rendering menu. The current geographic location of the Vessel is always
displayed in the Location text field.
Each vessel has a single point where the position is recorded, which is called a
tracked location (this may be a GPS sensor, or some other device). Usually a Vessel
will have a single tracked location; however, if multiple tracked locations exist on the
same object, click the Advanced button to view the Advanced Setup dialog as
discussed in section 4.10.4. By default, the tracked location is assumed to be at the
center of the object. If this is not the case, use the Advanced Setup dialog to change
the tracked location position.

Figure 4-59 - Vessel Controls

A number of options exist for controlling the shape of the Vessel object in the 3D
scene. The Model Type drop-down list can be used to select from three different built
models: the Basic ROV, a Cube, or a Cylinder. If the Custom type is selected from
the list, a custom model can be loaded by clicking on the Load Custom Model button.
The custom model being loaded must be a model that was imported using File >
Import > Import Model, and then saved as an SD object. Note that when saving a
model as an SD object, the model should be facing the positive x-axis (this can be
changed using the Transform Vertices button in the Solid Model interface).
The width, height, and depth of the Vessel can be specified in the Size text field. All
measurements are given in the units of the scene. Click the Scale button, enter a
value in the resulting dialog, and press Enter to uniformly scale the Vessel by that
value. For example, if the size was 10.00 10.00 6.00, clicking the Scale button and
entering 2.0 into the textfield and pressing Enter would cause the size to become
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20.00 20.00 12.00. To change the color of the Vessel, press the Change Color
button and select a color using the standard color selection dialog. Note that the
vertical exaggeration of the scene should be set to 1 when comparing distances
between the model and the scene.
In the display group, click the Show VesselManager to display the VesselManager
application which is used to configure the incoming vessel information. While
visualizing the scene, having multiple views of the Vessel can be quite useful. To
display an additional view, click the Show View button. This button opens another
window that is, by default, constantly focused on the Vessel. To change the how the
view is displayed, click the Options button (see Section 4.10.6 for more
information). Again, the display will not continually update unless in Interactive
Rendering mode. A monitoring dialog can be displayed by clicking the Show Monitor
dialog. This dialog displays important information about the Vessel and is discussed
in Section 4.10.5.

4.10.2

Vessel Distances Tab

Figure 4-60 Vessel Distances Tab

The Vessel Operations Class allows monitoring the distance between a point on the
Vessel and any point in the scene. Each distance monitor is displayed as a row in a
table on the Distances tab. Click the Add Distance Monitor to add a new distance
monitor to the bottom of the list, or select a row and click the Remove Distance
Monitor button to delete a monitor.
Each distance monitor by default measures from the center of the Vessel to another
point in the scene. To measure from another point on the Vessel instead of the
center, enter an offset in the Local Offset column in the units of the data. For
example, if an arm of an ROV is located 3 meters to the right, 2 meters forward, and
1 meter up from the center of the vessel, enter a Local Offset of 3 2 1 to measure
from that point.
The point in the scene that the distance monitor measures to changes depending
upon the value of the Distance Type column:
Pick Point Measures to the current pick point in the 3D scene. Select a new pick
point by entering Select mode in the main display and then clicking a point in the
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scene. The current pick point location will be displayed in the Target Location
column.
Object Measures to the center of another object in the scene. Choose the other
object using the Target Object drop-down list. To measure to another point on the
target object instead of the center, enter an offset in the Target Offset column (as you
would in the Local Offset column).
Line Object Measures the minimum distance from a point to a 3D lines object.
Select a lines object in the Target Object drop-down list to measure to that object.
This option is useful if a 3D lines object exists that indicates the shoreline of a river or
ocean, then a distance monitor of this type can indicate how close the vehicle is to
the shore.
Fixed Point Measures to a fixed point in the scene. Enter the coordinates of the
target point in the Target Location column.
Vertical Measures the distance vertically from the Vessel to the sea floor.
Line Object (+/-) Similar to the Line Object distance monitor, except displays a
positive distance if the vessel is to the right of the line or a negative distance if the
vessel is to the left of the line. This monitor is useful to measure the deviation of a
vessel from a planned path.
If the Visible toggle is turned on for a distance monitor, a line will be drawn in the
scene from the point on the Vessel to the target point. The color of this line can be
changed by clicking the rectangle in the Color column and selecting a new color. The
line width can be changed by entering a new value in the Line Width column. On
most of the distance monitor lines in the 3D scene, three numbers will be displayed:
the compass bearing in degrees from the Vessel to the point, the elevation angle to
the point, and the distance in meters to the point. Some distance monitor types only
display the distance in meters. The distance for each distance monitor is also
displayed in the Distance column, as well as in the Monitor dialog (see Section
4.10.5).
If a non-zero value is entered in the Warning Distance column, then the distance line
in the 3D scene will be displayed as a bold red line if the measured distance falls
below the warning distance. The distance will also be displayed in a red font in the
Monitor dialog. Use this option to warn if a vessel gets too close to another object in
the scene.
Clicking the Load Points of Interest button allows easily setting up a number of Fixed
Point distance monitors to points in the 3D scene. Click the button and select an XYZ
file containing the list of points to measure to, and the distance monitors will be
automatically created.

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4.10.3

Vessel Tools Tab

Figure 4-61 Vessel Tools Tab

A number of additional tools for the Vessel Operations Class are located on the Tools
tab at the bottom of the interface. The History section allows displaying a line
indicating the path the Vessel has taken in the 3D scene. Display the history line by
enabling the Visible toggle. The amount of time the history line indicates can be
controlled by entering a value in the Max. Length field in seconds and pressing Enter.
Clicking the Create Line Object button converts the current history line in a new SD
lines 3D object that will appear in the object list.
A profile can be displayed that tracks the Vessel by using the Profile group. If the
Visible toggle is enabled, the profile will constantly update and the profile window will
constantly be shown (note the Visible toggle must be disabled before the profile
window can be hidden). By default, the profile is locked to the center of the Vessel.
To lock the profile to another point, enter an offset in the Offset field. The offset is in
units of the scene and indicates the offset right, forward, and up from the center. The
Length field indicates the length of the profile, and the Rotate field can be used to
rotate the profile to different angles. For example, an angle of 0 means cross-track
and an angle of 90 means along-track. More options for the profile can be controlled
by clicking the Advanced button, as discussed in Section 4.10.7.
The Prediction group allows displaying a line in the 3D scene indicating where the
Vessel will be in the future. Enable the Visible toggle to display the prediction, which
appears as a straight dotted white line in the scene. The length of the line can be
controlled using the Length text field. The prediction line will not be displayed properly
unless your input format contains the course made good field.

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Vessel Advanced Setup Dialog

Figure 4-62 Vessel Advanced Setup Dialog

The Advanced Setup dialog is used to configure options for the tracked locations (or
sensors) on a Vessel, and is show in Figure 4-62. Display this dialog by clicking the
Advanced button in the Vessel Setup group.
Each tracked location is displayed as a row in the main table of the dialog. Enter an
Id number for the tracked location that corresponds to the number setup in
VesselManager. Clicking the Active toggle will activate or deactivate that sensor. The
current position of the tracked location will be displayed in the Location column when
in Interactive rendering mode.
By default, the tracked location is assumed to be at the center of the object. If the
tracked location is not at the center, enter an offset in the Offset column. The units for
the offset are in the units of the scene and indicate the amount right, forward, and up
from the center of the object.
To display the tracked location in the 3D scene, enable the Visible toggle. The
location will be drawn as a diamond and the color can be changed by clicking on the
Color column and selecting a new color.
Usually, a Vessel will only have one tracked location; however, some Vessels may
have multiple tracked locations (for example, an oil rig might have a tracked location
on each of its pylons). Add a tracked location to the bottom of the list by clicking on
the Add Tracked Location button, or remove a tracked location by clicking on a row in
the table and clicking the Remove Tracked Location button. Note that each tracked
location should have a separate Id number and a separate Offset. The first tracked
location is used for the position of the vessel, but the other tracked locations are
useful for showing the Vessel prediction.

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4.10.5

Vessel Monitor Dialog

Figure 4-63 Vessel Monitor Dialog

The Monitor dialog, as shown in Figure 4-63, is displayed by clicking the Show
Monitor button. This monitor displays important information about the Vessel in a
large font. The top part of the dialog displays each distance monitor as set up with
the Distances tab. The Type and Distance for each monitor is displayed and will
update continuously when the scene is in Interactive Rendering mode.
The bottom half of the dialog displays the list of tracked locations for the object.
Additional tracked locations can be added to the object by clicking the Advanced
button (see Section 4.10.4). For each tracked location, the current Location is
displayed, as well as the last time the position was updated in the Last Update Time
column (note that the Last Update Time is valid only if proper time information is
contained in your input format).
Click the Close button to hide the monitor.

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Vessel Display Options Dialog

Figure 4-64 Vessel Display Options Dialog

Figure 4-64 shows the Display Options dialog that is used to configure how the
camera in the main display and extra view will work. This dialog can be accessed by
clicking the Options button in the Display group on the main Vessel interface.
If the Lock Main View to Vessel toggle is enabled, the main Fledermaus window will
always be centered on the Vessel. The options in the New View group apply to the
extra view of the scene that is displayed when the Show View button is clicked in the
main Vessel interface. When the Lock New View to Vessel toggle is checked, the
view is always centered on the Vessel (this is on by default when the Show View
button is clicked). When the view is centered on the Vessel, the view direction can
also be locked to the Vessel by enabling the Lock View Direction to Vessel Direction
toggle. When this toggle is enabled, the extra view shows an image as if a camera is
positioned on the Vessel. The position of the camera can be controlled by entering
an offset in the Camera Offset field. This offset indicates the number of units right,
forward, and up from the center of the Vessel where the camera is located.
Note that when an option is changed in this dialog, the change will not take effect
until either the OK or Apply buttons are clicked. The OK button applies the changes
and closes the dialog, the Apply applies the changes without closing the dialog, and
the Cancel button closes the dialog without making any changes.

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4.10.7

Vessel Advanced Profile Dialog

Figure 4-65 Vessel Advanced Profile Dialog

A profile can be set up which follows the Vessel as it moves (see Section 4.10.3).
Clicking the Advanced button in the Profile section of the Tools tab displays the
Advanced Profile dialog, shown in Figure 4-65.
This dialog allows some extra information to be added to the Profile Window. Enable
the Visible toggle in the Rectangle group to display a rectangle indicating the bounds
of the Vessel. Input the horizontal bounds by entering the distance from the center of
the object in the Left and Right text fields. Enter the height above water level for the
top and bottom of the vessel in the Top and Bottom text fields. For example, if the
Vessel ranged from 2 meters above the water to 4 meters below the water, enter 2
and 4 in the Top and Bottom text fields respectively. If the Show Distances toggle is
checked a yellow line is drawn from the bottom corners of the rectangle to the profile.
This option could be used to tell how much a ship could move left or right before
hitting the banks of a river. If the Show Rectangle in Scene or Show Distances in
Scene toggles are enabled, the rectangle or yellow distance lines are drawn in the
actual 3D scene.
A line indicating the water height can be displayed by clicking the Visible toggle in the
Water Level group. The water level will appear as a light blue horizontal line in the
profile. Enter a new water height in the Water Height text field.
Note that before any changes are applied to the profile, the OK or Apply button must
be pressed. The OK button applies changes and hides the dialog, the Apply button
applies changes without hiding the dialog, and the Cancel button hides the dialog
without making changes.

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Chapter 5 - DMagic
5.1 Introduction
DMagic is an application designed to facilitate the management and preparation of
large amounts of source data for visualization and editing in Fledermaus. DMagic has
a number of key features:

an easy to use visual interface for importing and manipulating data;

project structure to help organize and manage large amounts of source

data;

source data display that allows interaction and processing of source data
before being converted to Fledermaus objects;

source data metadata system that provides additional information and

increases the speed of processing operations;

5.2 Starting DMagic

Depending on your operating system, there are multiple ways to start the DMagic
application. On a Windows based OS, click the DMagic icon from the Windows Start
Menu, or double click the DMagic desktop icon. Alternatively, the application can also
be launched directly from a command line.

5.3 User Interface

Figure 5-1 shows the six major regions of the main DMagic interface:

Display Region

Source Data

SD Data

Object Attributes

Control Bar

Menu Bar

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Figure 5-1 - DMagic Main Window

5.4 Display Region

The Display Region is the main visualization window of the application and consists
primarily of the large window that displays loaded SD objects and source data. It has
options that can be used to examine and manipulate the displayed surface.

5.5 Source Data Region

The Source Data region is divided into four main categories: Ungridded, Gridded,
Images, and Vectors. When source data is added to a project, it will be displayed
under one of these four categories. By right clicking on a group or an individual file, a
list of operations applicable to that object will be displayed. Please refer to the Menu
Bar section for a description of those tools.

5.6 SD Data Region

On the bottom left of the main window, there is a list box called SD Data . This list
contains the names of any SD files currently added to the active project. This list is
divided into two main categories: SD Files and PFM Files.

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5.7 Object Attributes Region

Shown to the right of the SD Data region is the object attributes control area. The
display will change depending on the type of object currently selected in the list.
These controls provide the ability to manipulate data type specific information related
to the selected object.
Refer to Chapter 4 -on Data Types, which describes in detail the function and
controls for each data object.

5.8 Control Bar

Figure 5-2 - Control Bar

The DMagic control bar is located on the right side of the main window and provides
a number of options for interacting with the display region. By default the control is
oriented vertically, however it can also be used horizontally, as shown in Error!
eference source not found..
The control bar has the following buttons:
Reset Camera (ESC Key): This command will reset the current camera location so
that all loaded data sets are now in view.
Zoom to object (Z Key): This command will move the camera so that you are viewing
the currently active data object.
Explore Mode (Space Key): The default explore mode is used for navigating around
the 2D display area using the middle mouse button, selecting object using the left
mouse button, and creating profiles with the right button.
Select Mode (S Key): The select mode allows the user to draw a rectangular
selection box that will then be used by many of the tools that DMagic provides.
Measure Mode (M Key): When the measure mode is active, the left mouse button
can be used to measure across any loaded SD surface. The measured distance will
be displayed in the information area located at the bottom left of the main window.
Clear Display (X Key): The clear display command will remove any selection boxes
or clicked points in the main display.

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Toggle Colormap Legend (C Key): This command will turn on/off the color map
legend display. When enabled the color map legend will automatically display the
color map for the currently active object.
Toggle Bounds (B Key): This command will turn on/off the bounding box and
associated coordinate labels.

5.9 Menu Bar

The Menu Bar provides access to the majority of the functionality that DMagic
provides and will be described in detail in this section.

5.10

File Menu

Figure 5-3 - DMagic File Menu

5.10.1

Create Project

Figure 5-4 - Create Project Dialog

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The 'Create Project' command is used to specify the directory in which the project
structure will be created. The project structure contains a number of sub-directories
for organizing data, in addition to a master project file. The 'Create Project' dialog is
shown in Figure 5-4. The default location for DMagic projects is in the
Users/username/FMData/Projects folder on your computer

Grids
Ancillary

Images

Metadata

Vectors

my.fmproj

PFM
Output
SD

Source
Figure 5-5 - Project Hierarchy

Once the project is created, a hierarchy of folders will be created as shown in Figure
5-5.
The primary folder at the top of the hierarchy will also contain the fmproject.xml file.
This XML file is a common structure that can be used by FMGT, FMMidwater and
DMagic to load projects. The key folders for FMGT are under the Output folder and
are used to store the interim data created by the staged processing

5.10.2

Delete Project

The Delete Project command will permanently delete an existing project and all the
data contained in its sub-directories.

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5.10.3

Open Project

Existing projects are opened using the 'Open Project' command. Note that DMagic
projects created in version 6.x are not compatible with version 7.x and cannot be
opened with this command.

5.10.4

Edit Project

Figure 5-6 Edit Project Dialog

After a project is created, the project options can be changed using the 'Edit Project'
menu command. The project options include the base coordinate system and vertical
datum as shown in Figure 5-6.

5.10.5

Close Project

This will close the currently opened project. The project is not deleted from disk.

5.10.6

Add Source Data

This command will add new source data to the current project using the add source
data wizard. During the process of adding the data, metadata for the source data will
be created (if none currently exists). Figure 5-7 shows the first stage of the wizard,
which is used to select the data type you would like to add.

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Figure 5-7 - Add Source Data Wizard (Stage 1)

The next stage of the wizard, shown in Figure 5-8, provides a number of
convenience functions for selecting the source data to be added to the project. The
controls on this stage of the wizard are:
Add File(s) : Select one or more input files using a multi-file selection dialog.
Add Directory : Allows all files in a directory to be selected at once. The Add File
Filter is used to restrict which files are added, and the Include Sub-Directories toggle
provides the ability to restrict the software from adding source data from any subdirectories.
Add Custom ASCII Files: Opens a dialog used to import customized ASCII files.
Load File List:: Used to select a text file containing a list of input files, one per line.
Save File List: Saves the current list of input files to a text file for future use.
Add HIPS Data: Used to add one or more lines from a CARIS hips project.
Select All: This command will select all currently loaded source files.
Deselect All: This command is used to clear the current selection of source files.
Remove File(s): Removes the currently selected file from the list.
Clear File List: Removes all files from the list of input files.
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Figure 5-8 - Add Source Data Wizard (Stage 2)

The last stage of the wizard is dependent on what data type was chosen during
stage 1. Figure 5-9, shows the last stage of wizard when Ungridded data was
selected.

Figure 5-9 - Add Source Data Wizard (Stage 3)

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Add SD File

Adds an existing SD file to the current project.

5.10.8

Add PFM File

Adds an existing SD PFM file to the current project.

5.10.9

Preference

Select the Preferences menu option to open the Preferences dialog box shown in
Figure X. Preferences are used to save settings for a number of options that effect
how DMagic runs.
The Preference Groups list box on the left-hand side of the dialog shows the
available preference groups. Selecting a preference group will display its controls on
the right hand side of the dialog. There are also a number of buttons along the
bottom of the dialog. The OK button applies all of the changed preferences and hides
the dialog from view. The Cancel button dismisses the dialog without saving any
changes. The Apply button sets all changed preferences without hiding the dialog
box. The Reset button will reset the preferences to their default (starting) values.
When DMagic exits, it writes the current preferences to a file for automatic loading on
start-up. Each user has a set of preferences normally saved in their home directory.

Figure 5-10 - DMagic Preferences - Display

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Startup Group
Ask to open Last Project Toggle: If this is turned on then at start up DMagic will
prompt the user to open the project that was last opened.
Display Group
Display Mode: This allows you to set the default starting display mode. See section x
for more information on the different display modes.
Colors: You can set the background and foreground color of the main display area
using this preference.
Windows: The 'Reset Display' button will reset all dockable windows to their default
location.
Color Map Legend Toggle: Sets whether or not the color map legend is toggled on
at start up.
Show Bounding Coordinates Toggle: Sets whether or not the bounding box and
associated coordinate labels is toggled on at start up.
Georeferencing Group

Figure 5-11 - DMagic Preferences - Georeferencing

Default Project Coordinate System: When creating a new project, this will be used as
the default coordinate system.
Geographic Format: Coordinates that are in geographic units will be displayed using
this format.
Projected Format: The display of project units will use the format specified by this
option.
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Always Show Bounding Coordinates: Determines if the bounding coordinates are

always displayed.

Shading and Color Maps Group

Figure 5-12 - DMagic Preferences - Shading and Color Maps

Default Color Map: Specifies which color map will be the default for any DMagic tools
that use the shading tools.
Default Shading Parameters: These values will be used as the default values any
time shading is used within DMagic. Refer to secion 5.6 for more information on
shading.
Source Data Group

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Figure 5-13 - DMagic Preferences - Source Data

Adding New Data: There are three options for determining what will happen when
new source data is added to a project. They are:
All Items On: Any data that is added will automatically be toggled on.
Children Items are On, Parent Items are turned Off: This allows groups to be toggled
on without having to toggle each child.
All Items Off: No items will be turned on unless the user toggles them.
Color Scheme: This section is use to change what colors are used for the different
types of source data that is displayed in DMagic.

5.10.10

Screen Capture

This option is used to save an image in the current visualization window to a file for
printing or publication. Selecting this option brings up the screen capture dialog box.

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Figure 5-14 - DMagic Screen Capture Dialog

The image can be saved as either a TIFF image, an encapsulated postscript (eps)
file, or a jpeg image. Choose the image format from the Image Type pop-up. The
entry field at the top displays the name of the image file to be saved. The Image Size
entry field gives the output size (width x height) of the generated image both in pixels
and in Megabytes. The image size is based on the dimensions of the visualization
window and the magnification factor specified by the Magnification slider bar.
Magnification of the current view allows for a much higher resolution image to be
saved than a standard screen capture would provide.

5.10.11

Pause

This option will pause the background scanning of source data.

5.10.12

Recent Projects

The Recent Projects menu option displays a continually updated list of recently
loaded projects. Clicking on any of the displayed files will load the corresponding
project.

5.10.13

Exit

The Exit menu command is used to stop running DMagic. It will bring up a message
dialog that asks you to confirm the quit operation. Quit DMagic by answering Yes to
the dialog box. Pressing the No button will return you to the application.

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5.11

View Menu

Figure 5-15 - DMagic View Menu

The View menu is used to hide and show both the Color Map Region and the
Analysis Tools Region. By hiding these regions, it increases the window size
available the Surface Display Region.
When DMagic is closed, it stores in its preference file the view options so the next
time it is run it will reload those view options.

5.12

Rendering Menu

The Rendering menu is used to configure the multistage rendering in DMagic.

Specifically, it determines how the high-resolution image is drawn when you pause in
your exploration; this is one of the important steps in the multi-stage interruptible
rendering algorithm.

Figure 5-16 - DMagic Rendering Menu

Rendering > Interactive In this mode the system continually redraws the scene
regardless of any user activity. The scene is drawn in the lower-resolution exploration
mode.
Rendering > Replace with Hi-Res - Renders the high-resolution image in the
background, then it clears the low-resolution image and replaces it with the high-

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resolution image. This provides an accurately rendered image but does not provide
any visual feedback while rendering the high-res imagery.
Rendering > Overlay with Hi-Res - Redraws the high-resolution image over top of the
low-resolution image. This is the most frequently used mode as one sees the high
resolution rendering as it progresses and can easily choose when to interrupt it.
Rendering > Overlay and Replace - Combines the previous two choices to provide
the best of both worlds: redraws the high resolution image both over the top of the
low resolution image and in the background, and clears the mixed low/high resolution
image and replaces it with the high resolution only.

5.13

Tools Menu

Figure 5-17 - DMagic Tools Menu

All tools apply to the currently selected files and are also available from right clicking
on the data object, or from right clicking in the graphical area.

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5.13.1

Plot Ungridded Files

This command will plot the points of the currently selected ungridded files in the
current view. If there is an active selection box, then only points within those bounds
will be plotted. Plotting points will activate the plotting toolbar as shown in Figure
5-18.

Figure 5-18 - DMagic Plotting Toolbar

The toolbar has the following commands:

Cell Size: This value is used to set the size of the 2D grid. This value will also be
used as the default cell size if the gridding wizard is launched.
Update Cell Size: This button will replace the current grid with a new grid set to
current cell size.
Value to Plot: By default the depth value will be plotted, however any additional value
available in the source files can also be used.
Toggle Grid: This will toggle on or off a 2D grid set to the size of the current cell size.
Point Size: This slider will adjust the size of each individual plot point.
Re-plot: This button is used to re-plot the points after the user has either moved the
camera position, or has adjusted the value to plot.
Close: This will close the plotting toolbar and clear any currently plotted points.

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5.13.2

R E F E R E N C E

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Grid Ungridded Files

Figure 5-19 - DMagic Gridding Wizard (Stage 1)

The grid ungridded files command is used to create a new gridded SD file from one
or more un-gridded files. If there is an active selection box, those bounds will be used
as the default bounds. Figure 5-19 shows the first stage of the gridding wizard.

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Figure 5-20 - DMagic Gridding Wizard (Stage 2)

Below the file type display is a table displaying all the input fields for the current input
files. The Mapping column indicates how a given field is used during the gridding
process. By changing the Mapping values, different fields can be used for both the
value to grid as well as the X and Y value. In addition to changing what fields are
used, any field can also be inverted by setting the Modifier column to Invert.
The second tab in the configuration dialog is the Flags control that is used to specify
which input flags are used to reject data during the gridding process. This table
contains two columns. One to display the flag name, and another to specify whether
to accept or reject data that has the given flag set to true.
The second stage of the wizard is displayed in Figure 5-20 and has a number of
different options for controlling the gridding algorithm. The Gridding Parameters
section controls how a set of points are gridded. The most important parameter when
gridding data is the Cell Size, which determines the dimensions of the surface to be
created. These dimensions are determined by taking the range of the input data in
the X and Y dimensions, dividing it by the cell size, and rounding up.
The Gridding Type pop-up menu specifies which algorithm to use when gridding.
There are three types of surfaces that can be used from irregularly spaced XYZ data:

Weighted Moving Average the default weighted average algorithm

Shallow Biased minimum value in the cell

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Median Filtered median value in the cell

Deep - the deepest value in the cell

Root Mean Square - uses a RMS algorithm

Figure 5-21 DMagic Gridding Wizard (Stage 3)

The next stage of the gridding wizard is used to specify the color map and shade
parameters used to build the SD file. This stage of the wizard is displayed in Figure
5-21.
.

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Figure 5-22 - DMagic Gridding Wizard (Stage 4)

The last stage of the gridding wizard is used to specify the output filename and if the
output should be a surface SD file (SonarDTM) or a scalar SD file. This stage of the
wizard is displayed in Figure 5-22.

5.13.3

Export Ungridded Files

This command is used to export ungridded files to another format. It will launch the
export wizard as displayed in Figure 5-23.

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Figure 5-23 - DMagic Export Ungridded Data Wizard (Stage 1)

The first stage of the wizard is used to confirm which files will be used during the
output process. Any file that you do not want to be exported can be disabled using
the checkbox located to the left of the file name.
The second stage displays the current coordinate system of the files being exported.
It also allows the user the specify which field value will be exported as the Z-Value.

Figure 5-24 DMagic Export Ungridded Data Wizard (Stage 2)

By default the exported files will be written in the same coordinate system they are in,
however the output coordinate system can be specified during stage 3 of the wizard.
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If the output coordinate system is different than the input coordinate system, each
point will be projected during the creation of the output file.

Figure 5-25 - DMagic Export Ungridded Data Wizard (Stage 3)

In addition to choosing the output format, there are also two options for deciding how
the output files are actually written:
All input files can be merged into a single output file
Each input file can be converted into a matching output file. In this case the use
specifies an output directory, and the output files will be created using the same base
name as the input files, except with _out added to the filename and the extension
changed to match the selected output format.

5.13.4

Apply Tides

The Apply tides operation allows offsetting the height of all soundings in an input file
according to a tide information file. The tides can only be applied to a set of FAU or
FU2 input files using a tide file in Nivel format. The Apply Tides dialog as shown in
Figure 5-26 will be displayed.

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Figure 5-26 - DMagic Apply Tides Dialog

To add a tide file to the list, click the Add Station and button and select a file or files
using the standard file select dialog box. The tide files must currently be in Nivel
format. A tide file may contain a number of Stations, which are positions where the
tide is recorded. To remove a tide file from the file, select the file and then click the
Remove Station button. Note that position information is not currently supported in
the Nivel format. Click the OK button to begin the tiding procedure, or click the
Cancel button to close the dialog without applying and tides.
When the tides are applied, each of the soundings in the input files are read. If a
timestamp for the sounding can be found in the tide file, the sounding height is offset
by the tide value. The input files are written to new files with -tided appended to the
file name. For example, tiding the file file001.fau would generate the file file001tided.fau. If the timestamp for any of the soundings cannot be found in the tide files,
an error is generated and the tiding operation is halted.

5.13.5

Build PFM

The PFM Wizard provides a user friendly and efficient interface for the creation of
PFM data sets. The following sections will outline the steps required for building a
new PFM with the wizard, appending new data, and unloading an edited PFM.

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Figure 5-27 - PFM Build Wizard (Stage 1)

Coordinate System
The second stage of the wizard is used to setup the coordinate system for the PFM
by displaying the coordinate system for both the ungridded input files and the output
PFM. If the PFM is set to a different coordinate system than the input files, DMagic
will project each data point into the PFM coordinate system.
Bounds
Once the coordinate system has been configured, the next stage is used to specify
the overall bounds for the PFM data set as shown in Figure 5-28. By default the
toggle Auto-Scan on Load is set to true, which means that no other set up is required
for this stage - before the actual loading is started, the Wizard will scan all the input
files in order to determine what bounds to be used. Alternatively, if the Auto-Scan on
Load toggle is turned off, the bounds need to be specified at this stage. The bounds
can be obtained by either loading an ISS-60 formatted area file (usually with
extension .are) using the Load From File button or the Scan Now button can be
used to perform a full scan of all the input files. An .are file is a simple ASCII file
consisting of four lines similar to that shown below.
N 30.26428, W 90.46645
N 30.26428, W 89.60689
N 29.95703, W 89.60689
N 29.95703, W 90.46645

Note that you can specify projected coordinate bounds as well. The system will
actually use the minimum bounding box that encloses all four corners for the PFM
area.
Once either option has completed and the bounds displayed, they can be manually
adjusted by replacing any value in the bounds fields.

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Figure 5-28 - PFM Build Wizard (Stage 2)

PFM Configuration
The PFM configuration stage of the wizard is used to specify some of the build
parameters for the new data set. At the top left of the wizard is the Z-Range selection
box, which is used to specify the approximate depth range for the PFM. In addition to
the four preset ranges, there are two other options Custom and Auto. When set to
Auto, the application will scan the data during the build operation in order to
determine what is the exact depth range of the input data. The last option, Custom,
can be used to set a user defined depth range for the PFM. The Bin Size field is used
to specify the size of each cell used in the PFM binned data structure. Note that the
binning has no affect on the underlying sounding data, which is always stored at full
resolution. The Vertical Resolution field is used to select a resolution close to the
expected vertical resolution of your data. The less resolution used, the less space the
PFM will require.

Figure 5-29 - PFM Build Wizard (Stage 3)

Extra Attributes
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In addition to the standard PFM data, three additional attributes can be selected and
included with the data set using the Wizard stage displayed in Figure 5-30. This
stage is optional and by default will not be displayed.
To include an extra attribute, the toggles on the left side of the Wizard can be turned
on. When creating a PFM with input files from two or more different file types, only
the format of the first input file added will be used. The next step is to select the
attribute from the source format that will be included in the PFM using the Configure
Attribute Mappings button. It is important to note that although a particular attribute
may be included in a format, there is no guarantee that the source files actually have
that field populated with real data.

Figure 5-30 - PFM Build Wizard (Stage 4)

Custom Filters (optional)

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Figure 5-31 - PFM Build Wizard (Stage 5)

The Custom Filters stage allows running filters on the individual soundings when the
PFM file is built. By default, no filters are used when building the file. To enable the
use of filters, click the Enable Custom Filters toggle.
Each filter has a Condition and an Action. If a sounding matches the condition, then
the action is applied to the sounding. Conditions are constructed by comparing the
value of one of the attributes of the file with a given value. Select the attribute to
compare in the drop-down list to the right of the If label. Select the comparison
method with the drop-down list to the right of the is label (options include Equal To,
Greater Than, Less Than, Not Equal To). Enter the value to compare in the field to
the right of this drop-down list. If the condition is met for a sounding, then an action is
applied to the sounding according to the drop-down list to the right of the --> symbol.
The action can either set one of the flags in the PFM file, or can exclude the sounding
from the PFM file.
Once a condition and action has been chosen, click the Add button and the filter will
be listed in the Filters list box. Only those filters listed in the Filters list box will be
applied to the data when the PFM file is built. Select a filter from the list and click the
Remove Filter button to delete the filter from the list. Click the Clear All button to
delete all filters from the list.
Final Stage and Area Based Filter
Before starting the build process, the location for the PFM data set needs to be
specified. The only required input at this stage is the file name and location for the
PFM list file both the Bin and Index filenames will be automatically created based
on the list file. If desired, these paths can be customized to accommodate a custom
configuration. This stage of the wizard can also be used to select both an optional
target file and an optional image file.
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Figure 5-32 - PFM Build Wizard (Stage 6)

The last stage of the wizard provides a confirmation of the PFM list filename and
path. The Finish button in the lower right of the wizard can then be used to start the
build process, during which a progress window will provide updates on the progress
of the build.
The last stage of the wizard provides the option to activate and configure the areabased filter. If enabled, the filter will automatically begin once the PFM data set has
finished building. Specify the standard deviation threshold for each cell in the Cell
Std. Deviation field.

5.13.6

Build Blank PFM

The Build Blank PFM command is used to build a PFM data set without adding any
initial data files. This allows a blank PFM to be set up as the first step before adding
data using one or more Append operations. Please refer to the previous section on
the PFM Build Wizard for a description of the options used when building a blank
PFM.

5.13.7

Unload PFM

Once you have edited a PFM data set in Fledermaus, the edits that have been
temporarily stored in the PFM can be applied back to the original source files using
the Unload PFM option. In order to support unloading the original format must have
validity flags that can be updated.

5.13.8

Append PFM

Additional source data can be added to an existing PFM by using the append
operation. The primary requirement for this operation is that the new data must be
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within the bounds of the PFM, otherwise any data that is outside those bounds will
not be included.

5.13.9

Delete Line from PFM

Figure 5-33 - PFM Delete Line Dialog

There is often the case when you need to delete one or more lines from a PFM but
do not want to rebuild the entire data set. The Delete Line utility allows you to select
one or more lines from a PFM and have the data records from those files removed
from the data set. Once the data is removed, the bin values are recalculated to
include only the remaining data.

5.13.10

Filter PFM

If you have an existing PFM that you would like to clean using the Area Based Filter
(as described in section 5.5.5) the Filter PFM menu option can be used. Once
selected, a wizard will launch in order to guide you through the steps of using the
area based filter.

5.13.11

Update/Verify PFM

Update/Verify PFM command launches a dialog to edit the internal hardcoded

pathnames within a PFM file. This is needed when a PFM has been moved from its
original location, or its source files have been moved.

5.13.12

View Histogram

This command will display a histogram for the currently selected un-gridded data file,
or the current active group of files. The currently active attribute that is displayed can
be adjusted using the Variable combo-box located at the bottom of the dialog, as
shown in Figure 5-34.

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Figure 5-34 - View Histograms Dialog

5.13.13

Convert Grid to SD

Figure 5-35 - Convert Grid to SD Wizard (Stage 1)

The Convert Grid to SD command is used to convert any supported source grid file
into either a surface (SonarDTM) surface SD file, or a Scalar SD file. The first stage
of the wizard displays the following options:
- Invert Z Range: This toggle will invert the z value of the incoming grid.
- Use User Defined Z-Range: By default the grid will be imported using the full z
range of the file, however a custom z-range can be provided to restrict the values.
- Output Coordinate System: Specifies the coordinate system for the resulting SD file.

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Figure 5-36 - Convert Grid to SD Wizard (Stage 2)

The second stage of the wizard is used to specify the colormap and the shade
parameters that will be used when shading the imported grid. Default shade
parameters are whats specified in the DMagic preference or the paramerters can be
loaded from a Shade Parameters file.

Figure 5-37 Convert Grid to SD Wizard (Stage 3)

The last stage of the wizard is used to specify the SD type (Surface DTM or Scalar)
and the filename for the SD file.

5.13.14

Convert Image to SD

This menu option will open a Save File Dialog to specify the name of the SD file that
the selected image will be saved to.
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5.13.15

Edit Image...

The Edit Image command is used to perform a wide array of operations directly on
raw image data. When this command is activated, the overall DMagic interface is
modified and the Edit Image Toolbar is displayed. While in the image editing mode,
all non image operations are disabled and only the currently active image is
displayed in the display area.

Figure 5-38 - DMagic Edit Image Toolbar

Save
The Save command will update the currently active image file with any changes that
have been made since the file was opened in the image editor.
Save As
If you want to save the current image to a new file, the Save As command can be
used. Any editing operations done after using this command will be applied to the
new image file.
Write TFW
The Write TFW option allows you to write the current geo-referencing data to a tiff
world file.
Undo / Redo
The Undo and Redo items which become active only when it is possible to undo the
last action or redo the last action (that is, undo the last undo).
Mode
Transparency
The Alpha (transparency) submenu gives you choices to add or remove an alpha
channel. You can also reset the alpha channel for the entire image with Clear Alpha
Channel. This makes the image transparent or opaque depending on the alpha level
used. In Fledermaus, the alpha channel is used as a switch to determine
transparency (<50% level is transparent, >50% is opaque). The Clear Alpha Channel
dialog box takes a value between 0 and 255 to set the alpha level. A value of 0 is full
transparency while a value of 255 is full opaqueness.
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Flip
The Flip Horizontal and Flip Vertical operations mirror the image across the horizontal
or vertical axis, respectively. The geo-bounds do not change for these operations, so
they are useful for correcting an image that is oriented incorrectly. Applying the same
operation twice returns the image back to its original form.
Resample
The resample operation can change the number of rows or columns in the image.
This is useful to change the resolution of an image, for example to make it smaller in
size. This operation does not affect the geo referencing bounds. By default, the ratio
of rows to columns is not allowed to change, that is the aspect ratio is preserved. By
un-checking the Constrain Ratio check box, the aspect ratio can be changed.
Crop
The Crop operation is used to extract a region of interest in the image you specify.
The geo-bounds are adjusted to reflect the section of the image extracted. First mark
the region of interest by clicking then dragging a box around the area using the left
mouse button. Then select the Crop operation.
Georeferencing
To manually change the georeferencing, enter the bounds in the boxes shown. The
western and eastern most bounds are on the top line, and the southern and northern
most bounds are on the second line respectively.
Reproject
The Reproject dialog can be used to change an image from one projection to
another, such as from Lat/Lon to UTM. The first step in the process is to select what
operation to perform using the drop down list at the top of the dialog. Depending on
which operation you select, you may then have to enter some additional information
about the image. There is also the option to enter the bounds manually.
Close Editor
When you are finished editing your image, the Close Editor button can be used to
close the special editing mode and return to the standard DMagic interface.

5.13.16

Convert Image to SD

This menu option will open a Save File Dialog to specify the name of the SD file that
the selected image will be saved to.

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5.13.17

Export Image to Google Earth

This menu option will open a dialog as seen in Figure 5-39 to export the selected
image to a Google Earth Image File.

Figure 5-39 DMagic Google Earth Export

5.13.18

Convert Vector to SD

This menu option will convert the selected Vector file into an SD File.

5.13.19

Edit Coordinate System

Figure 5-40 - DMagic Edit Coordinate System Dialog

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The coordinate system that was assigned to any source data file can be modified
using the Edit Coordinate System command, as shown in Figure 5-40.

5.13.20

Edit Configuration

Edit Configuration menu brings up a dialog to change which fields are mapped to X,
Y, and Z values for all ungridded files. Using the Preview Source File button will view
the currently selected ungridded file in Omniviewer.

Figure 5-41 DMagic Edit Configuration Dialog

5.13.21

View Metadata

All source data files that are displayed in DMagic have an associated metadata file
that provides a collection of summary information about those files. To view the full
metadata for any source data file, the View Metadata command can be used, as
shown in Figure 5-42.

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Figure 5-42 - DMagic View Metadata Dialog

5.13.22

Clean Metadata

This command will remove all of the temporary metadata files that have been create
with the current project.

5.13.23

Remove Errors

This command will remove all source files that could not be loaded due to some sort
of error.

5.14

Surface Sub-Menu

Figure 5-43 - Surface Sub-Menu

DMagic contains a number of tools for working with and manipulating gridded surface
data, which are located in the surface sub-menu, as shown in Figure 5-43.

5.14.1

Extract Area

It is possible to export a region of the currently selected surface by selecting Extract

Area from the Tools > Surface menu. This menu option brings up the Extract Area
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dialog box, where a rectangular sub-region of the surface may be extracted from the
currently selected surface or scalar object (see Figure 5-44).
A region to cut may be specified in one of three ways:
Custom Min and Max: specify a rectangular sub-section of the data by giving the
lower left and upper right coordinates of the box
Center and Radius: specify a rectangular sub-section of the data by giving the center
point, x radius, and y radius of the box

Corner and Size: specify a rectangular sub-section of the data by giving the lower left
corner plus the width and height

Figure 5-44 - DMagic Extract Area Dialog

5.14.2

Mask Area

Any surface can be masked using the Mask Surface tool. The surface file to be
masked will be the currently active data set and it will be displayed in the Apply Mask
To text field at the top of the dialog.
The Mask Source can be either an SD object or a supported geo-referenced image
file. The Mask Source will knock a hole in the loaded data component files whenever
data from the Mask Source is found intersecting any of the loaded data component
files. If the Mask Source is a geo-referenced image file, than the Ignore Transparent
Pixels checkbox will be activated. This gives the option to either ignore any
transparent pixels when masking the surface or not.

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Figure 5-45 - DMagic Mask Area Dialog

5.14.3

Export

It is possible to export a surface grid from DMagic by clicking the Export menu option.
This may be any surface grid that has been imported as a surface, either created in
DMagic or the Average Grid application. The following figure illustrates the Export
Surface dialog box that includes several options to tailor how the surface will be
exported. These include
ASCII Z,
ASCII XYZ,
ArcView ASCII Grid, or
Raw binary grid
NetCDF/GMT Grid
Floating Point TIFF

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Figure 5-46 - DMagic Export Dialog

Exported Surface can either be a SonarDTM or an Attched Scalar depending on

what you choose from Select Surface to Export.
When saving the data, areas of the surface containing no data may be included with
the output file if the Include Missing Data option is on. If missing data is included, a
special value is written for these data points, indicated by the No Data Value text
field.
When writing a binary file, you may specify either writing an 8-bit or 16-bit number, or
a 32-bit greyscale value containing red, green, blue, and alpha components.

5.14.4

Calculate Slope

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Figure 5-47 - DMagic Calculate Slope Dialog

Surface slopes can be calculated using the Tools > Compute Slope menu option. The
dialog box in Figure 5-47 allows the user to compute a surface that represents the
maximum slope at each grid center of the currently loaded SD. The generated
surface will have the same dimensions as the original surface file and represents the
maximum slope from each cell to any of its neighbouring cells.
For the generated surface, each cell represents the maximum slope to any of its
neighbours written in decimal degrees. You can optionally specify the slope range
bounds for the generated surface. This is useful if you want the range to correspond
to a particular range of colors in a given color map.
The created scalar file can then be used in the shading process to drape the scalar
color over the DTM. The values of the scalar can also be appended to the .sd when
the Fledermaus objects are assembled. This means that when the surface of the
object is picked in Fledermaus it will return X, Y, Z, and slope. Alternatively the user
may create another surface where the Z value of the DTM is the slope.
If the resulting surface will be an attached Scalar to the current SD or a copy of the
current SD, the SD can be re-shaded using the new attached scalar if Re-Shade with
attached scalar is toggled one.

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5.14.5

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Calculate Rugosity

Figure 5-48 - DMagic Calculate Rugosity

Dialog

Rugosity is a measure of surface roughness and it can be created using the

Calculate Rugosity command. By default the output surface will contain the full range
of rugosity values, however a custom range can be specified to restrict the output to
the user supplied values. There are three output options for the generated surface,
with the default being to attach it to the original source SD file. There is also an option
to create a copy of the source SD before attaching the rugosity, as well as an option
to create a standalone SCALAR file.
If the resulting surface will be an attached Scalar to the current SD or a copy of the
current SD, the SD can be re-shaded using the new attached scalar if Re-Shade with
attached scalar is toggled one.

5.14.6

Interpolate

The surface interpolation tool allows for small holes in a surface or scalar to be filled
in using values from one or more of the surrounding cells. The interface for setting up
the interpolation is displayed in Figure 5-49. Four options are available for
determining the interpolated values:
Average: Calculates the average value of all surrounding cells
Minimum Value: Uses the maximum of all surrounding cells
Maximum Value: Uses the minimum of all surrounding cells
Fixed Value: Uses the value supplied by the user
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Figure 5-49 - DMagic Interpolate Dialog

Once the interpolation method has been chosen, the next step is to determine what
cells will be filled in by the interpolator. This is done by setting the minimum number
of neighbours required for a cell to be filled in, ranging from 1 to 8. You can also set
the number of times the algorithm runs over the entire grid by setting the Number of
Iterations pull down menu.

5.14.7

Resample

The resample operation can change the number of rows or columns in a surface.
This is useful to change the resolution of an SD, for example to make it smaller in
size. This operation does not affect the geo referencing bounds. By default, the ratio
of rows to columns is not allowed to change, that is the aspect ratio is preserved. By
un-checking the Constrain Ratio check box, the aspect ratio can be changed, as
shown in Figure 5-50.

Figure 5-50 - DMagic Resample Dialog

Instead of resampling based on the number of rows or columns, the surface can also
be changed by specifying the X and Y cell sizes.
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5.14.8

R E F E R E N C E

M A N U A L

Surface Statistics

Figure 5-51 - DMagic Surface Statistics Dialog

Surface statistics of the loaded surface can be viewed using the Tools > Surface
Statistics menu option. The Surface Statistics dialog box, shown in Figure 5-51, will
appear. Properties of the current data set will be shown in the left text box, while the
Surface Statistics Information text box is populated with statistics about the data set.
The Save As button allows to save the statistics to specified text file.

5.15

Help Menu

The Help menu provides you with three options: Online Help, IVS Home Page, and
About. These options provide information on the product, the company, and the
software itself. The Help menu is illustrated in Figure 5-52.

Figure 5-52 - DMagic Help Menu

When you select the first option Online Help, it opens a web browser and loads the
local online documentation. The second option available is IVS Home Page
(http://www.ivs3d.com). When selected this option opens a web browser and loads
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the URL for the IVS Home Page. The third option available is About. When selected
it displays an about box that contains the version number of DMagic and IVS
company information such as our address, e-mail, and web site URL.

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Chapter 6 - FMGeocoder Toolbox

6.1 Introduction to FMGeocoder Toolbox (FMGT)

FMGT is a software program designed to visualize and analyze backscatter data
from multibeam and to a lesser degree sidescan sonars. In processing the source
files into mosaics, it is designed to perform as many corrections as possible to
maximize the information content within the backscatter signals.
The software can read multiple files of backscatter data, apply corrections, and then
create a 2D representation of the ocean floor called a backscatter mosaic (the
process of generating a mosaic is called mosaicing). Once the mosaic has been
generated, various statistics can be calculated and exported along with the
backscatter in a number of different formats. Angle range analysis (ARA) can also be
performed to attempt to classify the bottom types.
All of the processing pipelines of FMGT are multi-core aware to maximize throughput
of data and minimize any required reprocessing due to changes in desired output
mosaic resolution or addition of lines.

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6.2 FMGT Supported Data Formats

FMGT is currently designed to process backscatter, beam average or sidescan data
from the following base data formats.
GSF GSF files that contain beam averaged or beam time series data can normally
be mosaicked in FMGT.
XTF XTF files that contain sidescan data can be mosaicked. There is minimal
support for sidescan processing as FMGTs primary focus is multibeam time series
or beam average data.
GSF/XTF Pair Used to process Reson or R2Sonics data where the multibeam
depths come from a GSF file and the sonar beam time series data is stored in the
XTF file. FMGT will create a new GSF file containing both the multibeam depths and
the time series data and use that in the standard GSF processing flow.
GSF/S7K Pair Used to process Reson data where the multibeam depths come
from a GSF file and the sonar beam time series data is stored in the S7K file. FMGT
will create a new GSF file containing both the multibeam depths and the time series
data and use that in the standard GSF processing flow.
Kongsberg (.all) Files Depending on the sensor used to collect the information,
backscatter data can be directly mosaicked from the *.all files.

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6.3 FMGT Interface

Figure 6-1 - FMGT User Interface

The primary user interface for FMGT is shown in Figure 6-1. The interface can be
divided into 8 primary widgets that are summarized below and explained in detail in
later chapters.

Main Menu Bar

The Main Menu Bar displays a number of

options for the program. See section 6.6 for
more detail.

Source Files Panel

The Source Files tab of the tree view contains a

list of all files currently loaded for processing.
The Visual Objects tab displays a list of all
created visual elements such as mosaic,
statistical and ARA layers. See section 6.7 for
more detail.

Mosaic Information Panel

This panel displays the currently selected mosaic

resolution as well as general size and memory
requirements information. See section 6.8 for

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more detail.
4

Processing Panel

This is the key panel that controls the process

flow of FMGT. It allows the user to proceed
using automatic or manual control over the
processing pipeline. It also contains a tab which
displays the history of processing messages that
have been provided to the user during
processing stages. See section 6.9 for more
detail.

Status Bar

The Status Bar displays current geographic

position of the cursor when it is over the map. It
also displays the current directory during active
directory monitoring. For Windows users, it also
contains a control that displays the current
amount of memory utilized by FMGT. See
section 6.10 for more detail.

Map View

The Map View displays all of the visual layers of

the project. FMGT can have multiple mosaic,
statistic or ARA layers, all controlled by the user.
It can also display a reference bathymetric grid.
See section 6.11 for more detail.

Histogram/ARA Panel

The Histogram Panel displays the histogram of

the currently selected visual layer. The ARA
Panel displays the port/starboard response
curves of the currently selected ARA patch. See
section 6.9.4 and 6.9.5 for more detail.

Tool Bar

The Tool Bar contains all of the display and

editing controls for FMGT. See section 6.12 for
more detail.

Quick Start Guide

Getting up and running with FMGT begins with the creation of a Project. FMGT
projects allow you to manage your data processing flow and preserve any processing
steps that you have already accomplished. In order to give context to the following
sections of the reference manual, we will first go through a typical processing
scenario using an EM3002 survey of Little Bay in New Hampshire.

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6.3.1 Step 1 Create the Project

Use the File Menu described in section 6.6.1 to create a new project using the Create
Project Dialog (Figure 6-2). By default, the folder for your project will be in the
/Users/username/FMData/Projects directory. The created project will contain subfolders for storing interim processing data as well as created visual layers. The
complete directory structure is described in detail in section 6.6.1.1.

Figure 6-2 - Create Project Dialog

6.3.2 Step 2 Add Source Files

FMGT corrects multibeam time series data by using the associated processed
bathymetry for the associated beams. To accomplish this, FMGT has two primary
processing paths that support file formats containing both processed bathymetry as
well as backscatter time series data. These formats are the .all and .gsf. Other file
formats as defined in section 6.2 are supported by pairing data and generating a
new GSF file which is then used for processing through FMGT. For this
demonstration we will use .all files.
To add source files, use the File Menu->Add Source Files option to select files for
processing. The user will then be presented with the wizard dialog show in

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Figure 6-3 - Add Files Wizard, Page 1

Figure 6-4 - Add Files Wizard - Page 2

Figure 6-3 and Figure 6-4. The first page of the dialog lets you select a list of files or
a directory containing your files. If you select a directory, the directory hierarchy,
including sub-folders, will be reflected in the project tree view as well as all of the
processing output folders. This is explained in more detail in section 6.6.1.1.

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The second page of the wizard allows you to select the coordinate system for the
navigation of the input files. In our example, this is simply geographic, WGS_84.
After selecting Finish, FMGT will perform some preliminary processing that is
required to proceed to the actual backscatter processing stages. FMGT will first
index the files as shown in Figure 6-5.

Figure 6-5 - File Indexing

File indexing allows FMGT to access all datagram packets within a file in a non-linear
manner. This allows FMGT to process any part of a file without first having to read all
of the packets that came before. File indexing only occurs once unless the index
cache is deleted (see section 6.5 for details).
FMGT will then extract the metadata from each line as shown in Figure 6-6. The
metadata includes information such as file geographic extents, datagram packet
numbers, sonar modalities and sonar type.

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Figure 6-6 - File Metadata

After the metadata is extracted, FMGT will compute the coverage and extract the
navigation of each line as shown in Figure 6-7. Finally, a visual representation of
each line swath is created as shown in Figure 6-8 for display in the FMGT MapView
(Figure 6-9).

Figure 6-7 - File Coverage

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Figure 6-8 - Swath SD

Figure 6-9 - Files Loaded

As you can see, the files that were loaded appear in the Source Files tree view. The
checkbox next to each file serves a dual purpose. The first is to determine if the
object is to be displayed in the map view. The second, for source files, is to
determine if the file is to be used for any selected processing. This is a key part of
FMGTs workflow. If a source is checked, it will be included in any processing. If not,
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it will be ignored. You have many ways to check/uncheck files either using the
Check Select tool or the context menu Check options. These are described in
detail in later sections.

6.3.3 Step 3 Process the Data

Processing data loaded into FMGT can take two paths. The first way is to use the
Automatic Processing tab of the processing panel to select the desired output
products and simply click on the All button in the Build section of the panel. The
second is to use the Manual Processing tab. For our example, lets start by clicking
on the Mosaic button of the Build group on the Automatic tab.
FMGT will first adjust the backscatter data by performing backscatter extraction then
radiometric corrections based on sonar type and bottom topography. As this stage
progresses (Figure 6-10), it will persist the results of the backscatter adjustment to
the project hierarchy.

Figure 6-10 - Backscatter Processing

Next it will perform Filter processing which includes angle varying gain (AVG)
adjustments as well as anti-aliasing of the backscatter data. As this stage
progresses (Figure 6-11), it will also persist the results of the backscatter adjustment
to the project hierarchy.
Finally, FMGT will begin to create the desired mosaic as shown in Figure 6-12. It will
use the resolution as indicated in the Mosaic Info panel. For our example, this is
~15cm. This value is pre-computed by FMGT during coverage processing and is an
estimate based on the sonar beam configuration and along track coverage. This
value can be overridden at any time.

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Figure 6-11 - Filter Processing

Figure 6-12 - Mosaic Processing

Once complete, the mosaic will show up in the map view. If you click on the Visual
Objects tab of the Tree View, you open up the mosaic layer and see that it consists
of one tile (Figure 6-13). Survey areas can be tiled to allow for maximum resolution
of backscatter mosaics over large areas.
You can also choose to display no navigation lines by selecting None in the
Navigation combo-box directly below the map view. Alternatively, you can uncheck
the root Source node in the Source Files tab of the Tree View. Navigation in the map
view works exactly like DMagic. You can use the mouse wheel or track pad to zoom
in and out and left-click-drag to pan around the view.
Once zoomed in, you can use the histogram control to change the contrast stretch
over the image as shown in Figure 6-14 to increase the contrast quality of the
mosaic. Left-click/right-click in the histogram control or click-drag the ends of the
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composite control slider to set the range of data to be stretched over the full color
map.
Using those simple steps, you now have a mosaic that you can export to other
formats or you can simply save all of your visual elements as a scene and import
directly into Fledermaus.
As you move your cursor over the map view, you will notice that the status bar
updates to display the current position as well as the current backscatter value of the
point under the cursor. This is important as the status bar can relay different
information based on which layer is currently being viewed.

Figure 6-13 - Mosaic Visual Layer

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Figure 6-14 - Mosaic Layer Zoomed

Lets now perform statistical processing of our data (Figure 6-15). Since FMGT
maintains interim data on all processing stages, this will proceed very quickly. Simply
go back to the Automatic tab of the Processing panel and click on the Statistics
button. The statistical grid resolution has already been computed according to the
mosaic resolution but you can override this at any time. By default it is 20 times the
resolution of the underlying backscatter mosaic. For this example, the statistical grid
resolution is 10 meters.

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Figure 6-15 - Statistics Processing

After completion, the statistics layers will appear in the Map View as shown in Figure
6-16. As you move the cursor over the map, the status bar will update to show you
the current statistical parameter value. You can change layers by simply clicking on
the checkbox of one of the other layers. It will automatically uncheck the previously
selected layer.
You can also use the Opacity sliders to blend your layers together at any time. For
example, changing the opacity of the statistical layer allows you to view
corresponding features in the backscatter as shown in Figure 6-17.
Finally we can create the Angle Range Analysis (ARA) layer. Using the Automatic
tab of the Processing panel, simply click the ARA button in the Build group box. ARA
processing benefits the most from multi-core processing and scales almost linearly
as you add processing cores. If you plan to do much ARA processing, a
recommendation is to purchase a machine with as many cores as possible. As ARA
processing progresses (Figure 6-18), the results are persisted in the project.

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Figure 6-16 - Statistics Layers

Figure 6-17 - Transparent Statistical Layer

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Figure 6-18 - ARA Processing

Once ARA processing is complete, an ARA surface is created that reflects a

rasterized view of the overlapping ARA patches.

Figure 6-19 - ARA Visual Layer

In the same way that you could select individual parameter layers of the computed
statistics, you can easily change the currently viewed parameter by checking the
appropriate layer checkbox. Also, you can change the transparency of these layers
as well so that you can better correlate underlying features of the backscatter mosaic.
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Finally you should remember that all of these layers could have been created at once
by simply checking the desired products in the Build options group and clicking on
the All button.
Under normal workflow circumstances, when processing large data sets, you may
want to start working on a smaller part of the survey area in case you need to make
adjustments to either the beam pattern or processing parameters before proceeding
to process all of the data. See section 6.9for more information on optimizing the
workflow.

6.3.4 Step 4 Exporting Data

To export a visual layer, simply right click on the layer in the tree view and select the
export option from the context menu (Figure 6-20).

Figure 6-20 - Visual Layer Export Menu

You can also save the project as a Fledermaus scene by use the File->Save as
Fledermaus Scene option. Then simply load this scene into Fledermaus to use the
created mosaic for draping on existing bathymetry.

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6.4 FMGT Processing Pipeline

FMGT uses an optimized, multi-core, stage-based processing pipeline to accomplish
its job. Understanding how this pipeline proceeds can help you more efficiently use
FMGT. The generic pipeline architecture is shown in

Survey
Line

High
Performance
I/O

Stage
Processing

Stage
Results

Figure 6-21 Generic Processing Pipeline

FMGT uses our internal high-performance I/O library to maximize reading of survey
data from disk to achieve near theoretical maximum throughput. Results of a
processing stage are persisted in the user project to further eliminate the need for reprocessing when something in the project changes. FMGT then further increases
overall performance by parallelizing this stage processing architecture as shown in
Figure 6-22.

Figure 6-22 Parallel Stage Processing

FMGT stage processing not only reduces the need for re-processing under various
circumstances but also enhances protection against unexpected faults or system
failures. Since each stage mimics the same architecture, any failure will result in the
system picking up where it left off instead of starting back from the beginning when
restarted.

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Figure 6-23 FMGT Processing Stages

FMGT has five primary processing stages as shown in Figure 6-23. Each one of the
first three processing stages depends on the output of the previous stage. The final
two stages depend on the first three, but not on each other.
The three product stages shown in Figure 6-24 also depend on the first three
processing stages and additionally ARA or Statistics processing depending on the
selected layer.
This stage-dependency is an important concept to understand when using FMGT.
FMGT always knows what processing has been done to each line in the project.
When particular processing or products are requested, FMGT will know what needs
to be accomplished first before it proceeds.
For example, when you load lines, coverage processing is automatically performed
to extract the extents of the swath at each ping as well as navigation information that
will be used later. If you then click on the Mosaic button on the processing panel,
FMGT will perform backscatter processing, filter processing and finally mosaic
rendering. It knows that it needed to accomplish the other stages to provide the final
product you requested. If you then wish to change the mosaic resolution, FMGT will
proceed directly to mosaic rendering as reprocessing of the data is not necessary
when changing resolution.

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Figure 6-24 Generic Processing Pipeline

Certain changes to processing parameters as explained in section 6.6.3 will result in

stages requiring reprocessing. Typically, changes to processing parameters will
cause FMGT to invalidate the dependent stage flags for the project lines. So if the
user requests a new product, FMGT will know what needs to be reprocessed. The
user can also force reprocessing of a particular stage by clearing the processing flag
of that stage explicitly. All of this is explained in detail in section 6.9.2.

6.5 Preferences

Figure 6-25 - Preferences - General Tab

The Preferences Dialog allows you to change basic default settings for FMGT that
you want to use across all projects that you work on. The first tab of the dialog
contains the general preferences used by FMGT.

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The Shared Metadata options allow you to change the location for FMGT index files
to be written. These files are shared by both FMGT and FMMidwater. They are only
created once unless the contents of the file change, which FMGT will detect.
Occasionally, you may be having trouble loading a file. In such cases, you may
which to check the Force Rebuild checkbox which will rebuild the index file when it is
loaded. You can also completely clear your index cache by clicking the Clear Cache
button.
The Parallel Processing options allow you to force FMGT to use a specific number of
cores. When Auto is selected, FMGT will select the appropriate number of cores for
the parallel processing stages of FMGT. If you choose Manual, you can override this
with any value up to 24 cores. It is recommended that you do not exceed the
number of cores (real + hyper-threads) for a given system as it can cause
performance degradation of other applications you may be running.
The Ask to open last file option causes FMGT to prompt you with the last file you
were working on after restart. Unchecking this option will prevent FMGT from asking
you this question during start-up.
The Ask to recover failed processing option will have FMGT ask you if you wish to
pick up processing where you left off in the event of a system crash. Since no
software application is 100% bullet-proof (dont let anyone convince you otherwise),
there will be occasions when a source file may cause a system crash. If that
happens, when FMGT restarts, it can pick up processing where it left off if this option
is selected. It will ask you first and you will also be given the opportunity to skip the
file that was being worked on during the crash.
The Auto Reset Camera option is used if you want the map view to reset to center,
full view, when a product layer such as a mosaic is added. By default it is off as you
may be zoomed in and wanting to keep an area in context that you are changing in
some way, such as creating an inset high-resolution mosaic.
The Auto Scan option is on by default because FMGT will index then scan coverage
of a line when it is loaded. If you turn this option off, no preliminary work will be done
on a line and it will not yet be available for further processing.
The Metadata in tree option tells FMGT that you want to include the metadata nodes
in its source tree hierarchy. With very large survey datasets, you may want to turn
this option off to save time and memory.
The Pause on error option allows you to review error messages after completion of a
processing stage before the parallel processing window automatically closes.
Warning and Error messages are mirrored to the Messages tab in the main GUI but
you may want to know more clearly when an error occurs. This option allows you to
control that behavior.
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Figure 6-26 - Preferences - Coordinates Tab

The Coordinates tab of the Preferences Dialog is used to control the display of
coordinates in the status bar of FMGT. Simply select the way you want coordinates
to be formatted.

6.6 Main Menu Bar

6.6.1 File Menu
The file menu is used to create projects, load data and save Fledermaus scenes.

Figure 6-27 - FMGT File Menu

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6.6.1.1 Create Project

This menu option creates a new project for FMGT. If you currently have a project
open, it will save and close the current project before creating a new one. See the
creating projects section in the FMMidwater chapter for more details on projects.
6.6.1.2 Open Project
This menu option allows you to open an existing FMGT project. If you currently have
a project open, it will save and close the current project before opening a new one.
6.6.1.3 Close Project
This menu option will save and close the current open project.
6.6.1.4 Add Source Files
This menu option will open the Add Source Files dialog that is used to add a group of
files or a hierarchy of directories to your project. Click on Add File(s) to add files or
Add Directory to add a hierarchy of directories (Figure 6-28).

Figure 6-28 - Add Source Files Dialog Panel 1

After your files are added, click Next to proceed to the next dialog panel (Figure
6-29). Now you must select the coordinate system of the navigation for the incoming
data. Once you have selected the appropriate coordinate system, click on the Finish
button. The files will now be loaded into FMGT. They will be automatically indexed
and some initial processing such as navigation extraction and coverage will be
performed on each line. After completion the input file navigation lines will appear in
the FMGT Map View.

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Figure 6-29 - Add Files Dialog - Panel 2

6.6.1.5 Add Paired Files

This menu option is used to merge time series data from one file type with
bathymetry data from another file type. The support file pairings are XTF/GSF or
S7K/GSF. In both cases, processed bathymetry is expected in the GSF file. The
XTF or S7K will contain the time series data. The pairing operation will create a new
merged GSF containing both bathymetry and time series data and will be written to
your project directory in the Output/GSF folder.
When you select this option, you will active the Add Bathymetry/Backscatter File
Paris dialog (Figure 6-30).

Figure 6-30 - Bathymetry/Backscatter File Pairs Dialog - Panel 1

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You can select file pairs using the Add File(s) button or you can add a directory of
pairs using the Add Directory button. If you add a directory, be sure to change the
file extension combo box to the desired file types. After selecting the files, they will
appear in the dialog as shown in Figure 6-31.

Figure 6-31 - Bathymetry/Backscatter File Pairs Dialog - Panel 2

Click the Next button to proceed to the navigation source file correlation panel as
shown in Figure 6-32.

Figure 6-32 - Bathymetry/Backscatter File Pairs Dialog - Panel 3

If your files have similar naming schemes, FMGT will be able to determine which file
containing time series data, or snippets, matches the file containing the bathymetry.
If you file naming scheme is non-standard, you will have to choose the time series
source manually for each GSF file. Do this now before proceeding to the final panel.
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If your file pairs contain different time references for some reason, FMGT will not be
able to appropriately match pings from one file with another. If this is the case, you
will get an error indicating the time gap in seconds. To fix this, attempt to add the file
pairs again and additionally enter the appropriate value for the Time Gap in the
Options section of this panel. For example, if your time gap was 1 hour, you could
enter 1h or 3600s.
Click Next to proceed to the final dialog panel (Figure 6-33). Now you must select
the coordinate system of the navigation for the incoming data. Once you have
selected the appropriate coordinate system, click on the Finish button. The files will
now be merged into a new GSF and then loaded into FMGT. They will be
automatically indexed and some initial processing such as navigation extraction and
coverage will be performed on each line. After completion the input file navigation
lines will appear in the FMGT Map View.

Figure 6-33 - Bathymetry/Backscatter File Pairs Dialog - Panel 4

6.6.1.6 Add Reference Grid

Reference grids can be used to help correct backscatter when processing sidescan
files. Although the primary focus of FMGT is to focus multibeam backscatter data,
you can still process sidescan files (XTF) and use loaded bathymetric grids to help
correct the backscatter. Acceptable backscatter files are Fledermaus Sonar DTM
files. If you want to import another type, simply do it in Fledermaus and save the new
SD object for loading into FMGT. After loading the reference grid, it will appear in the
Map View as shown in Figure 6-34.
You can also load reference grids to help compare backscatter features in the
mosaic to the underlying bathymetry. Simply use the opacity sliders to allow you to
see through the mosaic, statistical or ARA layers.

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Figure 6-34 - Reference Grid

6.6.1.7 Import
This menu option provides means of importing PFM Edits that can be used during
processing of the backscatter data. Simply browse to the PFM SD file and use it to
load the sounding edits. The edits will be extracted and added to your project. If you
make further edits to your PFM, you have to re-import your PFM edits and re-process
your backscatter data. Figure 6-35 shows how some of the artifacts from suspended
objects in the water column can be removed using PFM edits.

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Figure 6-35 - PFM Edits

The Import menu also provides a location for Import plug-ins to be connected. If you
have installed 3rd party plug-ins or created your own import plugin, it will appear in
this sub-menu.
6.6.1.8 Preferences
This menu option displays the Preferences Dialog.
information.

See section 6.5 for more

6.6.1.9 Save as Fledermaus scene

This menu option will save the current contents of your Map View to a Fledermaus
scene.
6.6.1.10

Recent Projects

This menu option allows easy access to recently opened projects.

6.6.1.11

Encapsulate Project

This menu option will copy all source material and external ancillary files into your
project directory hierarchy. The file links in your project XML file will also be updated
so that you can easily move the project to another computer.
6.6.1.12

Quit

This menu option will quit FMGT. The currently loaded project will be saved before
FMGT exits.

6.6.2 View Menu

The view menu allows you to turn selected FMGT dockable panels on or off. If a
menu item is checked, the panel is visible. If it is unchecked, the panel is invisible.
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Figure 6-36 - FMGT View Menu

6.6.3 Settings Menu

The settings menu provides control over the processing options for FMGT. It also
allows you to edit the current project coordinate system or set up a directory for active
monitoring.

Figure 6-37 - Settings Menu

6.6.3.1 Processing Parameters

The Processing Parameters dialog provides options for the processing stages of
FMGT.

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Figure 6-38 - Processing Dialog Backscatter Options

If you modify any of the processing parameters, you must re-process your data. See
section 6.9 to see how to accomplish this.
6.6.3.1.1

Backscatter Options

Figure 6-38 shows the options available for the backscatter stage of processing.
The Do Tx/Rx Power Gain Correction option will turn on/off power gain correction
during processing of the backscatter data. This option is on by default and will apply
all of the radiometric correction algorithms appropriate for the particular sonar.
The Apply Beam Pattern Correction option applies a beam pattern correction file that
was created using the Beam Pattern Correction tool discussed in section 6.6.5.1. It
is on by default and applies a default beam pattern correction file that is all zeros.
The Keep data for ARA analysis option saves beam pattern patch data that can
later be used for ARA inversion. Turning this option off can speed up processing
slightly but you wont be able to do ARA inversion later unless you turn this option
back on and reprocess.
The Beam Angle Cutoff option allows you to change the incident angles of the beams
that are used for processing. This allows you to remove a part of the nadir or a part
of the outer beams.
The Backscatter Range option allows for processing of sonar data that is not
calibrated. This means that after corrections are applied, the sonar data will not be
in the nominal -70dB to +10dB range. If you have such sonar data, you will get a
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warning during filter processing. FMGT will tell you what the nominal range of your
data was. You can either change the range using this option, or, you can change the
dB reference value for this sonar in the Sonar Defaults options discussed later in this
chapter.
6.6.3.1.2

AVG Options

The AVG tab of the Processing Parameters Dialog can be seen in Figure 6-39.
Angle Varying Gain adjustments are on by default and can be applied over a
window of pings. The window size can be adjusted and is 30 pings by default.
AVG also has three algorithm options. These are Flat, Trend and Adaptive.
The Flat algorithm is generally the best default and will smooth out small variations
in backscatter level in an attempt to reduce noise in the signal. The Trend option
looks for a trend (or slope) in the backscatter signal and if found attempts to smooth
around the trend line. The Adaptive algorithm is a combination of the other two and
may work a little better in areas where the backscatter covers terrain with significant
slope variations.

Figure 6-39 - Processing Dialog - AVG Options

6.6.3.1.3

Statistics Options

Statistics can be computed in linear of logarithmic space. By default, logarithmic

space is used. These options can be seen in Figure 6-40.

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Figure 6-40 - Processing Dialog - Statistics Options

6.6.3.1.4

Navigation Options

Navigation options provide control over files with poor navigation. These options are
typically used for towed sidescan data. The default is to use standard linear
interpretation of the current navigation data.
The Course Made Good option computes a course made good for all heading values
of the line.
The Spline Smoothing option computes a smooth spline curve through the available
navigation. The edit field to the right of the option defines the skip factor. Larger
numbers create a smoother curve through the navigation data.
The Apply Layback option applies a fixed layback to every navigation point.

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Figure 6-41 - Processing Dialog - Navigation Options

6.6.3.1.5

Format Options (.ALL)

Format specific options for .ALL files as shown in Figure 6-42 provide control over the
source of the navigation and compensation for dual swath sonars.
The Navigation Source option allows the user to override the source of the navigation
data that is used in .ALL files. By default, FMGT automatically determines the
appropriate source. If multiple navigation sources were logged and the user wants to
override the automatic source, simply select the desired source (1,2,3).
The Dual Swath Compensation option provides a means of eliminating the
backscatter noise that is seen in some dual-swath files. Due to the frequency
variation in the two pulses, and the potential along track order of the data, standard
radiometric processing can result in an apparently noisy mosaic. To eliminate this,
FMGT simply uses the first or second pulse of the dual swath return.

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Figure 6-42 Processing Dialog - .ALL Format Options

6.6.3.1.6

Format Options (.XTF)

The specific options for .XTF files shown in Figure 6-43 primarily change the source
of backscatter (sidescan) and navigation data.
The Navigation source option uses navigation stored in either the Sensor or Ship
portion of the standard XTF sonar ping header. By default, Sensor is the selected
source.
The Altitude source option allows the altitude value to come from the Ship, Sensor or
Auxiliary field of the standard XTF sonar ping header. This value is important as it is
used for slant-range correction of the sidescan data.
The Sidescan Data Source option allows selection of sidescan source. This is useful
for systems that employ 2 channels of sidescan data.
The Bottom Detection option allows for use of a bottom detection algorithm when the
altitude field of the sonar ping header contains a zero value.

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Figure 6-43 Processing Dialog - .XTF Format Options

6.6.3.1.7

Sonar Defaults

The Sonar Defaults tab show in Figure 6-44 provides a means of changing the
nominal parameters used for backscatter processing of a specific sonar.

Figure 6-44 - Processing Dialog - Sonar Defaults

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These values are used when source files lack proper detailed information. Under
normal circumstances, they are overridden by the values in the source files.
The Automatic option means FMGT will automatically select the appropriate default
values according to the sonar type information found in the file. These values will
then be overridden by data values extracted from the file when they exist. For
example, the default pulse length value will be 500 microseconds, but if the file has a
non-zero value, such as 50 microseconds, the file value will be used. The dB
reference values are always used within the backscatter processing pipeline.
The Custom Defaults option allows the user to specify a custom set of default values.
You must either select an entry from the Sonar Type combo box, or create a new
entry specific to your needs. For example, if you are creating a custom version of the
Reson 7101 default values, simply select the Reson 7101 entry from the Sonar Type
combo box. Then click the Copy button to copy these values to a new entry with a
new name. You can then change the values directly for this configuration by typing
in the text fields. When complete, click on the Apply Edits button. As in the
Automatic option, the nominal values will be used when there is a lack of data in the
source files. The dB reference values that you have set will always be used.
The Custom Override All option will make FMGT use only the values that you have
chosen as sonar defaults. It will disregard the data or sonar type found in the source
files. This option is useful whenever you have file that have been either incorrectly
logged or incorrectly identified as a specific sonar type.
All of this data is kept in an XML file (Gc_SonarParameters.xml) in the
~./username/FMData folder.
It is important to note that FMGT expects to process data from a single sonar type.
Consequently, any of the options you select for processing will be used for all lines
within the project.
6.6.3.2 Mosaic Parameters
The Mosaic Parameters Dialog shown in Figure 6-45 is used to control mosaic
generation.
The Line Blending option controls how multiple samples that fall within the same
mosaic cell are blended. Normally the default is 50% which is an equal contribution
from both samples.
The Filter Type options are currently not used by FMGT and will be removed in a
subsequent version.
The Mosaic Style options provide control over how pixels are blended in overlapping
areas near nadir. By default, nadir pixels are blended with other overlapping pixels.
Using either of the No Nadir options provides two methods of weighting nadir pixels
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to reduce their effect when you have overlapping data from other lines. If your survey
lines do not overlap enough, these options will have no effect on the mosaic.

Figure 6-45 - Mosaic Options

The differences between the three mosaic styles can be seen in the images below.
Moving left to right, they represent Blend, No Nadir if Possible, and No Nadir if
Possible 2. The last option provides the best results for this survey.

Figure 6-46 - Mosaic Style Options

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6.6.3.3 Sensor Configuration

The Sensor Configuration Dialog shown in Figure 6-47 displays the project sensor
configuration. These values are extracted from the first added file and are saved to
the project XML file. The user can override the values of the sensor configuration
here which will save them to the project XML file.

Figure 6-47 - Sensor Configuration

It is important to note that FMGT is expecting to process one sensor type from one
vessel configuration within a project. Data from other sensors, vessels or projects
may be merged at a later time in Fledermaus.
6.6.3.4 Project Coordinate System
The Project Coordinate System dialog shown in Figure 6-48 allows you to view or
edit the project coordinate system. If you change the coordinate system, you must
re-process all of your data starting with the Coverage portion of the pipeline using the
Manual Processing part of the main GUI. See section 6.9.2 for information on
manual re-processing of data.

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Figure 6-48 - Project Coordinate System

6.6.3.5 Directory Monitoring

The Directory Monitoring Dialog show in Figure 6-49 allows FMGT to automatically
add files to a defined project. This capability is normally reserved for use during live
acquisition. When a sonar file gets added to the specified directory, FMGT will
automatically add it to the project, index it, and compute the coverage. In a
subsequent release of FMGT, this capability will be expanded to include further
processing. In the current release, the user must initiate processing of the file for
inclusion in a desired mosaic.

Figure 6-49 - Directory Monitoring

6.6.4 Processing Menu

The processing menu lets you activate specific parts of the processing pipeline either
through the menu option or a hot-key.

Figure 6-50 - Processing Menu

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For more on these options, see sections 6.9.1 and 6.9.2 on Automatic and Manual
processing of data.

6.6.5 Tools Menu

The tools menu contains advanced tools allowing finer control over the output mosaic
products.

Figure 6-51 - Tools Menu

6.6.5.1 Beam Pattern Correction

The Beam Pattern Correction menu option opens the dialog shown in Figure 6-52
which displays the beam pattern of the current virtual patch of data, the current
theoretical model beam pattern and the beam pattern correction plot which is the
difference between the actual and theoretical curves.
To begin, use the Edit Segment tool to select a portion of a track line as show in
Figure 6-53. When you initially activate the Beam Pattern Correction tool, it will read
the selected pings into a virtual patch that can be used by the ARA inversion
algorithm. Once the dialog is up, you can either manually select a bottom type or use
the FMGT ARA algorithms to compute the proper classification. After computing, the
dialog will be updated as show in Figure 6-54.

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Figure 6-52 - Beam Pattern Correction Dialog

Once the desired beam pattern correction has been defined, the user can either save
it to an external file using the Save As button or apply it to the current project using
the Apply button. Once applied, the user must re-process the backscatter data for
the file.

Figure 6-53 - Edit Selection Tool

It is important to note that the beam pattern correction file contains the delta between
the current backscatter value and the desired theoretical model value for each angle
(0..180).
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Figure 6-54 - Beam Pattern Correction - After Classification

6.6.5.2 Beam Pattern Viewer

The Beam Pattern Viewer menu option opens the dialog shown in Figure 6-55 allows
the user to view the previously applied beam pattern for the project.

Figure 6-55 - Beam Pattern Viewer

The user can then load another external beam pattern correction file or clear the
beam patter correction for the currently loaded project.

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6.6.5.3 Patch Analyzer

The Patch Analyzer menu option opens the Angle vs. Range Analysis dialog shown
in Figure 6-56 and is used to view and edit the output of the ARA Inversion stage of
FMGT processing. If the user has not run ARA Inversion, the default characterization
will be shown by the blue line. At this point, the user could manually select the
appropriate values or run the model for the current patch.

Figure 6-56 - Angle vs. Range Analysis Dialog

Angle vs. Range Analysis (ARA) is a method of seafloor characterization which

compares the actual backscatter angular response to expected acoustic response
curves based on a mathematical model (the Jackson Model). Due to the nature of
the process, we prefer to use the term characterization rather than classification. For
this process you have a mathematical model (The Jackson Model) which generates
an expected acoustic response curve as a function of grazing angle vs. returned
backscatter intensity. This is a complex model where many sediment properties and
acoustic frequency contribute to the overall modeled curve. As the parameters are
adjusted the resulting modeled curve changes accordingly. The goal of the ARA is an
attempt to characterize the measured response curve from the survey data to a best
fit of a modelled curve. If a good match is found we expect that tells us something
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about the sediment properties. However, many things can affect the veracity of the
results starting with the quality of the system calibration and the appropriateness of
the radiometric corrections applied. Many systems that have been well calibrated,
have shown good correlation between the characterized sediment types and
measured sediment types. However, the ARA process is still in its infancy and much
more ground truthing work needs to be done. One shouldnt automatically assume
because it worked well for one sonar (an EM3002 for example) means it will
automatically work as well for all systems. As stated above, good calibration is key to
any hope of reasonable results from the ARA. The survey environment will also
affect the results as ARA requires a wide coverage of grazing angles. In deeper
water where you often have limited grazing angles the process will not work or not
work very well.
6.6.5.4 Backscatter Adjustment
The Backscatter Adjustment menu option opens the dialog shown in Figure 6-57. It
allows the user to offset the processed dB value for the currently selected line. This
is useful if you have a line where the overall brightness level is different from the
surrounding lines. After selecting a line, FMGT will create a dynamic mosaic of the
currently selected line and mosaic in the dialog. As you adjust the offset the effect on
the mosaic will be apparent.

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Figure 6-57 - Backscatter Adjustment Dialog

Simply use the Bias slider to change the offset value that you want to apply to the
line. Once you hit the OK button, FMGT will apply the offset and refresh the currently
selected mosaic.
6.6.5.5 Plot Roll/Pitch
The Plot Roll/Pitch option displays the roll and pitch plots for the currently selected
line as shown in Figure 6-58. For more information on using plotting widgets, see
section 6.13. This dialog is also accessible from the context menu of the source file
tree (i.e. if you right click the mouse on a file in the list of source files).

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Figure 6-58 - Plot Roll/Pitch

6.6.5.6 Plot Heading

The Plot Heading option displays heading plot for the currently selected line as
shown in Figure 6-59. For more information on using plotting widgets, see section
6.13. This dialog is also accessible from the context menu of the source file tree.

Figure 6-59 - Plot Heading

6.6.5.7 Plot Heave

The Plot Heave option displays the heave plot for the currently selected line as show
in Figure 6-60. For more information on using plotting widgets, see section 6.13. This
dialog is also accessible from the context menu of the source file tree.

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Figure 6-60 - Plot Heave

6.6.5.8 Plot Power/Gain

The Plot Power/Gain option displays the power and gain plots for the currently
selected line as show in Figure 6-61. For more information on using plotting widgets,
see section 6.13. This dialog is also accessible from the context menu of the source
file tree.

Figure 6-61 - Plot Power/Gain

6.6.5.9 Examine Backscatter

The Examine Backscatter option allows you to view the raw backscatter data stored
in a file external to your current project. This works just like the context menu of a
source line except it allows you to view information about files external to your
project. It brings up the dialog shown in Figure 6-62 that display a waterfall like
image of the data.
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Figure 6-62 - Backscatter Dialog

Use the scroll bar to scroll up/down through the data. The first ping is at the bottom
of the display area and the last ping is at the top. You can change the histogram
settings to bring out features but the dialog will have to re-render the waterfall. You
can also change the color map by clicking on the color map button.
6.6.5.10

Examine Beam Average

The Examine Beam Average option allows you to view the beam average data
stored in a file external to your current project. This works just like the context menu
of a source line except it allows you to view information about files external to your
project. It brings up the dialog shown in Figure 6-63.

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Figure 6-63 - Beam Average Dialog

Use the scroll bar to scroll up/down through the data. The first ping is at the bottom
of the display area and the last ping is at the top. You can change the histogram
settings to bring out features but the dialog will have to re-render the waterfall. You
can also change the color map by clicking on the color map button.

6.6.6 Help Menu

The help menu gives you access to version information as well as a link to the online
help.

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Figure 6-64 - Help Menu

6.6.6.1 Online Help

This menu option will bring up the online documentation which is a PDF of this
document.
6.6.6.2 IVS Home Page
This menu option will bring up the IVS home page.
6.6.6.3 About FMGT
This menu option will display the FMGT About Box shown in Figure 6-65 that shows
the current build number and provides access to licensing details.

Figure 6-65 - FMGT About Box

If you click on the Show License Status button, you will get the dialog shown in
Figure 6-66.

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Figure 6-66 - Licensing Dialog

6.7 Source Files Panel

This panel contains information about all of the data loaded into the Map View, which
includes the track lines of the loaded source files as well as all of the visual layers.
The panel is broken up into two tabs, source files and visual objects. This is a
powerful control as you can access lots of information about a loaded line simply by
using the associated context menu.

6.7.1 Source Files

The Source Files tab of the Source Files Panel shown in Figure 6-67 shows all of the
files currently loaded into a project. If you have loaded directories of files, the
directory hierarchy will be preserved in the Source Files Tree.

Figure 6-67 - Source Files Tab

When you select a file in the Source tree view, the related nadir and swath track lines
will be highlighted in the Map View. This makes it easy to see where a line is
spatially in your scene. Also, when you select a line by clicking in the Map View, the
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corresponding source file node will be highlighted in the tree view. This makes it
easy to correlate lines back from the Map View to the Tree View.
The checkbox for a source file node controls three key behaviours. The first is
whether this line will be included for any type of processing requested by the user. If
the line is unchecked, it will be skipped during any processing. The second
behaviour is that the checkbox controls whether the associated track lines are visible
or not in the tree view. The last behaviour is that the checkbox can easily
add/remove lines from an existing mosaic. If you want to remove a line, simply
uncheck it in the tree view and refresh the desired mosaic using the context menu
for that mosaic or the refresh toolbar button for the currently selected mosaic.
There are many helper context menu items that can be used to automatically
check/uncheck files in the source tree. These are discussed in section 6.7.1.2.
6.7.1.1 Source File Metadata
When you click on the caret next to a source line, you display the metadata
associated with a specific file as shown in Figure 6-68. The metadata provides an
easy way to debug files that have been problematic during processing stages. For
example, you may be missing backscatter information, have no valid navigation or
the file may contain only a few pings of data.

Figure 6-68 - Source File Metadata

The Extents node displays the navigation 2D extents of the data. This information
was created during indexing of the file and may not include the outer edges of the
swath.
The Sonar node has information on sonar type, sonar modes and number of heads.
The Modes node displays all of the available logged modalities of the sonar.
The Datagrams node displays the count of each datagram type present in the source
file.
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6.7.1.2 Source File Context Menu Root Node

When you right click on a source file node, or the source root node, you will get the
source file context menu. Different parts of the menu will be highlighted based on the
node type you clicked on and other states of your project.
When right-clicking on the root node of the source tree, you will get the menu options
shown in Figure 6-69.
The Add Sonar Files menu option will bring up Add Source Files Dialog as discussed
in section 6.6.1.4.
The Add Sonar Pairs menu option will bring up the Add Sonar Pairs Dialog as
discussed in section 6.6.1.5.
The Remove All option will remove all source files from the project. You will be
prompted to confirm this option before proceeding.

Figure 6-69 - Source Root Node Context Menu

The Check menu option has a sub-menu that allows you to check files based on their
processing state. You can also have FMGT check all lines that are currently within a
currently selected area. See section 6.12 for a description on to do an area-based
selection in FMGT.
The Check All option will check all files in the project.
The Uncheck All option will uncheck all files in the project.
The View and Export sub-menus will be disabled as they are specific to a source file
node and not the root node.

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6.7.1.3 Source File Context Menu Source File Node

When you right-click on a specific sonar node, the menu options in the context menu
will adjust accordingly as shown in Figure 6-70.
The Remove option will remove this particular file. You will be prompted to confirm
the removal request.
The Check sub-menu will allow you to check only this file or all except this source file.
This is handy when you want to eliminate a file that is causing problems from the
processing pipeline.
The View sub-menu show in Figure 6-71 allows you to activate plot or waterfall
dialogs for viewing of particular navigation or backscatter data within a file. It
activates the same controls as described by the Tools menu in section 6.6.5.

Figure 6-70 - Source File Node Context Menu

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Figure 6-71 - Source File Node - View Sub-Menu

The Export sub-menu allows you to export data related to a specific file as shown in
Figure 6-72.
The ASCII Navigation option will export a text file containing the navigation data that
has been extracted for a line. It will contain the Time, X Position, Y Position, Roll,
Pitch, Heading and Heave values.
The ASCII Nadir Track option will export a text file containing the projected Easting
and Northing of the nadir track line.
The ASCII Port Track option will export a text file containing the projected Easting
and Northing of the port track line.
The ASCII Starboard Track option will export a text file containing the projected
Easting and Northing of the starboard track line.

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Figure 6-72 - Source File Node - Export Sub-Menu

The ASCII ARA option will export a text file containing the projected Easting and
Northing of each patch section (port and starboard) as well as the Depth, Gradient,
Intercept, Mean Total, Mean Near, Mean Far, Mean Outer, Impedance, Roughness,
Phi, Fluid Factor, Distance, Volume and classification ID.
The Point ARA Object option will export a point SD object that is the same as the
visualization used in the previous implementation of GeoCoder (FMGeocoder
versions 7.2.2e and earlier) as shown in Figure 6-73.

Figure 6-73 - Points ARA Object

The FMGT File option creates a native FMGT file that can be used as input to
another project. It is the processed version of a source file.
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6.7.2 Visual Objects

The Visual Objects tab of the Source Files Panel as shown in Figure 6-74 allows the
user to interact with the visual layers of the Map View.

Figure 6-74 - Visual Objects Tab

When nodes are unchecked, they will not be rendered in the Map View. If the root
node of a specific type such as Mosaics is unchecked, all mosaics in the Map View
will be hidden. Right clicking on specific nodes will bring up the context menu that is
associated with that node type.
Under each mosaic node are the tiles that have been created for that mosaic. If tiling
was not specified, there will be only one tile.
Under each Statistics node will appear all of the associated statistical layers as show
in Figure 6-75.

Figure 6-75 - Statistics Layers

As you show one layer in the statistics tree, FMGT will automatically hide the
previous layer by unchecking it. FMGT will also display the histogram associated
with the selected layer in the Histogram tab of the Processing Panel.
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Under each ARA node are all of the ARA layers associated with that ARA object as
shown in Figure 6-76.
As you show one layer in the ARA tree, FMGT will automatically hide the previous
layer by unchecking it. FMGT will also display the histogram associated with the
selected layer in the Histogram tab of the Processing Panel.

Figure 6-76 - ARA Layers

Under the Grid node are all of the loaded reference grids. Each visible grid will be
used during processing of sidescan data to help correct the processed backscatter.
If you do not wish to use a reference grid during processing, simply uncheck it.
Reference grids are only used for visual reference when processing standard time
series data using processed bathymetry.
The Layout node contains the extents of the currently defined survey area. This is
typically the extents of the loaded files but can be overridden using the Settings>Survey Area menu option.
6.7.2.1 Mosaic Context Menu
Right-click on a mosaic root node, mosaic node or mosaic tile node to activate the
context menu shown in Figure 6-77. Different components of this menu will be active
based on the node level you select. During export, if the layer node is selected, all
tiles will be exported with the selected filename as a prefix and _Tile_N as the
suffix. When selecting an individual tile, only the single tile will be exported.
The Remove option is used to remove a single mosaic from the project. The user will
be prompted to confirm this action.
The Remove All option is available if you click on the root node and will remove all
mosaic layers from the project. The user will be prompted to confirm this action.

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The Check All option is available if you click on the root node and will check all
mosaic layers in the project.

Figure 6-77 - Mosaic Context Menu

The Uncheck All option is available if you click on the root node and will uncheck all
mosaic layers in the project.
The Load option is available if you click on a specific mosaic tile. If the tile is currently
unloaded, FMGT will attempt to load the tile. If you are running a 32-bit install of
FMGT, memory availability may prevent loading of a specific tile into the Map View.
The Unload option is available if you click on a specific mosaic tile. If the tile is
currently loaded, it will unload the tile from the scene.
The Load Tile Layout option is available if you click on a specific mosaic layer and
allows you to load the layout of that mosaic. This is an easy way to get back the tiling
layout if you want to produce more mosaics using the same tiled structure.
The Refresh option is available if you click on a specific mosaic layer and will update
a mosaic based on changes to the checked state of specific source files. This
provides an easy way to add or remove lines from a mosaic layer.
The Export sub-menu provides a way to export your mosaic tiles to another format.
The Grayscale Geo TIFF option exports the mosaic as a single plane GeoTIFF file.
The Color Geo TIFF option exports a color version of the mosaic. The Surface
option launches the surface exporter dialog shown in Figure 6-78. The mosaic
surface can be exported in several formats. These include:

ASCII Z

ASCII XYZ
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ArcView ASCII Grid, or

Raw binary grid

NetCDF/GMT Grid

Floating Point TIFF

When saving the data, areas of the surface containing no data may be included with
the output file if the Include Missing Data option is on. If missing data is included, a
special value is written for these data points, indicated by the No Data Value text
field.
When writing a binary file, you may specify either writing an 8-bit or 16-bit number, or
a 32-bit greyscale value containing red, green, blue, and alpha components.

Figure 6-78 - Surface Export Dialog

The Transfer to ArcGIS option on the sub-menu allows the user to export all tiles of a
mosaic directly to an ArcGIS database. When selected, the user will be presented
with the ArcGIS export dialog shown in Figure 6-79. This option will only be available
if you have the ESRI software installed and have a valid fmgis license feature.
The Name field should contain the intended prefix name of the transferred raster.
Since a mosaic can contain multiple tiles, it will be named as Name_Tile1,
Name_Tile2, etc. If you are exporting to a folder workspace, be sure to keep the total
name length under 13 characters.

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If you select the 1-band option, you will export a single plane raster containing the
backscatter values of the mosaic. If you select the 3-band option, you will export an
RGB image of the mosaic.
The Workspace type field is used to define what workspace types are browsed by
the dialog. Once a workspace is selected, the top level feature classes and datasets
can be viewed in the tree view. Click OK to proceed with the export to ArcGIS.

Figure 6-79 - ArcGIS Export Dialog

6.7.2.2 Statistics Context Menu

Right-click on a statistics layer or specific statistics attribute layer to activate the
context menu shown in Figure 6-80.

Figure 6-80 - Statistics Context Menu

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Different components of this menu will be active based on the node level you select.
During export, if the layer node is selected, all specific statistic layers will be exported
to the selected filename as a prefix and layername as the suffix. When selecting a
specific layer, such as Mean, only the single layer will be exported.
The Remove option is used to remove a statistics layer from the project. The user
will be prompted to confirm this action.
The Remove All option is available if you click on the root node and will remove all
statistics layers from the project. The user will be prompted to confirm this action.
The Check All option is available if you click on the root node and will check all
statistics layers in the project.
The Uncheck All option is available if you click on the root node and will uncheck all
statistics layers in the project.
The Export sub-menu works just like the mosaic context menu and is described in
the section 6.7.2.1.
6.7.2.3 ARA Context Menu
Right-click on an ARA layer or specific ARA attribute layer to activate the context
menu shown in Figure 6-81.

Figure 6-81 - ARA Context Menu

Different components of this menu will be active based on the node level you select.
During export, if the layer node is selected, all specific ARA layers will be exported to
the selected filename as a prefix and layername as the suffix. When selecting a
specific layer, such as Classification, only the single layer will be exported.
The Remove option is used to remove an ARA layer from the project. The user will
be prompted to confirm this action.
The Remove All option is available if you click on the root node and will remove all
ARA layers from the project. The user will be prompted to confirm this action.
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The Check All option is available if you click on the root node and will check all ARA
layers in the project.
The Uncheck All option is available if you click on the root node and will uncheck all
ARA layers in the project.
The Export sub-menu works just like the mosaic context menu and is described in
the section 6.7.2.1.

6.7.2.4 Reference Grid Context Menu

Right-click on a reference grid layer to activate the context menu shown in

Figure 6-82 - Reference Grid Context Menu

The Remove option is used to remove a reference grid from the project. The user
will be prompted to confirm this action.
The Remove All option is available if you click on the root node and will remove all
reference grids from the project. The user will be prompted to confirm this action.
The Check All option is available if you click on the root node and will check all
reference grids in the project.
The Uncheck All option is available if you click on the root node and will uncheck all
reference grids in the project.

6.8 Mosaic Information Panel

The Mosaic Information Panel shown in Figure 6-83 displays details about the
current survey area or the selected area using the Area Selection tool. The width
and height of the mosaic area are displayed in meters and pixels.

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Figure 6-83 - Mosaic Information Panel

The amount of memory needed to allocate the mosaic for processing is also
displayed. If the number is green, it is within the tolerance of the current binary and
its associated memory limits. The mosaic and statistic pixel sizes are also displayed.
The initial value is pre-computed by FMGT during coverage processing and is an
estimate based on the sonar beam configuration and along track coverage. These
are automatically computed by FMGT but can be overridden at any time. The
Compute button will recompute the nominal mosaic pixel size according to the active
source files in the project and the selected backscatter source. This is useful if the
user changes to a custom resolution but desires to get back to the resolution as
computed by FMGT.

6.9 Processing Panel

The Processing Panel of FMGT is the primary control over all processing of the user
source data. It is divided into Automatic and Manual processing. Automatic
processing requires the least user interaction as it runs all stages of backscatter
processing through generation of specific output layers. Manual processing provides
the user with finer control of specific processing stages of FMGT. Both of these
paths are defined in detail in the following sections.

6.9.1 Automatic Processing Tab

The Automatic Processing tab provides the simplest way to get to an output product.
As shown in Figure 6-84.

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Figure 6-84 - Automatic Processing Tab

The build All button will run all required processing stages and create the output
layers that are selected by the checkboxes. With this single button, FMGT can run
all processing and produce a mosaic layer, statistics layer and ARA layer for the
active lines of the project.
The individual build Mosaic, ARA and Statistics buttons will perform all required
processing stages and produce the specified output layer.
The Backscatter Source combo box is representative of the contents of the loaded
files. By default, if FMGT loads files with Beam Time Series data, this will be the
primary option selected regardless of other modes such as Beam Average. If the
user changes the backscatter source, the entire processing pipeline must be done
again. See the following section on manual processing to see how to accomplish
this.
The Visual Options section of this tab allows the user to control the opacity of visual
layers within the Map View. This allows visual correlation between characteristics of
different output layers. Changing opacity for a layer type changes the opacity for all
layers of that type.

6.9.2 Manual Processing Tab

The Manual Processing Tab shown in Figure 6-85 provides direct control over
specific stages of the FMGT processing pipeline as defined in Figure 1-23.

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Figure 6-85 - Manual Processing Tab

6.9.2.1 Backscatter Processing

The Backscatter group of buttons provides direct control over the backscatter
processing stages. These three primary stages, Adjust, Filter and ARA Inversion are
cascaded in that they depend on the previous stage being accomplished first.
However, whenever a button is pressed on this tab, FMGT will determine what needs
to be accomplished first by interrogating file state flags of each active line. It will then
perform the required processing before moving on to the user activated processing.
Before selecting any of the manual processing stages, the user must first clear the
associated processing flag. Clicking on the Clear Flags button will display the Clear
Flags Dialog as shown in Figure 6-86.

Figure 6-86 - Clear Flags Dialog

6.9.2.2 Product Layers

The Product Layers group allows the user to initiate generation of specific product
layers. This works the same way as the Mosaic, ARA and Statistics buttons on the
Automatic tab.

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6.9.2.3 Mosaic Tiles

By default, all visual object layers are created as a single tile whose bounds equal
either the total survey area or a user defined selection area. For very large surveys,
the tile size may be too large to fit into memory at full resolution. Sometimes the
survey may not be large but the layout of the survey lines run diagonally across the
survey area as shown in Figure 6-87.

Figure 6-87 - Diagonal Survey Line

If the user tried to build a mosaic of this size and resolution (~8cm), the required
memory size required for processing of the tile would be 2.91 GB as shown in the
Mosaic Memory text field. The on disk memory for this single tile would be
approximately 500 MB.
If you create a default tile layout of 2048x2048 pixels, FMGT will create the tile layout
shown in Figure 6-88 which spatially allocates tiles of the desired size along the track
line.

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Figure 6-88 - Tile Layout

By using the selection tool the user can see that the tile size requirements have been
reduced to ~45 MB. After clearing the selection and clicking on the Mosaic button,
FMGT processes the backscatter and renders the 18 tiles of the layout as shown in
Figure 6-89. The total on disk memory for all 18 tiles has been reduced from an
initial 500 MB down to 150 MB while keeping the maximum possible resolution of the
data.
Of course the user could easily select a lower resolution for the output mosaic but
this demonstrates FMGTs ability to spatially manage large or high resolution data
sets through the addition of tiled mosaics.

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Figure 6-89 - Rendered Tiles

To clear the tiles and select a new tile size, simply change the tiling resolution and
click the Create New button again. If the user wishes to go back to using the survey
bounds, simply click the Clear button.
FMGTs rendering engine will use the tile layout, survey bounds or area selection as
the target for all mosaic output. Statistics and ARA surfaces cannot be tiled. They
will always use either the survey bounds or the current selection area. Typically, the
larger resolution of these surfaces precludes their need for tiling. If FMGT cannot
allocate a statistics or ARA surface, you must change the resolution until FMGT can
properly allocate the surface.

6.9.3 Messages Tab

The Messages Tab will display all processing messages as well as warnings and
errors that occurred during any processing stage as shown in Figure 6-90. You can
clear this list by clicking on the Clear button. At this time, FMGT does not persist this
data between project sessions. If want to save it, you will need to copy and paste it
into a text document.

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Figure 6-90 - Messages Tab

6.9.4 Histogram Panel

The Histogram Tab contains the Histogram Control shown in Figure 6-91, which
displays the data histogram for any of the selected visual layers. The left and right
text boxes show the currently selected range of the data. The center text box shows
the value of the data for the current cursor location when over the control. To change
the range, use the composite control by click-dragging on either end, or simply left or
right click in the display to set the minimum and maximum desired value.

Figure 6-91 - Histogram Control

The Histogram control will stretch the selected data range over the full color map.
This provides a quick and easy way to do a contrast stretch for gray-scale
backscatter data.

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Click on the Color Map tool button to change the current color map. Use the Apply
All tool button
to apply the current histogram settings to all layers of the same
type.

6.9.5 ARA Tab

The ARA Tab contains the ARA Control shown in Figure 6-92. It displays the
backscatter plots for the currently selected patch. If the user has run ARA Inversion,
the model curve (in blue) will represent the current class for each side of the patch. If
the user has not run ARA Inversion, they can use the Quick Modeling tools by
clicking on the show/hide tool button at the bottom of the control.

Figure 6-92 - ARA Control

This will bring up the quick modeling tools shown in Figure 6-93 which are a subset
of the tools the user gets when accessing the full Patch Analyzer as described in
section 6.6.5.3.

Figure 6-93 - ARA Quick Modeling Tools

The user can use the grain size slider to try to fit the modeling curve to the observed
data or click on the Compute button to have FMGT do the modeling automatically.
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To preserve the results, simply click on the Apply button for the side of the patch that
was changed.
Click on the Patch Analyzer tool button
for this patch.

to bring up the full Patch Analyzer Dialog

See section 6.13 for information on how to use the plotting tool buttons.

6.10

Status Bar

The Status Bar shown in Figure 6-94 displays the current Map View coordinates of
the cursor when it is over the Map View panel. It also displays the value of the visual
layer under the cursor. If you are over the mosaic, it will display the backscatter
value. If you are over an ARA or statistic layer, the status will tell you what value you
are seeing as shown in Figure 6-95.

Figure 6-94 - Status Bar

Figure 6-95 - ARA and Statistical Layer Status

The currently monitored directly will be displayed after the Directory= portion of the
status line. If directory monitor is off, it will indicate Off.
The widget at the end of the status bar indicates the current application memory
usage for FMGT. As you approach the memory limits imposed by either the platform
build (32-bit vs. 64-bit) or the physical memory, the widget will go from green to
yellow to red. This widget is only available on the Windows version of FMGT.

6.11

Map View

The Map View of FMGT is very similar in nature to the DMagic map view or the
Fledermaus Plan View mode. The map view will display all visual layers of your
project that are currently active and all track lines for the loaded lines that are active.
The mouse buttons, mouse wheel or track pad (on Mac) are used to navigate within
the Map View.
Panning is accomplished by left-click dragging in the scene. Zooming in and out is
accomplished either using the mouse-wheel or a two-finger drag on a Mac track pad.
To center the scene on a selected point, use the center mouse button (mouse wheel
button). This action is not available on the track pad.
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Figure 6-96 - Map View Panel

To select a particular track line in the scene, left-click near the desired track line. This
will show the port and starboard swath extents for the entire line as shown in Figure
6-97.

Figure 6-97 - Line Selection

It will also cause the corresponding source file node to be highlighted in the source
files tree view. The currently selected patch will also appear as a green and red
polygon either side of the nadir track line.

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6.12

Tool Bar

The Tool Bar show in Figure 6-98 is used to control the Map View, the action tied to
the cursor and the activation of specific processing and edit tools.

Figure 6-98 - Tool Bar

6.12.1
6.12.1.1

Camera
Reset Camera

This tool button will reset the Map View such that the entire scene will be visible.
6.12.1.2

Zoom to Object

This tool button will zoom the scene to the currently selected survey line.

6.12.2
6.12.2.1

Cursor Modes
Explore

This cursor mode is the default mode used to navigate within the current scene as
explained in section 6.11.

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6.12.2.2

Select Mosaic Area

This cursor mode shown in Figure 6-99 will draw a selection area in the scene using
a left-click mouse dragging motion. The selected area will then become the new
extents of the mosaic area.

Figure 6-99 - Select Mosaic Area

6.12.2.3

Check in Area

This cursor mode shown in Figure 6-100 is used to automatically check source files
in a project that are within certain spatial extents. Simply left-click and drag out the
selection area. When the mouse is released, the source file tree will update to show
the lines that intersect the selection area. This also becomes the new extents of the
mosaic area.

Figure 6-100 - Check in Area

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6.12.2.4

Select Segment

This cursor mode shown in Figure 6-101 is used to select a segment of a line for
editing or beam correction processing. Left mouse click to select the starting point
(green) and right click to select the ending point (red). The user must click near the
nadir track line of the desired source file in the tree. To have the selection snap to
the start or end of a line, hold down the CTRL key while right or left mouse clicking.

Figure 6-101 - Select Segment

6.12.2.5

Measure

The measure cursor mode is used to measure a straight line distance in the scene.
Left-click and drag between the desired spatial points and the status bar of FMGT will
display the associated distance.

6.12.3
6.12.3.1

Display Options
Color Map

This tool bar button will turn on/off the display of the color map widget.
6.12.3.2

Clear Area

This tool bar button will clear the current selection area and/or the currently selected
line segment.
6.12.3.3

Show Bounds

This tool bar button will turn on/off the display of the scene bounding box.
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6.12.3.4

Show Selection Highlight

This tool bar button will turn on/off the display of the selection box.

6.12.4
6.12.4.1

Editing Tools
Line Brightness

With a line selected, this tool button will activate the Backscatter Adjustment tool
described in section 6.6.5.4.
6.12.4.2

Refresh

This tool button will refresh the currently selected mosaic. If lines have been turned
on/off via a checkbox, this tool will update the mosaic layer.
6.12.4.3

Cut Segment

When a line segment is selected as shown in Figure 6-102, this tool button will
remove the selected part of the line and update the associated mosaic.

Figure 6-102 - Cut Segment

6.12.4.4

Add Segment

With a line segment selected as shown in Figure 6-103, this tool button will add back
the selected part of the line and update the associated mosaic.

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Figure 6-103 - Add Segment

6.12.4.5

Force on Top

This tool button will force the selected line as shown in Figure 6-104 to be on-top
during mosaic rendering. To clear this flag, you must re-filter your data before
rendering another mosaic.

Figure 6-104 - Force on Top

6.12.4.6

Fill Gaps Only

This tool button will force the selected line as shown in Figure 6-105 to only be used
for gap filling in the mosaic. It will not be used to blend with overlapping pixel data.

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Figure 6-105 - Fill Gaps Only

6.12.5
6.12.5.1

Beam Tools
Beam Pattern Correction

With a current line segment selected, this tool will activate the Beam Pattern
Correction tool described in section 6.6.5.1.
6.12.5.2

Patch Analyzer

With a patch selected, this tool button will activate the ARA Analysis tool described in
section 6.6.5.3.

6.13

Plotting Widgets

All plotting widgets have the same capabilities. The plot widget for roll and pitch of a
selected file is shown in Figure 6-106. As you move your cursor over the plotting
area, the cursor location values update in the text box at the bottom of the widget.

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Figure 6-106 - Plot Widget

You can zoom into a portion of the plotting area by click-dragging a selection on the
plot surface as shown in Figure 6-107.
If you wish to zoom back out, simply click on the zoom out icon
the plot widget.

in the toolbar of

If you wish to save the current plot to an image, simply click on the Save As icon
the plot widget tool bar.

of

The settings icon

will bring up the settings dialog as shown in Figure 6-108. Here
you can change the axis label names, colors and ranges. When you are finished,
simply click OK to apply the values.
The color buttons in the toolbar of the plot widget allow you to quickly hide or show a
field of the plot. This can be useful in multi-plot widgets.

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Figure 6-107 - Plot Widget Zooming

Figure 6-108 - Plot Widget Settings

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Chapter 7 - Routeplanner

7.1 Introduction
Multiple routes can be laid over most of the SD objects that Fledermaus supports,
including SonarDTMs and GeoImages. Routeplanner also supports interactively
editing routes, changing circle radii, and profiling along routes or straight lines.

7.2 Starting Routeplanner

There are two ways to start the Routeplanner application. Click the Routeplanner
icon from the Windows Start Menu...

7.3 User Interface

The interface for Routeplanner is divided into the following five regions:
Route Display Region
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Control Bar
Control Region
Object Manager
Profile Region
Menu Bar Region
Each region is shown in Figure 7-1 and is described in more detail in the following
sections.

Figure 7-1 - Routeplanner Interface Overview

7.4 Route Display Region

The Route Display Region is the main black area in the center of the window where
SD objects and routes are displayed. All manipulation is done using the mouse and
the function of the mouse buttons depends upon the current mode the application is
in. The current mode is indicated by one of the buttons located in the Control Bar.

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7.4.1 Bottom Display Bar

The Bottom Display Bar displays the geographic coordinates of the mouse cursor as
the cursor moves over the surface. The coordinates will also display the z coordinate
(height) if the mouse is over an area that contains valid data.

Figure 7-2 - Routeplanner Bottom Display Bar

7.5 Control Bar

The Control Bar is located to the right of the display region and has three buttons,

Figure 7-3 Control Bar Command Icons

which are used to adjust the camera and interaction mode of the application.
The Reset Camera button will reset the display to show the entire dataset(s). The two
buttons on the right set the mode for Routeplanner.
The arrow indicates exploration mode, useful for zooming in on a specific area of the
surface or otherwise manipulating the view. The Edit button allows you to create a
route or change or add to the current route (selected in the object manager). When
in Edit mode, profiling is along the route rather than in straight sections.
7.5.1.1 Exploration Mode
Exploration mode allows you to move the dataset around. Click and drag with the left
mouse button to move the surface up, down, right or left. Use the middle mouse
button or scroll wheel to zoom in and out. Clicking on a point on the surface with the
middle mouse button will center that point on the screen. You can profile along a
straight line by using the right mouse button.
The following table lists the uses for each of the mouse buttons:
Mouse Button

Operation

Left

Click and drag to move the viewpoint north,

south, east, or west.
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Middle

Click and drag right to zoom in. Click and drag

left to zoom out.

Right

Click and drag to profile along a straight line.

Scroll Wheel

Zoom in or out.

Table 7.1 - Use of Mouse Buttons in Exploration Mode

7.5.1.2 Route Editing Mode

The Route Editing Mode is used for editing routes. A route is displayed as a white
line in the Route Display Region. A series of purple points along the active route
indicate which points are movable. These points are displayed at the end points of
the route and at the tangent points between a circle and the neighbouring lines. If the
circle centers are shown, they are visible as yellow dots. If the intersection points are
shown, they are visible as white dots. The following table lists the uses for each of the
mouse buttons:
Mouse Button

Operation

Left

Click and drag a tangent point (purple) to move

the point to a new position. Click and drag a
center point (yellow) right to enlarge the circle
radius or left to shrink the circle radius.

Middle

Click near a route line or one of the endpoints to

add a new point to the active route. New circles
are created with the radius given in the Default
Radius textfield. A new route will be created
automatically if needed.

Right

Click and drag along the active route to profile

the route.
Table 7.2 - Use of Mouse Buttons in Route Editing Mode

Note that when a node is selected in Route Editing Mode, the selected circle will be
indicated in the Nodes list along the left side of the application and the circle will be
displayed as a dotted line. The Route Editing Mode can be entered using the M key
when the Route Display Region is selected.

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7.6 Profile Region

The Profile Region shows a vertical cross section of a surface. Create a profile by
clicking and dragging with the right mouse button in either the Exploration or Route
Editing Mode. In Exploration mode, the profile will be a straight line. In Route Editing
Mode, the profile will stretch along the active route.
The colors under the profile correspond to the color of the surface along the profile.
The axes are labelled with the height of the profile and the distance. By clicking and
dragging on the profile display, you can measure the distance and slope angle for a
specific part of the profile. An example of this is shown in Figure 7-4 near the upper
right, denoted by a solid white bar with the distance and slope angle above and
below the bar respectively. This bar can then be repositioned anywhere along the
profile.
Below the profile window are features for loading and saving profiles, changing the
display of the profile and information about the profile. The length of the profile, the
vertical exaggeration and the profile's end points are displayed in Distance, V-Scale
and End Points boxes on the right. As the mouse cursor is moved over the profile,
the slope at the point the mouse is over is displayed in the Gradient text field.

Figure 7-4 - Profile

By default each time you drag a new profile the vertical scale automatically adjusts its
value. The Lock Scale toggle button locks the vertical exaggeration to whatever value
is entered. Thus new profiles will maintain the same vertical scale. This option is
useful when trying to do comparative profiles.
Click on the Profile button, at the bottom left, to show drop-down menu with a number
of options for profiles. Select the Save Profile menu option to save the current profile
to a disk. Profiles are saved as a text file with the extension .pfl. Each point in the
profile will be written out to the file as a distance along the profile and an x, y, and
height position. A profile that has been saved can be loaded from disk by clicking the
Open Profile menu option and selecting the profile using a file dialog box. Click the
Clear Profile menu option to erase the current profile. The Screen Capture menu item
can be used to save an image of the current profile to either a TIFF or EPS file. Click
the Screen Capture option and select the destination image file and type using the
file dialog box.
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7.7 Object Region

The Object Manager provides control over the routes in the current scene. All routes
will be displayed below the Routes label. Selecting a route in the list will make that
route the currently active route. The active route is indicated in the Route Display
Region by a series of purple points along the route. To create a new route, click the
New Route button or start adding points when no route currently exists.
Delete nodes from the current session by selecting the objects or nodes you want to
delete in the Object Manager and then clicking the Delete Route button.

Figure 7-5 - Routeplanner Object Manager

7.8 Control Region

The Control Region along the left side of the application allows for control of the
routes and surfaces.
7.8.1.1 Route Controls
The Route Controls, shown in Figure 7-6, are used to control various attributes of
routes and also how the routes are displayed. The Default Radius textfield indicates
the radius in meters of any new nodes that are added to the route. To enter a new
value, click on the textfield, enter a new value, and press Enter. The Default Radius
is also used when importing a file of XY Intersections.
When either exporting or profiling a route, a number of points are sampled along the
route. The Sample Interval indicates the spacing of these points in meters. For
example, for a value of 10, points every 10 meters along the pipeline would be
exported.

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Figure 7-6 - Route Controls

The Line Width text field controls the visual width of the route in pixels and does not
affect any other operation on the route. Make sure to press Enter after the line width
has been changed. Below the text fields are three toggles that affect the display or
behaviour of the route.
The Show Circle Centers toggle controls whether the center of the circles are drawn
(indicated by yellow dots). The Show Intersections toggle controls whether the
intersection points between neighbouring lines are displayed (indicated by white
dots). The toggle Lock Intersections changes how the route behaves when moved.
When Lock Intersections is selected the straight run sections of the route will not
move (except for the one section being moved). Instead, the radii of the nodes will
change to accommodate the new route. This keeps the intersection points the same
while allowing you to make changes to the route.
The Nodes list displays all internal nodes in the route (excluding the end points) and
the radius of the circle for each node. Selecting a node in the list will cause that node
to be highlighted by a dotted circle in the Route Display Region. The radius of a circle
and intersection point of a node can be edited by double clicking on the node or by
clicking on the node and pressing the Edit Properties button. The Node Properties
dialog, shown in Figure 7-7, will be displayed where a different radius or intersection
point can be entered. The node tangent points will be displayed, but cannot be
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edited at this time. To delete a node, select the node from the list and click the Delete
button.

Figure 7-7 - Node Parameters Dialog

7.9 Menu Bar

Figure 7-8 File menu

7.9.1 File Menu

7.9.1.1 Open Data Object/Scene
The loaded SD objects need only be in the approximate area of the routes to be
planned as the routes can be laid anywhere, including areas where there is no data
(shown as black on the main screen). To load SD objects, click the File > Load SD
Object menu option and select one or more files using the standard file selection
dialog.

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7.9.1.2 Open Route

To load one or more routes, click the File > Load Route menu option. This action will
display the standard file selection dialog which can be used to select route files which
have the extensions .plf.
7.9.1.3 Save Route
To save the currently active route, select the File > Save Route menu option and
select a file name for the route. Note that if the filename does not have the extension
.plf, it will automatically be added to the end of the name.
7.9.1.4 Clear Scene
Any loaded SD files can be removed from the Routeplanner application using the
Clear Scene menu command. Active routes are not removed by this command.

7.9.2 Import Menu

7.9.2.1 Import XY Intersections
The File > Import > Import XY Intersections menu option allows importing a route
from an ASCII file containing a set of X and Y points. Each X and Y pair should be on
a separate line in the file. Routeplanner will generate a route using the given points
as intersection points and using the radius in the Default Radius textfield for the route
nodes.

7.9.3 Export Menu

7.9.3.1 Export SD

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As shown in Figure 7-9, the File > Export > Export Line SD File menu option allows
exporting of the current route to a line SD file that may be read by Fledermaus.
7.9.3.2 Export XY
The Export XY File command writes an ASCII file containing the x and y coordinates
of a set of points along the line.
7.9.3.3 Export XYZ
The Export XYZ File writes an ASCII file containing the x, y, and z coordinates.
Note that the Sample Interval text field is used to determine how many points are
Figure 7-9 Export menu options

output in either of the files.

7.9.3.4 Export Cross Profiles
Selecting this option brings up the following dialog box which allows one to
control how the cross profiling is done and what type of output will be generated.

Figure 7-10 Export cross profile control dialog

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The top half of the dialog contains the parameters that control how the cross
profiling is performed. The along pipe sample interval specifies how often along
the route a cross profile is taken. The cross profile sample interval is the spacing
between the sampling points in the cross profile itself and the cross profile radius
controls the overall width of the cross profile. The total width is twice the cross
profile radius. Thus a cross profile sample interval of 10 meters with a cross
profile radius of 100 meters will generate a total of 21 sample points over a 200
meter profile centered on the route.
The starting and ending KP point are specified in units of the data (as are all the
fields here). Thus if your data set is in meters then all the units here are meters
as well. A value of -1.0 indicates the start or end of the route should be used.
The lower half of the dialog provides options that affect the structure of the
generated output file. Currently two output formats are supported. The Abaqus
format and a basic ascii XYZ export format. The number of decimal places field
value controls how many decimal places are written for the x and y coordinates.
Currently the z coordinate is always written to two decimal places. For the
Abaqus format an additional input field is provided to specify the starting node ID.
The default is one. Finally the reference coordinates to 1st node toggle makes the
1st node have a coordinate of 0.0, 0.0 in x and y with all other coordinates relative
to it. The z coordinate is not affected by this option. Some sample outputs are
shown below.
7.9.3.5 Exit
The Exit menu command is used to stop running Routeplanner.

7.9.4 Help Menu

The Help menu provides you with three options: Online Help, IVS Home Page, and
About. These options provide information on the product, the company, and the
software itself.

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Chapter 8 - Crosscheck

8.1 Introduction
Crosscheck is a point versus surface comparison tool that is designed to generate
the difference statistics for comparing survey line data with a reference set of data.
The reference data may consist of either ground truth data or other survey lines.
The program can either be used as a background process that takes the given data
and generates an output statistics file or as an interactive graphical analysis package
that allows for interactive inspection of the resulting statistics and histogram data.

8.2 Starting Crosscheck

The crosscheck program can be run completely via the command line or through the
graphical interface as desired.

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Figure 8-1 Crosscheck command line

-data: The data files to perform the crosscheck test on are specified through the
data option. Note that one or more files can be specified. When multiple files are
specified the crosscheck analysis is both for each file separately and also for the
entire combined data sets.
-gt: If you want to generate a reference surface at run time you need to specify the
source point file via the gt option.
-cell: A cell size for the surface must also be specified (in units of the source files) via
the cell option.
-dia: a weighting diameter via the dia option. Normally for this application the
diameter should be 3.
-retsurf: To directly load a prepared SD file as the reference surface use the refsurf
option followed by the SD file name.
-out: The program can write the surface file it creates via the out option if you want
to save the generated reference file for use later.
-stats: If the stats option is specified then the resulting calculated statistics are
written to the given filename. This option is normally used if the program is run as a
background application but can be used anytime.
-batch: If the program is run as a background application than the batch option
should be specified. This prevents the graphical interface from being displayed.

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8.3 User Interface

The main display is divided into the five major regions:

Data Sets

Surface Display

Histogram

Data Analysis

Menu Bar

Each region is labelled in the figure. This chapter will examine each of these regions
and explain how to make use of all the capabilities Crosscheck has to offer.

Figure 8-2 - Crosscheck Main Window

8.4 Data Sets Region

The Data Sets Region is located to the left of the surface display areas and lists all
line files that are being used as part of the analysis. Selecting any line will display the
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analysis statistics, histogram and intersecting points for that line. A special top level
parent is called ALL_DATA_SUMMARY and will display statistics and histogram for
all line files together.

8.5 Surface Display

The Surface Display region is used to display two important data sets: the reference
surface that is being used, and any points that intersect between the reference
surface and the ungridded line files. Before running the analysis, only the reference
surface will be displayed. Once the analysis is complete, the points for the selected
line (or all lines if ALL_DATA_SUMMARY) will be displayed. The size of the points
can be adjusted using the slider directly below the surface display region.

8.6 Histogram
The frequency count display bins the sample point difference range into a series of
512 bins. Each sample is then sorted into a bin and the numbers of entries in each
bin are counted. This gives of the frequency of occurrence distribution of the
difference points.

8.7 Data Analysis Region

The application computes seventeen statistics from the comparison calculations,
which are described in turn. The process proceeds by looping across all points in the
data files. For each data sample, the geographic position is used to inquire the height
from the reference surface at the same location. For successful tests, this reference
height along with the point height, and difference amount (data_height ref. height)
is stored and forms the basis for the statistical calculations.
The computed values include:
Number of Data Points

Number of points tested for which a reference height was

found.

Data Mean

Average height of the source data files.

Reference Mean

Average height of the matching sample reference points.

Difference Mean

Average value of the (ref-source) difference.

Difference Median

The median difference height (50% above, 50% below).

Difference Std. Deviation

The standard deviation calculation of the height

differences.

Data ZRange

The overall Z(height) range of the source data.

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Reference Z-Range

The overall Z(height) range of the matching reference

data.

Difference Z-Range

The overall range of the difference data.

Order 1 Error Limit

The IHO Order 1 error limit for the average data depth.

Order 2 Error Limit

The IHO Order 2 error limit for the average data depth.

Order 1 P-Statistic

The Order 1 P-Statistic (percentage confidence)

Order 2 P-Statistic

The Order 2 P-Statistic (percentage confidence)

Order 1 - # Rejected

Number of soundings rejected in the target population.

Order 2 - # Rejected

Number of soundings rejected in the target population.

IHO Order 1 Test Status

Pass/Fail for an IHO Order 1 Survey Quality

IHO Order 2 Test Status

Pass/Fail for an IHO Order 2 Survey Quality

8.8 Menu Bar

8.8.1 File Menu

Figure 8-3 - Crosscheck File Menu

8.8.1.1 Open Reference Surface

Before doing any analysis, a reference surface needs to be loaded using the Open
Reference Surface command. The surface needs to be a SonarDTM object.
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8.8.1.2 Open Lines

One or more un-gridded data files can be loaded using the Open Lines command.
8.8.1.3 Open Line List
In order to save time when working with groups of files, a text file containing one
filename per line can be loaded using the Open Line List command.
8.8.1.4 Input Configuration
The default configuration for the data lines can be adjusted using the input
configuration dialog, which is shown in Figure 8-4.

Figure 8-4 - Input File Configuration Dialog

8.8.1.5 Save List

The Save List command can be used to save a text file containing a list of all
currently loaded line files.
8.8.1.6 Open Project
If you have previously saved a Crosscheck project, you can load it using the Open
Project command. This will restore the reference surface, lines, and configuration.
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8.8.1.7 Save Project

The Save Project command is used to save the current setup of reference surface,
data lines, and configuration.
8.8.1.8 Save Statistics
The save statistics menu option will write an ASCII statistics file. It is designed to be
easily readable by other programs so the results can be easily fed into a parent
application.
Statistic records are written for each input file as well as the combined record entitled
ALL_DATA_SUMMARY. The numbers are shown first followed by a comment that
starts with the hash mark that explains what the number is.
8.8.1.9 Save Depth vs. Difference
This menu option will save a single ASCII file that contains a record for each point
that intersects with the reference surface. Each record will have two columns, the first
column is the depth of the reference surface, and the second column is the difference
between the reference surface and intersecting point.
8.8.1.10

Save Position vs. Difference

The Save Position vs. Difference menu option is very similar to the Depth vs.
Difference option, however it creates an ASCII file with 5 columns. The columns
contain the following data: x-value, y-value, difference between reference surface
and the point, reference surface depth, and point depth.
8.8.1.11

Exit

The Exit menu command is used to stop running Crosscheck.

8.9 Object Menu

Figure 8-5 - Crosscheck Object Menu

8.9.1 Surface Projection

The Surface Projection command can be used to change the projection parameters
for the currently loaded reference surface. Once selected, the coordinate system
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dialog will be displayed, as show in Figure 8-6. It is especially important to set the
proper coordinate system for older SD objects that may not have a full coordinate
system specified.

Figure 8-6 - Crosscheck Reference Surface Coordinate System Dialog

8.9.2 Line Projection

When line files are first added to Crosscheck, you will be prompted to set the
coordinate system, however the Line Projection command can be used to change
the coordinate system at any time. Note that if the coordinate system of the line files
do not match the coordinate system of the reference surface, the line files will be
projected into the same coordinate system as the reference surface.

Figure 8-7 - Crosscheck Input Line Coordinate System Dialog

8.10
8.10.1

Import Menu
Import un-gridded data

A reference surface can be built from one more ungridded files using the Import
Ungridded Data command. For more details on the un-gridded import wizards, see
the DMagic chapter.

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Help Menu

The Help menu provides you with three options: Online Help, IVS Home Page, and
About. These options provide information on the product, the company, and the
software itself.

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Chapter 9 - Vessel Manager

9.1 Vessel Manager
The vessel management tool is designed to support remote operated vehicle
operations, vessel tracking and other similar real-time tracking tasks. It serves to
gather the realtime data from appropriate sources and present it to Fledermaus so
that vessels, ROVs, and other moving objects can be tracked, measured, and
analyzed. At its core, Vessel Manager understands standard NMEA strings, a special
customized NMEA like data string, and the PLO (a US Navy) format. Data in any of
these formats can be read in via a file, a serial port connection, or via network UDP
packets (added in v6.5.1). Previous versions of Vessel Manager could only support
one vehicle when using standard NMEA data however as of version 6.5.1 multiple
vehicles are supported based on the 1st two characters of the NMEA message
strings. Figure 9-1 below is the display when the application is started. The main
display area is used to verify that the input navigation is being successfully read and
processed. The area to the left shows the list of active vehicles configured to receive
data.

Figure 9-1 - VesselManager application window

The controls on the front panel are mostly limited to showing the setup/preferences
dialog and buttons to start and stop the data acquisition. The data input source and
current status are also shown on the front panel. When toggled on the Audio
Feedback check box causes a beep to be emitted each time a valid input navigation
message is processed.
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Setting up the workflow for vessel manager is a three step process. Configure the
method of data input, specify its format, and setup the vehicle list. The basic data flow
for working with real time navigation data is shown in Figure 9-2.

Figure 9-2 - VesselManager data flow

From the diagram, vessel manager acts as a middle man interpreting navigation data
that comes in from a variety of sources and parsing it into vehicle structures that are
constantly updated with the latest navigation information. To visualize and analyze
the vehicle information Fledermaus is used. Adding vessel objects in Fledermaus
connects to the vehicle structures generated by VesselManager through the vehicle
ID (a number between 0 and 9). All interaction with the vessels is done in
Fledermaus. Once vessel manager is configured, using it is simply a matter making
sure the correct configuration is selected and clicking the start acquisition button. If a
configuration file is saved with the auto-start option checked then acquisition begins
automatically when that configuration is selected.
Before VesselManager can be used it is necessary to create an acquisition profile file
that configures how the system will receive and process the received data. This is
done via the Setup/Preference button in the lower left corner of the main display.
Once the application is configured, the settings can be saved as defaults or an
appropriate configuration file can be saved. This makes using the application again in
the future trivial. The setup dialog box is shown in Figure 9-3 and contains a tabbed
display that covers most of the dialog and steps one through the setup process. As
the tabs suggest, one needs to configure the data source (Communication Setup), its
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format (Message Configuration), and vehicle setup. If logging of the received data is
desired than it can be configured in the final setup. Once you have finished the setup
you can choose to make it the application default by clicking the Save As Defaults
button, or choose Apply to make it the current configuration. Clicking Cancel exits the
dialog without changing the current configuration.

Figure 9-3 - Setting up VesselManager

Below the tabbed display is a check box which when checked tells the system to start
acquiring data immediately once the configuration is loaded. Generally configurations
that auto-start should not be saved as the default configuration for the application.
Starting with the Communication Setup tab as shown in Figure 9-3 the 1st choice is to
specify how the application will receive its navigation data. There are three choices
that include receiving data from a TCP/IP network, via the serial port, or as played
back from a logged data file. Clicking on the appropriate choice activates any
additional setup parameters required for the chosen method.
To use network based UDP packets you must specify the IP network address and
network port number. The lower port numbers are often reserved for other system
related activities so generally ports in the 30000-60000 range are recommended.
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You must specify the resolved IP address (the 4 numeric triplets for example
192.168.0.45) and not a machine name (for example: mymachine.com ).
To receive data via the serial port it is necessary to identify which serial port and the
expected baud rate. Generally the baud rate will be 9600 although 4800 is also fairly
common. The serial port name on Windows machine will be COMn where n is a
number, usually 1 or 2. For UNIX machines this will be a serial device name. For
example on Linux for serial port #1 the serial port name is something similar to
/dev/ttyS0.
Lastly there is a file playback option. This is used to replay an existing log file saved
to disk and is a handy option for re-analyzing how a job went or showing others. To
use the file playback option you need to select the file and specify the file playback
rate. A playback rate of 1 is real time and larger numbers playback the file at n
times the speed for quick reviews. In previous versions of vessel manager file
playback was a separate dialog now it is integrated in here.
The second tab, called Message Configuration as shown in Figure x.x is used to
identify what the format of the data received will be. The system currently supports
three different data formats, all which now support multiple vehicles. These include
standard NMEA messages, a specific IVS defined custom message, and PLO
formatted messages.
The Message Configuration tab is used to identify the format of navigation data being
read. Three formats are currently supported which includes standard NMEA style
navigation strings, a custom (IVS) formatted string, and the US Navy PLO binary
format. NMEA is most commonly used when vessel manager is directly reading raw
navigation data via the serial port or off a network connection. The custom IVS string
is generally used in conjunction with a navigation package such as WinFrog.
WinFrog, as a full featured navigation system, can receive a wide variety of
navigation strings from multiple sources and create the appropriate custom string that
vesselmanager uses. The format of this string is discussed below.

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Figure 9-4 Message Configuration Setup

NMEA standard strings have no extra configuration options. The system reads a
limited number of the standard strings as described below. All NMEA strings start
with a dollar sign followed by a five digit code. For example: $GPGGA is a standard
satellite navigation string. The actual message type is defined by the last three
character of the string header. In the previous example that is the GGA portion of
the message. Vessel manager uses the 1st two letters as the vehicle name. In this
example GP would be the name of the vehicle. The NMEA message strings
currently understood by vesselmanager include (xx means any two characters):
Message Header

Overview

$xxGGA

Provides geographic x, y positioning

$xxGLL

Provides geographic x, y positioning

$xxHDT

Provides heading information

$xxDPT

Provides depth which is negated to turn into a height. (z

coordinate)

$xxRMC

Provides heading information

$xxHDG

Provides heading information

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The second input format shown in Figure x.x is Custom which is designed to look like
NMEA data strings but it supports a custom message string which can be output by
navigation programs such as WinFrog. Currently this input format is the any method
to have full access to vehicle yaw, pitch, and roll information. The controls for this
format include the ability to identify the NMEA string header (defaults to $C&C). A
small sample of input in this format looks like:
$C&C,SIM,00:00:00.0,541175.375000,167894.781000,296.088928,0.0,0.0,-2.568574,0.0
$C&C,SIM,00:00:00.0,541173.578779,167895.660529,296.088928,0.0,0.0,-2.564224,0.0
$C&C,SIM,00:00:00.0,541169.088227,167897.859352,296.088928,0.0,0.0,-2.553348,0.0

The strings follow NMEA conventions are a set of comma separate set of fields.
Following the $C&C header the fields include:
Vehicle Name -> A string. In the example the name is SIM.
Time -> hh:mm:ss.s for hours, minutes, seconds and fractional secs.
X-Coordinate -> Can be a projected easting or decimal geographic longitude
Y-Coordinate -> Can be a projected northing or decimal geographic latitude
heading -> in degrees [0, 360]
pitch -> in degrees ( +ve is pitch up )
roll -> in degrees ( +ve is roll to starboard )
height -> in units of the data (+ve is up)
altitude -> in units of the data (currently not used)

The input message contains a string which represents the vehicle name as the 1st
argument. In the example above the vehicle name is SIM. If this string matches the
name given to one of the active vehicles than the relevant navigation data will be sent
to that vehicle.
The last data format option is PLO, which is a binary input format used by the US
Navy. It contains a series of records where each record contains a vehicle ID, and
appropriate positioning information.
Once the data format is selected, one can optionally adjust the output projection of
the x, and y coordinates. Standard NMEA and PLO always provide the x, and y
coordinates as geographic longitudes and latitudes. The custom format can provide
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data in that way or projected into Universal Transverse Mercator(UTM), or Universal

Polar Stereographic(UPS). Thus there is an extra check box for the custom format to
specify whether the data is geographic or projected. By default geographic data is
expected.
The output projection area below the data format lets one project data on the fly if
desired. By default the output format is selected to be geographic to match the
default input format but one can choose UTM or UPS and have the system
automatically project the data as necessary then use the resulting coordinates as the
x and y position. When selecting options other than geographic it will be necessary to
set the appropriate projection parameters. For UTM, the zone normally defaults to
auto in which case the 1st geographic coordinate read is used to select the nearest
zone. Alternately the zone can be directly specified. For Polar Stereographic
projection, the hemisphere must be specified.
Geographic Output

Universal
Transverse Universal
Polar
Mercator Output
Stereographic Output

Figure 9-5 - Data output coordinate format

Navigation logging is the final section of the setup dialog and lets one specify a
directory in which the log files are written. If Log Raw Nav Strings is on then a file of
The 3rd tab is used to perform the vehicle setup. This identifies the names and/or IDs
of particular vehicles of interest present in the incoming data stream and is used to
route data to the appropriate vehicle slot.

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Figure 9-6 Vehicle Setup

The Vehicle Setup tab contains a set of up controls for up to ten vehicles. Each
vehicle has an integer ID shown at the left hand edge of the controls labeled from
zero to nine. When using Fledermaus, when you add a vessel, this is the ID # that
you need to enter to activate the vessel inside Fledermaus. The vehicle name
identifies the vehicle. How it is used depends on which data format was selected in
the previous tab.
For standard NMEA messages a vehicle name is always two characters long. These
characters must match the 1st two characters of the NMEA message header after the
dollar sign. Thus if the NMEA message starts with $V1HDT then one must name
a vehicle V1 (without the quotes) to match it. Any NMEA strings received that start
with $V1 send their data to the V1 vehicle.
For custom formatted data strings the 1st comma separated field after the header is
the vehicle name. For example, for messages of the form $C&C,HMCSHalifax,
the vehicle name is HMCSHalifax.
Finally for PLO formatted data, the vehicle name is an integer number that matches
the appropriate vehicle ID send inside the PLO data.
The final tab is used to setup logging. If this option is activated then all received data
is sent to a log file. This is useful to replay a job in the future. The resulting log files
can be played back by using the file in the file playback option available in the
communication setup tab previously described. To create a log file it is necessary to
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select the directory in which it will be created and a base name. Log files will be
created in that directory with the name <baseName>-<JulianDay>.log. The Julian
day is automatically appended onto the filename and is based on the current date
when the logging starts. For example for the base name shown in the dialog below if
the current date is January 1st then the resulting filename would be mplog-1.log.

Figure 9-7 Data Logging Setup

Once the setup is complete, clicking Apply will make the settings active for the
current session and return one to the main display.
From the main display there are several menu options available as shown in Figure
9-8. The current settings can be saved to a configuration file using the File > Save
As command. File names will automatically be given the extension .vmf which
stands for vessel manager file. This file saves all the settings used to configure
vesselmanager for a particular project. Once a configuration file is saved, it can be
loaded back in simply using the File > Open option and selecting the saved .vmf file.
Often this file can be immediately loaded just by looking at the File > Open Recent
menu. If the .vmf file has been used recently it will be shown and can be loaded
simply by clicking its name.

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Figure 9-8 File Menu for VesselManager

The final two screen captures show VesselManager receiving data across a network.
The first screen shows the raw message view and the 2nd one the processed
message view.

Figure 9-9 Raw Acquired Message Display

When viewing raw messages, as long as you are seeing data and it appears properly
formatted then VesselManager is receiving the data. The processed messages
displays vehicle update messages. Whenever a processed message appears this
means that VesselManager has successfully parsed a raw data message matched it
to an active vehicle and has updated the vehicles navigation information.
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Figure 9-10 Processed Navigation Message Display

Showing processed messages is the best method to verify that VesselManager is

running as expected.

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Chapter 10 - Omniviewer

10.1

Introduction

Omniviewer is a program that displays XYZ and multivariate data from a variety of
formats from a simple ASCII XYZ files to vendor specific formats such as HDCS.

10.2

Starting Omniviewer

There are two ways to start the Omniviewer application. Click the Omniviewer icon
from the Windows Start Menu...
To start Omniviewer via the command line, the following start-up option may be
specified. The square brackets indicate which part of the text is optional.
omniviewer

[ -in ]
[ -start ]
[ -rows ]

The file option lets you load a specific sounding file.

The rows option lets you specify how many rows to display at once.
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The start option lets you specify the ping and beam values to start reading the
sounding file at. .
The -h option displays command line help.

10.3

User Interface

The main display is divided into the 3 major regions:

Menu Bar

Data View

Control Panel Region

Each region is labelled in the figure. This chapter will examine each of these regions
and explain how to use them for viewing ungridded data files.

Figure 10-1 - Omniviewer Main Window

10.4

Data View

The Data View area provides a spreadsheet style view for a subset of the source
ungridded file. Along the top of the display are multiple columns, one for each
attribute found in the source file. These columns are populated by the number of
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rows specified in the Display Rows text field, which is described in the following
section.

10.5

Control Panel Region

The number of records display will depend on the amount entered in the text field
Display Rows. After the data has been loaded, to change the amount of records
displayed at once, simply change the amount entered in the text field Display Rows
and hit return. To retrieve the next or previous set of records, select either the Next>>
or <<Previous buttons. To display a specific record, enter in the desired records ping
and beam number (or record and subrecord) in the text fields Ping and Beam, then
select the Go To button. If the record is found, it will be displayed at the top of the
records list.

10.6

Menu Bar

The Omniviewer menu bar contains additional functionality for loading a new file and
for viewing any header information that a source file may contain. The following
section will describe these commands in detail.

10.6.1

File Menu

Figure 10-2 - Omniviewer File Menu

10.6.1.1

Load File

To load a new file, select from the menu File > Load File. A file selection dialog will
be displayed to select a file. When a file is loaded, its data will be displayed in the
main application as shown in Figure 10-1. This will display the data for all input fields
and flags for the specified file.

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10.6.1.2

View Header

If the file format being read contains header data, this information can be displayed
using the File > View Header command.

Figure 10-3 - Omniviewer View

Header Window

10.6.2

Help Menu

The Help menu provides you with three options: Online Help, IVS Home Page, and
About. These options provide information on the product, the company, and the
software itself.

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Chapter 11 - Fledermaus and GIS

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11.1

Introduction to Fledermaus ArcGIS Connectivity

Fledermaus allows direct connectivity to an ESRI ArcGIS workspace through the

new SD ArcWorkspace object type. Having this SD object in your scene allows you
to browse an ArcGIS workspace for Fledermaus compatible objects and load them
directly into your scene. Conversely, you can take ArcGIS Aware SD objects from
your scene and transfer them directly to any connected ArcGIS workspace.
Fledermaus allows your scene to have multiple connections so that you can move
data to and from any number or type of ArcGIS workspace objects.
The capability is currently supported only under the Windows 32-bit version of
Fledermaus due to ArcGIS being Windows-only software, and a 32-bit limitation in
the ArcGIS Engine. The 32-bit version of Fledermaus is supported on both 32-bit
and 64-bit Windows platforms.
Your system must also have ArcGIS installed and you must be licensed to operate
the standard toolset for the ArcGIS capabilities to be exposed within Fledermaus. As
of this writing you will also require the ArcGIS option to be active in your Fledermaus
license file.

11.2

Bathymetry Quick Start Guide

With this Quick Start Guide, we will demonstrate exporting bathymetric information
from a PFM. The guide assumes that you have a pre-existing Fledermaus scene
with a PFM SD object loaded.

11.2.1

Step 1 Creating the Workspace

The first thing to do when working with ArcGIS data is to create a workspace object
that will give you proper connectivity to the workspace. When licensed properly, the
Fledermaus Create menu will have the additional option Add ArcGIS Workspace as
shown in Figure 11-1.

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Figure 11-1 Create Menu

After creation, you will have a new SD Arc Workspace object that when selected will
display the attribute panel shown in Figure 11-2.
A workspace can contain both spatial and non-spatial information. It can be
configured as a file system, a local database or a remote database. Fledermaus
allows four types of workspace connections. These are the Folder, File, Personal
and ArcSDE workspaces. The Folder workspace is used for standard file system
folders that contain shape or raster files. The File workspace is an ArcGIS .GDB file
and is considered a local database. The Personal workspace is a Microsoft Access
.MDB file also considered to be a local database. The ArcSDE workspace provides
connectivity to a local or remote SQL-based database such as SqlExpress,
SqlServer and Oracle.

Figure 11-2 - Arc Workspace Attribute Panel

Using the attribute panel you can either connect to an existing workspace or create a
new workspace. Fledermaus can only connect to, not create, an ArcSDE workspace.
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Creation of these types of workspaces is done using the ArcGIS tools, typically
ArcCatalog.
A local file-based geodatabase will be used for the example. Select the File
connection radio button and click on the Create button. You will be presented with a
File Save dialog to name your database. An important note is that the local File
database creates a folder with the name mydbname.gdb. You should never alter the
contents of this folder as these are the files that the geodatabase engine sets up.
Once you have named your database and clicked OK on the dialog, you will notice
that the attribute panel has a progress icon indicating that the database connection is
initiating as shown in Figure 11-3.
Once the database has been created and the connection is successful, you will see
the new connection in the Features group on the attribute panel. The root of this tree
is always the database name. As you add features to the database from
Fledermaus, you will see these features appear in the tree view.

Figure 11-3 - Workspace Creation

Alternatively, you could connect to a pre-existing workspace. This is done by

selecting the workspace type and clicking on the Connect button. When the
connection is completed, Fledermaus will query all of the top-level objects within the
workspace. These will appear in the tree view on the attribute panel as shown in .

Figure 11-4 File Workspace Connection

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For more information on creating the different types of workspaces, see section 11.3.

11.2.2

Step 2 Transferring Fledermaus Data to ArcGIS

Every SD object within a Fledermaus scene that is ArcGIS Aware will have an
ArcGIS button on the attribute panel that allows you to move data from Fledermaus
to ArcGIS. The currently supported set of SD objects includes GeoImage,
Interpretation, Lines, PFM, Points, Scalar, and Surface. For more on transferring
these types, see section 11.5.
Select the PFM object that you have in your scene. The attribute panel should look
like the one shown in Figure 11-5. Be sure to extract a selection or the entire PFM
from the Coverage Map. Also note that some of the objects you transfer are
controlled by the type of surface you are currently viewing, as listed under Surface
Display Options. For example, if you are viewing the Shallow Edited Surface, that is
the surface that will be transferred if you choose bathymetric raster as a transfer
option.

Figure 11-5 - PFM Attribute Panel

The ArcGIS button located under Edit Control will pop-up a menu that will allow you
to transfer individual components of the PFM to your workspace or transfer all of the
available items at once using a wizard. The available object types include
soundings, BAG, survey area, bathymetry raster and sun illuminated image raster.
11.2.2.1

Transfer Soundings

If you select Transfer Soundings from the ArcGIS pop-up menu, you will launch the
dialog shown in Figure 11-6.

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Figure 11-6 - Transfer Soundings

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This dialog is very similar to the one accessed from the Tools button with the
exception that you are not exporting to a disk file. To see more on how this dialog
operates, please see section 4.8 in the Fledermaus Reference Manual.
For our example, assume that the plotted sounding selection filter has been run at a
chart scale of 5000:1. So in the ArcGIS Soundings Transfer dialog we select the
entire PFM, accepted soundings only and the plotted soundings option. After you hit
the OK button, Fledermaus will launch the ArcGIS Transfer Options dialog as shown
in Figure 11-7.

Figure 11-7 - Transfer Options

In this dialog you first select a name for your new object. This name must be unique
to the database and contain no spaces. Next you select which ArcGIS connection
you will be targeting for the transfer. When you select the workspace, the Destination
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tree view will show you the layout of that workspace. You must then select the
Destination of the transfer within the workspace. Depending on the object type, this
will be the root object node, an ArcGIS Feature Dataset or Raster Catalog. Finally,
you can change the coordinate system of the transfer. This allows you to re-project
data during the transfer into ArcGIS. After you have filled out the dialog, click the OK
button and the soundings will be transferred. When complete, you will see the new
object reflected in the tree view of your connection as shown in Figure 11-8.

Figure 11-8 - ArcGIS Transfer Complete

If we open ArcCatalog, we can browse to our workspace and see that the data has
been transferred as shown in Figure 11-9.

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Figure 11-9 - ArcCatalog Soundings

If you select Table from the Preview combo box of ArcCatalog, you will notice that
the soundings are transferred as Z-enabled Point objects with the additional
attributes of Depth and Mask. The depth attribute is a repeat of the Z value from the
point and the mask attribute is the flag mask from the PFM.
11.2.2.2

Transfer BAG

If your PFM has a Cube surface, you can transfer the Bathy Attributed Grid (BAG) as
a set of attributed Z-enabled points to your workspace. See section 3.16 of the
Fledermaus manual for more on Cube surfaces. The additional attribute in this case
will be uncertainty. When you select Transfer Bag from the pop-up menu of the
ArcGIS button, you will get the same Transfer Options dialog shown in Figure 11-7.
11.2.2.3

Transfer Survey Area

You can transfer the survey area of a PFM to ArcGIS as a polygonal object with
holes (the holes being where there is a data holiday/no data). The ability to account
for holes in the data ensures that the Shape_Area that is reflected in the attribute
table of the object represents the correct computed area of coverage for the PFM.
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This area is a planar computation is does not account for surface variation. When
you select Transfer Survey Area from the pop-up menu of the ArcGIS button, you will
get the same Transfer Options dialog shown in Figure 11-7. If you refresh your
connection in ArcCatalog after transfer, you will see the survey area polygon as
shown in Figure 11-10.

Figure 11-10 - Survey Area Polygon

If you switch ArcCatalog to Table view, you will see a single entry with the
appropriate computed shape length and shape area. The shape length is the length
of all boundaries in the polygon. The area is the computed area in square meters of
the object.
11.2.2.4

Transfer Bathymetry Raster

This option will transfer the currently extracted PFM surface as a single band ArcGIS
raster object. The single band will contain floating point values of the bathymetry.
When you select Transfer Bathy Raster from the pop-up menu of the ArcGIS button,
you will get the same Transfer Options dialog shown in Figure 11-7. If you refresh
our connection in ArcCatalog after transfer, you will see the bathy raster as shown in
Figure 11-11.
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Figure 11-11 - Bathymetry Raster

11.2.2.5

Transfer Bathymetry Image

This option will transfer the currently extracted PFM surface as a sun-illuminated 3band ArcGIS raster object. The three bands will contain RGB values of the sunilluminated image. When you select Transfer Image Raster from the pop-up menu of
the ArcGIS button, you will get the same Transfer Options dialog shown in Figure
11-7. If you refresh your connection in ArcCatalog after transfer, we will see the
bathy image raster as shown in Figure 11-12.

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Figure 11-12 - Image Raster

After all of these individual transfers, your workspace attribute panel will reflect all of
the recent workspace additions as shown in Figure 11-13.

Figure 11-13 - Workspace Using Individual Transfers

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11.2.2.6

Transfer Wizard

Another way to transfer data from a PFM is to use the Transfer Wizard option from
the ArcGIS pop-up menu. This will allow you to transfer all selected object types at
once as shown in Figure 11-14.

Figure 11-14 PFM Transfer Wizard

The name that you use will be used as a prefix for all of the objects. For example,
our Plotted Soundings object will be named Test_Plotted. Our BAG object will be
named Test_BAG. For this demonstration, the Feature Soundings option is deselected as this PFM has no tagged features. If you leave this object selected and
there is nothing to transfer, Fledermaus will simply not attempt to transfer that object
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type. After completion your workspace connection will be updated to show the
transferred objects as seen in Figure 11-14.

Figure 11-15 - Image Raster

11.2.3

Step 3 Loading ArcGIS Data to a Fledermaus Scene

Data can be transferred to a Fledermaus scene in a very simple manner. The

current object types available for transfer include ArcGIS feature class objects where
the geometry type is Point, Multipoint, Line, Polyline or Polygon. You can also
transfer raster dataset objects with 1-4 bands of data. For more information on
loading data from ArcGIS into a Fledermaus scene, see section 11.6.

Figure 11-16 Workspace Context Menu

To load ArcGIS data into a Fledermaus scene, right click on the object in the tree
view of the connected workspace to get the context menu shown in Figure 11-16.

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Figure 11-17 Load Feature to Scene Dialog

If the Load to Scene option is selected, this object will be loaded to your Fledermaus
scene. Depending on the object type, the Feature Loading dialog will allow you to
change the type of SD you will create. The configuration for loading a Point feature
class is shown in Figure 11-17.
The default name of the object is the name of the feature in the ArcGIS workspace.
You can enter a name for your object and then use the Field Mapping Options table
to determine which ArcGIS fields are mapped to the SD object type. Click on the
combo-box in the Mapping column to make appropriate changes. If you need to
modify any fields, such as negation, use the combo-box in the Modifier column of the
table.
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Once you are done, click the OK button and the ArcGIS feature class will be loaded
into your Fledermaus scene.

11.3

Creating ArcGIS Workspaces

This section describes how to create the various workspace types for ArcGIS
connectivity. Your first step is to create the workspace object by selecting the Add
ArcGIS Workspace option from the Create menu of Fledermaus as shown in Figure
11-18.

Figure 11-18 Fledermaus Create Menu

11.3.1

Folder Workspace

After you have created an ArcGIS Workspace object, select Folder from the
Connection group and click the Create button. Use the folder browse dialog to create
your new folder and click the OK button. A new empty folder workspace will appear
in the attribute panel tree view as shown in Figure 11-19. The Folder workspace is
not considered a database but instead a collection of shape and raster files.

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Figure 11-19 Folder Workspace

11.3.2

File Workspace

After you have created an ArcGIS Workspace object, select File from the Connection
group and click the Create button. Use the file save dialog to create your new .GDB
file and click the OK button. A new empty file workspace will appear in the attribute
panel tree view as shown in Figure 11-20. You should note that the File workspace
creates a folder with the extension .GDB. You should never manually edit the files
within this folder. The File workspace is a local file system geodatabase.

Figure 11-20 File Workspace

11.3.3

Personal Workspace

After you have created an ArcGIS Workspace object, select Personal from the
Connection group and click the Create button. Use the folder browse dialog to create
your new .MDB file and click the OK button. A new empty Personal workspace will
appear in the attribute panel tree view as shown inFigure 11-21. The MDB file is a
Microsoft Access database file. The Personal workspace is a local file system
geodatabase.

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Figure 11-21 Personal Workspace

11.3.4

ArcSDE Workspace

After you have created an ArcGIS Workspace object, select ArcSDE from the
Connection group and click the Create button. This is a bit confusing in that you are
not creating the workspace, but instead an object that contains your connection
information to the database (database name, username, login information, etc.).
When you connect to an ArcSDE database, you select the connection object (.sde)
and not a database. For this option, you must have already configured a workspace
using ArcCatalog within the database server you are using. The configuration dialog
is shown in Figure 11-22.

Figure 11-22 SDE Configuration Dialog

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Figure 11-23 SDE Workspace

After clicking the OK button, a new empty ArcSDE workspace will appear in the
attribute panel tree view as shown in Figure 11-23. The ArcSDE workspace can be a
local or remote SQL geodatabase.

11.4

Connecting to Workspaces

To connect to a previously created workspace, start by creating an ArcGIS

Workspace object as described in section 11.3. Then select the workspace type
from the Connection option on the attribute panel and click the Connect button. This
will bring up a File Open dialog where you can select a folder, .gdb, .mdb or .sde file
depending on the selected workspace type. Fledermaus will do an automatic toplevel query of your workspace and display the ArcGIS objects in the Features tree
view of the attribute panel as shown in Figure 11-24.

Figure 11-24 Workspace Connection

If the object in the Features tree view is a Raster Catalog or Feature Dataset, it is the
root node of a sub-hierarchy containing children. To query ArcGIS for these children,
right click on the object and select Get Children as shown in Figure 11-25.

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Figure 11-25 Get Children

When you have made the query, the tree view will fill in with the loaded child objects
as shown in Figure 11-26.

Figure 11-26 Get Children Complete

11.5

Transferring Data to ArcGIS

This section describes how to transfer data from a Fledermaus scene to ArcGIS.
Each SD object in a Fledermaus scene that is ArcGIS Aware will have an ArcGIS
button on the attribute panel. This will contain the pop-up menu with options for
transferring your data to an ArcGIS workspace. Transfer of specific SD types is
detailed in the following sections.
Transferring data to ArcGIS requires a connected workspace. Be sure that the
intended target workspace is in a connected state. The root icon will display with a
red X when disconnected as shown in Figure 11-27.

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Figure 11-27 Disconnected Workspace

11.5.1

SD Points

The SD Points object can be transferred to an ArcGIS feature class using the pop-up
menu on the ArcGIS button of the Points attribute panel as shown in Figure 11-28.

Figure 11-28 Points Attribute Panel

This will launch the ArcGIS Transfer Options dialog as shown in Figure 11-29. Select
an output name for the feature class which is unique to the workspace. Then select
the ArcGIS connection and the destination for the transfer.

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Figure 11-29 Transfer SD Points

Valid destinations for this object type include the workspace root as well as Feature
Dataset objects with the same spatial reference. Finally you can select the output
spatial coordinate system. Once the transfer is complete, a new node with the
selected name will be added to the workspace Features tree view. A completed
transfer of points to ArcGIS is shown in Figure 11-30. In this figure you see the
points as viewed in Fledermaus and ArcCatalog.
All attributes of the SD Points object are transferred as fields to the new feature class
object in your ArcGIS workspace. You can view these using the Table option from
the ArcCatalog Preview combo-box.

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Figure 11-30 SD Point Transfer

11.5.2

SD Lines

The SD Lines object can be transferred to an ArcGIS feature class using the pop-up
menu on the ArcGIS button of the Lines attribute panel as shown in Figure 11-31.

Figure 11-31 Lines Attribute Panel

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SD Lines can be transferred as either ArcGIS lines or ArcGIS polygons. Use the
pop-up menu option to select which geometry type to create on transfer. These
choices will launch the ArcGIS Transfer Options dialog as shown in Figure 11-31.
Perform the same operation as you did for transferring points.

Figure 11-32 Lines Transferred as Lines or Polygons.

Once the transfer is complete, a new node with the selected name will be added to
the workspace Features tree view. A completed transfer of lines to ArcGIS as lines
or polygons is shown in Figure 11-32. In this figure you can see the SD lines as
viewed in Fledermaus and the lines and polygons as viewed in ArcCatalog.

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11.5.3

R E F E R E N C E

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SD GeoImage

The SD GeoImage object can be transferred to an ArcGIS raster dataset using the
pop-up menu on the ArcGIS button of the Image attribute panel as shown in Figure
11-33. This will launch the ArcGIS Transfer Options dialog as shown in Figure
11-29. Perform the same operation as you did for transferring points and lines.

Figure 11-33 GeoImage Attribute Panel

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Figure 11-34 GeoImage Transferred as 1-Band or 3-Band

You have the additional option of selecting 1-band (grayscale) or 3-band (RGB)
raster formats. Once the transfer is complete, a new node with the selected name
will be added to the workspace Features tree view. A completed transfer of the
GeoImage to ArcGIS as 1-band or 3-band is shown in Figure 11-34. In this figure
you see the GeoImage as viewed in Fledermaus, and the 1-Band and 3-Band image
raster as viewed in ArcCatalog.

11.5.4

11.5.4 SD Surface

The SD Surface object has three options when transferring to ArcGIS. You can
transfer the Survey Area, Bathymetry Raster or Image Raster using the pop-up menu
on the ArcGIS button of the Surface attribute panel as shown in Figure 11-35.
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Figure 11-35 Surface Attribute Panel

Selecting Transfer Survey Area will launch the ArcGIS Transfer Options dialog as
shown in Figure 11-29. Perform the same operation as you did for transferring points
and lines. This option will transfer a single polygon object defining the boundaries
and holes of the SD Surface object. You can view the computed area of the DTM by
using the Table option from the preview panel of ArcCatalog. This area will be the
total area of the boundary polygon minus the area of the holes.
Selecting Transfer Bathy Raster will transfer the bathymetry information to ArcGIS as
a single band floating point raster.
Selecting Transfer Image Raster will transfer the sun-illuminated bathymetry image to
ArcGIS as a 3-band raster. If you have backscatter draped on top of the bathymetry,
this view will be transferred as the image (rather than the sun-illuminated bathymetry
colored by depth).
Once the transfer is complete, a new node with the selected name will be added to
the workspace Features tree view. A completed transfer of the Surface as Survey
Area, Bathy Raster or Image Raster is shown in Figure 11-36. In this figure you see
the Surface as viewed in Fledermaus, and the survey area, bathy raster and image
raster as viewed in ArcCatalog.

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Figure 11-36 Surface Transfer

11.5.5

SD PFM

The SD PFM object has several options when transferring data to ArcGIS. You can
transfer the Soundings, BAG, Survey Area, Bathymetry Raster or Image Raster
using the pop-up menu on the ArcGIS button of the PFM attribute panel as shown in
Figure 11-37. You can also do a batch transfer using the Wizard option.

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Figure 11-37 - Image Raster

Selecting the Transfer Soundings option will launch the ArcGIS Soundings Transfer
dialog as shown in Figure 11-38. This dialog is very similar to the one accessed from
the Tools button with the exception that you are not exporting to a disk file. To see
more on how this dialog operates, please see section 4.8 in the Fledermaus
Reference Manual.

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Figure 11-38 PFM Soundings Transfer Dialog

Selecting the Transfer BAG allows you to transfer Z-enabled points with an
uncertainty field. A BAG is a gridded file, and the points represent the grid node
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value for each cell and the associated uncertainty. Your PFM must have a Cube
surface to be able to do this. The transfer is very similar to a standard point transfer
with the exception that there is an additional field for the uncertainty.
Selecting the Transfer Survey Area option will transfer a single polygon object
defining the boundaries and holes of the currently loaded surface of the PFM. This is
similar to the survey area transfer for a Surface.
Selecting Transfer Bathy Raster will transfer the bathymetry information from the
loaded surface of the PFM. Again, this is similar to the bathy raster transfer from a
Surface.
Selecting Transfer Image Raster will transfer the sun-illuminated bathymetry image
from the loaded surface of the PFM. This is a 3-band RGB image raster, the same
as the image raster transfer from a Surface.
Selecting the Transfer Wizard will launch the ArcGIS Transfer Options dialog with the
PFM Transfer Options exposed as shown in Figure 11-39. This dialog allows you to
transfer all relevant PFM details at once. The feature class names will use the Name
field as the prefix followed by _Plotted, _Feature, _Area, _BAG, _Bathy, and _Image.
Note that Plotted soundings require that you have run a plotted soundings selection
filter. Feature soundings require that you have run a feature soundings selection
filter. The BAG transfer requires that your PFM have a Cube surface.

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Figure 11-39 PFM Transfer Wizard

Once the transfers are complete, new nodes with the selected names will be added
to the workspace Features tree view.
A completed transfer of the PFM as
Soundings, BAG, Survey Area, Bathy Raster or Image Raster is shown in Figure
11-40. In this figure you see the PFM in Fledermaus and the plotted soundings,
BAG, survey area, bathy raster and image raster as viewed in ArcCatalog.

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Figure 11-40 PFM Transfer

11.5.6

Interpretation

The SD Interpretation object can be transferred to an ArcGIS feature class using the
pop-up menu on the ArcGIS button of the Interpretation attribute panel as shown in
Figure 11-41.

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Figure 11-41 Interpretation Attribute Panel

This will launch the ArcGIS Transfer Options. Perform the same operation as you did
for transferring points and lines. The data from an SD Interpretation object will create
a polygon feature class in ArcGIS with appropriate sub-type information. There will
be a one table entry for each Key Name in the interpretation. The entries will be
displayed as polygons with holes in the correct locations. When viewing the Table
preview in ArcCatalog, the listed Shape_Area field will match the Area field shown in
the Interpretation Information table of the attribute panel.
Once the transfer is complete, a new node with the selected name will be added to
the workspace Features tree view. A completed transfer of interpretation data to
ArcGIS is shown in Figure 11-42. In this figure you see the interpreted polygons in
Fledermaus, and as viewed in ArcCatalog.

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Figure 11-42 Interpretation Transfer

11.5.7

SD Scalar

The SD Scalar object has three options when transferring to ArcGIS. You can
transfer the Survey Area, Scalar Raster or Image Raster using the pop-up menu on
the ArcGIS button of the Scalar attribute panel as shown in Figure 11-43.
Selecting Transfer Survey Area will launch the ArcGIS Transfer Options dialog as
shown in Figure 11-29. Perform the same operation as you did for transferring points
and lines. This option will transfer a single polygon object defining the boundaries
and holes of the SD Scalar object. You can view the computed area of the Scalar by
using the Table option from the preview panel of ArcCatalog. This area will be the
total area of the boundary polygon minus the area for the holes.
Selecting Transfer Scalar Raster will transfer the scalar information to ArcGIS as a
single band floating point raster.
Selecting Transfer Image Raster will transfer the scalar image to ArcGIS as a 3-band
raster.
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Figure 11-43 Scalar Attribute Panel

Once the transfer is complete, a new node with the selected name will be added to
the workspace Features tree view. A completed transfer of the Scalar as Survey
Area, Scalar Raster or Image Raster is shown in Figure 11-44. In this figure you see
the Scalar as viewed in Fledermaus and the survey area, scalar raster and image
raster as viewed in ArcCatalog

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Figure 11-44 Feature Tree

11.6

Scalar TransferLoading Data from ArcGIS

This section describes how to load ArcGIS data into a Fledermaus scene.
Fledermaus currently supports loading ArcGIS Raster Dataset and Feature Class
objects of certain geometry types. When an object type is recognized as loadable in
Fledermaus, the Load to Scene menu option of the workspace context menu will be
active as shown in . This menu option will launch the Feature Loading or Raster
Loading dialog as described in the following sections.

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Figure 11-45 Load to Scene

11.6.1

Feature Loading

ArcGIS feature class objects can be loaded into Fledermaus if they are Point,
Multipoint, Line, Polyline or Polygon geometry types. The geometry type will
determine the options for loading the data as a particular SD object.
11.6.1.1

Point Geometry

ArcGIS feature classes containing Point geometry can be loaded directly into
Fledermaus with their attributes. When Load to Scene is selected from the tree view
context menu, it will launch the Feature Loading dialog as shown in Figure 11-46.
The default name will be the name of the feature in the ArcGIS workspace. You can
enter a name for the SD object that will appear in your Fledermaus scene. For some
objects you can also change the SD type using the Load As combo-box. In the case
of Point geometry features, they can only be loaded as SD Point objects.
You can also change the output coordinate system so that the points get re-projected
on their way into the scene.
The final key piece is the Field Mapping Options table. This is where you specify the
source of the X, Y, and Z values of the 3D point. For example, some feature class
objects in ArcGIS may be only 2D with their Z component in one of the attribute
fields. Use the Mapping combo-box to set the mapping for each of the attributes you
wish to use. Color will let you color the points based on that attribute, while Label will
allow you to label the points based on that attribute. If None is selected, that attribute
will be ignored during the load process.
In the sample shown in Figure 11-46, we are mapping the Depth attribute to the SD
Point label.

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Figure 11-46 Point Loading Options

After proper sizing of the labels, draping to a DTM and a color change to solid white,
we can see the new SD object as loaded to Fledermaus in Figure 11-47.

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Figure 11-47 Points Loaded to Scene

If you select Other as a mapping option, that field will be mapped directly as a
named attribute in the new SD Point object. For example, your point feature may
have associated density, temperature, salinity with each point. You could use the
Other option to ensure these are mapped in as attributes of the Point object in your
scene. Currently, all numeric values in ArcGIS will be cast as floating point double
types within the SD Point object. A future update of the SD Point class will support all
ArcGIS numeric types without recasting.
11.6.1.2

Multipoint Geometry

Multipoint geometries are usually very large point datasets in ArcGIS. Attribution of a
multipoint object is at the collection leveleach individual point does not carry its
attributes with it. Attribution of SD Point objects is at the point leveleach point has
a set of attributes. Because of this difference, multipoint attributes do not carry
through when the points are transferred to Fledermaus. Therefore you are limited to
only X, Y and Z for your mapping options when loading multipoint objects as shown
in Figure 11-48.
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Figure 11-48 Multipoint Loading Options

11.6.1.3

Line & Polyline Geometry

Line and Polyline geometries are load to Fledermaus scenes as SD Line objects.
The Feature Loading dialog will only allow mapping of the X, Y and Z values as
shown in Figure 11-49.

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Figure 11-49 Line & Polyline Loading Options

After the line load is complete, we can see the new SD object as loaded to
Fledermaus in Figure 11-50.

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Figure 11-50 Lines Loaded to Scene

11.6.1.4

Polygon Geometry

Polygon geometry objects are loaded as SD Line or SD Interpretation objects. Use

the Load As combo-box to select which type. If the feature has sub-type information,
the default for the load is an SD Interpretation object as shown in Figure 11-51.

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Figure 11-51 Polygon Load as Interpretation

The color values are randomly chosen from a default color map as the workspace
does not expose color information. At this point you can double-click on the color
and the standard color picker dialog will launch allowing you to change the color. An
alternative method is to use the Color from template... button which will allow you to
select an SD Interpretation object from your file system to use as a template. The
feature loader will attempt to match the key field names to the ones in the template.
If a match is found, the color will be changed to the color saved in the template.

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After the line load is complete, we can see the new SD object as loaded to
Fledermaus in Figure 11-52.

Figure 11-52 - Interpretation Loaded to Scene

11.6.2

Raster Loading

ArcGIS raster dataset objects can be loaded into Fledermaus as a number of SD

object types depending on the number of bands that the raster contains. If the raster
is 3 or 4-Band, it can be loaded to Fledermaus as an SD GeoImage. If it has a single
band, it can be loaded as an SD GeoImage (Image), SD Scalar (Scalar), or SD
Surface (Surface). Use the Load as option on the Raster Loading Dialog as shown
in Figure 11-53 to select which object type to load. With a single band raster, you
also have the opportunity to invert (negate) the value that is stored in the raster. For
example, if your workspace raster has bathymetry stored as positive down, you need
to invert these values so that they will match the coordinate space of Fledermaus
which is Z down.

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Figure 11-53 Raster Loading

11.6.3

Other Workspace Operations

There are other operations that you can perform on a workspace when using the
right-click menu from the Features tree view. These are described in the following
sections.
11.6.3.1

Create Blank PFM

The Create Blank PFM option shown in Figure 11-54 is used to build a PFM without
adding any initial data files. Please see section 5.13.5 of the Fledermaus Reference
Manual for details on using this wizard. The major difference to the wizard as
described in section 5.13.5 is that the coordinate system and the bounds will be
automatically set by the spatial reference of the ArcGIS object you selected in the
workspace tree view.

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Figure 11-54 - Create Blank PFM

For our example, we will use points that were previously transferred to our ArcGIS
workspace. The first page of the wizard is shown in Figure 11-55 and is primarily for
setup of the PFM file name. If you would like to create a CUBE surface when the
PFM is generated, turn that on here as well.

Figure 11-55 - Create Blank PFM Wizard Page 1

The second page of the wizard shown in Figure 11-56 is for assigning the spatial
reference for the PFM that is created.

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Figure 11-56 - Create Blank PFM Wizard Page 2

The third page shown in Figure 11-57 sets up the X and Y bounds of your PFM.
These values are set by default to the workspace object that you right-clicked on.

Figure 11-57 - Create Blank PFM Wizard Page 3

The fourth page of the wizard shown in Figure 11-58 sets the minimum and
maximum depth range of your PFM. These values are set by default to the
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workspace object that you right-clicked on. It also sets the bin size, vertical reference
and CUBE parameters if CUBE processing was enabled on page 1 of the wizard.

Figure 11-58 - Create Blank PFM Wizard Page 4

The fifth page of the wizard shown in Figure 11-59 allows you to set custom
attributes for your PFM. When appending data to this PFM, you can map fields from
your ArcGIS feature to these custom attributes.

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Figure 11-59 Create Blank PFM Wizard Page 5

The sixth and final page of the wizard shown in Figure 11-60 allows you to set
custom flags for your PFM. When appending data to this PFM, you can map fields
from your ArcGIS feature to these custom flags. When you click Finish, the blank
PFM object will be created and added to your scene.

Figure 11-60 Create Blank PFM Wizard Page 6

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11.6.3.2

Append to PFM

The Append to PFM option shown in Figure 11-61 allows you to append soundings
from an ArcGIS workspace object to a PFM that is currently loaded in your scene.

Figure 11-61 Append to PFM

This option will launch the Select PFM dialog as shown in Figure 11-62. After you
have selected the PFM, the PFM Append Wizard will be launched.
The first page of the wizard show in Figure 11-63 allows you to change the selected
PFM. The second page of the wizard shown in Figure 11-64 allows you to determine
how the ArcGIS feature fields are mapped to the corresponding PFM fields, attributes
and flags. The final page of the wizard shown in Figure 11-65 allows you to set any
custom filters. Please see section 5.13.5 of the Fledermaus Reference Manual for
details on setting custom filters.

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Figure 11-62 Select PFM

Figure 11-63 PFM Append Wizard Page 1

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Figure 11-64 PFM Append Wizard Page 2

Figure 11-65 PFM Append Wizard Page 3

Once the PFM append operation is complete, your PFM object in the Fledermaus
scene will update to show the new coverage map as shown in Figure 11-66.

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Figure 11-66 PFM Append Coverage Map

11.6.3.3

Rename Object

The Rename Object option as shown in Figure 11-67 of the workspace context menu
allows you to rename a specific feature class. Certain feature classes, such as graph
or network feature classes, will have the Rename Object option disabled.

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Figure 11-67 Rename Object

11.6.3.4

Delete Object

The Delete Object option as shown in Figure 11-68 of the workspace context menu
allows you to delete a workspace object in your geodatabase. Occasionally the
object will not be able to be deleted due to a lock by another viewing application. If
this is the case, Fledermaus will return an error that the deletion could not be
accomplished. Certain feature classes such as network and topology feature classes
will have the Delete Object option disabled.

Figure 11-68 Delete Object

11.6.3.5

Add Dataset

The Add Dataset option as shown in Figure 11-69 will create a new ArcGIS feature
dataset object. This option is only available from the root node of the tree view.
When selected, it will launch a text entry dialog for you to name your feature dataset.

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Figure 11-69 Add Dataset

If you click OK, it will then launch a coordinate system edit dialog as shown in Figure
11-70. All objects added to this feature dataset in the future must have the same
coordinate system.

Figure 11-70 Feature Dataset Coordinates

You can now use this dataset as a destination when transferring data from
Fledermaus to ArcGIS as shown in Figure 11-71. In this example, we are
transferring plotted soundings from a PFM that were generated at a chart scale of
5000:1 to our newly created sounding feature. Once the transfer is complete, we can
see the new node added as a child of the feature dataset as shown in Figure 11-72.

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Figure 11-71 Feature Dataset Transfer Destination

Figure 11-72 Feature Dataset Tree View

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11.6.3.6

Add Raster Catalog

The Add Raster Catalog option as shown in Figure 11-73 will create a new ArcGIS
raster catalog object. When selected, it will launch a text entry dialog for you to name
your raster catalog.

Figure 11-73 - Image Raster

If you click OK, it will then launch a coordinate system edit dialog as shown in Figure
11-74. All objects added to this raster catalog in the future must have the same
coordinate system.

Figure 11-74 Raster Catalog Coordinates

You can now use this catalog as a destination when transferring raster data from
Fledermaus to ArcGIS as shown in Figure 11-75. You can also use the Add Raster
option described in 11.6.3.7 to add raster objects from another workspace, such as a
folder-based workspace. When transferring a new raster, Fledermaus will create a
raster object at the root level and then add an entry to the raster catalog as shown in
Figure 11-76.

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Figure 11-75 Raster Catalog Transfer Destination

Figure 11-76 Raster Catalog Tree View

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11.6.3.7

Add Raster

The Add Raster option allows you to add raster entries in a raster catalog. The raster
objects can be in any of your connected workspace objects. When selected, it
launches the transfer wizard so that you can select the raster object to insert as
shown in Figure 11-77. In this example we are selecting a raster contained in a
folder-based workspace. Once complete, we can see the raster entry in the catalog
of our file-based workspace as shown in Figure 11-78

Figure 11-77 Add Raster to Catalog

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Figure 11-78 Raster Catalog Entry

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Chapter 12 - FMMidwater

12.1

Introduction to FMMidwater

FMMidwater is a software program designed to rapidly extract relevant water column

features from a range of sonar file formats. Raw sonar files are first converted to a
Generic Water Column format (GWC) for use in further processing and visualization.
A simple graphical user interface is used to perform threshold filtering on a number of
key parameters to help with feature extraction. FMMidwater also provides multiple
views of the water column features and finally allows for easy export to a variety of
Fledermaus visualization objects and text files.
Use of the tool is broken up into four simple steps:

Import sonar file(s)

Convert to GWC format

Identify features of interest using threshold filtering

Export to Fledermaus for visualization or ASCII for custom processing

The following sections describe in detail how to use FMMidwater.

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FMMidwater Supported Data Formats

FMMidwater supports a range of file formats that contain water column time-series
data from either single beam or multibeam systems. Ancillary file types can also be
loaded to aid in processing. Currently supported sonar file types are is listed below.
Kongsberg (.all) Files Support for .all files containing datagram 0x6B. Example
sonars logging this file type include the EM 122, EM 302, EM 710, EM 2040, EM
3002 and ME 70.
Kongsberg (.wcd) Files Support for .wcd files containing datagram 0x6B.
Depending on the settings of the topside, water column data can be logged to a
separate file type while all other packets are logged to a .all file. If the .wcd file lacks
navigation and system configuration information, the user needs to additionally load
the matching .all file which contains required system configuration and navigation
data. This type of processing is explained in more detail in section 12.7.3.1.
Example sonar types are the same as the .all format.
Kongsberg / Simrad (.raw) Files Support for .raw files containing datagram
RAW0 datagram. Example sonars logging this file type include the ME 70, EK 60,
and ER 60.
Kongsberg / Simrad (.ek5) Files Support for .ek5 files containing datagram
0x3356 (VolumeBS_1), 0x3256 (VolumeBS_2) and 0x3356 (VolumeBS_3).
Example sonars logging this type include the EK 500.
Imagenex Delta-T (.83b) Files Support for .83b files containing datagram 83b
(Beam Output).
Reson (.s7k) Files Support for .s7k files containing datagram 7008 or 7018.
Example sonars include 7125 and 7101.
SEGY (.seg, .sgy, .segy) Files Support for SEGY files containing trace datagram.
Example sonars logging this type include EdgeTech Chirp systems. Typically, subbottom time-series data contains part of the water column prior to seabed
penetration. FMMidwater simply treats the sub-bottom channel as a single beam
echosounder.
DBM (.dbm) Files DeBeers mining format.
Triton Imaging (.xtf) Files Support for .xtf files containing Sonar (type 0) datagram
with sub-bottom channel.
POSPac (sbet*.out) Files POSPac data can be loaded as the navigation source
during the GWC file creation. This is explained in more detail in section 12.7.3.1.

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12.3

FMMidwater Interface

Figure 12-1 - FMMidwater User Interface

The primary user interface for FMMidwater is shown in Figure 12-1. The interface
can be divided into 9 primary tools that are detailed in Table 3.
Table 3 - FMMidwater User Interface

Main Menu Bar

The Main Menu Bar displays a number of options

for the program. This control is explained in detail
in section 0.

Source
Files/Visual The Source Files tab contains a list of all files
Objects Tree View
currently loaded for processing and visualization
within FMMidwater. The 3 major categories are
Sensor, Navigation and Midwater. All raw sensor
data will be loaded under the Sensor node. All
loaded external navigation (POSPac) will be
loaded under the Navigation node. All converted
GWC files will be loaded under the Midwater node.
All exported SD files will appear under the SD Files
node in the Visual Objects tab. This control is
explained in detail in section 12.8.

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Map View

The Map View displays an overhead view of all

loaded files containing navigation data. This view
works identically to the map view of DMagic.

Beam View Options

The Beam View Options on the display control

panel allow the user to change the Water Column
View as well as select threshold settings for beam
number, beam range and displayed depth. This
control is explained in detail in section 12.13.

Water Column View

The Water Colum View displays the currently

selected GWC file. This display supports Swath,
Polar, Stacked and Beam views of the water
column data. These views are explained in detail
in section 12.9. Polar view is reserved for future
support of radial ping sonars.

Time Bar Control

The Time Bar Control allows the user to move to

any point in time in the currently selected GWC file.
This control works identically to the Timeline
control found in Fledermaus. This control is
explained in detail in section 12.15.

Signal Options/Picking

The Signal Options tab allow the user to change

aspects of the displayed signal by adjusting the
histogram or changing the signal function. The
Picking tab allows the user to see the coordinates
of Picking Tool actions. This control is explained in
detail in section 12.14.

Tool Bar

The Tool Bar contains cursor modality controls for

the Map View and Midwater (Water Column
View). This control is explained in detail in section
12.11.

Status Bar

The Status Bar display current information about

the current Timeline or cursor position. This control
is explained in detail in section 12.16.

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12.4

Quick Start Guide

Getting up and running with FMMidwater is rather straightforward. In order to give

context to the following sections of the reference manual, we will first go through a
typical processing scenario using a line of EM 3002 data taken off the coast of New
Hampshire. This data comes from a survey that was done over a group of fish traps
suspended in the water column via mooring lines and anchorages. This file (.all)
contains all relevant packets required for processing.

12.4.1

Step 1 Create the Project

Use the File Menu described in section 12.7.1 to create a new project using the
Create Project Dialog (Figure 6-2). By default, the folder for your project will be in the
/Users/username/FMData/Projects directory. The created project will contain subfolders for storing interim processing data as well as converted GWC files and
exported visual objects. The complete directory structure is described in detail in
12.5.

Figure 12-2 - Create Project Dialog

12.4.2

Step 2 Add Source Files

FMMidwater converts sonar specific file formats to a Generic Water Column format
(.GWC) which contains full resolution or subsampled time series data in ping records
containing all relevant navigation information. These GWC files are then used as a
processing source for extraction relevant feature information from the water column.
To add source files, use the File Menu->Add Source Files option to select files for
processing. The user will then be presented with the wizard dialog show in Figure
6-3 and Figure 6-4. The first page of the dialog lets you select a list of files or a
directory containing your files. If you select a directory, the directory hierarchy,
including sub-folders, will be reflected in the project tree view as well as all of the
processing output folders. This is explained in more detail in section 12.5.

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Figure 12-3 - Add Files Wizard, Page 1

Figure 12-4 - Add Files Wizard - Page 2

The second page of the wizard allows you to select the coordinate system for the
navigation of the input files. In our example, this is simply geographic, WGS_84.
After selecting Finish, FMMidwater will perform some preliminary processing that is
required to proceed to the actual GWC conversion stage. FMMidwater will first index
the files as shown in Figure 6-5.
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Figure 12-5 - File Indexing

File indexing allows FMMidwater to access all datagram packets within a file in a
non-linear manner. This allows FMMidwater to process any part of a file without first
having to read all of the packets that came before. File indexing only occurs once
unless the index cache is cleared (see section 12.6 for details).
FMMidwater will then extract the metadata from each line as shown in Figure 6-6.
The metadata includes information such as file geographic extents, datagram packet
numbers, sonar modalities and sonar type.

Figure 12-6 - File Metadata

After the metadata is extracted, FMMidwater will compute the coverage and extract
the navigation of each line as shown in Figure 6-7. Finally, a visual representation of
each line is created as shown in Figure 6-8 for display in the FMMidwater MapView
(Figure 6-9).
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Figure 12-7 - File Coverage

Figure 12-8 - Swath SD

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Figure 12-9 - Files Loaded

As you can see, the files that were loaded appear in the Source Files tree view. The
checkbox next to each file serves a dual purpose. The first is to determine if the
object is to be displayed in the map view. The second, for source files, is to
determine if the file is to be used for any selected processing. This is a key part of
FMMidwater workflow. If a source is checked, it will be included in any processing. If
not, it will be ignored. You have many ways to check/uncheck files either using the
Check Select tool or the context menu Check options. These are described in
detail in later sections.

12.4.3

Step 3 Converting Files

The next step of the process is to convert the sonar file to the Generic Water Column
format (GWC). Conversion to GWC is done for a number of reasons. There are a
variety of raw sonar formats with a heterogeneous mix of packet logging and format
styles. Not only are the packets formatted differently depending on the manufacturer,
but the packets may not be complete. Due to intranet constraints during acquisition,
some of water column packets are actually broken up into multiple packets. Also,
navigation is stored in different packets. A GWC water column packet contains all
beam data in addition to navigation, attitude and calibration information. Another
reason for conversion to GWC is that during this step, the operator has the
opportunity to downsample the data. Some sonar models highly oversample their
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data which causes file sizes to be extremely large. For visualization purposes, the
full resolution is often not needed.
To start the conversion processes, go to the Tools menu and select Convert Sonar
Data. This will bring up the GWC Conversion Wizard. The first page of the wizard
(Figure 12-10) displays the checked files loaded into FMMidwater that contain water
column packets and are available for conversion. If you have loaded valid files,
simply proceed to the second page of the wizard.

Figure 12-10 - GWC Wizard - Page 1

The second page of the wizard (Figure 12-11) displays the relationship between the
source of water column packets and the source of navigation. FMMidwater attempts
to determine this based on the contents of the loaded data in the tool. For example,
if you are using external POSPac files, you could select these under the Navigation
Source column within the table. Under Navigations Options, you have the
opportunity to select navigation filtering for your data. Certain file types have very
slow navigation update rates and this smoothing filter can help the overall
appearance of the data. Typically, you would leave this off and proceed to the next
page of the wizard.

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Figure 12-11 - GWC Wizard - Page 2

The third page of the wizard (Figure 12-12) is where you select the level of
resampling that you want to do to the time series data for each beamthis is the
Downsample Factor. A value of 2 for example will reduce the time series data by
half. If you have 1000 samples per beam, the tool will take every 2 samples,
compute the maximum, and use that as the value with a new adjusted sampling
interval. If you selected 4, your data would be reduced to 250 samples and the
maximum value of every 4 samples would be used. Obviously selecting None will
leave the data in its full resolution state. Click Finish and your data will be
automatically converted to integrated water column packets in the GWC format.
They are called integrated in that they contain everything required for visualization.
This includes time series data for every beam, beam configuration information and all
navigation and motion parameters correlated to the ping time.

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Figure 12-12 - GWC Wizard - Page 3

After completion of the wizard, the processing dialog (Figure 12-13) will show the
progress of the file conversion. After the conversion completes, you will see the
GWC file added to the Midwater node of the Tree View and the Water Column View
will update to show you the first packet of the GWC file as shown in Figure 12-14.
This wizard is explained in detail in section 12.7.3.1.

Figure 12-13 - GWC Conversion Dialog

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Figure 12-14 - GWC Files Loaded

12.4.4

Step 4 Threshold Filtering

The next step of the process involves adjusting thresholds so that you can focus in
on the specific water column features that you want to export. The fastest way to do
this is to change the Water Column View to Stacked mode. Stacked mode presents
all of the data for the entire line in a single snapshot as seen in Figure 12-15. It is an
oblique view through the water column. Its as if the entire line was stretched out and
you were looking through the water column from a point perpendicular to the track.
The horizontal axis of this view is along track, with packet 0 at the far left and packet
N at the far right. The top of the display is at the transducer and the bottom of the
display is maximum range. The Stacked view takes all of the beams in the swath,
collapses them down together in an overlapped manner and displays the maximum
signal level for every discrete range increment in the display. This view is not
geometrically corrected and is intentionally distorted so that the operator can see as
many of the water column features as possible.

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Figure 12-15 - Stacked View

When in the Stacked View, you can easily zoom into a particular area by left-clicking
and dragging out a selection area within the view. When you release the mouse
button, the data is re-stacked to adjust to the new bounds of the display area. When
you do this, also notice that the Range composite slider in the Beam Options Panel
updates appropriately showing the new minimum/maximum displayed beam range.
To zoom out, simply select the zoom out button from the Midwater Toolbar.
In this view, one can easily see the fish traps suspended in the water column. Now
we need to remove the ambient noise from the water column. We can do this by
eliminating beams or changing the histogram thresholds.
The simplest way to do this is to adjust the histogram display in the Signal Options
Panel, using the composite slider. FMMidwater incorporates the use of composite
sliders as shown in Figure 12-16.

Figure 12-16 - Composite Slider

Each end of the slider can be clicked/dragged to change either the minimum or
maximum value of the threshold. The center of the control can also be
clicked/dragged to move the entire min/max over the desired range. Moving the
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minimum value of the histogram composite slider allows us to easily clip out the
background ambient noise. Notice that as you move this slider, you see the new
histogram (in magenta) that is the stretched histogram covering our color range.
Reducing the maximum will give you better color saturation. Leave the Clip
checkbox unchecked so that you clamp the data at the high end instead of clipping it.
When clipping below a minimum range, data will not be displayed or exported if it is
below the minimum value of the histogram settings. If clipping is off, all data below
the minimum range will be included in display and export but will be clamped to the
minimum color of the color map.
When clipping above the maximum range, data will not be displayed or exported if it
is above the maximum value of the histogram settings. If clipping is off, all data
above the maximum range will be included in display and export but will be clamped
to the maximum color of the color map.
At this point we are ready to export our data. The histogram control is explained in
detail in section 12.14.

Figure 12-17 - Final Stacked View

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12.4.5

R E F E R E N C E

M A N U A L

Step 5 Data Export

FMMidwater allows the operator to export to a number of visualization and

processing formats. Exporting of data is achieved through the File Menu by selecting
either the Export SD or Export Data sub-menus. Exporting of SD objects uses the
Export Dialog as shown in Figure 12-18. Typically, all of the appropriate values will
be selected by FMMidwater and the operator can simply hit the OK button and enter
an SD file name. Depending on the output format type, this dialog will show/hide
certain selectable options. This is further described in section 12.7.1.8. Additionally,
all FMMidwater generated SD objects must be in projected space. The source data
can be Geographic (latitude and longitude), but the output objects must be output in
projected space.
Once SD objects are exported, you can either load them into Fledermaus or doubleclick the SD object name in the Tree View under the SD Files node to open iView4D.

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Figure 12-18 - SD Export Panel

12.4.5.1

Exporting SD Objects Beam Fan Object

The Beam Fan SD object is a 4D visualization of the water column swath data. Once
exported, the SD object can be loaded into Fledermaus. The appearance of the
object is shown in Figure 12-19. This object is time aware in that as the time line is
moved in Fledermaus, the Beam Fan object will move through the scene. This
object is also know as a dynamic dependence object in that it is dependent on and
references a specific GWC file and updates its appearance by loading data from the
GWC appropriate to the current time indicated by the Fledermaus time bar. This is
different from most SD objects that are self-contained in that the SD file has all data
necessary for display within the visualization.

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Figure 12-19 - Beam Fan SD Object

12.4.5.2

Exporting SD Objects Beam Line Object

The Beam Line SD object is a 4D visual representation of a single beam from the
entire GWC file and is shown in conjunction with a Beam Fan object in Figure 12-21.
It is similar to a Vertical Curtain in that it contains imagery data with the addition of
being aligned to the beam angle at each point in time. It is also time aware so it
grows as the time bar is moved within Fledermaus.
A simple way to export this object is to use the Beam option from the Beam View
Options panel (Figure 12-20) and select the desired beam number. One could then
zoom in to a specific feature, threshold out the ambient noise and proceed directly to
exporting of the Beam Line.

Figure 12-20 - Beam View Options

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Figure 12-21 - Beam Line SD Object

12.4.5.3

Exporting SD Objects Point Object

The Point Object is a 4D visualization representation of the bore site (acoustic axis of
a directional sonar beam) positions of the filtered samples. Each point can be
attributed with signal level, time, ping and beam so that you can use Fledermaus to
change colors based on any of these attributes, including depth. When this object is
exported with time, it is time aware and grows according to the current time bar
position as shown in Figure 12-22.

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Figure 12-22 - Points SD Object

1.4.4.4 Exporting SD Objects Volume Object

The Volume Object (Figure 12-23) is a 3D brick that is divided into voxels of a userdefined size. This brick is grid-aligned and created by ray tracing the instantaneous
beam sample position from each filtered ping, beam and sample into the volume.
The highest signal level that intersects a voxel is used in the final volume. This
volume is then used by Fledermaus to render ISO surfaces based on an ISO level
chosen by the user.
The key to generating a good volume object is to have feature data that is spatially
coherent and reasonably dense. Good features to export as Volume Objects are fish
schools and the plumes detected from seafloor vents. You must choose a proper
voxel cell size during export; voxel cell sized is based on your beam spacing and
water depth. Cell size is defined on the SD Object Panel shown in Figure 12-18.

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Figure 12-23 - Volume SD Object

12.5

Project Files

FMMidwater uses an XML file and a folder hierarchy to store all of the relevant
information required for saving projects. When the project is created, you are
actually creating a system folder with the extension .fmproj. That folder will also
contain the XML file, fmproject.xml and all of the related folder hierarchies.

12.5.1

Creating Projects

When you create a project file, you are creating a directory structure where
FMMidwater will save metadata and the results from all of the processing stages.
Using the File->Create Project menu option, it will activate the Create Project Dialog
show in Figure 12-24.

Figure 12-24 - Create Project Dialog

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The default location for projects is in the Users/username/FMData/Projects folder on

your computer. A key step in defining the project is to define the FMMidwater
coordinate system that is used for all of the created data. For FMMidwater, this must
be a geographic coordinate system and not projected.

Grids
Ancillary

Images

Metadata

Vectors
GWC

my.fmproj

Navigation
Output
PFM

Source
SD
Figure 12-25 - Project Hierarchy

Once the project is created, a hierarchy of folders will be created as shown in Figure
12-25.
The primary folder at the top of the hierarchy will also contain the fmproject.xml file.
This XML file is a common structure that can be used by FMMidwater, FMGT and
DMagic to load projects. The key folders for FMMidwater are under the Output folder
and are used to store the interim data created by the file processing.

12.5.2

Opening Projects

When opening a project, you are actually using a folder browser dialog to find the
primary *.fmproj folder. If FMMidwater created the project, the data will be loaded
and will appear as you left it when you closed the project. If another application
created the project and this is the first time that you have opened it with FMMidwater,
you will be presented with the dialog shown in Figure 12-26.

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Figure 12-26 - Opening Other Projects

This is to ensure that the proper coordinate system is set up for the FMMidwater
project. As during project creation, you must select a geographic coordinate system
for your FMMidwater project.

12.6

FMMidwater Preferences

There are some general preferences that affect the operation of FMMidwater. To
access them, use the File Menu and select the Preferences option. This launches
the dialog shown in Figure 12-27.

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Figure 12-27 - Preferences Dialog General Tab

The General tab of the dialog allows you to control several key options. The first is
the Metadata option group. Use the Browse button to select a location for the
metadata that is generated when parsing sonar, GWC and navigation files. The
metadata is critical for accessing all the various packet types supported by
FMMidwater. If you ever suspect that you are having trouble reading a particular file,
or had a fault during reading, it is best to select the Force Rebuild option. This will
force FMMidwater to rebuild all metadata for files loaded in the current session. You
could also select Clear Cache to clear all metadata that has been created by
FMMidwater. Note that the Force Rebuild option does not persist as a preference if
you exit the application. This is to prevent unnecessary rebuilding of metadata each
time a file is loaded.
The Parallel Processing Setup section enables you to control how FMMidwater uses
multiple CPU cores. By default, it will use one less than the available hyper-threads
in the system to do the processing. If you wish to change this, simply click on
Manual and change to the desired number of cores.
The Startup Options section has 2 components. The first allows FMMidwater to ask
you to open the previous project after startup. By default this option is on. To disable
this feature simply uncheck the option. The second option allows FMMidwater to
attempt to recover processing after a fatal error. By default this option is on. To
disable this feature simply uncheck the option.
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The Rendering group allows you to force FMMidwater to render the real beam
pattern when Fan is the selected beam display option of the Water Column View.
Typically FMMidwater will compute an optimal beam spacing to reduce aliasing
during rendering of the beam fan.
The Colors option group allows you to select default colors for the Water Column
View background, the Map View background, the Zoom Box used during cursor
click-drag zooming and finally the Measure Box used during measurement
operations.
The Default Color Map is the color map used for displaying the water column data.
To change the color map, simply click on the button to the right of the color map
name text field.
The Default Signal Ranges section allows you to set default min/max values for all of
the signal options available in FMMidwater.
The Coordinates tab shown in Figure 12-28 allows you to select how FMMidwater
displays coordinates in the status bar.

Figure 12-28 - Preferences Dialog - Coordinates Tab

The Coordinate System group allows you to preset input/output coordinate

systems to simplify SD export. If the Auto-Compute checkbox is set, the output
coordinate system will be computed as the proper UTM zone for navigation data
of the GWC. If you wish to set a specific output coordinate system, or match the
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import geographic coordinate system, simply uncheck this box and select the
desired input/output projections.
The Format Specific tab shown in Figure 12-29 allows you to change options
related to specific format types. For now the only format that has additional
options is the SEGY format.
The Force Single Channel option will tell FMMidwater to ignore the SEGY
information on number of channels and treat each trace record as a sequence of
pings of the same channel.
The Force Fixed Length Trace option tells FMMidwater to use the trace length as
defined in the binary header as opposed to the trace length defined in the trace
header.

Figure 12-29 - Preferences Dialog - Format Specific Tab

12.7

Main Menu Bar

The main menu bar contains the File, View, Tools, Filter and Help menus.

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12.7.1

File Menu

Figure 12-30 - File Menu

The File Menu shown in Figure 12-30 is the primary menu used to both load data into
FMMidwater and export data to a variety of output formats. The detail of each menu
option is explained later in this section.
12.7.1.1

Create Project

This menu option creates a new project for FMMidwater. If you currently have a
project open, it will save and close the current project before creating a new one.
See section 12.5.1 for more on creating projects.
12.7.1.2

Open Project

This menu option allows you to open an existing FMGT project. If you currently have
a project open, it will save and close the current project before opening a new one.
See section 12.5.2 for more on opening projects.
12.7.1.3

Close Project

This menu option will save and close the current open project.
12.7.1.4

Add Sonar Files

This menu option will display a File Open dialog box where the user can choose
which sonar files (.all, .wcd, .raw, .s7k, etc.) to load into FMMidwater. This same
operation is accomplished through drag and drop of sonar files from the file system
onto the Map View control.

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12.7.1.5

Add Navigation Files

This menu option will display a File Open dialog box where the user can choose
which navigation files (sbet*.out) to load into FMMidwater. This same operation is
accomplished through drag and drop of navigation files from the file system onto the
Map View control.
12.7.1.6

Add GWC Files

This menu option will display a File Open dialog box where the user can choose
which GWC files (.gwc) to load into FMMidwater. This same operation is
accomplished through drag and drop of GWC files from the file system onto the Map
View or Water Column View.
12.7.1.7

Screen Capture

This menu option will display a File Save dialog so that the current Water Column
View is saved to an image file. Selectable file formats are TIFF, PNG, BMP and
JPEG. The output image size will be the size of the Water Column View control.
12.7.1.8

Export SD

This menu option has a sub-menu that allows you to select the output type for the SD
object. When you select an SD object, the Export Panel dialog is shown as in Figure
12-31. Depending on which SD object you select, certain parts of this dialog may be
hidden. See section 12.4.5 to see the type of SD objects you may export. The
majority of these values are filled in properly by the system with the exception of Cell
Size during Volume SD export; in most cases the user can simply click OK.
The Limits group shows you the currently selected ping and beam limits. These
values are filled in automatically by the program based on your selections. If you are
in stacked view and have zoomed, this will alter the ping limits. If you have changed
the beam composite slider or are in single beam view mode, the beam selection will
be updated accordingly. At this point, you can choose to override these values.
The Beam Stabilization group allows the user to indicate if the current sonar is pitch
and roll stabilized. This is used by the output transformation routines when exporting
the SD object.
The Z Offset group allows the user to add a Z offset to the exported SD. This can be
used to represent an instantaneous tidal value.
The Heading group allows the user to force the exported SD object to use computed
course made good values for the heading.
The Attributes group allows the user to determine if certain attributes will be exported
to the SD object. For instance, if Time is unchecked and the user is exporting a Point
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SD object, the object will not be time aware when displayed in Fledermaus. The
Beam attribute allows you to color points by their beam number in Fledermaus.
The Blanking group allows the user to blank data above, below or at the computed
nadir bottom detect. For example, if you have done a nadir bottom detect (see
section 1.6.6.3) on a single beam file, you can use blanking to easily remove
everything below the bottom detection when exporting a Beam Line object. The Bias
value is used differently by the three types of blanking. For example, if the bottom
detect value was 100m and the bias is 5m, blanking below will remove all data below
95 meters. Blanking Above will remove all data above 105 meters. Blanking at will
remove all data between 97.5 and 102.5 meters.

Figure 12-31 - Export Panel

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The Volume Options group is used exclusively by the Volume SD export. Cell Size
specifies the size of each voxel cell within the three-dimensional volume. Use Single
ISO exports all data at a constant maximum ISO.
The Volume Object is a 3D brick that is divided into voxels of a user-defined size.
This brick is grid-aligned and created by ray tracing the instantaneous beam sample
position from each filtered ping, beam and sample into the volume. The highest
signal level that intersects a voxel is used in the final volume. This volume is then
used by Fledermaus to render ISO surfaces based on an ISO level chosen by the
user or the chosen constant ISO value.
The key to generating a good volume object is to have feature data that is spatially
coherent and reasonably dense. Good features to export as Volume Objects are fish
schools and the plumes detected from seafloor vents. You must choose a proper
voxel cell size during export; proper voxel cell sized is based on your beam spacing
and water depth.
The ASCII Export group is used to select which values are exported during an ASCII
export session. This is explained in the following section.
The Input Coordinate System group shows the coordinate system of the current
GWC object, which is based on the coordinate system of the input sensor and
navigation files.
The Output Coordinate System group shows the coordinate system of the SD or
ASCII files you are about to export. If your Input Coordinate System is in geographic
space (latitude and longitude), this will default to the corresponding UTM zone.
Remember that all FMMidwater output SD objects must be in projected space.
12.7.1.9

Export Data

This menu option has a sub-menu that allows you to select the type of data you wish
to export. If you select ASCII, you will be presented with the export panel shown in
Figure 12-31. You can then decide which types of data you want to export in your
file. The output ASCII file will contain a file header explaining the contents of the file.
A sample file header is show in Figure 12-32. It will be followed by columns of all of
the data defined in the header.

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Figure 12-32 - ASCII Out

You can also select Navigation export. This will export an ASCII file containing time,
position X and position Y.
12.7.1.10

Export Contact

This menu option displays the Midwater Contact dialog box (Figure 12-33). This
menu option is active when you have measured an object of interest in the beam
view. It allows you to export a contact XML file with an associated JPEG image. The
JPEG will have your measured area of interest highlighted so that it can be viewed
in context as opposed to just exporting the image data inside the measured area.
The XML file will contain key information such as start/end vessel position, depth and
time of the measured area. You can also enter comments and observer information
for this contact. This menu option is intended for use with single beam sonars as no
position or depth transformations are done based on different beam angles when
viewing data from multibeam sonars.

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Figure 12-33 - Midwater Contact Dialog

12.7.1.11

Preferences

This menu option displays the Preferences Dialog.

information.
12.7.1.12

See section 12.6 for more

Recent Projects

This menu option allows easy access to recently opened projects.

12.7.1.13

Encapsulate Project

This menu option will copy all source material and external ancillary files into your
project directory hierarchy. The file links in your project XML file will also be updated
so that you can easily move the project to another computer.

12.7.2

View Menu

The View menu shown in Figure 12-34 sets the visibility of some of the FMMidwater
controls. Each menu option allows you to change the visibility of the corresponding
dockable area.

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Figure 12-34 - View Menu

12.7.3

Tools Menu

The Tools menu shown in Figure 12-35 contains processing controls for
FMMidwater. The detail of each menu option is explained later in this section.

Figure 12-35 - Tools Menu

12.7.3.1

Convert Sonar Data

This menu option starts the GWC conversion wizard explained in section 12.17.
12.7.3.2

Integrate New Navigation

This menu option is used if you have externally re-processed navigation data that
you want to integrate into an already existing GWC file. The file format must be one
that FMMidwater supports. After loading, FMMidwater will use time tag matching to
replace the current navigation in the GWC file with the selected navigation.
12.7.3.3

Plot Selected Area

This menu option is used to plot a vertically projected view of the water column data
onto the selected area of the map. It is important to threshold-out excess data and
and restrict your location prior to using this tool. To do this, use the following steps:
First, get your data properly filtered in your stacked view by adjusting the appropriate
thresholds (Figure 12-36).
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Figure 12-36 - Fish Traps - Stacked View with Thresholds Applied

Next, move the time bar control so that the vertical time bar bar appears at the center
of your stacked view. Notice where the ship position appears in your map view and
use the Select button on the Map toolbar to put the cursor into select mode. Click
and drag a selection around your current vessel position to tell the system what area
to plot as shown in Figure 12-37.

Figure 12-37 - Map View - Selected Area

Once you have the area selected, choose the Plot Selected Area menu option to plot
the water column data as shown in Figure 12-38.
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Figure 12-38 - Map View - Plotted Water Column Data

The data is plotted at the resolution of the current Map View. If you want a higher
resolution plot, simply zoom in to the level you want.
12.7.3.4

Nadir Bottom Detect

The Nadir Bottom Detect method allows you to easily pick a rough bottom track that
can be used for Blanking (see Figure 12-31) during SD export. This is especially
useful when you are trying to export a water column feature close to the seabed,
where the seabed has a noticeable slope. When this is the case, having a square
select in the Stacked View will not prevent you from exporting some unwanted
bottom information.
To use this function, you must first have the Water Column View in Beam mode. If
you are using multibeam data, be sure to select the nadir beam. In our example, we
will use some single beam EK 60 data as shown in Figure 12-39.

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Figure 12-39 - Nadir Detect - Step 1

Figure 12-40 - Nadir Detect Step 2

Next, use the composite slider to adjust the histogram minimum value (Figure 12-40)
so that everything is eliminated from the view except the bottom track. You can also
adjust the Range composite slider so that the seabed is more vertically centered as
shown in Figure 12-41.

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Figure 12-41 - Nadir Detect Step 3

Now simply select Nadir Bottom Detect from the menu and the result will appear as a
red line in the Water Column View as show in Figure 12-42. The computed bottom
detection is saved in the GWC file for later use.

Figure 12-42 - Nadir Detect - Step 4

Now re-adjust the histogram so that you get your features back in the Water Column
View but still have the noise eliminated. In our single beam example, we can now
export a Beam Line object, being sure to select Below from the blanking option in the
export panel. The SD loaded into Fledermaus appears in Figure 12-43.

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Figure 12-43 - 'Blanked' Beam Line SD

12.7.3.5

Clear Nadir Detect

This menu option will clear the nadir detection stored in the GWC from a previous
Nadir Detect operation.
12.7.3.6

Edit Sensor Configuration

This menu option will launch the Vessel Configuration dialog shown in Figure 12-45.
This dialog displays all of the installation information relating to the selected GWC
file. You can change any of these values and they will be saved to the GWC file.
This data is very important for proper geo-location of the exported feature detections.
Typically this data comes directly from the processed source file. If the source file
contains no configuration data, you must ensure that you enter the proper values for
export. The coordinate system of a GWC is shown in Figure 12-44.

Figure 12-44 - Vessel Reference Frame

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The X-axis is alongship positive out the bow. Roll is around the X-Axis with positive
roll resulting in port side up. The Y-axis is athwartship positive to starboard. Pitch is
around the Y-Axis with positive pitch resulting in bow up. The Z-axis is positive
down. Heading is positive clockwise about the Z-axis.

Figure 12-45 - Sensor Configuration Dialog

Note that linear offsets are all in meters and angular offsets are all in degrees. There
is also separation between Transducer 1 and Transducer 2 configuration to support
dual-head systems.
12.7.3.7

Plot Heading/CMG

This option launches a Plot Dialog that plots the heading and course made good
(CMG) value as shown in Figure 12-46. When the cursor is moved over the surface,
the current location is displayed in the text window below the plot. The color buttons
on the right of the dialog allow you to turn on/off a particular plot. Simply click and
drag a selection rectangle to zoom in on a section of the plot. To zoom out, click on
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the

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icon. To save the plot to an image file, click on the

settings for the plot dialog, click on the

shown in Figure 12-47.

icon. To change

icon. This will bring up the settings dialog

Figure 12-46 - Plot Dialog

You can change the labels on the Y-Axis by typing in the text boxes. You can also
change the color of the plotted line by clicking on the color button next to the text
label.

Figure 12-47 - Plot Settings

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The X-Axis label can be changed by typing a new label in the text box.
Finally, change the axis limits to set the zoomed out X/Y range of the plot. You can
also invert the Y axis by clicking the Invert checkbox.
12.7.3.8

Plot Pitch/Roll

This launches the same plot dialog as section 12.7.3.7 except this time it will plot
pitch and roll data from the GWC.
12.7.3.9

Plot Heave

This launches the same plot dialog as section 12.7.3.7 except this time it will heave
data from the GWC.

12.7.4

Filter Menu

The Filter menu shown in Figure 12-48 contains filter controls for FMMidwater. The
detail of each menu option is explained later in this section.

Figure 12-48 - Filter Menu

12.7.4.1

AGC

The AGC (Automatic Gain Control) option is used to clean the imagery from subbottom chirp systems. An example of the before and after effects of using the AGC
filter can be seen in Figure 12-49 and Figure 12-50 (Data courtesy of USGS).

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Figure 12-49 - Chirp Data - No AGC

Figure 12-50 - Chirp Data - With AGC

12.7.4.2

Beam Control

This option launches the Beam Selector dialog shown in Figure 12-51. This dialog
will explicitly turn beams on or off; this controls whether or not the beams are used in
the water column visualization and consequently in any exported data. The Save
button in the dialog can be used to save the configuration to a .bcf file and the Load
button can be used to load a previously stored configuration. This dialog is especially
handy for sonars with overlapping beam configurations.
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Figure 12-51 - Beam Selector Dialog

12.7.5

Help Menu

The Help menu is shown in Figure 12-52.

explained later in this section.

The detail of each menu option is

Figure 12-52 - Help Menu

12.7.5.1

Online Help

This menu option will open up a browser window with the current FMMidwater
documentation.
12.7.5.2

IVS Homepage

This menu option will open up a browser window to the IVS homepage.
12.7.5.3

About

This menu option will display a dialog with the current version and build information
for FMMidwater.

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12.8

R E F E R E N C E

M A N U A L

Tree View

The Tree View control shown in Figure 12-53 is where you can see a list of the
currently loaded source and navigation files as well as the processed GWC files and
exported SD files.

Figure 12-53 Source Files Tree View

12.8.1

Source Files Sensor Node

This node will list all currently loaded sensor files. If you click on the caret next to the
filename, you will expose the packet counts for each packet type found in the sonar
file. Packet types are defined by the particular sonar manufacturers specification.
When a sensor file is selected that contains navigation data, the corresponding
navigation line in the Map View is highlighted. Conversely, if you select a line in the
Map View, the appropriate node will be highlighted in the Tree View. The checkbox
next to the file name is used to show/hide the line rendering in the Map View. It is
also used to indicate which files you want to send to the GWC Wizard when you start
the conversion process.
When you right click on an item of the Sensor Node, you will activate the context
menu for this item type as shown in Figure 12-54.
The Add Sonar Files menu option is performs the same task as the primary File
menu option described in section 12.7.1.4. The Remove menu option will remove
the currently selected item. The Remove All option will remove all nodes under the
root node. The Find option is used the find source files that have been inadvertently
moved on disk. If a source file is moved after the FMMidwater project is created, you
can use this option to reconnect the file. FMMidwater will then attempt to reconnect
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all files in the same relative folder as the file you picked. The Check All menu option
checks all files under the root node. The Uncheck All will uncheck all files under the
root node. The Check Only option checks only the currently selected item. The
Check All Except checks all items except for the currently selected item. Remember
that checked items are the only ones used for processing. The Edit Coordinate
System option is used to change the coordinate system of a source file in the project.

Figure 12-54 - Sensor Node Context Menu

12.8.2

Source Files Navigation Node

This node displays the currently loaded external navigation files.

currently supports only POSPac navigation files.

FMMidwater

When you right click on an item of the Sensor Node, you will activate the context
menu for this item type as shown in Figure 12-55.
The Add Nav Files menu option is performs the same task as the primary File menu
option described in section 12.7.1.5. The Remove menu option will remove the
currently selected item. The Remove All option will remove all nodes under the root
node. The Check All menu option checks all files under the root node. The Uncheck
All will uncheck all files under the root node. The Check Only option checks only the
currently selected item. The Check All Except checks all items except for the
currently selected item. Remember that checked items are the only ones used for
processing. The Edit Coordinate System option is used to change the coordinate
system of a source file in the project.

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Figure 12-55 - Navigation Node Context Menu

12.8.3

Source Files Midwater Node

This node contains all of the loaded (either explicitly loaded or converted during the
current session) GWC files. Clicking on the caret next to the file name shows the
packet information for the particular GWC file. Once a GWC file has been created,
you no longer need the original source files and you can simply load the GWC in a
future working session.

12.8.4

Visual Objects SD Files

This node displays the current SD files exported in the current session. Doubleclicking on one of these nodes will launch iView4D with the designated SD file.
When you right click on an item of the Sensor Node, you will activate the context
menu for this item type as shown in Figure 12-56.

Figure 12-56 - Midwater Node Context Menu

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The Add GWC Files menu option is performs the same task as the primary File
menu option described in section 12.7.1.6. The Remove All option will remove all
nodes under the root node. The Check All menu option checks all files under the
root node. The Uncheck All will uncheck all files under the root node. The Check
Only option checks only the currently selected item. The Check All Except checks all
items except for the currently selected item. Remember that checked items are the
only ones used for processing. The Plot menu options plot navigation information
found in the GWC file. Use of the Plot Widget is described in section 6.13. The Edit
Coordinate System option is used to change the coordinate system of a source file in
the project.

12.9

Water Column View

The Water Column View has 3 primary modalities. These are the Fan, Stacked and
Beam view. Polar view is reserved for future support of radial ping sonars. These
views are used to see the water column features from different viewpoints to aid in
the threshold filtering step of water column processing. This view is active when you
have a GWC file selected from the Tree View control. To change the current view,
use the radio buttons at the top of the Beam View Options panel as shown in Figure
12-57.

Figure 12-57 - Beam View Options

12.9.1

Water Column View Fan

This view is a traditional along-track view of the water column data. The viewpoint is
from directly astern looking towards the bow and underwater. Port side is on the left
of the screen, starboard to the right of the screen. Moving the time bar control will
change the fan display to the appropriate ping in the GWC file.
You can zoom on this display by click-dragging a selection rectangle on the view as
shown in Figure 12-58. When you do this, you will notice that the Depth composite
slider updates appropriately to indicate to currently zoomed depth range. To zoom
out, click on the Zoom Out button on the Midwater toolbar.
As you move the cursor over this view, the status bar will update with the
approximate depth at this location. The depth is relative to the transducer head at
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zero and uses the sound speed at the transducer head to compute the depth. At this
time, it does not account for linear offsets, vessel motion or refraction.

Figure 12-58 - Fan View Zooming

12.9.2

Water Column View Beam

This view provides a complete look at the time series data for an entire line, from one
beam. Use the Beam View Options spin control to select the beam number. The
horizontal axis of the view is along-track, with ping 0 at the left of the window and
ping N at the right. The top of the view is the minimum range. The bottom of the
view is the maximum range as set by the Range composite slider in the Beam View
Options panel.
You can zoom on this display by click-dragging a selection rectangle on the view as
shown in Figure 12-59. When you do this, you will notice that the Depth composite
slider updates appropriately to indicate the currently zoomed depth range. To zoom
out, click on the Zoom Out button on the Midwater toolbar.

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Figure 12-59 - Beam View Zooming

12.9.3

Water Column View Stacked

This view is similar to the Beam view described above with the exception that you are
seeing all time series information from all currently selected beams stacked on top
of each other. There is no geometry correction for beam angle so it is as if all beams
are collapsed to nadir. The stack uses and displays the maximum signal level at a
given time based pixel. This allows the user to see all of the water column data in a
single snapshot.
The horizontal axis of the view is along-track, with ping 0 at the left of the window and
ping N at the right. The top of the view is the minimum range and the bottom of the
view is the maximum range as set by the Range composite slider in the Beam View
Options panel. The beam data used for the stack is determined by the Beam
composite slider settings in the Beam View Options panel. If you want to change the
beams used, simply go back to the Fan view, change the composite slider settings,
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and then return to the Stacked view. The Beam composite slider is locked while in
stacked view due to the computational requirements for re-stacking.
You can zoom on this display by click-dragging a selection rectangle on the view as
shown in Figure 12-60. When you do this, you will notice that the Depth composite
slider updates appropriately to indicate to currently zoomed depth range. To zoom
out, click on the Zoom Out button on the Midwater toolbar.
As you move the cursor over this view, the status bar will update with the range and
signal amplitude at this location. The range is beam relative with zero range at the
transducer head.

Figure 12-60 - Stacked View Zooming

12.10 Map View

The Map View displays the navigation data from the current lines loaded in
FMMidwater. If you have a GWC line selected in the Tree View, it will also indicate
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the current vessel position as shown in Figure 12-61. As you move the time bar
control, the vessel position indicator will update.

Figure 12-61 - Vessel Position

To pan within the view, simply click and drag the map. To zoom, use the mouse
scroll wheel to zoom in and out. To reset the Map View display, simply click on the
Reset Camera button in the Map toolbar.
If you single click in the display, the system will select the closest track line and
highlight it in the Tree View.
The Map View is also a dockable control. Click and drag on the control title bar to the
left of the map to float it outside the main application window. To dock, just drag it
over the main application window until the docking box highlights. Release the
mouse button and the control will dock.

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12.12 Tool Bar

The tools bar shown in shown in Figure 12-62 is used to control both the Map View
and the Water Column View. The top half of the tool bar controls the Map View while
the bottom half of the tool bar is for the Water Column Display.

Figure 12-62 - Tool Bar

12.12.1
12.12.1.1

Map View Tools

Reset Camera

This tool button will reset the Map View such that the entire scene will be visible.
12.12.1.2

Zoom to Object

This tool button will zoom the scene to the currently selected survey line.
12.12.1.3

Explore

This cursor mode is the default mode used to navigate within the current map view
as explained in section 12.10.
12.12.1.4

Select Area

This cursor mode is used to select an area of the map that will be used for plotting
with the Plot Selected Area tool.

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12.12.1.5

Measure

The measure cursor mode is used to measure a straight line distance in the map
view. Left-click and drag between the desired spatial points and the status bar of
FMMidwater will display the associated distance.
12.12.1.6

Clear Selection

This tool bar button will clear the current selection in the map view.
12.12.1.7

Show Bounds

This too bar button will turn on/off the display of the scene bounding box.
12.12.1.8

Show Selection Highlight

This tool bar button will turn on/off the display of the selection box.

12.12.2
12.12.2.1

Water Column View Tools

Reset Camera

This tool button will reset the Water Column View such that the entire fan, beam or
stacked view will be visible.
12.12.2.2

Explore

This cursor mode is the default mode used to see current navigation and depth or
range on the status bar as you move your cursor over the water column view. You
can also click/drag a selection rectangle for zooming in any of the views.
12.12.2.3

Pan

This cursor mode allows you to pan around either the beam or stacked view. This is
only available when you have more data to display then can fit in the currently
selected zoom window. To pan, simply click and drag the display. When you
release the mouse button, the display will refresh with the new location. You will be
prevented from panning past the top, bottom, left or right of the min/max data range.
When in Explore mode, you can also pan by using the arrow keys. This will pan the
display 50% of the current zoom view.

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12.12.2.4

Select

M A N U A L

This cursor mode allows you to select a non-rectangular area in either the Beam or
Stacked views for use during SD exporting. Just click out an area for export as
shown in Figure 12-63.

Figure 12-63 - Area Select Tool

12.12.2.5

Pick

This cursor mode allows you to do geo-picking in the fan or beam view as shown in
Figure 12-64.

Figure 12-64 - Beam View Picking

As you pick features, the Picking tab of the Signal and Picking control panel will fill
with the appropriate coordinates. You can then use this panel to export as SD
objects or to an ASCII file. See section 12.18 for more information.

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12.12.2.6

Measure

The measure cursor mode allows you to measure between two points in the Stacked
or Beam view as shown in Figure 12-65. The status bar will show the along-track
distance (dX), beam range (dZ) and time difference (dT) between the points.

Figure 12-65 - Measure Tool

12.12.2.7

Clear Selection

This tool bar button will clear the current measured area in the water column view.
The Zoom Out tool will zoom the current display out one level.
maintains a stack of viewing rectangles as you zoom into a feature.

FMMidwater

The Show/Hide mask tool allows you to suppress data from displaying in the Fan
view if it is outside of the beam or range limits. Figure 12-66 shows the mask tool off
in the left image (default) and on in the right image. Masking can speed rendering for
high resolution data sets during time bar playback or time bar dragging.

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Figure 12-66 - Mask Tool Show/Hide

The 1:1 tool button changes the horizontal zoom range of the display so that you get
1 ping per pixel in the horizontal axis. The vertical range will still be distorted. Note
that if you change the size of the viewing window, you must click the 1:1 button again
to get 1 ping per pixel.

12.13 Beam View Options

The Beam View Options panel shown in Figure 12-67 allows you to change the
water column view and set a number of key threshold values for reducing the water
column data you may export.

Figure 12-67 - Beam View Options

At the top of the panel are the controls for changing the display mode of the Water
Column View panel. The current options are Fan, Stacked and Beam view. Polar
view is reserved for future support of radial ping sonars. When Beam view is
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selected, there is a spin control to change the beam number. The button at the far
right will launch the Beam Selector dialog as described in section 12.7.4.2.
The three composite sliders are used to set min/max thresholds for the beams used,
range used and depth used. Each end of the sliders can be click/dragged to change
either the minimum or maximum value of the threshold. The center of the control can
also be click/dragged to move the entire min/max over the desired range. You can
also click the button to the right of the composite slider, which will launch a dialog for
you to enter the min/max values directly.
The Beam composite slider is only enabled while in Fan mode. As you change the
min/max values for this slider, you are eliminating beams for use during the export
process. Prior to export, check the water column view to remind you of your
changes. The data outside of the limits will be slightly transparent and desaturated.
The Range composite slider is available in all view modes. It sets a near and far
range limit for your data processing.
The Depth composite slider is only enabled while in Fan mode.

12.14 Signal Options

The Signal Options panel shown in Figure 12-68 controls the computed value of the
time series data displayed in the water column view. It is also a key control used to
reduce the amount of low-level signal that appears in the visualization and
consequently in any SD objects that are exported.
The top of the control allows you to change what you are viewing in the water column
view. The default is Amplitude. This is the raw time series sample value present in
the source sonar file. The second option is Power (in dB). This is a computed value
and is a function of the type of sonar used. The third value, Sv (volume backscatter
in dB), is only available for calibrated sonars such as the Kongsberg ME-70. This
changes the water column view to show volume scattering. The final option, Ts
(target strength in dB), is also only available for calibrated sonars and changes the
display to show target strength. As you select the different modes, the histogram will
update accordingly.
The next part of the control is the color map. These are the colors that are mapped
across the stretched histogram. To select a new color map, simply click on the
button to the right of the color map display.
The next section of the panel is the histogram display. The cyan histogram is the
base histogram for the currently loaded file. As you change the composite slider
below the histogram, you will see a magenta histogram that represents the
stretched part of the histogram that you have selected. The vertical cyan dotted
lines represents the portion of the main histogram that your are stretching.
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The Clip check boxes on the left and right of the histogram allow you to either clip or
clamp signal values outside of the minimum or maximum of the composite slider.
This allows you to clip or clamp data to the minimum and maximum limits. Clipping
eliminates data while clamping. During minimum clamping, if value is less than the
minimum limit, the value is set to the minimum value. During maximum clamping, if
the value is greater than the maximum limit, the value is set to the maximum limit.
The Lock button will cause these settings to be used for all currently loaded GWC
files.

Figure 12-68 - Signal Options Panel

The composite slider at the bottom of the panel is used to set min/max thresholds for
the type of signal that is used. Each end of the slider can be click/dragged to change
either the minimum or maximum value of the threshold. The center of the control can
also be click/dragged to move the entire min/max over the desired range. You can
also click the button to the right of the composite slider, which will launch a dialog for
you to enter the min/max values directly.

12.15 Time Bar

The time bar control shown in Figure 12-69 is the same control used in Fledermaus.
Please see section 2.4 in the main Fledermaus Reference Manual for details on
using this control.

Figure 12-69 - Timeline Bar

12.16 Status Bar

The status bar at the bottom of the GUI is used to display cursor information.
Depending on the part of the GUI that the cursor is over, the status bar will update
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accordingly to show things such as current geographic location, depth, or range. The
button to the right of the status bar allows you to pop-up a Cursor Info window as
shown in Figure 12-70 that can be used to provide more detailed information while in
Beam or Stacked view. This window also shows the current zoomed location of your
display.

Figure 12-70 - Cursor Info Dialog

12.17 Converting Source Files to GWC Format

Before any analysis of water column data can occur, FMMidwater must first convert
the source files to the GWC file format. Using the Tools->Convert Sonar Data option,
you launch the conversion wizard shown in Figure 12-71 thru Figure 12-73. The
majority of the options for this wizard are set by the system, based on extracted
metadata of the files. The user is given the opportunity to make changes on each
page of the wizard.

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Figure 12-71 - GWC Wizard - Page 1

The first page of the wizard displays currently loaded sonar files that contain water
column packets. On this page you can deselect files for processing or add more files
using the Add Files button. Once you are satisfied with the settings on this page,
simply click the Next button. To cancel, click the Cancel button.

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Figure 12-72 - GWC Wizard - Page 2

The second page of the wizard allows you to correlate water column files with the
files that contain the proper navigation. Typically these files will have the same file
names, with different extensions. Some topside systems break out acquisition into
two files so that water column packets are in one and all the other packets are in
another. An example of this is the Kongsberg .all and .wcd file pair. In some cases,
the water column files and navigation files will be the exact same file. This occurs
when water column packets and all required navigation and configuration data are
contained in the same file. Finally, the combo box in the Navigation Source column
allows you to change the selection on the navigation source, in the case that the
system chose the wrong file or no file could be found.
The Navigation Options group allows you to first select the source of the navigation.
FMMidwater has 3 options for this.
The Use File option is for using a single external navigation file for all water column
source files. This option is useful if you are recording and processing a single
POSPac file for an entire day of survey operations where you have logged multiple
water column files.
The Use Selected option is the default option and will use the matched navigation file
as listed in the main area of the dialog.
The No Navigation option allows you to process the data without navigation. You will
not be able to export data from these GWC files until you integrate proper navigation.
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For information on how to do integrate navigation into an existing GWC file, see
section 12.7.3.2.
The Nav Smoothing option allows you to enable a box-car (simple window-based
moving average) filter for smoothing navigation information. Typically this is not
used, but if required, it will help smooth out poor navigation. Just click on the
checkbox and enter a box-car window size.

Figure 12-73 - GWC Wizard - Page 3

The final page of the wizard allows you to select a downsample amount for the time
series data. Resampling is only done on the time series and not on the beam count
or number of pings. A factor of 2 (2:1) resample will reduce the number of samples
in a beam by one half. It will take every two samples and preserve the maximum. It
will also properly adjust the sample interval within the GWC file so that the samples
appear in the correct location.
The Transducer Selection is used for multi-channel systems. A GWC file can contain
data from only 1 transducer source. This option allows you to select which
transducer to use.
The file name of the GWC will reflect both of the above selections. For example, if
the source file name was 0005_20040617_145627_Pingeline.all, the output GWC
file name will be 0005_20040617_145627_Pingeline_R2_CH1.gwc. The R2
signifies the resample amount and the CH1 signifies channel 1.
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The Concatenation option allows you to export a single GWC file from all of the
currently loaded source files. This is especially useful for topside software that
changes file names based on a small disk size when acquiring lines. The system
virtually concatenates the metadata from all of the source files, and uses that to
export a single processed GWC file. You must remember to enter an output
filename for this option. For this option, the data must have non-overlapping times
and some relative time coherency.

12.18 Picking Features for Export

The Picking tool described in section 12.12.2.5 is used to extract water column
features to another format or file. To use the tool, you must be in fan or beam view.
The stacked view cannot be used as the picked beam becomes ambiguous and you
cannot extract the proper position. As you pick features as shown in Figure 12-74, a
circular highlight appears in the window.

Figure 12-74 - Feature Picking

As you pick, the corresponding coordinates will appear in the table of the Pick tab as
shown in Figure 12-75

Figure 12-75 - Pick Table

To export the points as a line or point SD object, simply use the Table Action combo
box. You can also use the Export button to export to a standard X,Y,Z ASCII file.

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To clear the table, click the Clear All button or select some of the table rows and click
on the Clear Selected button.

12.19 Plotting Widgets

All plotting widgets have the same capabilities. The plot widget for roll and pitch of a
selected file is shown in Figure 6-106. As you move your cursor over the plotting
area, the cursor location values update in the text box at the bottom of the widget.

Figure 12-76 - Plot Widget

You can zoom into a portion of the plotting area by click-dragging a selection on the
plot surface as shown in Figure 6-107.
If you wish to zoom back out, simply click on the zoom out icon
the plot widget.

in the toolbar of

If you wish to save the current plot to an image, simply click on the Save As icon
the plot widget tool bar.

of

The settings icon

will bring up the settings dialog as shown in Figure 6-108. Here
you can change the axis label names, colors and ranges. When you are finished,
simply click OK to apply the values.
The color buttons in the toolbar of the plot widget allow you to quickly hide or show a
field of the plot. This can be useful in multi-plot widgets.

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Figure 12-77 - Plot Widget Zooming

Figure 12-78 - Plot Widget Settings

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Chapter 13 - Interpretation

13.1

Introduction to Fledermaus Interpretation

Interpretation in Fledermaus is accomplished by the addition of a new SD

Interpretation object. This object is meant to seamlessly move interpretation
information to and from ArcGIS workspaces. The SD Interpretation object can also
exist in a standard Fledermaus scene for users that dont have ArcGIS installed on
their system.
Interpretation is done by defining Key Names that will be used to segment the
interpreted areas of a scene. Adding areas to a key is accomplished using the built in
Fledermaus selection tools. The user simply selects an area of interpretation then
adds it to a specific key name. The following sections describe how to set up and use
the SD Interpretation object.
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13.2
13.2.1

Quick Start Guide

Step 1 Adding Interpretation Objects

To add SD Interpretation objects to your scene, select the Add Interpretation object
from the Fledermaus create menu as shown in Figure 13-1.

Figure 13-1 - Fledermaus Create Menu

This will add an empty interpretation object containing the default key type
Unclassified as shown in Figure 13-2.

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Figure 13-2 Empty Interpretation Object

13.2.2

Step 2 Editing Key Names

You must now define the key names for your interpretation. This can be done one of
two ways. The first way is to use the Edit Keys button in the Tools Group of the
Interpretation attribute panel. This will launch the key editor dialog so that you can
add key/color pairs to your interpretation. You can also change the name of the
default key as shown in Figure 13-3. Click in the text area to edit the key name and
double-click the color to launch the color picker dialog. The controls are fully
explained in 13.3.5.

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Figure 13-3 - Key Field Editor

In our example weve added Sand, Mud, and Rock as key field names.
Corresponding colors are brown, green and orange. After clicking the OK button, you
will now be ready to perform your interpretation as shown in Figure 13-4.
The alternative method for editing the key fields is to load them from a template. A
template is simply an SD Interpretation object that has been saved as an empty
interpretation. It has all of the key/color pairs defined but all areas are zero size. Use
the Load Template menu option from the Tools drop-down menu on the attribute
panel.
*Note* A shortcut method of adding an interpretation object is to open the template
object directly using the Fledermaus File->Open Data Object / Scene menu. Once
you save your scene, your original template will still be preserved and your SD
Interpretation object will be saved in the scene.

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Figure 13-4 - Edited Key Fields

13.2.3

Step 3 Creating Interpretation Areas

To add an area in the scene to a specific key field, select the key field then use one
of the selection modes from the Fledermaus toolbar (Select, Polygon Select, or Area
Select) to drag out a selected area in the scene as shown in Figure 13-5. Once you
are ready, simply click on the Add button in the Select Actions group of the attribute
panel. Your selected area will create a poly-line object in the color of your key field as
shown in Figure 13-6.

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Figure 13-5 Selecting an Area

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Figure 13-6 Add To Key

It is important to note that the number of points in the poly-line selection change
according to the zoom level of the scene. This allows you to dynamically refine your
interpretation by zooming in and selecting high detail areas as well as zooming out to
select coarser detail areas. The complexity of the poly-line will change with your
zoom level.
Now simply continue with your interpretation, selecting new areas, selecting new key
names, and using Add, Remove or Overwrite from the Select Actions group of the
attribute panel. To learn more about these actions, please see section 13.3.4.

13.2.4
Step 4 Saving, Exporting, or Transferring
Interpretation
Since your interpretation object is a standard Fledermaus SD, it can be saved by
simply saving the scene. It can also be saved as a standalone SD by using the rightclick context menu in the Fledermaus Data Sets tree view.
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Other options include exporting to ASCII, exporting a report or transferring to an

ArcGIS workspace. See sections 13.3.5.4 to 13.3.5.5 for more information on these
options.

13.3

SD Interpretation Control Panel

The control panel for the SD Interpretation object is shown in Figure 13-7. This
control panel is presented in the Object Attributes panel of Fledermaus whenever this
type of SD object is selected in a scene.

Figure 13-7 SD Interpretation Control Panel

13.3.1

Display Options

The Display Options group contains controls that affect the display of your
interpretation within the scene. The first control is the Hole Marker Is combo box that
allows you to change the marker type that is used to display holes in a particular key
type. The Marker Size slider allows you to change the size of the drawn marker.
Holes are drawn using markers and enclosed areas are drawn with lines. This is to
facilitate the need to have an island of one interpretation type within a larger,
enclosing second interpretation type; an example is shown in Figure 13-8.

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Figure 13-8 Hole Markers

In this example, a rocky zone is displayed using the purple line. The rocky zone is
completely enclosed by near shore ramp, which is represented by the color green.
Green diamonds on the purple polyline means that the purple rocky zone cuts a hole
in the green near shore ramp.
The size of the line can be changed using the Line Width slider and the height of the
line above the interpreted surface can be controlled using the Offset slider.
The number of markers shown is dynamically adjusted so that they do not obscure a
valid enclosed area.

13.3.2

Draping Options

Interpretation lines are automatically draped on available surfaces whenever you add
new selections to a key. There are times when you may want to un-drape or re-drape
the lines due to a change in surface. You may also wish to do this if you are importing
interpretation data from ArcGIS. In the later case, interpretation objects are typically
polygon feature class objects that contain sub-typing attribute information. Since they
are polygon objects, they will come into Fledermaus with no Z value. Using the Drape
button, all components of the interpretation object will be draped on available
surfaces in the scene. Using the Un-Drape button will return all
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components of an interpretation to a Z value of zero.

13.3.3

Interpretation Information

This control contains a table with detailed information about the interpretation object.
The primary columns are Color, Area and Key Name. The Color is the color used to
draw the lines or hole markers for a particular key. The Area is the current area in
square meters or square kilometers of all enclosed areas, minus holes, for a
particular key. The Key Name is the assigned name for each interpretation type.

13.3.4

Select Actions

This control group contains the buttons that are used to build your interpretation.
Once you have made a selection in the scene, simply select the appropriate Key
Name in the Interpretation Information table and then click the Add, Remove or
Overwrite button.
13.3.4.1

Add Action

The Add button will add the current selection to the selected key in the Interpretation
Information table as shown in Figure 13-9. If you have overlapped a previous
selection, you will merge the new selection into the old as shown in Figure 13-10.
The Area for the key will automatically update in the Interpretation Information table.
If the new selection does not overlap, you will simply create a new enclosed area that
will be added to the total area for the key.

Figure 13-9 Initial Area Selection

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Figure 13-10 Add Overlapped Areas

Add selection actions with new areas will always conform to the boundaries of
currently existing interpreted areas. Notice in below that the selection area in the
second frame overlaps the sand type. When I click the Add button with the mud key
selected, the system creates a new poly-line that conforms to the edges that were
defined in the existing interpretation (last frame). In this way, no data is inadvertently
overwritten and no gaps are left over.

Figure 13-11 Add New Overlapped

13.3.4.2

Remove Action

The Remove button will remove an area from the currently selected key in the
Interpretation Information table as shown in below.

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Figure 13-12 Removing an Area

The Area for the key will automatically update. If the new selection does not overlap,
the interpretation area will not change. If the area to be removed is completely
enclosed by one of the interpretation poly-lines, you will cut a hole in the enclosed
area as shown in below. Notice that the hole is drawn using the selected Hole Marker
Type as described in 13.3.1.

Figure 13-13 Remove an Enclosed Area

13.3.4.3

Overwrite Action

The Overwrite operation will behave differently based on whether our selection is
overlapping an existing area or completely enclosed by an existing area. Lets look at
the first case where we have overlap. In this example, we want to designate the area
in the upper right of our interpretation as mud. We see in Figure 13-14 that our
selection area will cut-out the existing interpretation of sand and add our new
selection area of mud. If we turn off the mud key by clicking the checkbox in the
Interpretation Information table, we will see that our sand polygon has changed
shape.

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Figure 13-14 Overwrite Overlapping Area

The second type of overwrite operation is when your selection area is completely
enclosed by an existing interpretation. The first frame of Figure 13-15 shows our
current interpreted area. The second frame is zoomed in and we have selected a
small area we believe to be mud. The last frame is the result of clicking the Overwrite
button. The system has cut a hole in the sand poly-line object as indicated by the
brown diamonds. The system has then added the mud region as shown by the green
poly-line. Holes in interpreted areas are shown using markers so that the user can tell
the difference between an enclosed area and a hole. The coloring of the markers
tells you which key type the hole belongs to.

Figure 13-15 Overwrite Enclosed Area

13.3.4.4

Fill Action

The Fill action will allow you to fill the selected key in the Interpretation Information
table with all remaining un-interpreted areas on a particular surface. When you click
this button, you are presented with a dialog box containing all current surfaces in the
scene (Figure 13-16).
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Figure 13-16 Object Selection

This action should be done near the end of your interpretation session, to create a
complete interpretation where all areas are placed into some key (and all surface
area is accounted for in some key). It is best to do near the end so that the remaining
operations are not slowed by the necessary Boolean logic operations that are
computed every time you Add, Remove, or Overwrite new interpretation areas.
13.3.4.5

Clip Action

The Clip action should be done at the end of your interpretation session. This action
will clip all interpretation areas to the visible surfaces in the current scene. It will clip
areas outside of a surface and cut holes in the interpretation wherever there are
holes in the surface. This will yield more accurate Area values in the Interpretation
Information table. Images before and after a Clip operation are shown in Figure
13-17 and Figure 13-18.

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Figure 13-17 Clip Before

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Figure 13-18 Clip After

13.3.5

Tools

The Tools control group contains tools for editing keys, saving and loading templates,
generating image layers and transferring interpretations to ArcGIS.
13.3.5.1

Edit Button

The Edit button will launch the edit control dialog box as shown in Figure 13-19.
When you first create an interpretation object from the Fledermaus Create menu
option, it will contain only one default key name, Unclassified.

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Figure 13-19 Key Field Edit Dialog

To add a new field, click the Add button. You can then click in the Key Field Value
text box to edit the field name. To change the color, double-click the Color value
which will open a standard color picker dialog box. To remove a field, select the field
you wish to remove and click the Remove button. You are not allowed to remove the
first field in the list. If you wish the name to be something other than Unclassified,
click in the text box and edit the name. Once you are done, click the OK button and
your interpretation will have all of your assigned key field names.
This operation can be done at any time during your interpretation session. Know that
if you delete a key field, you will lose all of the associated interpretation areas.
13.3.5.2

Clear Button

The Clear button will clear all areas from the selected key in the Interpretation
Information table. This button is only enabled when you have selected a key value.
The Area will also update to show a zero value.
13.3.5.3

Clear All Button

The Clear All button will clear all areas from every key in your Interpretation
Information table.
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13.3.5.4

Tools Button

The Tools button has a pop-up menu shown in Figure 13-20.

Figure 13-20 Tools Menu

13.3.5.4.1 Create GeoImage Object

This menu option will launch the dialog shown in Figure 13-21. This allows you to
select some options for the output of a new SD GeoImage object.

Figure 13-21 Generate Interpretation Image Dialog

The pixel resolution controls the image resolution in meters per pixel. As you change
this value, you will see the resultant image size to the right of the text box. Take care
not to create an image that is too large for the given memory of your system. The
image bounds will be taken from the bounds of all of your visible interpretation keys.

You have several options for filling the background color of the image. The default
option is Transparent. You could also choose to fill in using a color from one of your
key fields or specify a custom color. If Custom is chosen, double-click on the color
box to launch the standard color picker dialog. If you have chosen From Class, use
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the combo box to select the key field name. Once you click the OK button,
Fledermaus will render a new GeoImage SD object and it will be added to the scene.
A GeoImage SD object generated using the transparent fill option is shown in Figure
13-22.

Figure 13-22 GeoImage SD

13.3.5.4.2 Save Template

This menu item will save an SD object that can be used as a template the next time
you do an interpretation. You are presented with a standard File Save dialog box for
saving the template. It will save an SD Interpretation object with all the assigned key
names and colors, but with no interpretation areas. In other words, you will have the
key fields set up, but the areas will all be zero.
13.3.5.4.3 Load Template

After creating an Interpretation SD object, you can use this tool to load a previously
saved template. Dont forget that if the template contains keys that you dont need,
you can always use the Edit Keys dialog to remove them.

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13.3.5.4.4 Export ASCII

This menu option will save all of the current interpretation polygons in an ASCII file.
Each point of a polygon has 4 fields. These are the X, Y, and Z position as well as a
field that indicates if the polygon is a hole (1) or normal (0) polygon. Each polygon is
preceded by a starting indicator (9999 9999 9999) and the key name.
13.3.5.4.5 Export Report

This menu option will export a simple report containing details about the
interpretation object. It will contain name, area and boundary length totals for each
key field in the interpretation.
13.3.5.5

ArcGIS Button

This button displays the ArcGIS specific pop-up menu (Figure 13-23). It is used to
transfer the interpretation object to ArcGIS. It will launch the workspace selector
dialog so that you can select a target ArcGIS workspace. This action is described in
detail in the Fledermaus chapter on Using ArcGIS in Fledermaus.

Figure 13-23 ArcGIS Menu

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