Spectra Manager

Spectra Analysis
Software Manual

P/N: 0302-7001J November 2016

Preface
This instruction manual serves as a guide for using this software. It is intended to instruct
first-time users on how to properly use the software, and to serve as a reference for
experienced users.

Before using the software, read this instruction manual carefully, and make sure you fully
understand its contents. This manual should be easily accessible to the operator at all times
during software operation. When not using the software, keep this manual stored in a safe
place. Should this instruction manual be lost, order a replacement from your local JASCO
distributor.

Note: With this software you can use the same graphic user interface to analyze
a wide variety of data from various spectroscopic instruments. This
manual explains all the functions offered by this software using data from a
JASCO spectrometer. We have tried to ensure that all functions are
explained clearly for users of any JASCO instrument compatible with this
software, but if you cannot find an explanation for a specific function
please contact your local JASCO representative.

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Servicing
Contact your local JASCO distributor for instrument servicing. In addition, contact your JASCO
distributor before moving the instrument to another location. Consumable parts should be
ordered according to part number from your local JASCO distributor. If a part number is
unknown, give your JASCO distributor the model name and serial number of your instrument.

Do not return contaminated products or parts that may constitute a health hazard to
JASCO employees.

Notices
(1) JASCO shall not be held liable, either directly or indirectly, for any consequential damage
incurred as a result of product use.
(2) Prohibitions on the use of JASCO software

Copying software for purposes other than backup

Transfer or licensing of the right to use software to a third party
Disclosure of confidential information regarding software
Modification of software
Use of software on multiple workstations, network terminals, or by other methods
(not applicable under a network licensing agreement concluded with JASCO)

(3) The contents of this manual are subject to change without notice for product
improvement.
(4) This manual is considered complete and accurate at publication.
(5) This manual does not guarantee the validity of any patent rights or other rights.
(6) If a JASCO software program has failed causing an error or improper operation, this may
be caused by a conflict from another program operating on the PC. In this case, take
corrective action by uninstalling the conflicting product(s).
(7) Windows is a registered trademark of Microsoft Corporation in the United States and
other countries. In general, company names and product names are trademarks or
registered trademarks of the respective companies. However, the TM and ® marks are not
used in all cases in this manual.
(8) JASCO and the JASCO logo are registered trademarks of JASCO Corporation in Japan
and other countries.

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Limited Warranty
Products sold by JASCO, unless otherwise specified, are warranted for a period of one year
from the date of shipment to be free of defects in materials and workmanship. If any defects in
the product are found during this warranty period, JASCO will repair or replace the defective
part(s) or product free of charge.

THIS WARRANTY DOES NOT APPLY TO DEFECTS RESULTING FROM THE

FOLLOWING:

(1) IMPROPER OR INADEQUATE INSTALLATION

(2) IMPROPER OR INADEQUATE OPERATION, MAINTENANCE, ADJUSTMENT OR
CALIBRATION
(3) UNAUTHORIZED MODIFICATION OR MISUSE
(4) USE OF CONSUMABLE PARTS NOT SUPPLIED BY AN AUTHORIZED JASCO
DISTRIBUTOR
(5) CORROSION DUE TO THE USE OF IMPROPER SOLVENTS, SAMPLES, OR DUE
TO SURROUNDING GASES
(6) ACCIDENTS BEYOND JASCO'S CONTROL, INCLUDING NATURAL DISASTERS
(7) CONSUMABLES AND PARTS OF WHICH WARRANTY PERIOD IS SPECIFIED
OTHERWISE.

THE WARRANTY FOR ALL PARTS SUPPLIED AND REPAIRS PROVIDED UNDER THIS
WARRANTY EXPIRES ON THE WARRANTY EXPIRATION DATE OF THE ORIGINAL
PRODUCT. FOR INQUIRIES CONCERNING REPAIR SERVICE, CONTACT YOUR JASCO
DISTRIBUTOR AFTER CONFIRMING THE MODEL NAME AND SERIAL NUMBER OF
YOUR INSTRUMENT.

JASCO Corporation
2967-5, Ishikawa-machi, Hachioji-shi
Tokyo 192-8537,
JAPAN

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Notation Used
The following notational conventions are used throughout this manual:

General Notation
Notation Meaning
[Measurement] menu Names of menus, commands, and text boxes are enclosed in
[Parameters...] command square brackets ‘[ ]’, followed by a description indicating
whether the function is a menu, command, text box, etc.
Shortcut keys used to select menus or commands are
underlined.
<OK>, <Cancel> Names of buttons are enclosed in angular brackets ‘< >‘.

Keyboard Operations
Notation Meaning
Shift Ctrl The key is enclosed in a square and shown in boldface.
Alt , F Keys that are to be pressed in succession are separated by
commas. In the example shown on the left, the Alt key is to
be pressed and released, followed by the F key.
Shift + Keys that are pressed simultaneously are separated by a
"plus" sign. In the example shown on the left, press the
key while holding down the Shift key.

Mouse Operations
Notation Meaning
Point Move the mouse pointer to the specified item.
Click Quickly press and release the mouse button.
Double-click Click the mouse button twice in rapid succession.
Drag Point to an item, click and hold down the mouse button.
Move the mouse with the button held down, and release
the button when the pointer is in the desired position.

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Contents
Preface......................................................................................................................... i
Servicing .................................................................................................................... ii
Notices........................................................................................................................ ii
Limited Warranty ...................................................................................................... iii
Notation Used ........................................................................................................... iv
Contents ..................................................................................................................... v
1. Introduction ......................................................................................................... 1
1.1 How to Use This Manual......................................................................................... 1
1.2 Overview of the [Spectra Analysis] Program ........................................................ 2
2. Introduction to [Spectra Analysis] Program ..................................................... 3
2.1 Overview of Spectra Analysis Operation .............................................................. 3
2.2 Logging on to [Spectra Manager CFR] .................................................................. 3
2.3 Starting [Spectra Analysis] program and opening spectra ................................. 5
2.4 Finding Peaks in the Spectrum.............................................................................. 8
2.5 Displaying and Printing the Results .................................................................... 10
2.6 Saving and Signing .............................................................................................. 11
2.7 Exiting [Spectra Analysis] Program and [Spectra Manager CFR] ..................... 12
3. [Spectra Analysis] Program Reference ........................................................... 13
3.1 Program Window and Menus ............................................................................... 13
3.1.1 Program Window ........................................................................................... 13
3.1.2 Menu List ....................................................................................................... 14
3.1.3 Toolbars ........................................................................................................ 17
3.1.4 View Area Basic Operations .......................................................................... 19
3.1.4.1 Zooming in on a spectrum using the mouse............................................ 19
3.1.4.2 Displaying spectra coordinates ............................................................... 19
3.1.4.3 Overlaying spectra using the mouse ....................................................... 19
3.1.4.4 Changing the active spectrum................................................................. 20
3.1.4.5 Moving or copying all spectra in a View simultaneously .......................... 21
3.1.4.6 Vertically offsetting multiple spectra within a View .................................. 22
3.2 [File] Menu............................................................................................................. 23
3.2.1 [Open...]......................................................................................................... 23
3.2.2 [Overlay...] ..................................................................................................... 25
3.2.3 [Close] ........................................................................................................... 25
3.2.4 [Save] ............................................................................................................ 26
3.2.5 [Save As...] .................................................................................................... 27
3.2.6 [Import...] ....................................................................................................... 29
3.2.7 [Export...] ....................................................................................................... 30
3.2.8 [Open View...] ................................................................................................ 30
3.2.9 [Save Active View...] ...................................................................................... 31
3.2.10 [Print...] .......................................................................................................... 32

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 3.2.11 [Print Preview...] ............................................................................................ 34
3.2.12 [Print Setup...] ................................................................................................ 36
3.2.13 [Exit] .............................................................................................................. 37
3.3 [Edit] Menu ............................................................................................................ 38
3.3.1 [Copy as Picture] ........................................................................................... 38
3.3.2 [Copy as Bitmap] ........................................................................................... 38
3.3.3 [Cut Spectrum]............................................................................................... 38
3.3.4 [Copy Spectrum] ............................................................................................ 38
3.3.5 [Paste Spectrum] ........................................................................................... 38
3.3.6 [Delete Spectrum] .......................................................................................... 39
3.3.7 [Select All] ..................................................................................................... 39
3.3.8 [Comments...] ................................................................................................ 39
3.4 [View] Menu........................................................................................................... 40
3.4.1 [Toolbars] ...................................................................................................... 40
3.4.2 [Status Bar].................................................................................................... 40
3.4.3 [Work Space] ................................................................................................. 40
3.4.4 [Monitor Bar] .................................................................................................. 40
3.4.5 [Scales...]....................................................................................................... 41
3.4.6 [Patterns...] .................................................................................................... 42
3.4.7 [Fonts...] ........................................................................................................ 43
3.4.8 [Gridlines...] ................................................................................................... 44
3.4.9 [Styles...]........................................................................................................ 45
3.4.10 [Horizontal Axis Units...]................................................................................. 46
3.4.11 [Information...]................................................................................................ 46
3.4.12 [Normalize] .................................................................................................... 47
3.4.13 [Peak Indicators...] ......................................................................................... 48
3.5 [Processing] Menu................................................................................................ 49
3.5.1 [Corrections] submenu................................................................................... 49
3.5.1.1 [Baseline...] ............................................................................................. 49
3.5.1.2 [Smoothing...] ......................................................................................... 51
3.5.1.3 [Noise Elimination...] ............................................................................... 52
3.5.1.4 [Deconvolution...] .................................................................................... 53
3.5.1.5 [FFT Filter...] ........................................................................................... 54
3.5.1.6 [Truncate Data...] .................................................................................... 57
3.5.2 [Operations] submenu ................................................................................... 59
3.5.2.1 [Arithmetic...]........................................................................................... 59
3.5.2.2 [Derivatives...] ......................................................................................... 61
3.5.2.3 [K-K Transform...] ................................................................................... 62
3.5.3 [Peak Processing] submenu .......................................................................... 64
3.5.3.1 [Peak Find...] .......................................................................................... 64
3.5.3.2 [Peak Height...] ....................................................................................... 67
3.5.3.3 [Peak Area...] .......................................................................................... 70
3.5.3.4 [FWHM...] ............................................................................................... 73
3.5.4 [Subtraction...] ............................................................................................... 74

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 3.5.4.1 Automatic calculation of factor ................................................................ 76
3.5.5 [X Unit Conversion...] ..................................................................................... 77
3.5.6 [Y Unit Conversion...] ..................................................................................... 78
3.5.7 [Common Options] ......................................................................................... 79
3.5.7.1 [Curve Fitting...] ...................................................................................... 79
3.5.7.2 [Data Dump...] ........................................................................................ 79
3.5.7.3 [Data Accumulation...] ............................................................................. 80
3.5.7.4 [Arithmetic between Data...] .................................................................... 80
3.5.7.5 [Channel Conversion...] .......................................................................... 82
3.5.7.6 [Arithmetic between Channels...] ............................................................ 84
3.5.7.7 [Photon X Unit Conversion...] .................................................................. 86
3.5.7.8 [Time Axis Offset...] ................................................................................ 87
3.5.7.9 [Peak Normalization...] ............................................................................ 88
3.5.7.10 [Run KnowItAll] ....................................................................................... 89
3.5.8 IR Options ..................................................................................................... 90
3.5.8.1 [ATR Correction...] .................................................................................. 90
3.5.8.2 [Spectrum to Interferogram...] ................................................................. 92
3.5.8.3 [Auto Baseline] ....................................................................................... 93
3.5.8.4 [Interferogram to Spectrum...] ................................................................. 94
3.5.8.5 [H2O Reduction] ...................................................................................... 95
3.5.8.6 [CO2 Reduction] ...................................................................................... 96
3.5.8.7 [Data Comparison] .................................................................................. 97
3.6 [Window] Menu ................................................................................................... 103
3.7 [Other] Menu ....................................................................................................... 104
3.7.1 [Customize Toolbar...].................................................................................. 104
3.7.2 [Options...] ................................................................................................... 105
3.7.2.1 [View] tab .............................................................................................. 105
3.7.2.2 [Print] tab .............................................................................................. 106
3.7.2.3 [Data Processing] tab............................................................................ 107
3.7.3 [Decimal Places...] ....................................................................................... 110
3.8 [Help] Menu ......................................................................................................... 111
3.8.1 [Contents] .................................................................................................... 111
3.8.2 [Search Topic] ............................................................................................. 111
3.8.3 [About...] ...................................................................................................... 111
4. Appendix .......................................................................................................... 112
4.1 JCAMP-DX Format Files ..................................................................................... 112
4.1.1 JCAMP-DX File Structure ............................................................................ 113
4.1.1.1 Labeled-Data-Records (LDRs).............................................................. 113
4.1.1.2 Lines ..................................................................................................... 113
4.1.1.3 Data labels............................................................................................ 113
4.1.1.4 Blocks ................................................................................................... 113
4.1.2 Reserved Labels.......................................................................................... 113
4.1.3 User-defined Labels..................................................................................... 115
4.1.4 Adding Comments ....................................................................................... 115
4.2 Smoothing Methods ........................................................................................... 116

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 4.2.1 Moving Average Method .............................................................................. 117
4.2.2 Simple Moving Average Method .................................................................. 117
4.2.3 Savitzky-Golay Method ................................................................................ 118
4.2.4 Adaptive Smoothing Method ........................................................................ 120
4.2.5 Binomial Method .......................................................................................... 121
4.3 Self-deconvolution Method ................................................................................ 122
4.4 Kubelka-Munk Transform (K-M Transform) ...................................................... 124
4.4.1 Principle of K-M Transform .......................................................................... 124
4.5 Kramers-Kronig Transform (K-K Transform) .................................................... 125
4.5.1 Principle of the Kramers-Kronig Transform .................................................. 125

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1. Introduction
1.1 How to Use This Manual
This section describes the structure and use of this manual. The manual consists of 4 chapters
including this one. An explanation of each chapter is given below. For this manual, Microsoft
Windows is referred to as Windows and personal computer as a PC.

1. Introduction
This chapter describes how to use this manual and gives an overview of the [Spectra Analysis]
program. Read this chapter first.

2. Introduction to [Spectra Analysis] program

This chapter describes procedures for starting the program, opening saved spectra, finding
peak positions, and saving/printing results, for practice in operating the [Spectra Analysis]
program. Users unfamiliar with Windows or first-time users of the [Spectra Analysis] program
should follow the procedures described in this chapter for a general overview of how to operate
the program.

3. [Spectra Analysis] Program Reference

This chapter provides reference information for the [Spectra Analysis] program. Read this
chapter as required.

4. Appendix
This appendix provides technical information and file types for the [Spectra Analysis] program.

1
1.2 Overview of the [Spectra Analysis] Program
[Spectra Analysis] is a common program for the entire range of JASCO analytical instruments,
including UV/Vis, near-infrared, infrared, fluorescence, Raman, polarimetry and circular
dichroism spectrometers. This program can analyze spectrum data and time-course data
measured by the analytical instruments.
The main functions of the [Spectra Analysis] program are summarized below. Other optional
functions are also available depending of the instrument used to measure data. Refer to
Chapter 3 “[Spectra Analysis] Program Reference” for details.

(1) [File] menu: saves/opens spectra, and prints data.

(2) [Edit] menu: copies spectra to the clipboard or between Views and deletes spectra.
(3) [View] menu: changes scales, colors, and fonts of spectra. Shows or hides results of
peak processing.
(4) [Processing] menu:
Baseline Correction
Smoothing
Noise Elimination
Deconvolution
FFT Filter (noise elimination)
Interpolation and Truncation
Arithmetic (between spectra or a spectrum and a constant)
Deviation
Kramers-Kronig Transformation
Peak Find
Peak Height, Peak Height Ratio
Peak Area, Peak Area Ratio
Full Width at Half Maximum
Subtraction
X and Y Unit Conversion

Note: The units for the data depend on the analytical instrument being used. Also,
the windows that appear in the program vary depending on the type of data
obtained.

(5) Other functions: used to show or hide windows, set the print format and customize the
display after data processing.

2
2. Introduction to [Spectra Analysis] Program
This chapter describes procedures for starting the program, opening saved spectra, finding
peak positions, and saving/printing results, for practice in operating the [Spectra Analysis]
program. Users unfamiliar with Windows or first-time users of the [Spectra Analysis] program
should follow the procedures described in this chapter for a general overview of how to operate
the program.

Note: This section is described based on the fact that the initial settings have already
been performed by a Windows administrator and the [Spectra Manager]
administrator. Refer to the separate manuals “Setup Guide Security Settings
based on Access Control” and “Spectra Manager CFR Administrative Tools
Software Manual” for the initial settings.

2.1 Overview of Spectra Analysis Operation

Logging on to [Spectra Manager CFR] Refer to Section 2.2

Starting the [Spectra Analysis] Program and Opening a Spectrum Refer to Section 2.3

Finding Peaks in the Spectrum Refer to Section 2.4

Displaying and Printing the Results Refer to Section 2.5

Saving and Signing Refer to Section 2.6

Exiting the [Spectra Analysis] and [Spectra Manager CFR] Programs

Refer to Section 2.7

2.2 Logging on to [Spectra Manager CFR]

(1) Select [Program] - [JASCO] - [Spectra Manager] from the Windows [Start] menu or
double-click the [Spectra Manager] icon on the Windows desktop. The dialog box in Fig.
2.1 is displayed.

Figure 2.1 Logging on to Spectra Manager CFR

3
(2) Type the user name and the password in the [Username] and [Password] text boxes,
respectively. Clicking the <Logon> button starts the [Spectra Manager CFR] program
(Fig. 2.3). Clicking the <Cancel> button exits [Spectra Manager CFR].

Note 1: If the current password has expired, or the user is logging on to the program for
the first time, the following dialog box in Fig. 2.2 is displayed. Type a new
password to continue the logon procedure.

Figure 2.2 [Enter New Password] dialog box

Note 2: If an incorrect password is entered five times consecutively during a logon

attempt, the user is locked out and an error message is displayed. If this
happens, a [Spectra Manager CFR] administrator will need to unlock the user
by assigning a new password to the user using the [Administrative Tools]
program.

Details display field

Application display field

Figure 2.3 [Spectra Manager CFR] window

4
The left field of the window (application display field) shows a list of instruments, measurement
programs and analysis programs in hierarchical order (a tree), and the right field (details
display field) displays any details about the selected item.

Note: The contents of the window vary depending on the logged-on user.

2.3 Starting [Spectra Analysis] program and opening

spectra
(1) Starting the [Spectra Analysis] Program
1) Click [Spectra Analysis] in the application display field. The details display field shows
detailed information concerning [Spectra Analysis] (Fig. 2.4). The upper pane of the
details display field shows a list of file names in the selected folder and the lower pane
shows the contents of the file selected in the upper pane.

Figure 2.4 [Spectra Manager CFR] window (when [Spectra Analysis] is selected).

2) Select [Start] from the [Application] menu to start [Spectra Analysis] (Fig. 2.5).

Note 1: Programs can be started by double-clicking the program name.

Note 2: Programs can be started by opening data. After selecting a data file, select
[Open Data] from the [Application] menu to open the file. Programs can also
be started by double-clicking a corresponding file.
Note3: In the [Spectra Manager CFR] window, files can be located using the search
function. Refer to the separate “Spectra Manager CFR Administrative Tools
Software Manual” for details.

5
 Figure 2.5 [Spectra Analysis] window

(2) Opening a spectrum

1) Select [Open...] from the [File] menu to display the [Open Data] dialog box (Fig. 2.6).

Figure 2.6 [Open Data] dialog box

Note: Select [Import...] from the [File] menu to open old format standard files (*.jws,
j1d, jsp, spc), JASCO files (*.f8k, *.jrs), or dx or txt files.

2) Select the target spectrum file and click the <Open> button. The spectrum file opens
and the spectrum is displayed in the View.

6
 Figure 2.7 [Spectra Analysis] window

The [Spectra Analysis] window consists of two main components: a dockable [Work
Space] window and the View windows. The [Work Space] window shows the names of
open files and numbered Views in a tree-like hierarchy, and spectra are displayed in the
View windows. (Fig. 2.7)
Two or more windows may be opened simultaneously to display multiple spectra. Each
of these windows is referred to as a "View". In addition, multiple spectra can be overlaid
in a single View.

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2.4 Finding Peaks in the Spectrum
(1) Select [Processing] - [Peak Processing] - [Peak Find...] to display the [Peak Find] dialog
box (Fig. 2.8).

Figure 2.8 [Peak Find] dialog box

The [Peak Find] dialog box consists of three main components: a peak table, parameters,
and the spectrum display area.

(2) Setting parameters and finding peaks

1) Select “Top (peaks)”, “Bottom (valleys)”, or “Both (peaks and valleys)” from the [Peak]
drop down list.
2) Input a value in [Noise level] text box. Peaks with intensities less than the input value
are regarded as noise.
3) Select the [Upper limit] and [Lower limit] check boxes to input values, if necessary. The
values can also be set by dragging the limit setting bar displayed in the spectrum
display area.
4) Click the <Apply> button. Peaks are detected with the parameters and results are
displayed in the peak table. Peak positions are indicated with short bars.
(3) Adding peaks
1) Drag the long bar to the target peak position to activate the <Add> button.
2) Click the <Add> button to add the peak to the peak table.
(4) Deleting peaks
1) Select a target peak to be deleted. Select the peak in the peak table or move the long
bar to the peak position to activate the <Delete> button.

8
 2) Click the <Delete> button to delete the peak from the peak table.
(5) Copying peak table
Click the <Copy> button to copy the values in the peak table to the clipboard. For
instance, the copied data can be pasted into Windows Notepad.

(6) Writing the results of Peak Find to memory

Click the <OK> button. The results of Peak Find displayed on the spectrum are written to
memory.

9
2.5 Displaying and Printing the Results
(1) Displaying results of Peak Find on the spectrum
Select display mode from [View] - [Peak Indicators] to display the peak indicators on the
spectrum. The indicators in Fig. 2.9 are displayed with the [Bar, X] mode.

Figure 2.9 [Spectra Analysis] window (spectrum with peak indicators)

(2) Displaying print images
1) Select [Print Preview] from the [File] menu to display the [Print Preview] window (Fig.
2.10).

Figure 2.10 [Print Preview] window

(3) Printing results

Click the <Print> button after checking the print image. Spectrum and results of Peak
Find are printed.

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2.6 Saving and Signing
(1) Select [Save As...] from the [File] menu to display the [Save As] dialog box (Fig. 2.11).

Figure 2.11 [Save As] dialog box

Note: In the CFR version, a spectrum can only be saved in the workgroup folder and
its subfolders. Folder settings can be changed in [Administrative Tools] only by
the [Spectra Manager CFR] administrators. Refer to the separate “Spectra
Manager CFR Administrative Tools Software Manual” for details.

(2) After typing a file name and password, click the <Save> button.

Note: To add “Approval” and “Review” signatures to a saved spectrum by Managers,

display the [Spectra Manager CFR] window. Refer to the separate “Spectra
Manager CFR Administrative Tools Software Manual” for details.

11
2.7 Exiting [Spectra Analysis] Program and [Spectra
Manager CFR]
(1) Exiting [Spectra Analysis] program
Select [Exit] from the [File] menu. The [Spectra Analysis] program window closes,
leaving the [Spectra Manager CFR] window displayed.

Note: When spectra have not been saved, the following message is displayed. Save
spectra, if necessary. A message will be displayed for each unsaved
spectrum.

Figure 2.12 Error message when spectra have not been saved

(2) Exiting the [Spectra Manager CFR] program

Select [Exit] from the [Program] menu to close the [Spectra Manager CFR] window and
return to Windows.

(3) Exiting Windows

Exit Windows in accordance with standard Windows procedures.

12
3. [Spectra Analysis] Program Reference
3.1 Program Window and Menus
3.1.1 Program Window
Select [Spectra Analysis] on the [Spectra Manager CFR] window to start the [Spectra Analysis]
program (Fig. 3.1).

Note: When the [Send to Analysis] command is selected in measurement programs,

the [Spectra Analysis] program runs automatically and opens a new View to
display the measured spectrum.

Toolbars Views

Workspace

Status bar

View area

Figure 3.1 [Spectra Analysis] window

Work space The workspace is divided vertically into two panes by a bar. The
upper pane displays View numbers and associated file names, and
the lower pane displays information about the currently active
spectrum.
View area Views are displayed in separate windows in this area.
Views A window that displays a single spectrum (or overlaid spectra).
Multiple spectra can be displayed in one View. The file name of the
active spectrum is displayed in the title bar of the View window. (If a
spectrum has not been saved to file, the title will be displayed as
Memory-#, where # is number)
Toolbars The toolbars contain shortcuts to frequently used functions. The
toolbar buttons for data processing functions can be customized.
Status bar Displays the x and y data values of the currently selected position in
the active spectrum. To select a position, move the mouse pointer to
the desired position over the spectrum and left-click the mouse.

13
3.1.2 Menu List
[File] menu
[Open...] Opens one or more spectra files.
[Overlay...] Overlays one or more spectra files to the active View.
[Close] Closes the active View.
[Save] Saves the active spectrum.
[Save As...] Saves the active spectrum with a new file name.
[Import...] Imports a spectrum in a format other than the standard Spectra
Manager format. JASCO old standard format (*.jws), JCAMP-DX
format (*.dx), text format (*.txt), JASCO FT format (*.j1d), J-700
DOS format (*.jsp), V-500 DOS format (*.spc), JASCO F8K
format (*.f8k), or JASCO iRM format (*.jrs) is available.
[Export...] Saves data in the JASCO old format (*.jws), ASCII format (*.txt),
JCAMP-DX format (*.dx), CSV format (*.csv), JASCO iRM format
(*.jrs), or ASCII XY format (*.txt).
[Open View...] Opens an existing View file in a new View.
[Save Active View...] Saves the active View with a new name.
[Print...] Prints the active spectrum.
[Print Preview...] Displays a print preview of the active spectrum.
[Print Setup...] Designates the target printer and print parameters.
[Exit] Exits the [Spectra Analysis] program.
[Edit] menu
[Copy as Picture] Copies a spectrum to the Windows clipboard as a picture.
[Copy as Bitmap] Copies a spectrum to the Windows clipboard as a bitmap.
[Cut Spectrum] Removes the currently selected spectrum from the active View
and places it onto the Spectra Analysis clipboard.
[Copy Spectrum] Copies the currently selected spectrum in the active View to the
Spectra Analysis clipboard.
[Paste Spectrum] Pastes the contents of the Spectra Analysis clipboard into the
active View.
[Delete Spectrum] Deletes the currently selected spectrum in the active View.
[Select All] Selects/clears all spectra in the active View.
[Comments...] Comments regarding a spectrum may be added or edited using
this window.
[View] menu
[Toolbars] Main
View
Data Processing
View Command
[Status Bar] Shows or hides the status bar.
[Work Space] Shows or hides the workspace.
[Monitor Bar] Shows or hides the monitor bar.

14
 [Scales...] Changes the scale for the active View.
[Patterns...] Selects the line style and color for the active View.
[Fonts...] Selects the font settings and text orientation for the active View.
[Gridlines...] Adds/removes vertical and/or horizontal grid lines to the active
View.
[Styles...] Changes the scale settings for the active View.
[Horizontal Axis Units...] Changes the quantity or units displayed on the horizontal axis.
[Information...] Displays the spectrum information.
[Normalize] Normalizes the scale of each spectrum displayed in the active
View.
[Peak Indicators...] Designates how the peak value or peak position for the active
spectrum should be displayed.
[Processing] menu
[Corrections] [Baseline...] Corrects a spectrum using a specified
baseline.
[Smoothing...] Smooths the spectrum.
[Noise Elimination...] Eliminates noise for which the cause is
known.
[Deconvolution...] Separates overlaid peaks.
[FFT Filter...] Eliminates interferometric noise from a
spectrum.
[Truncate Data...] Creates a spectrum with the desired data
interval and wavelength range
[Operations] [Arithmetic...] Performs arithmetic operations between
spectra or between a spectrum and a
constant.
[Derivatives...] Calculates derivatives for a spectrum.
[K-K Transform...] Performs a Kramers-Kronig Transformation.
[Peak Processing] [Peak Find...] Finds spectrum peaks (or valleys).
[Peak Height...] Calculates the peak height and peak height
ratio.
[Peak Area...] Calculates the peak area and peak area ratio.
[FWHM...] Calculates the full width at half maximum
value.
[Subtraction...] Calculates a difference spectrum.
[X Unit Conversion...] Converts the x-axis units of the spectrum.
[Y Unit Conversion...] Converts the y-axis units of the spectrum.
[Common Options] [Curve Fitting] Transfers a spectrum to the [Curve
Fitting] program.
[Data Dump] Displays values of measurement data.
[Data Accumulation] Averages data overlaid in the same
View.
[Arithmetic between Data] Performs arithmetic operations between

15
 data overlaid in the same View.
[Channel Conversion] Converts channels of data in a View and
extracts data with the desired channel
from overlaid spectra or multiple
channels in a View.
[Arithmetic between Performs arithmetic operations between
Channels] channels displayed in the same View.
[Run KnowItAll] Transfers a spectrum to the search
software (Sadtler) (not available in
Spectra Manager CFR).
[IR Options] [Data Comparison] Compares spectra to identify the
measured data.
[ATR Correction...] Corrects the absorption intensity
relationship between the high
wavenumber and low wavenumber
regions of a spectrum.
[Interferogram to Converts an interferogram (IF) into a
Spectrum...] single-beam spectrum.
[Spectrum to Converts a single-beam spectrum into
Interferogram...] an interferogram (IF).
[Auto Baseline...] Automatically performs baseline
correction.
[H2O Reduction] Eliminates the absorption bands of water
vapor in a spectrum.
[CO2 Reduction] Eliminates the absorption bands of
carbon dioxide in a spectrum.

[Window] menu
[Cascade] Cascades all open Views.
[Tile Horizontally] Arranges Views as non-overlapping horizontal tiles.
[Tile Vertically] Arranges Views as non-overlapping vertical tiles.
[Arrange Icons] Arranges minimized View icons at the bottom of the window.
[Close All] Closes all Views.
[Other] menu
[Customize Customizes the [Processing] toolbar.
[Toolbar...]
[Options...] Changes the View and print style options.
[Decimal Places...] Sets the number of decimal places of the vertical and horizontal
axes.
[Help] menu
[Contents] Displays the help window with the contents tab selected.
[Search Topic] Displays the help window with the index tab selected.

16
 [About...] Displays information about the version of the [Spectra Analysis] and
product license information.

3.1.3 Toolbars
The toolbars contain buttons for frequently used functions, such as saving files, changing scale
settings and performing data processing. The buttons are of four basic types and are thus
arranged in four separate toolbars: Main, View Toolbar, Processing and View Command. Each
of these toolbars can be hidden or displayed independently. In addition, the Processing toolbar
buttons can be customized if necessary.

Note: Refer to 3.7.1 [Customize Toolbar] to learn more about customizing the
Processing toolbar.

Main
Opens one or more spectra files. Shortcut to [File]-[Open...].
Saves the active spectrum. Shortcut to [File]-[Save] or [File]-[Save As...].
Prints the active spectrum. Shortcut to [File]-[Print...].
Displays a print preview of the active spectrum. Shortcut to [File]-[Print Preview...].
Displays version information about the program. Shortcut to [Help]-[About].
View
When selected, the following buttons can be used to modify the x-axis scale settings.
Reduces the spectrum horizontally.
Expands the spectrum horizontally.
Moves the spectrum to the left.
Moves the spectrum to the right.
When selected, the following buttons can be used to modify the y-axis scale settings.
Reduces the spectrum vertically.
Expands the spectrum vertically.
Moves the spectrum up.
Moves the spectrum down.
Automatically scales the vertical axis.
Automatically scales both axes so that all measured data is displayed in the current
View.
Returns to default scale settings.
Tracing mode: The mouse is used to display spectrum x and y coordinate data.
Zoom mode: The mouse is used to zoom in on a region of the spectra.
Offset mode: The mouse is used to offset overlaid spectra vertically within a View.
Changes the active spectrum within an overlaid View.

17
Data Processing
[Baseline]
[Smoothing]
[Noise Elimination]
[FFT Filter]
[Interpolation/Truncation.]
[Arithmetic]
[Deconvolution]
[Derivatives]
[K-K Transform]
[Peak Find]
[Peak Height]
[Peak Area]
[FWHM]
[Subtraction]
[Y Unit Conversion]
[X Unit Conversion]
View Command
[Scales]
[Patterns]
[Fonts]
[Gridlines]
[Styles]
[Peak Indicators]
Toggles between Overlay/Normalize. Normalize is used to display overlaid spectra
using independent auto-scaling.
Displays spectrum information. Shortcut to [View]-[Information].

18
3.1.4 View Area Basic Operations
3.1.4.1 Zooming in on a spectrum using the mouse

Click the button on the toolbar. The button is displayed as depressed and the mouse
changes to zoom mode. When the mouse pointer is moved over a spectrum View while in this
mode, the mouse pointer changes into a crosshairs. At one corner of the desired range,
left-click and drag the pointer diagonally to specify the desired range. When the mouse button

is released, the selected area is rescaled to fill the entire View. Click the button to return to
the original scale.

Note 1: The coordinates of the mouse cursor are displayed on the status bar. These
can be used as a reference for performing the scale expansion.
Note 2: This method does not set the edges of the scale to exact values. To change
the scale limits to specific values, select [Scales...] from the [View]- menu.
Note 3: To revert to the zoom settings that were used immediately prior to zooming in,
right-click the mouse button.

3.1.4.2 Displaying spectra coordinates

To display coordinate data at an arbitrary point within the spectrum, click the button on the

toolbar. The button is displayed as depressed and the mouse is set to trace mode. Move
the mouse pointer over an arbitrary point on the spectrum and left-click to display the data
corresponding to the position indicated on the status bar.

Note: If the mouse button is held down while the mouse pointer is moved, the status
bar is updated as the mouse moves.

3.1.4.3 Overlaying spectra using the mouse

The following is the procedure for overlaying spectra by dragging from one View to another
using the mouse. This can be done when two or more Views are open.

Note: Although multiple spectra can be opened in a single View, only eight patterns
(colors, line styles) can be defined in each View. Thus, when more than eight
spectra are overlaid in a single View, the patterns will be repeated from the
ninth spectrum on.

(1) Select [Window]-[Tile Horizontally] from the menu. All open View are tiled (displayed side
by side).

(2) Click in the View containing the spectra to be moved. The View is activated.
(3) Moving the mouse pointer over the spectrum changes the cursor into the shape of a
tweezers . Left-clicking the mouse changes the mouse pointer to . Drag the mouse
and release the button over the View in which you want to overlay the spectrum (this
procedure is called “drag and drop”). The spectrum is moved from the original View and

19
 is overlaid in the View. If the original View only contained a single spectrum, the View is
closed automatically.

Note 1: Overlaying spectra automatically updates the vertical axis scale. The
horizontal axis does not change.
Note 2: Overlaid spectra can be split into separate Views by dragging and dropping a
spectrum outside of the View.
Note 3: When dragging the spectrum, holding the Ctrl key down while pressing the
mouse button changes the mouse pointer to . The spectrum is then copied
by dragging and dropping, with the original View left unchanged.
Note 4: Spectra can be overlaid in the workspace. Select a file name in the workspace
and drag it to the desired View number to overlay or split it.

3.1.4.4 Changing the active spectrum

When multiple spectra are overlaid in a View, operations such as file saving, spectrum copying
and data processing are performed only on the active spectrum within that View. The name of
the active spectrum is displayed in the title bar of the View and is highlighted in the [Work
space] pane when the View is active.

Note: The units for the vertical axis of the spectrum change according to the active
spectrum.

Active spectra can be selected in four different ways as outlined below: using the mouse, using
the [Work space] pane, using the toolbar button, or using the keyboard.

(1) Using the mouse

1) Verify that the button (Tracing mode) on the toolbar is depressed.

2) Move the mouse pointer over the spectrum to be activated. The mouse pointer turns
into the shape of tweezers . Left-click to activate the selected spectrum.
3) Verify with the View title bar or in the [Work space] pane that the active spectrum has
been changed.
(2) Using the [Work space] pane
Click on the file name in the [Work space] pane. The file name will be highlighted and the
spectrum will become active.
(3) Using the button on the toolbar

(4) Click the button on the toolbar to cycle through the spectra in the View. Click the
button until the required spectrum becomes active (as shown in the [Work space]
pane or in the View title bar).

20
(5) Using the keyboard
Pressing the [ ] or [ ] cursor keys changes the active spectrum in the active View. Use
the cursor keys until the necessary spectrum file name appears in the View title bar.

3.1.4.5 Moving or copying all spectra in a View simultaneously

All spectra in a View can be moved or copied by performing a single operation when two or
more Views are open.
This can be accomplished either by dragging and dropping using the mouse or by using the
edit menu. The method of dragging and dropping using the mouse is as follows:
(1) Select [Tile Horizontally] from the [Window] menu to ensure that all View are visible.
(2) Click within the View, but outside of the bounding rectangle of the graph, and the mouse

pointer will change to . Drag the mouse pointer over the destination View and release
the button. All spectra are overlaid and the original View closes.

Note1: If the Ctrl key is held down while the mouse is pressed and dragged, the
mouse pointer changes to (different from above). All spectra in the View
can then be copied by dragging and dropping using the mouse. That is, the
original View remains unchanged.
Note2: Spectra can be moved or copied in the workspace. Select a file name in the
workspace and drag it to the desired View number to move (or copy by
pressing the Ctrl key) or split it.

21
3.1.4.6 Vertically offsetting multiple spectra within a View
Arranges overlaid spectra in a View along the y-axis direction so that they can be more easily
compared.
Vertical offset parameters can be entered numerically using a dialog box or can be set visually
by dragging spectra within a View using the mouse.

(1) Setting vertical offsets numerically

1) Click the button on the toolbar. The button is displayed as depressed, and
the mouse enters offset mode.
2) Press and hold the right mouse button in a View. A red vertical cursor is displayed. To
numerically set the vertical offset between spectra, a reference wavenumber from
which vertical offsets are calculated must be selected. Move the vertical cursor to the
appropriate location and release the button to display the following dialog box. (Fig.
3.2) Enter the reference x coordinate and offset interval, and click the <OK> button.
If zero is entered as the offset interval, the spectra will be shifted vertically to overlap at
the reference x-coordinate.

Figure 3.2 [Offset Settings] dialog box

(2) Dragging spectra in the View

1) Click the button on the toolbar. The button is displayed as depressed, and
the mouse enters offset mode.
2) Move the mouse pointer onto the spectrum to be moved. The mouse pointer changes
into a double-ended vertical arrow. Click and hold the left mouse button, and drag the
spectrum up or down within the View as desired. Release the mouse button to confirm
the offset location.

Note: To reset all offsets, hold down the Ctrl key and right-click the mouse.

22
3.2 [File] Menu
Saves or opens a measured data or parameter file.
3.2.1 [Open...]
Select [Open] from the [File] main menu to display the [Open Data] dialog box, which is used to
open a spectrum (or spectra) in a new View. Multiple files can be selected simultaneously and
opened in the same or separate Views.

Figure 3.3 [Open Data] dialog box

[Look in] Selects a drive or folder to browse using the drop-down list. Files
saved in the currently opened folder are displayed in the file name list.
To select multiple non-sequential files, click on the desired spectra file
names while holding down the Ctrl key. To select any number of
sequential files, click on the first and last file names of the desired list
while holding down the Shift key.
[File name] Enters the file name for the spectrum to open. To select multiple files,
input their names enclosed by “” and separated by a space. The
extension may be omitted. If an incorrect extension is entered, the
default extension is substituted automatically.
[Files of type] Lists the file types (extensions) that can be opened in the [Spectra
Analysis] program.

Note: In [Spectra Manager CFR], only Standard Files (*.jws)

can be selected using the [Open Data] dialog box. To
open files in other formats, use the [Import] function
(see 3.2.6).

[Multi view] Select this checkbox to open multiple files in separate Views. If [Multi
view] is not selected the spectra are overlaid in a single View.
<Preview> Click the <Preview> button to display a preview of the selected
spectrum and information about the currently selected file. When
multiple files are selected, the preview panel displays information
about the last file selected.

23
 Figure 3.4 [Open Data]-[Preview]

<Open> Opens a data file and closes the dialog box.

<Cancel> Closes the dialog box without opening a data file.

Note: In the CFR version, the [Look in] list cannot be used to select a folder from the
drop-down list. However, a subfolder within the prespecified folder can be
selected.

24
3.2.2 [Overlay...]
Select [Overlay] from the [File] menu to display the [Overlay Data] dialog box used to add a
spectrum (or spectra) to the active View. (Fig. 3.5) Multiple files can be selected and added
simultaneously.

Note: If the [Automatically scale display range when a spectrum is opened or

overlaid.] check box is selected in the [View] tab of the [Options] dialog box
([Other] – [Options...]), the vertical axis is automatically re-scaled so that all of
the spectra to be overlaid are displayed. However, the horizontal axis is not
changed.

Figure 3.5 [Overlay Data] dialog box

3.2.3 [Close]
Closes the active View. The dialog box in Fig. 3.6 is displayed when there are spectra that
have not been saved. Click the <Yes> button to save the spectra before closing. Click the
<No> button to close the View without saving. Click the <Cancel> button to leave the active
View open.

Figure 3.6 Message displayed before closing unsaved spectra

25
3.2.4 [Save]
Select [Save] from the [File] menu to save the data in the active View or the measurement
parameter file using the same file name. In the CFR version, the data file can be overwritten
only if the raw data is not changed by data processing. The files that can be overwritten vary
depending on the Workgroup user rights and the signature for the file.

Table 3.1 Privileges assigned to Save function

Managers Analysts Operators
Creation signature only ✔ ✔
Creation and review signatures ✔
Creation, review, and approval signatures

Figure 3.7 [Create Signature] dialog box

[Username] Displays the name of the logged-on user. It cannot be edited.

[Password] In the CFR version, an electric signature is required for saving the
file. Type a password in the text box.
<Sign> Saves the selected data and closes the dialog box.
<Cancel> Closes the dialog box without saving the selected data.

26
3.2.5 [Save As...]
Select [Save As] from the [File] menu to display the [Save Data] dialog box, which is used to
save the active spectrum in the active View using a new file name and/or in a new location (Fig.
3.8).

Figure 3.8 [Save Data] dialog box

[Save in] Selects a drive or folder to browse using the drop-down list. Files
saved in the currently opened folder are displayed in the file name
list.
Only files and subfolders in the workgroup folder can be searched.
Users in the workgroup cannot access folders higher than the
specified workgroup folder.
[File name] Enters the file name for saving the selected data. The extension may
be omitted since it is automatically appended. If an existing file name
is designated and the <Save> button is clicked, the following dialog
box is displayed.

Figure 3.9 Dialog box displayed when overwriting an existing file

Note: Spectrum can be overwritten according to Table 3.1

“Privileges according to Save function”.

[Save as type] Selects the file types under which a file can be saved. Files other
than Standard Files (*.jws) cannot be selected.

27
 Note: To save files in the JASCO-DX or ASCII formats, use
the [Export] function (see 3.2.7).

[Username] Displays the name of the user logged on to [Spectra Manager CFR]
and cannot be changed.
[Password] In [Spectra Manager CFR], saving a spectrum requires an electronic
signature. Type the password for the current user.
<Save> Saves the data file and closes the dialog box.
<Cancel> Closes the dialog box without saving the data file.

Note: In the CFR version, the [Look in] list cannot be used to select a folder from the
drop-down list. However, a subfolder within the prespecified folder can be
selected.

28
3.2.6 [Import...]
In Spectra Manager CFR, [Import...] is used to open a spectrum saved in a format other than
the Standard Files (*.jws) (Fig. 3.9).

Note: In Spectra Manager CFR, this function can also be used to open an old format
file that is saved in a folder other than that of a logged-on Workgroup.

Figure 3.10 [Import] dialog box

The operating procedure is as described in 3.2.1 “[Open...]”. However, the file types described
below can be selected.

[Files of type] Lists the types of files that can be opened by the [Spectra Analysis]
program. If the extension is omitted when the file name is entered,
the file extension designated here is automatically appended. When
[All files] is selected, .jws is the default extension.

The following file types can be selected:

Old Format Standard Files (*.jws):
Data measured and calculated using the
Spectra Manager ver.1.5# (the file extensions
(*.j1d, *.jsp, *.spc) are also included).
JCAMP-DX (*.dx): Data in JCAMP-DX 4.24 format. Refer to the
Appendix “JCAMP-DX Format Files” for a
description of the file formats that can be used.
Text file (*.txt): Data in text format. Refer to the Appendix 4.1
“JCAMP-DX Format Files” for a description of
the file formats that can be used.
All files (*.*): Designates all files. Files not in one of the
above formats or in ASCII format cannot be
loaded.

29
3.2.7 [Export...]
Saves data in the Old Format Standard Files, JCAMP-DX (*.dx), ASCII Files (*.txt), CSV Files
(*.csv), JASCO iRM Files (*.jrs) or XY ASCII (*.txt) format.The operating procedure is the same
as described in 3.2.5 “[Save As...]”.

Note: In Spectra Manager CFR, this function can be used to save a file in a folder
other than that of a logged-on Workgroup.

3.2.8 [Open View...]

Select [Open View...] from the [File] menu to display the [Open View] dialog box, which is used
to open a View.

Note: In Spectra Manager CFR, this function cannot be used.

Figure 3.11 [Oven View] dialog box

[Look in] Selects a drive or folder to browse using the drop-down list. View files
saved in the currently opened folder are displayed in the file name list.
[File name] Enters the file name for View to open.
[Files of type] Selects the files (type of extension) to display in the file name list.
Files other than View Information Files (*jwsv) cannot be selected.

30
3.2.9 [Save Active View...]
Select [Save Active View...] from the [File] menu to display the [Save Active View] dialog box,
which is used to save the active View using a new file name and/or in a new location.

Note: In Spectra Manager CFR, this function cannot be used.

Figure 3.12 [Save Active View] dialog box

[Save in] Selects a drive or folder to browse using the drop-down list. Files
saved in the currently opened folder are displayed in the file name list.
[File name] Enters the file name for saving the selected View. The extension may
be omitted since it is automatically appended. If an existing file name
is designated and the <Yes> button is clicked, the following dialog box
is displayed.

Figure 3.13 Dialog box displayed when overwriting an existing file

[Save as type] Selects the file types under which a file can be saved. Files other than
View Information Files (*jwsv) cannot be selected.

31
3.2.10 [Print...]
Prints the selected data. The spectrum line style, frame, gridlines, and font, for example, are
printed according to the parameters designated in [Patterns], [Fonts], and [Styles] in the [View]
menu. The measurement parameters, comments, peak information and data processing
histories can be printed.

Note 1: If the [Prompt the user to type title before printing] check box is selected in the
[Print] tab of the [Options] dialog box ([Options] in the [Other] menu), when
[File] - [Print...] is selected, the dialog box in Fig. 3.14 or 3.15 is displayed.
Note 2: “Unsigned” will be watermarked on the printed page when no creation
signature is assigned to the analysis data.

Figure 3.14 [Print] dialog box (when [Default format] is selected in the [Print] tab of the
[Options] dialog box)

[Title] Prints the title. Enter a desired title in the text box.
[Legend] Prints the legends.
[Comments] Prints the sample name, comment, user name, workgroup
name (only for CFR version), division and company names.
[Data information] Prints information about the data such as the creation date
and the start and end wavelengths.
[Measurement information] Prints measurement information such as the creation date,
instrument name, accessory name and measurement
parameters.
<Print> Prints the data.
<Cancel> Closes the dialog box without printing the data.
<Print Setup...> Specifies the target printer and print parameters.
<Preview...> Displays a print preview of the data.

32
Figure 3.15 [Print] dialog box (when [Print format] is selected in the [Print] tab of the [Options]
dialog box)

[Print title] Prints the title. Enter a desired title in the text box.
Legend Prints the legends.
[Always] Prints the legend always.
[When multiple data Prints the legend only when two or more spectra are displayed
displayed] in the active View.
[Never] Do not print the legend.
Print form Designates the print format.
[Standard form] Select to print using the standard format.
[Fixed form] Select to print using the fixed format.
[User form] Select to print using a template file created in JASCO Canvas.
Click the <Browse...> button and designate the JASCO Canvas
template file to be used.
<Setup...> Opens the [Print Setup] dialog box used to designate the target
printer and printer parameters (See Section 3.2.12).
<Preview...> Shows a preview of what the active View will look like when
printed.
<Print> Prints the active View using the settings declared within the
[Print] dialog box.
<Cancel> Cancels the [Print] of the active View.

33
3.2.11 [Print Preview...]
Displays a print preview of the active View. Clicking on the preview window zooms in or out.

Note: This window varies depending on the settings in the [Print] tab of the [Options]
dialog box from [Options...] in the [Other] menu.

left: when [Default format] is selected right: [Print format] is selected (in the [print]
tab of [Options] dialog box)
Figure 3.16 [Print Preview] window

<Print> Prints the active View.

<Close> Closes the [Print Preview] window without printing.

The functions for the tool buttons in the left of Fig. 3.15 are as follows.

(Print items) Selects the items to print (see Fig. 3.14). In the CFR version, Managers
or Analysts authority is required to select print items.
(Margins) Specifies the paper margins in inches or millimeters. In the CFR version,
Managers or Analysts authority is required to specify margins.

Figure 3.17 [Margins] window

34
(Fonts) Specifies the font for the title, information and data (Fig. 3.18). In the
CFR version, Managers or Analysts authority is required to specify
fonts.

Figure 3.18 [Fonts] window

(Print) Prints the data.

35
3.2.12 [Print Setup...]
Select [Print Setup...] from the [File] menu to designate the target printer and print parameters
(Fig. 3.19).

Figure 3.19 [Print Setup] dialog box

Printer Displays the available printers. To add a new printer, select [Control
Panel] - [Printers] from the Windows task bar and select [Add
Printer...].
Paper Selects the paper size and paper source tray.
Orientation Selects the orientation of the paper for printing.
<OK> Applies the changes to the [Print Setup] settings and closes the dialog
box.
<Cancel> Closes the dialog box without applying any changes to the [Print
Setup] settings.

36
3.2.13 [Exit]
Select [Exit] from the [File] menu to exit the [Spectra Analysis] program. The following
message is displayed when unsaved spectra exist (Fig. 3.20). To save the unsaved spectra,
click the <Yes> button. A warning message is displayed for each unsaved data.

Figure 3.20 Message displayed when there are unsaved spectra

<Yes> Saves the selected data. The [Save As] dialog box is displayed.
<No> The [Spectra Analysis] program ends without saving the data.
<Cancel> Cancels the [Exit] command and returns to the active View.

37
3.3 [Edit] Menu
Copies, cuts or pastes the spectrum, or edits the comments.

3.3.1 [Copy as Picture]

Select [Copy as Picture] from the [Edit] menu to copy a spectrum to the Windows clipboard as a
picture. The picture format allows the spectrum to be edited using vector-type software, such
as Microsoft Powerpoint.

3.3.2 [Copy as Bitmap]

Select [Copy as Bitmap] from the [Edit] menu to copy a spectrum to the Windows clipboard as a
bitmap. The bitmap format is suitable for raster-type software, such as Microsoft Paint. The
image becomes distorted if the bitmap is greatly expanded or reduced. Therefore, the size of
the window (spectrum) should be adjusted accordingly before copying. A clear image can be
obtained if care is taken not to change the aspect ratio between the horizontal and vertical
scales when reducing or expanding the pasted image. A large change in the aspect ratio
always distorts the image.

3.3.3 [Cut Spectrum]

Select [Cut Spectrum] from the [Edit] menu to remove the currently selected spectrum from the
active View and transfer it to the [Spectra Analysis] clipboard. When [Select All] (Section 3.3.7)
is checked, all spectra in the active View are cut and the View is closed. Use this command or
the [Copy Spectrum] command (Section 3.3.4), (or the drag-and-drop feature) to place spectra
from different Views into one View.

3.3.4 [Copy Spectrum]

Select [Copy Spectrum] from the [Edit] menu to copy the currently selected spectrum in the
active View to the [Spectra Analysis] clipboard. The original spectrum remains in the active
View. When [Select All] (Section 3.3.7) is checked, all spectra in the active View are copied.
Use this command to place spectra from different Views into one View.

3.3.5 [Paste Spectrum]

Select [Paste Spectrum] from the [Edit] menu to paste the contents of the [Spectra Analysis]
clipboard into the active View.

38
3.3.6 [Delete Spectrum]
Select [Delete Spectrum] from the [Edit] menu to delete the currently selected spectrum in the
active View. When [Select All] is checked, all spectra in the active View are deleted and the
View closes.

Note: When a spectrum is deleted or cut from a View containing multiple spectra, the
color of the remaining spectra may change.

3.3.7 [Select All]

Select [Select All] from the [Edit] menu to select/clear all spectra in the active View. When
[Select All] is checked, all spectra in the active View are selected. This function can be used in
combination with [Cut Spectrum], [Copy Spectrum] and [Delete Spectrum].

3.3.8 [Comments...]
Select [Comments] from the [Edit] menu to display the [Comments] dialog box used to add or
edit comments (Fig. 3.21).

Figure 3.21 [Comments] dialog box

[Sample name] Enters a sample name (maximum 63 single-byte characters).

[Comment] Enters a comment. Use as required (maximum 127 single-byte
characters).
[User] Enters a user name.
[Division] Enters a division name.
[Company] Enters a company name.
<OK> Applies the changes to the [Comments] dialog box and closes the
dialog box.

Note: In the [Spectra Manager CFR], [User], [Division], and [Company] cannot be
edited.

39
3.4 [View] Menu
Specifies the View options.

3.4.1 [Toolbars]
Shows or hides toolbars.
Buttons are divided into four categories on four separate toolbars: Main, View, Data
Processing and View Command. Each of these toolbars can be hidden or displayed
independently. In addition, the Data Processing toolbar buttons can be customized.
Refer to Section 3.7.1 [Customize Toolbar...] for details.

3.4.2 [Status Bar]

Shows or hides the status bar.

3.4.3 [Work Space]

Shows or hides the workspace.

3.4.4 [Monitor Bar]

Shows the monitor bar in the lower pane of the window to display the vertical and horizontal
values specified using the trace bar. Inputting a horizontal value in the text box and clicking the
<Apply> button displays the measured horizontal and vertical values that are nearest to the
entered value.

Figure 3.22 Monitor bar

40
3.4.5 [Scales...]
Specifies the display scale for the spectrum.

Figure 3.23 [Scales] dialog box

Horizontal axis Enters the scale for the horizontal axis. Selecting the [Auto] check box
displays the entire range irrespective of the entered values.
Vertical axis Enters the scale for the vertical axis. Selecting the [Auto] check box
displays the graph at the optimal scale for the specified horizontal axis
range.
<OK> Applies the changes to the [Scales] settings and closes the dialog box.
<Cancel> Closes the dialog box without applying any changes to the [Scales]
settings.

Note 1: When the [Apply scale settings to all views.] check box in the [View] tab of the
[Options] dialog box (see Section 3.7.2) is selected, the scale settings are
applied to all Views.
Note 2: This operation can also be performed by clicking the tool button [Scales].

41
3.4.6 [Patterns...]
Selects the display color and line style for the spectrum. These pattern settings are applied
when data are printed.

Figure 3.24 [Patterns] dialog box

[Item] Selects an item to change its color, line style, and line width. These
vary depending on the selected graph type.
Options: Spectra 1 to 16, Frame, Gridlines, Auxiliary gridlines
[Color] Shows the available colors for the selected item in the drop-down list.
[Line style] Shows the available line styles. The currently selected item in the
[Item] drop-down list is displayed with the selected line style.
[Line width] Shows the available line widths. The currently selected item in the
[Item] drop-down list is displayed with the selected line width.
Sample Displays a sample of the selected pattern.
[Set as default] Applies the selected patterns to all subsequently opened spectra.
<OK> Applies the changes to the [Patterns] settings and closes the dialog
box.
<Cancel> Closes the dialog box without applying any changes to the [Patterns]
settings.

Note 1: When the [Apply view settings to all spectra.] check box in the [View] tab of the
[Options] dialog box (see Section 3.7.2) is selected, the pattern settings are
applied to all Views.
Note 2: This operation can also be performed by clicking the tool button
[Patterns].

42
3.4.7 [Fonts...]
Specifies the display fonts for the spectrum. These pattern settings are applied when data are
printed.

Figure 3.25 [Fonts] dialog box

[Item] Selects an item to change its font settings.

[Axis label]: Character ([Abs], [nm], or other)
[Scale label]: Numeric value
[Peak indicators]: Numeric value
[Font name] Lists available font names.
[Style] Lists available styles.
[Size] Lists available sizes.
Effects Selects strikeout and underline effects.
[Strike out]: Draws a line through the middle of the text.
[Underline]: Underlines the text.
[Color] Shows the available colors for the selected item in the drop-down list.
Sample Displays a sample of the specified font.
Orientation Selects the orientation for displaying the axis label.
[Horizontal]: Displays the y-axis label horizontally
[Vertical]: Displays the y-axis label vertically
[Set as default] Applies the specified fonts to all subsequently opened spectra.
[Script] Selects the language for the specified font.
<OK> Applies the changes to the [Fonts] settings and closes the dialog box.
<Cancel> Closes the dialog box without applying any changes to the [Fonts] settings.

Note 1: When the [Apply view settings to all spectra.] check box in the [View] tab of the
[Options] dialog box (see Section 3.7.2) is selected, the fonts settings are
applied to all Views.
Note 2: This operation can also be performed by clicking the tool button [Fonts].

43
3.4.8 [Gridlines...]
Shows or hides the gridlines for the spectrum.

Figure 3.26 [Gridlines] dialog box

Main gridlines
[Horizontal] Displays major horizontal axis gridlines.
[Vertical] Displays major vertical axis gridlines.
Auxiliary gridlines
[Horizontal] Displays minor horizontal axis gridlines.
[Vertical] Displays minor vertical axis gridlines.
[Set as default] Applies the selected gridlines to all subsequently opened spectra.
<OK> Applies the changes to the [Gridlines] settings and closes the
dialog box.
<Cancel> Closes the dialog box without applying any changes to the
[Gridlines] settings.

Note 1: When the [Apply view settings to all spectra.] checkbox in the [View] tab of the
[Options] dialog box (see Section 3.7.2) is selected, the gridline settings are
applied to all Views.
Note 2: This operation can also be performed by clicking the tool button
[Gridlines].

44
3.4.9 [Styles...]
Specifies the display style for the spectrum. These style settings are applied when data are
printed.

Figure 3.27 [Styles] dialog box

[Axis] Selects an item to change its display style.

Interval
[Auto] Automatically selects the gridline format.
[Manual] Manually specifies the gridline format for the main and auxiliary
scales.
Tick type
[None] Displays no ticks on the axis
[Outside] Displays ticks on the outside of the axis.
[Inside] Displays ticks on the inside of the axis.
[Cross] Displays ticks on both sides of the axis.
[Decimal places] Selects the number of decimal places for the display values on
the horizontal and vertical axes.
[Display the max. and min. Displays maximum and minimum values at the main ticks.
values at the main ticks] Values at the auxiliary ticks are not displayed.
[Set as default] Applies the specified styles to all subsequently opened spectra.
<OK> Applies the changes to the [Styles] settings and closes the
dialog box.
<Cancel> Closes the dialog box without applying any changes to the
[Styles] settings.

Note: This operation can also be performed by clicking the tool button [Styles].

45
3.4.10 [Horizontal Axis Units...]
Changes the units for the horizontal axis.

Figure 3.28 [Horizontal Axis Units] dialog box

[Axis list] Lists the available formats for the horizontal axis.
<OK> Applies the changes to the [Horizontal Axis Units] settings and
closes the dialog box.
<Cancel> Closes the dialog box without applying any changes to the
[Horizontal Axis Units] settings.

3.4.11 [Information...]
Displays information for the currently selected spectrum in the active View.

Figure 3.29 [Spectrum Information] dialog box

46
3.4.12 [Normalize]
Automatically normalizes the scale for each overlaid spectrum in the active View. The purpose
of this function is so that spectra having different vertical axis scales can be viewed
simultaneously in a single View window. When the [Normalize] function is active, a box
appears around the vertical axis label in the active View.
For example, for two spectra displayed in %T and Abs modes, without [Normalize], the
spectrum displayed in Abs mode is not visible, as shown in Fig. 3.30(a).
By switching to [Normalize], both spectra are visible, as shown in Fig. 3.30(b).

Figure 3.30(a) Overlaid View Figure 3.30(b) Normalized View

Note 1: This function can also be performed by clicking . When this button is
selected (shown as depressed), the normalized View is displayed. Clicking the
tool button again toggles the View display mode.
Note 2: Unlike in the overlaid View, changing the scale in the normalized View
changes only the scale of the active spectrum. The [Scales] dialog box for the
normalized View is shown below (Fig. 3.26). Change the scale after selecting a
spectrum from the drop-down list at the top of the dialog box.

Figure 3.31 [Scales] dialog box for normalized View

47
3.4.13 [Peak Indicators...]
Displays a submenu allowing the method for indicating the peak values and peak positions in
the active spectrum to be designated when the [Peak Find...] command is executed.

[None] Peak positions are not indicated.

[Bar] Indicates peak positions using a vertical bar.
[Bar, Data No.] Indicates peak positions using a vertical bar, and displays the
peak number.
[Bar, X] Indicates peak positions using a vertical bar, and displays the
horizontal axis value.
[Bar, Y] Indicates peak positions using a vertical bar, and displays the
vertical axis value.
[Bar, X, Y] Indicates peak positions using a vertical bar, and displays both
the horizontal and vertical axes values.

Note: Specify the orientation of the x- and y-axes labels as in Fig. 3.25 of Section
3.4.7. This can be changed as desired.

48
3.5 [Processing] Menu
Specifies, opens and saves the data processing parameters.
3.5.1 [Corrections] submenu
3.5.1.1 [Baseline...]
Corrects the active spectrum using a free baseline (Fig. 3.32). A baseline having a maximum of
32 variable points (including both ends) can be created. The variable points can be connected
by a straight line or by a spline curve.

Figure 3.32 [Baseline Correction] dialog box

[Line] Connects adjacent variable points by a straight line.

[Spline] Connects adjacent variable points by a spline curve.
<Reset> Restores the baseline to its original shape (i.e., two variable
points connected by a straight line).
<Delete Point> Erases a single variable point. Darkened points or points having
thick square frames can be erased. If a variable point on the left
or right end is erased, the next successive point will become the
end point.
<Scales...> Sets the display scales for the upper spectrum. The x-axis scale
is applied for both spectra.
Spectrum display area Set the spectrum baseline in the upper spectrum to display the
results below it. Move the small squares on the baseline (initially
only at the ends) to change the baseline shape. When the pointer
approaches a square, the shape of the pointer changes to a set of
tweezers that can be used to drag the square to another
location.
When the pointer approaches the baseline, the shape of the

49
 pointer changes to a syringe . Click the left mouse button to
add variable points.
<OK> Applies the baseline settings and displays a new View with the
calculated baseline correction after closing the dialog box.
<Cancel> Closes the dialog box without performing baseline correction.

50
3.5.1.2 [Smoothing...]
Smooths the active spectrum and reduce the apparent noise in the spectrum (Fig. 3.33). The
following four smoothing methods are available: Means-Movement, Savitzky-Golay,
Adaptive-Smoothing and Binomial.

Figure 3.33 [Smoothing] dialog box

[Method] Selects the smoothing method.

[Convolution width] Sets the number of data points to be bundle together during the
smoothing process. Only odd numbers can be set. Values are
immediately recalculated after each change.
<Apply> Applies the set convolution width, and then performs the
calculation.
Spectrum display area The original spectrum is displayed in gray (if the [Display
original data] box is selected) while the smoothed spectrum is
always displayed in red.
<Scales...> Sets the display scale for the spectrum.
[Auto scale y-axis] Displays the results using the auto-scaling function. Clear to
view the changes resulting from the smoothing calculation.
[Display original data] Overlays a spectrum before smoothing. The original spectrum
is displayed in gray and the processed spectrum is displayed in
red.
<OK> Applies the smoothing parameters and displays a new View
with the smoothed spectrum after closing the dialog box.
<Cancel> Closes the dialog box without calculating the smoothed
spectrum.

Note: Refer to Section 4.2 “Smoothing Methods” in the Appendix for details on each
method.

51
3.5.1.3 [Noise Elimination...]
Eliminates false peaks due to noise of known origin (Fig. 3.34). A peak is eliminated by
connecting the points at two designated horizontal axis positions by a straight line. The
horizontal axis range can also be changed.

x-axis
display area

Figure 3.34 [Noise Elimination] dialog box

Spectrum display area The top and bottom spectra are the same when the dialog box is
opened. Specify the range for eliminating peaks by dragging the
two vertical bars in the top spectrum and click the <Execute>
button to display the resulting spectrum. Undesired peaks can
be eliminated by repeating this procedure.
x-axis display area Displays the position of the active x-axis cursor. Input an x-axis
value, and then click the <Apply> button to shift the active x-axis
cursor to the designated position.
<Apply> Moves the active x-axis cursor to the designated position.
<Execute> Performs noise elimination.
<Undo> Undoes the most recently performed noise elimination.
<Reset> Resets the spectrum to its original condition before noise
elimination.
<Scales...> Specifies the display scale for both spectra.
[Auto scale y-axis] Displays the results for the lower spectrum using the
auto-scaling function. Clear to view the change in the size of the
calculated spectrum.
<OK> Applies the parameter settings and displays a new View with the
calculated spectrum after closing the dialog box.
<Cancel> Closes the dialog box without performing noise elimination.

52
3.5.1.4 [Deconvolution...]
Analyzes bands that may contain overlapping Lorentzian curves having the same full width at
half maximum and accurately distinguishes the peak positions for each band (Fig. 3.35).

Note: The region outside the wavelength range of interest will also be influenced by
the deconvolution calculation, and the spectral profile will change.

Figure 3.35 [Deconvolution] dialog box

FWHM Specifies the full width at half maximum for the expected
Lorentzian waveform.
<Apply> Performs the deconvolution using the input value.
<Scales...> Specifies the display scale for the spectrum.
[Auto scale y-axis] Displays the results using the auto-scaling function. Clear to view
the change in the size of the calculated spectrum.
[Display original data] Overlays the original spectrum before deconvolution. The original
spectrum is displayed in gray and the calculated spectrum is
displayed in red after processing.
<OK> Applies the final [Deconvolution] settings and opens a new View
with the calculated spectrum after closing the dialog box.
<Cancel> Closes the dialog box without performing the deconvolution.

Note: Before clicking <OK> and confirming the changes, the deconvolution
calculation can be performed with different full widths at half maximum any
number of times. For more details on deconvolution refer to Section 4.3
“Self-deconvolution Method” in the Appendix.

53
3.5.1.5 [FFT Filter...]
Separates the spectrum into frequency components using a fast Fourier transform and
eliminates noise having a particular periodicity. (Fig.3.36) A filter containing a maximum of 32
variable points (including both ends) can be created. However, if the heights of the peaks and
the noise are approximately equal, the noise cannot be removed.

Note: [FFT Filter] processing is not compatible with data having an irregular data
point interval (pitch). In order to conduct [FFT Filter] processing, it is necessary
to perform interpolation to obtain a regular data point interval by using
[Truncate Data] in advance.

Figure 3.36 [FFT Filter] dialog box

Spectrum display area Displays the shape of the FFT filter in the upper spectrum and the
results in the View below it. Move the small squares on the filter to
change the filter shape. When the pointer approaches a square,
the shape of the pointer changes to a set of tweezers that can
be used to drag the square to another location.
When the pointer approaches the filter, the shape of the pointer
changes to a syringe . Click the left mouse button to add
additional filter points. The X and Y coordinates of the currently
selected filter point are shown at the upper right, together with the
period of the noise (cm-1).
<Delete Point> Erases a single variable point. The minimum number of variable
points is two. If only two points exist, neither can be erased.
Darkened points or points having thick square frames can be
erased. If a variable point on the left or right end is erased, the
next successive point will become the end point.
<Reset> Returns the filter to its original shape.
<Scales...> Sets the vertical and horizontal axis scales for the filtered
spectrum.

54
 [Display original data] Overlays a spectrum before applying the FFT filter. The original
spectrum is displayed in gray and the processed spectrum is
displayed in red.
<OK> Applies the parameter settings and displays the calculated
spectrum in a new View after closing the dialog box.
<Cancel> Closes the dialog box without performing the FFT.

[Example of application of FFT filter]

The FFT filter can selectively eliminate only noise having a specific period. The example below
describes the elimination of noise using the supplied sample data file “fftfilt.jws”.

Figure 3.37 fftfilt.jws

First, open the spectrum fftfilt.jws, change the scale and display the range as shown in the
figure above (Fig. 3.37) (accuracy is not necessary). This is a spectrum with a large amount of
noise.
Determine the noise period by using a simple trace. Determine the start and end wavenumbers
for the noise period by referring to the figures below (Fig. 3.38). In this example, one period is
approximately 10 cm-1. This value should be noted for later use.

Figure 3.38 Determination of the noise period

55
When the noise period is known, apply the FFT filter. The following dialog box is displayed (Fig.
3.39).

Figure 3.39 [FFT Filter] dialog box

Referring to the noise period displayed at the upper right of the dialog box in Fig. 3.39, move
the two small squares to the neighborhood of 10 cm-1 to indicate that noise having a period of
less than 10 cm-1 will be eliminated. Each time the filter shape is changed, the filtered spectrum
is redrawn. Checking [Display original data] overlays the data before calculation, allowing the
filter shape to be changed while comparing the resulting spectrum to the original data (Fig.
3.40).

Figure 3.40 [FFT Filter] dialog box

A complex filter may also be set by increasing the number of rectangles. However, if only
short-period noise is to be eliminated, a simple shape such as that shown above will suffice.

56
3.5.1.6 [Truncate Data...]
Creates a spectrum having a defined data interval with a specified x-axis range. Data in any
region of the x-axis can also be cut without changing the data point interval (Fig. 3.41).
This function is used, for example, when converting data having an irregular data point interval
(pitch) into data having a regular pitch in order to conduct [Derivatives], [Curve Fitting] or [FFT
Filter] processing.

Figure 3.41 [Interpolation and Truncation] dialog box

Note: Figure 3.41 shows spectra before (upper pane) and after (lower pane) data
interpolation and truncation. Before processing was carried out, the same
spectrum appeared in both panes.

Spectrum display area The original spectrum is displayed at the top, and the
calculated spectrum following data truncation and
interpolation (if applied) is displayed below it.
[Method] Selects the method of data interpolation. The following
options are available (see reference section below).
[Lagrange]: Lagrange interpolation
rd
[3 order spline]: Tertiary spline interpolation
[No correction]: Select this to simply truncate
the data.
[Data interval] Specifies the data point interval for the data to be created.
[x-axis (L)] Specifies the upper x-axis value for the data to be created.
[x-axis (R)] Specifies the lower x-axis value for the data to be created.
<Apply> Performs data interpolation and truncation using the
entered values.
<OK> Applies the parameter settings and displays a new View
with the calculated spectrum after closing the dialog box.

57
 <Cancel> Closes the dialog box without performing interpolation and
truncation.

Reference: Methods of data interpolation

Data interpolation determines the interpolation function F that satisfies Yi = (Xi); i=1,2,3,... N
from the data points {(Xi,Yi); i=1,2,3,...N} obtained by measurement in order to estimate Y with
respect to X (except for known Xi).
“Lagrange interpolation” and “Tertiary spline interpolation” are representative methods of data
interpolation.
(1) Lagrange interpolation
This method determines a function F that passes through all data points in a specified
range for interpolation. For N data points, F is a complicated (N - 1)th-order function.
However, in practice, the calculation is performed through special operations.

(2) Tertiary spline interpolation

This method calculates the values between N data points within a specified range using
(N - 1) different tertiary functions Fi. The interpolation functions Fi and Fi+1 for adjacent
sections are determined such that the values of the functions and their first and second
derivatives agree at the boundary.

58
3.5.2 [Operations] submenu
3.5.2.1 [Arithmetic...]
Performs an arithmetic operation between spectra or between a spectrum and a constant(s)
(Fig. 3.43). When only one spectrum is displayed in the active View, the arithmetic operation is
performed using a constant(s). When two spectra are displayed, the arithmetic operation is
performed between the two spectra. When three or more spectra are displayed, the second
spectrum to be used in the arithmetic operation must be designated from the [Select Spectrum]
dialog box (Fig. 3.42), which opens before the [Arithmetic] dialog box (Fig. 3.43). The active
spectrum in the View is always selected as the primary spectrum for the arithmetic operation.

Figure 3.42 [Select Spectrum] dialog box

Figure 3.43 [Arithmetic] dialog box (left: when a single spectrum is displayed, right: when two
spectra are displayed)

The operation to be performed is shown at the top of the dialog box (Fig. 3.43). S1 and S2
represent the selected spectra and are defined immediately below the arithmetic expression to
be calculated. Enter constants into the appropriate text boxes and select the desired arithmetic
operator from the drop-down list to generate an arithmetic expression.

<Apply> Performs the calculation using the designated parameters.

<Exchange> Reverses the order of spectra S1 and S2.
Spectrum display area The original spectrum or spectra is (are) displayed at the top, the
results of the arithmetic operation are displayed below it.
<Scales...> Specifies the display scales for the upper spectrum. The x-axis

59
 scale is applied for both spectra.
[Auto scale y-axis] Displays the results using the auto-scaling function. Clear to view
the change in the size of the calculated spectrum.
<OK> Applies the settings for the arithmetic expression and displays the
calculated spectrum in a new View after closing the dialog box.
<Cancel> Closes the dialog box without performing calculation.

Note 1: To perform an arithmetic operation between one spectrum and a constant,

input 0 for the factor for the second spectrum and a constant not related to the
desired operation.
Note 2: The result of dividing between single beams (SB) is converted to %T. When
adding or subtracting %T (%R), the values are added or subtracted using the
same units. (Addition of 100% and 100% yields 200% and subtraction of 100%
and 100% yields 0%. This is in contrast to the difference spectrum obtained
using [Subtraction...]).

60
3.5.2.2 [Derivatives...]
Determines the derivative of a spectrum (Fig.3.44). First-, second-, third-, and fourth-order
derivative calculations can be performed using a [Subtract] or [Savitzky-Golay] algorithm.

Note: [Derivatives] processing is not compatible with data having an irregular data
point interval (pitch). In order to conduct [Derivatives] processing, it is
necessary to perform interpolation to obtain a regular data point interval by
using [Truncate Data] in advance.

Figure 3.44 [Derivatives] dialog box

Spectrum display area Displays the original spectrum at the top, and the calculated
spectrum below it.
[Algorithm] Selects the derivative algorithm from the drop-down list.
[Order of derivatives] Select the order of the derivative. Choose a 1st, 2nd, 3rd, or 4th order
derivative function from the drop-down menu.
[Order of polynomial] Selects the order of a smoothing polynomial for the
[Savitzky-Golay] algorithm. Choose a 1st, 2nd, 3rd, 4th or 5th order
polynomial from the drop-down menu.
Data points Selects the interval between data points, in effect, the data point
interval for [Subtract] and the number of data points to be used,
centered on the point being smoothed using the [Savitzky-Golay]
algorithm.
<Apply> Performs the smoothing using the interval selected in [Data points].
<Scales...> Specifies the display scale for the upper spectrum. The x-axis scale
is applied for both spectra.
<OK> Applies the parameter settings and displays a new View after
closing the dialog box.
<Cancel> Closes the dialog box without performing differentiation.
Note: When differentiating a spectrum containing a high level of noise, it is
recommended to conduct smoothing first or use a higher number of [Data
points].

61
3.5.2.3 [K-K Transform...]
Determines the absorbance from a specular reflection spectrum (Kramers-Kronig transform)
(Fig. 3.45). Only available for spectra for which the vertical axis is absorbance (Abs), %T
or %R.
Since the specular reflection spectrum is affected by the refractive index and absorption index
of the sample, the measured spectrum has an appearance similar to that of a first derivative.
This spectrum can be divided into components corresponding to the absorption index (k) and
the refractive index (n), by subjecting the reflectance spectrum to a Kramers-Kronig (K-K)
transform. This can only be performed effectively when the spectrum looks like a first derivative
and both ends are flat (no peaks present).. In addition, when applying a K-K transform to only a
specific region, select a region for which both ends are flat.

Note: Only the displayed area is calculated, and data in other areas are truncated
from the original spectrum.

Figure 3.45 [K-K Transform] dialog box

Note: Figure 3.45 shows spectra before the K-K transform is performed. All three
spectra in the spectrum display area are the same. After execution, the top
spectrum is the original spectrum, the middle spectrum is the K-K-transformed
spectrum and the bottom spectrum is the refractive index spectrum obtained
as a result of the calculation (Fig. 3.46).

Spectrum display area The top spectrum is the original spectrum, the middle spectrum is
the K-K-transformed spectrum and the bottom spectrum is the
refractive index spectrum obtained as a result of the calculation
(Fig. 3.45).
[Thinning] Specifies the interval between data points to be used for
calculation. Calculation is faster when this value is large.
<Apply> Performs the calculation using the set parameters. The

62
 K-K-transformed spectrum is in Abs mode.
<Scales...> Specifies the display scale for the top spectrum. The x-axis scale
is applied for all the spectra.
<OK> Applies the calculation parameters and closes the dialog box.
Spectra for the absorption index (k) spectrum and the refractive
index (n) are displayed in two separate Views.
<Cancel> Closes the dialog box without performing the K-K transform.

Figure 3.46 [K-K Transform] result dialog box

63
3.5.3 [Peak Processing] submenu
3.5.3.1 [Peak Find...]
Detects the peaks and/or valleys in the spectrum (Fig.3.47). The peak table and marker display
on the spectrum can be updated by changing the peak find parameters in the parameters
group and clicking the <Apply> button.

Peak table

Figure 3.47 [Peak Find] dialog box

Peak table Displays the peak find results for the active spectrum. Clicking on a
value causes a vertical line cursor to appear at the selected
top/bottom position in the spectrum display area below. The
top/bottom position and the intensity are displayed as x- and y-axis
values, respectively, to the right of the peak table.
[Peak] Lists the modes available for detecting the peaks or valleys in the
spectrum.
Top: Detects peaks.
Bottom: Detects valleys.
Both: Detects both peaks and valleys.
[Noise level] Enters a threshold value used to recognize the top/bottom of the
peak. When the difference between the start of the top/bottom of a
peak and its apex (valley to peak to valley) does not meet or
exceed this value, the peak will not be recognized. The units are
the same as those used for the active spectrum.
[Upper limit], Specifies the upper and lower limits for photometric values for valid
[Lower limit] peaks. Selecting the check boxes enables the corresponding text
boxes and displays horizontal line cursors indicating the upper and
lower limits in the spectrum display field. When these check boxes

64
 are selected, the [Peak Find] function searches the portion of the
spectrum currently specified by the upper and/or lower horizontal
cursor(s). Therefore, by changing the position of the cursor(s) it is
possible to select those peaks or valleys within a specific y-axis
range of the spectrum.
When this check box is not selected, the [Peak Find] function
searches the entire y-axis range for the spectrum. The upper and
lower limits can also be set by dragging the cursors using the
square bar handles ( ).
<Apply> Performs peak finding using the specified [Peak Find] parameters.
Spectrum display field By clicking on the short bar that indicates a peak position, the
vertical line cursor will move to that position and the selected value
in the peak list becomes highlighted. This operation is identical to
clicking on a value in the peak list.
The vertical line cursor can also be moved to locations other than
the selected top/bottom positions by left-clicking the desired
position within the spectrum. The wavelength (wavenumber) and
y-axis value for the selected position, as indicated by the x-axis
and y-axis values, respectively, are displayed above the spectrum
display area. To add a peak or valley, click on the desired
peak/valley position, and then click the <Add> button.
<Print...> Opens the [Print Preview] window. For details refer to Section
3.2.11 [Print Preview...].
<Scales...> Specifies the display scale for the spectrum.
Peak finding is performed only within the x-axis range set here.
Clicking the <Apply> button after changing the scale updates the
peak table.
<Add> Adds a peak/valley. Click the <Add> button after clicking on the
desired position within the spectrum.
<Delete> Deletes a peak/valley. Select the peak(s) to be deleted in the peak
list or in the spectrum display and then click the <Delete> button.
<Copy> Copies the peak table to the clipboard. The result of [Peak Find]
can also be copied to the Windows clipboard by selecting the peak
table and pressing Ctrl + C.
<OK> Accepts the [Peak Find] parameters within the dialog box and
displays the calculated peak labels in the original View after closing
the dialog box. The peak label format can be pre-selected prior to
execution of [Peak Find] by choosing a peak mark setting from the
[View] - [Peak Indicators] submenu (Section 3.4.13).
<Cancel> Closes the dialog box without attaching the detected peak
information to the original data.

65
Note: Easy detection of peak top (bottom)
This is a convenient function that can be used when a peak that is smaller than
the noise level is to be added. Dragging the mouse in the x-axis direction while
holding down the Ctrl key moves the vertical line cursor to the position at
which the vertical axis value is the largest (or smallest, in the case of a valley)
in the range over which the mouse is dragged. Clicking the <Add> button adds
the selected peak (or valley). Dragging the mouse pointer while holding down
the Ctrl key displays a red line on the spectrum display that indicates the
x-axis range to be examined for the maximum or minimum value (peak or
valley).

66
 3.5.3.2 [Peak Height...]
Determines the peak height and peak height ratio for a selected peak(s) (Fig. 3.48).

How to draw the baseline

Figure 3.48 Methods for determining peak height

Note 1: It is always best and more accurate to calculate peak heights by using a
spectrum in the absorbance format.
Note 2: The [Peak Height] function has many parameters that can be set. Follow the
procedure below to learn about general ideas concerning [Peak Height].

Operating procedure

This example shows how to calculate the peak height for a spectrum by using [Two-point base
(auto)].

(1) Select [Peak Height] from the [Peak Processing] submenu to display the [Peak Height]
dialog box.

Information Results
display field display field

Figure 3.49 [Peak Height] dialog box

67
(2) Select the [P1] check box to calculate the peak height.

Note: Select the [P1] and [P2] check boxes to calculate the peak height ratio.

(3) Select [Two-point base (auto)] from the [Calculation method] drop-down list.
(4) Select Base 1 and Base 2 to set the base range for the horizontal axis by using the
vertical line cursors. The base range can also be set by typing values in the two text
boxes and clicking the <Apply> button. The peak height for the spectrum is calculated
and the results are displayed in the results display field.

Note: To calculate the peak height ratio, follow steps (3) and (4) after selecting a
peak to be set in the information display field.

(5) Click the <Print...> button to display the [Print Preview] window. Clicking the <Print>
button in the dialog box prints the results.

[Peak], [Base 1], [Base 2] Displays horizontal axis fields for Peak, Base 1 and Base 2.
Enter the values and click the <Apply> button. Alternatively,
the displayed vertical line cursors can be dragged to the
desired positions for the Peak, Base 1 and Base 2 fields. Items
to be set vary with [Calculation method].
[P1], [P2] check boxes P1 and P2 represent Peak 1 and Peak 2, respectively. Items
having a check in the check box are ascertained and
calculation results are displayed in the results display field.
[Calculation method] Selects how to draw the baseline for peak height calculation
and how to set the peak position (manually or automatically).
When (Auto) is set for [Two-point base], the maximum
absorption position is recognized as a peak within the range
specified by Base 1 and Base 2. (Auto) cannot be set in the
case of a [One-point base).
Click the drop-down menu for [Calculation method] and select
the desired calculation method.
One-point base
Two-point base (manual)
Two-point base (auto)

The method used to draw the baseline is described in Fig.

3.48.
Information display field Displays the peak and base positions for peaks ([P1], [P2]) for
calculating the peak height/height ratio. The horizontal range
can be changed using the vertical line cursors or by entering
the desired values into the peak and base fields and clicking
the <Apply> button.

68
Spectrum display area The peak and base positions can be set by dragging the
vertical line cursors on the spectrum. The peak height and
peak height ratio are calculated simultaneously upon setting
the x-axis values. The y-axis value for the active line cursor is
displayed in the [Data] field.
Results display field Displays the calculation results for the peak height/height
ratio. The results are calculated and re-displayed each time
the peak and base position(s) are changed.
<Apply> Clicking this button after the values for Peak, Base 1 and Base
2 have been entered moves the appropriate vertical line
cursors to the specified position and performs the peak height
calculation.
<Copy> Copies the [Peak Height] calculation results and the
associated information to the clipboard.
<Print...> Opens the [Print Preview] window. Refer to Section 3.2.11
[Print Preview...] for more information.
<Scales...> Specifies the display scale for the spectrum.
<OK> Performs the peak height/peak height ratio calculation using
the defined parameters and closes the dialog box. The results
are attached to the original spectrum file as metadata and the
file must be saved for the results to be retained.
<Cancel> Closes the dialog box without attaching the peak height
calculation results to the original data.

69
3.5.3.3 [Peak Area...]
Determines the peak area and peak area ratio for a selected peak(s) (Fig. 3.50).

How to draw the baseline

(1) [Two-point base]: Determines the total area within the baseline range
(2) [No base]: Assumes 0 Absorbance or 100%T as the baseline
(3) [Independent base]: Sets the baseline and peak ranges separately

Peak height Peak height Peak height

Baseline Baseline Baseline

Designate these points Designate these points Designate these points

(1) Determines total area (2) Assumes 0 Abs or 100%T (3) Sets the baseline and peak
within baseline Peak area as the baseline Peak area ranges separately
Figure 3.50 Peak Area determination methods

Calculation methods
(1) Ignore under baseline
(2) Subtract under baseline
(3) Add under baseline
To calculate peak area aa’ + bb’ in Fig. 3.51(a), designate a [Two-point base] from Point A to
Point B and select [Add under baseline]. To calculate peak area aa’, designate a [Two-point
base] from Point A to Point B and select [Ignore under baseline]. To calculate peak area aa’ -
bb’, designate a [Two-point base] from Point A to Point B and select [Subtract under baseline].

Figure 3.51(a) Example 1 Figure 3.51(b) Example 2

In Fig. 3.51(b), when a baseline is designated from Point A to Point B, all three methods give
the same result.

70
Note1: It is always better and more accurate to calculate peak areas using a spectrum
in the absorbance format.
Note2: The [Peak Area] function has many parameters that can be set. Follow the
procedure below to learn about general ideas concerning [Peak Area].

Operating procedure
This example shows how to calculate the peak area for a spectrum by using [Independent
base (manual)].
(1) Select [Peak Area] from the [Peak Processing] submenu to display the [Peak Area]
dialog box.

Information Results
display field display field

Figure 3.52 [Peak Area] dialog box

(2) Select the [P1] check box to calculate the peak area.

Note: Select the [P1] and [P2] check boxes to calculate the peak area ratio.

(3) Select [Two-point base] and [Ignore under baseline] from the [Calculation method]
drop-down list.

(4) Select the baseline range for Peak 1 by using the vertical line cursors. The baseline
range can also be set by typing values in the two text boxes and clicking the <Apply>
button. The peak area for the spectrum is calculated and the results are displayed in the
results display field.

Note: To calculate the peak area ratio, follow steps (3) and (4) after selecting a peak
to be set in the information display field.

(5) Click the <Print...> button to display the [Print Preview] window. Clicking the <Print>
button in the dialog box prints the results.

71
[Range (area)], Specifies the peak area calculation range and the peak baseline
[Range (baseline)] range. Enter the values and click the <Apply> button to set the
area and baseline values. Alternatively, drag the vertical line
cursors to the desired positions for the area and baseline fields.
Items to be set vary with [Calculation method].
[P1], [P2] check boxes P1 represents peak area 1 and P2 represents peak area 2. Items
having a check in the check box are ascertained and the
calculation results are displayed in the results display field.
[Calculation method] Selects how to draw the baseline for peak area calculation and the
method of peak area calculation.
Select P1 or P2 and click the drop-down menu for [Calculation
method].
Baseline: Two-point base, No base, Independent Base
Method: Ignore under baseline, Subtract under baseline, Add
under baseline
The method used to draw the baseline and the calculation
properties are described in Figs. 3.50 to 3.51.
Information display field Displays the area calculation range for peaks ([P1], [P2]) for
calculating the peak area/area ratio and the horizontal axis value
for the baseline calculation range. The horizontal range can be
changed using the vertical line cursors or by entering the desired
values into the base fields and clicking the <Apply> button.
Spectrum display field The area calculation range and base calculation range can be set
by dragging the vertical line cursors on the spectrum. The peak
area and peak area ratio are calculated simultaneously upon
setting of the line cursors. The y-axis value for the active line
cursor is displayed in the [Data] field.
Results display field Displays the calculation results for the peak area/area ratio. The
results are calculated and re-displayed each time the area and
baseline range are changed.
<Apply> Clicking this button when the values of the [Range (area)] and
[Range (baseline)] are entered moves the vertical line cursors to
the specified position and performs the area calculation.
<Copy> Copies the [Peak Area] calculation results and the associated
information to the clipboard.
<Print...> Opens the [Print Preview] window. Refer to Section 3.2.11 [Print
Preview...] for more information.
<Scales...> Specifies the display scale for the spectrum.
<OK> Performs the peak area/peak area ratio calculation using the
defined parameters and closes the dialog box. The results are
attached to the original spectrum file as metadata and the file
must be saved for the results to be retained.
<Cancel> Closes the dialog box without attaching the peak area calculation
results to the original data.

72
3.5.3.4 [FWHM...]
Calculates the full width at half maximum (Fig. 3.53).

Results
display field

Information
display field

Figure 3.53 [FWHM] dialog box

Spectrum display field Sets the full width at half maximum calculation range by dragging
the vertical line cursors on the spectrum. The full width at half
maximum value is calculated simultaneously. Alternatively, the full
width at half maximum calculation range can be entered directly in
[x-axis (L)] and [x-axis (R)] and the <Apply> button clicked.
[y-axis] Displays the y-axis value where the active vertical line cursor
intersects the spectrum.
[x-axis (L)] Enters the lower x-axis value for the full width at half maximum
calculation range.
[x-axis (R)] Enters the upper x-axis value for the full width at half maximum
calculation range.
[FWHM] Displays the result of the full width at half maximum calculation.
<Apply> Clicking this button when the values for [x-axis (L)] and [x-axis (R)]
are entered moves the vertical line cursors to the specified position
and performs the full width at half maximum calculation.
<Copy> Copies the [FWHM] calculation results and the associated
information to the clipboard.
<Print...> Opens the [Print Preview] window. For details refer to Section
3.2.11 [Print Preview...].
<Scales...> Specifies the display scale for the spectrum.
<OK> Performs the full width at half maximum calculation using the
defined parameters and closes the dialog box. The results are
attached to the original spectrum file as metadata and the file must
be saved for the results to be retained.
<Cancel> Closes the dialog box without attaching the full width at half
maximum calculation results to the original data.

73
3.5.4 [Subtraction...]
Determines a difference spectrum from two spectra (Fig. 3.54).
One method of identifying an unknown sample is to compare the spectrum of the sample with other
known spectrum. To identify the components of an unknown mixture, the spectrum of the known
component(s) can be removed, leaving only the spectrum containing the unknown component(s) of
the mixture. Thus, if the spectrum of the mixture is assumed to be A, and the spectrum of a known
component is assumed to be B, the difference spectrum can be determined using the formula ((A
coefficient) - B) or the formula (A – (B coefficient)). The coefficient is then selected to cancel the
intensity of a common absorption peak (key band) present in the two spectra.
The coefficient can be applied using one of two methods. The first method involves
continuously changing the coefficient to remove the key band by trial and error while viewing
the spectrum. The second method involves calculating the coefficient from an observed peak
height or area in order to remove the key band.

The number of spectra overlaid in the View determines which dialog box opens first when
[Subtraction] is performed.
When two spectra are displayed, the [Subtraction] dialog box appears (Fig. 3.54).
When three or more spectra are displayed, select the unknown spectrum from which
you wish to subtract the known component(s). When [Subtraction] is selected, the
[Select Spectrum] dialog box is displayed (Fig. 3.42). Select the spectrum that contains
the component(s) to be subtracted from the unknown spectrum.

Note: [Subtraction] is not valid when only one spectrum is displayed in the View.
Perform [Subtraction] after overlaying at least one additional spectrum
containing a known component of the mixture.

Figure 3.54 [Subtraction] dialog box

The calculated result is displayed in the spectrum field at the bottom.
[Factor] Enters a multiplication factor. The factor can also be changed
using the arrow keys . Each click on the arrow keys

74
 increases or decreases the factor by the amount designated in
[Step]. The difference spectrum is recalculated each time the
factor is changed.
[Step] Designates the amount by which [Factor] increases or
decreases each time an arrow key is clicked.
<Exchange> Exchanges the spectrum to be multiplied by the factor. In Fig.
3.49, clicking the <Exchange> button will change the calculation
from (Std-5.jws – (Factor Std-2).jws) to ((Factor
Std-5.jws) – Std-2.jws).
<Exchange Data> Click to exchange the spectra. In Fig. 3.49, clicking the
<Exchange Data> button will change the calculation from
(Std-5.jws – (Factor Std-2).jws) to (Std-2.jws – (Factor
Std-5).jws).
<Scales...> Specifies the display scale for the upper spectrum. The x-axis
scale is applied for both spectra.
<Apply> Performs the subtraction calculation after [Factor] has been
entered, and shows the subtraction result in the lower spectrum
display field.
<Auto Factor> Displays the [Subtraction – Auto Factor] dialog box used to
calculate the factors that cancel a particular peak. These factors
can be calculated using a peak height or peak area. (The
contents of the [Subtraction – Auto Factor] dialog box are
described below (Fig. 3.50).
<Offset> Toggling offset calculates the overall spectrum, where the
difference at an arbitrary x-axis value for two spectra is zero.
Move the vertical cursor to any position or enter the x-axis value
and click the <Apply> button.
[Auto scale y-axis] Select the checkbox to view the results using the auto-scaling
function. Clear the checkbox to view the change in the size of
the resulting difference spectrum.
<OK> Applies the [Subtraction] parameters and displays the
subtraction result in a new View after closing the dialog box.
<Cancel> Closes the dialog box without calculating the subtracted
spectrum.

75
3.5.4.1 Automatic calculation of factor
Calculates a factor that cancels a peak of interest by subtraction. The factor can be calculated
from either the peak height or peak area.
The factor in the subtraction equation displayed at the upper left of the spectrum changes in
real time.

Factor

Figure 3.55 [Subtraction – Auto Factor] dialog box

[Peak Parameters] Sets the method for calculating the subtraction factor (either peak
height or peak area) and how the baseline is defined.
Height (two-point base)
Height (one-point base)
Area (two-point base)
Area (one-point base)
For more information about how to define the baseline and the
calculation range, refer to 3.5.3.2 [Peak Height] and 3.5.3.3 [Peak
Area].
[Range (peak)] Items to set differ depending on the calculation method selected
[Range (baseline)] and how the baseline is to be defined. Select a specific x-axis
position using the vertical cursor or enter the horizontal axis value
and click the <Apply> button.
<Apply> Moves the vertical cursor(s) to the specified position when the
values of the [Range (peak)] and [Range (baseline)] are entered and
performs the subtraction calculation.
[Data] Displays the current y-axis values for the active vertical cursor.
<OK> Applies the entered parameters and displays the result within the
[Subtraction] dialog box after closing the [Subtraction – Auto
Factor] dialog box.
<Cancel> Closes the dialog box without changing the settings for the [Auto
Factor] parameters.

76
3.5.5 [X Unit Conversion...]
Converts the x-unit units for a spectrum and opens a new View for the converted spectrum (Fig.
3.56).

Note: The units for the x-axis can be changed by choosing [Horizontal Axis Units...]
from the [View] menu, but this only changes the apparent units for the View
window, while the units for the data in memory remain the same.

Figure 3.56 [X Unit Conversion] dialog box

[Horizontal units] Selects the x-axis units after conversion.

<OK> Converts the x-axis units and displays the spectrum in a new View.
<Cancel> Closes the dialog box without converting the x-axis units.

77
3.5.6 [Y Unit Conversion...]
Converts the y-axis units for the spectrum (Fig. 3.57).
This function is applicable for spectra for which the vertical axis is absorbance (Abs), %T
or %R.

Note: When a spectrum is selected for which the vertical axis is intensity, a [Data
mode error] message will appear.

Figure 3.57 [Y Unit Conversion] dialog box

[Vertical units] Selects the y-axis units after conversion.

<OK> Converts the y-axis units and displays the spectrum in a new View.
<Cancel> Closes the dialog box without converting the y-axis units.

78
3.5.7 [Common Options]
The contents of [Common Options] vary depending on the instrument.

3.5.7.1 [Curve Fitting...]

Selecting [Processing] – [Common Option] – [Curve Fitting] runs the [Curve Fitting] program.
The active spectrum is automatically transferred to the program. Refer to the separate [Curve
Fitting] program manual for details.

3.5.7.2 [Data Dump...]

Displays data values for a spectrum. The values can be copied to the clipboard.

Parameters
setting field

Spectrum
display field

Data value
display field Vertical line
cursors

Figure 3.58 [Data Dump] dialog box

[Range] Enters the range within which to list the data values. The range can
also be input by moving the vertical line cursors.
[Thinning] Designates the interval between data points to be used for data
value display.
<Apply> Moves the vertical line cursors to the specified positions when the
values of the [Range] are entered, and lists the data values.
<Close> Closes the dialog box.
<Copy> Copies the data values to the clipboard.
<Scales...> Sets the display scale for the spectrum.

79
 3.5.7.3 [Data Accumulation...]
Obtains the average of spectra overlaid in the same View and displays the new spectrum in a
new View. This function cannot be performed on spectra that have different data modes, data
intervals, or measurement ranges.

3.5.7.4 [Arithmetic between Data...]

Performs an arithmetic operation between spectra overlaid in the same View. This function
cannot be performed on spectra that have different data modes or data intervals. An arithmetic
operation is performed only on the overlapping ranges of the spectra. When only one spectrum
is displayed in the active View, the arithmetic operation is performed using a constant(s).

Arithmetic expression

Calculated spectrum Before calculation After calculation

Overlaid spectra

Figure 3.59 [Arithmetic between Data] dialog box (left: 1 channel data, right: multiple channel data)

The operation to be performed is shown at the top of the dialog box (Fig. 3.59). S1 and S2
represent the selected spectra and are defined immediately below the arithmetic expression to
be calculated. Enter constants into the appropriate text boxes and select the desired arithmetic
operator from the drop-down list.

Spectrum display field Displays overlaid raw spectra on the left side and calculated
spectra on the right side.
<Apply> Performs the calculation using the designated parameters.
<Exchange> Reverses the order of spectra S1 and S2.
<Scales...> Specifies the display scale for the spectrum before calculation (on
the left side). The x-axis scale is applied for both the spectra before
and after calculation.
[Auto scale y-axis] Displays the results using the auto-scaling function. Clear to view
the change in the size of the calculated spectrum.

[Calculation] Selects the calculation channel for multiple channel data.

<OK> Applies the settings for the arithmetic expression and displays the
calculated spectrum in a new View after closing the [Arithmetic
between Data] dialog box.
<Cancel> Closes the dialog box without performing the calculation.

80
Note 1: To perform an arithmetic operation between one spectrum and a constant in a
View in which multiple spectra are displayed, open the dialog box via the same
procedure as when performing an arithmetic operation between data. Input 0
for the factor of the spectrum and a constant not related to the desired
operation even if there are multiple spectra.
Note 2: The dialog box in Fig. 3.60 is displayed when performing this function on a
single spectrum. In the dialog box, an arithmetic operation between one
spectrum and a constant can be performed.

Figure 3.60 [Arithmetic between Data] dialog box when a single spectrum is displayed

81
3.5.7.5 [Channel Conversion...]
Converts channels of data in a View and extracts data having a desired channel from overlaid
spectra or multiple channels in a View . To process data with a channel number of 2 to 4, either
the data must be converted to channel 1 using this function, or extracted and opened in a new
View, where it will be in channel 1.

Note1: Data processing is performed only on channel 1 data.

Note2: Spectrum data measured using FT-IR or UV/Vis spectrophotometer have only
one channel. The data processing results are displayed with the specified
spectra arranged lengthwise in one dialog box.

Channel data
to be selected.

Spectrum
display field

Figure 3.61 [Channel Conversion] dialog box

[Channel data] Selects channel data from the drop-down list. The data is displayed
on the spectrum display field. Click the <Add> button to register the
data to [New data image]. Data is numbered according to the order
that it is added. Repeat this procedure to convert all channels.
Then, select the required channel to display the desired data.

Note: To convert the channel for multiple data, display the

data in one View before conversion.

[New data image] Displays the registered data in the list. The maximum number of
data that can be added is 4.
<Add> Adds the selected data in the [Channel data] drop-down list to the
[New data image] list.
<Delete> Deletes the selected data in the [New data image] list.

82
<Up> Moves the selected spectrum to a lower channel number.
<Down> Moves the selected spectrum to a higher channel number.
<OK> Displays registered data in a new View after closing the [Channel
Conversion] dialog box.
<Cancel> Closes the dialog box without performing the conversion.

Note: Spectrum data measured using a FT-IR or UV/Vis spectrophotometer have

only one channel. The data processing result is displayed with the specified
spectra arranged lengthwise in one dialog box.

Figure 3.62 View after channel conversion

83
3.5.7.6 [Arithmetic between Channels...]
Performs an arithmetic operation between channels of data displayed in the same View. The
[Arithmetic between data] function performs an arithmetic operation between overlaid spectra.
This function performs arithmetic operation by selecting two data sets from multiple channel
data displayed in the same View. The attributes of the vertical axis can also be selected. This
function is performed on the horizontal axis range covered by both data sets.

Note: Spectrum data measured using a FT-IR or UV/Vis spectrophotometer have

only one channel. In those cases, the operation is the same as the [Arithmetic]
function.

File name
display field

Figure 3.63 [Arithmetic between Channels - Settings] dialog box

[Select data] Displays channels and file names in the [S1] and [S2] drop-down
lists. Click on the button to display file names of data overlaid in
the same View. Select a data set and channel.
[Data attribute after Selects an attribute after processing. When the data attribute
processing] changes, select the [Select attribute] check box and select an
attribute from its drop-down box. For example, attribute after
dividing a single beam by another single beam, it becomes %T.
<OK> Displays the dialog box for specifying calculation parameters (Fig.
3.64).
<Cancel> Closes the dialog box without performing the calculation.

84
 Arithmetic operation

Overlaid spectra

Calculated spectrum

Figure 3.64 [Arithmetic between Channels] dialog box

Spectrum display field S1 and S2 represent the selected spectra and are defined
immediately below the arithmetic operation. Enter constants into
the appropriate text boxes and select the desired arithmetic
operator from the drop-down list to generate an arithmetic
expression. Refer to 3.5.7.4 “[Arithmetic between Data]” for details.
Click the <Back> button to return to the dialog box in Fig. 3.63.
<OK> Applies the settings for the arithmetic expression and displays the
calculated spectrum in a new View after closing the [Arithmetic
between Channels] dialog box.
<Cancel> Closes the dialog box without performing the calculation.

85
3.5.7.7 [Photon X Unit Conversion...]
Converts the horizontal units (wavenumber, wavelength or energy) for a spectrum to the
selected units and displays the converted spectrum in a new View. In [Photon X Unit
conversion], the vertical axis value is divided by the conversion factor for the horizontal axis
units to maintain the peak area after conversion.

Figure 3.65 [X Unit Conversion - Photon] dialog box

<OK> Applies the settings for the X-unit conversion and displays the
converted spectrum in a new View after closing the [X Unit
Conversion - Photon] dialog box.
<Cancel> Closes the dialog box without performing the conversion.

Note: This function cannot be performed on data converted using [X Unit

Conversion...].

86
3.5.7.8 [Time Axis Offset...]
Sets the specified time of the time-course data to zero.

Time setting bar

Time-course
data display field

Figure 3.66 [Time Axis Offset] dialog box

Time-course data Displays the original and offset time-course data in the upper and
display field lower graphs, respectively. When the dialog box is first opened, the
data displayed in the lower graph is not offset. Drag the time setting
bar in the upper graph to select the offset position.
[Offset at] Specifies the time to offset the time-course data in the upper graph.
<Apply> Offsets the data with the time specified in the [Offset at] text box and
displays the result in the lower graph.
<Scales...> Specifies the display scale for the time-course data displayed in the
upper graph. The x-axis scale is applied for both the data.
<OK> Applies the settings for the offset and displays the calculated spectrum
in a new View after closing the [Time Axis Offset] dialog box.
<Cancel> Closes the dialog box without performing the calculation.

87
3.5.7.9 [Peak Normalization...]
Normalizes the intensity of the specified peak position to an arbitrary intensity. [Peak
Normalization] can also be used for overlaid spectra. Select [One-point base] for [Baseline] to
normalize the intensity difference at peak and base wavelengths.

Spectrum display field

Figure 3.67 [Peak Normalization] dialog box

Spectrum display The upper and lower graphs show the original and normalized
field spectra, respectively.
[Normalization Specifies the intensity after normalization.
value]
[Display] Displays the spectrum in the spectrum display field.
[Legend], Displays the line style and name for the spectrum.
[Spectrum Name]
[Position] Specifies the wavelength for normalizing the spectrum.
[Baseline] Selects the correction method for the baseline. Double-click the text
box to display a drop-down list with [No base] and [One-point base]
options. Select [One-point base] to normalize the intensity difference
at the peak and base wavelengths.
[Base] Specifies the base wavelength. [Base] can be specified only when
[One-point base] is selected for [Baseline].
[All position] Applies the normalization wavelength for a spectrum to the other
spectra. This command can only be selected when two or more
spectra are opened in [Peak normalization].
[All base] Applies the base wavelength for a spectrum to the other spectra. This

88
 command can only be selected when two or more spectra are opened
in [Peak normalization].
<Auto Detect> Locates the wavelength of the spectrum with the maximum intensity
and specifies this wavelength as the normalization position.
<Apply> Normalizes the data with the specified parameters.
<Scales...> Specifies the display scales for the upper spectrum. The x-axis scale
is applied for both spectra.
<OK> Applies the settings for the normalization calculation and displays the
normalized spectra in a new View after closing the [Peak
Normalization] dialog box.
<Cancel> Closes the dialog box without performing the normalization.

3.5.7.10 [Run KnowItAll]

Transfers an active spectrum to the search software KnowItAll. The KnowItAll is the spectrum
search program of Bio-Rad Laboratories, Inc., and is a standard program of FT-IR series.
Refer to the separate KnowItAll manual for details.

Note: Installation of KnowItAll software on the PC is required.

89
3.5.8 IR Options
Analysis functions for data collected by an FT-IR are displayed on the [IR Options] menu.
Some instruments have standard menu items that are registered when the infrared
spectrometer driver is installed.

3.5.8.1 [ATR Correction...]

Two types of ATR correction method are prepared. Select the ATR correction method from
[Method].

Figure 3.68 [ATR Correction] dialog box

[Method]: Penetration Depth

The penetration depth method corrects the relative intensity ratios for high wavenumber and
low wavenumber data such that the ATR data more closely corresponds to spectra data
collected using the transmission method. It is not necessary for the penetration depth
correction to input the correction parameters.

[Method]: Anomalous Dispersion

The peaks of ATR spectrum will shift to lower wavenumber due to anomalous dispersion
compared with the peaks of transmission spectrum. The anomalous dispersion correction
makes this effect reduced. Input wavenumber range, measurement parameters, and sample
refractive index into the correction parameters.

Correction Parameters
[Range] Enters the correction range for the spectrum.
[Repeat] Enters the number of times to repeat the correction.
[Incident angle] Enters the incidence angle for ATR.

90
[Prism refractive Selects the type of prism used for the measurement. [Diamond],
Index] [ZnSe], [Ge], [KRS5], [Si], [ZnS] are registered by default. If other ATR
prism is used, it must be newly registered. Input the prism name and
refractive index. To delete a user-defined registered prism, erase the
prism name. The selected user-defined prism is erased from the
[Prism refractive Index] list.
[Sample refractive Enters the sample refractive index. The refractive index of the general
index] organic matter is approximately 1.5.
<Apply> Starts the ATR correction.
<Retry> Erases the corrected spectrum and retries the ATR correction to reset
the correction parameters.
[Normalize] Normalizes the spectra before and after ATR correction.
<Scales...> Specifies the display scale for the spectrum.
<OK> Applies the settings for the ATR correction and displays the corrected
spectrum in a new View after closing the [ATR correction] dialog box.
<Cancel> Closes the dialog box without correcting the spectrum.

Note1: When [Normalize] is selected, the scale for the spectrum cannot be changed.
Note2: The baseline for the ATR spectrum should be Abs > 0 for [Anomalous
Dispersion].
Note3: To register a user-defined prism, Manager or Analysts privileges in the
workgroup are required.

91
3.5.8.2 [Spectrum to Interferogram...]
Converts a single-beam spectrum (Single) into an interferogram (IF) (Fig. 3.69). There are no
parameters to be set for this dialog box.

Figure 3.69 [Spectrum to Interferogram] dialog box

<OK> Applies the reverse transform settings and displays the

interferogram in a new View.
<Cancel> Closes the dialog box without performing the reverse FFT
transform on the single-beam spectrum.

92
3.5.8.3 [Auto Baseline]
Automatically corrects a spectrum baseline. Entering a fitting range or setting the range
with the vertical line cursors and clicking the <Apply> button performs the baseline
correction.

Figure 3.70 [Automatic Baseline Correction] dialog box

[Order] Selects the order of the baseline correction. Setting an order and
clicking the <Apply> button performs the correction and re-displays
the corrected spectrum.
[Fitting range] Sets a correcting range. Setting a range and clicking the <Apply>
button performs the correction and re-displays the corrected
spectrum.
<Apply> Performs the baseline correction according to the set conditions
and displays the corrected spectrum.
<Scales...> Specifies the display scale for the spectrum.
<OK> Applies the baseline correction parameters and displays the
corrected spectrum in a new View after closing the [Automatic
Baseline Correction] dialog box.
<Cancel> Closes the dialog box without performing baseline correction.

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3.5.8.4 [Interferogram to Spectrum...]
Converts an interferogram (IF) into a single-beam spectrum (Single) (Fig. 3.71). Eleven types
of apodization functions are available for the FFT for the interferogram.

Spectrum display field

Figure 3.71 [Interferogram to Spectrum] dialog box

Spectrum display field Displays the original spectrum in the upper spectrum display field,
and the transformed single-beam spectrum in the lower spectrum
display field.
[Apodization] Selects the desired apodization function for the FFT transform.
[Resolution] Selects the transformed spectrum resolution. Note that a
resolution lower than that of the interferogram cannot be selected.
[Zerofilling] Selects the amount of zero filling to be done.
<Apply> Performs the calculation using the designated parameters and
displays the transformed spectrum in the lower spectrum display
field.
<OK> Displays a transformed spectrum in a new View.
<Cancel> Closes the dialog box without performing the FFT transform on
the interferogram.

94
3.5.8.5 [H2O Reduction]
Water vapor in the air may affect the spectrum being measured by obscuring some of the
analyte peaks. This function eliminates the water vapor absorption in the infrared spectrum
(Fig. 3.72).

Figure 3.72 [H2O Reduction] dialog box

[Start] [End] Sets the range for conducting water vapor reduction. After entering a
range in the text box, click the <Add> button. The range is registered in
the table. The range can also be set using the vertical line cursors. Up
to 16 spectral ranges can be set.
[Function] Selects a weighting function from Constant (0-th order), Linear
(primary) and Quadratic (secondary) functions.
<Add> Registers a new water vapor reduction range.
<Delete> Deletes the currently selected range from the display field.
<OK> Applies the water vapor reduction parameters and displays the
corrected spectrum in a new View.
<Cancel> Closes the dialog box without performing the water vapor reduction.

95
3.5.8.6 [CO2 Reduction]
Carbon dioxide in the air may affect the spectrum being measured by obscuring some of the
analyte peaks. This function eliminates the CO2 absorption in the spectrum (Fig. 3.73).

Figure 3.73 [CO2 Reduction] dialog box

[Start] [End] Sets the range for conducting CO2 reduction. Enter a spectral range for
the reduction in the text box, and then click the <Append> button. The
range is registered in the display field at the bottom. Up to 16 spectral
ranges can be set.
[Function] Selects a weighting function from Constant (0-th order), Linear (primary)
and Quadratic (secondary) functions.
<Add> Registers a new CO2 reduction range.
<Delete> Deletes the currently selected range.
<OK> Applies the CO2 reduction parameters and displays the corrected
spectrum in a new View.
<Cancel> Closes the dialog box without performing the CO2 reduction.

96
3.5.8.7 [Data Comparison]
Compares a measured spectrum with a reference spectrum.

Note: When the driver for the FT-IR spectrometer is installed, this command is in [IR
Options] in the [Processing] menu. When it is not installed, this command is in
[Common Options...] in the [Processing] menu. If the user has an FT-IR
spectrometer and other instruments, this command is installed in both
[Common Options] and [IR Options].

Results display field

Figure 3.74 [Data Comparison] dialog box

[Algorithm] Displays the comparison algorithm selected in Fig. 3.75.

[No. of data] Enters the number of comparison results to display in the results
display field. Enabled when [Folder] is selected in Fig. 3.75. Clicking
the <Apply> button performs the comparison calculation. The results
are displayed in descending matching order.
<Compare Specifies the comparison parameters. The [Data Comparison
Settings...> Settings] dialog box is displayed (Fig. 3.75).
<Export...> Saves the comparison results in text format.
The target file name for comparison, parameters (algorithm,
calculation range and threshold) and comparison results (matching
order numbers, score, pass or fail results and reference file names)
are saved.
<Print Preview...> Displays the print preview dialog box (Fig. 3.78).

97
<Scales...> Specifies the display scale for both spectra.
<Decimal Places...> Selects the number of decimal places to display for the score,
threshold or calculation range.
<OK> Performs the comparison calculation using the defined parameters
and closes the dialog box. Results are attached to the original
spectrum file as metadata and the file must be saved for the results to
be retained.
<Cancel> Closes the [Data Comparison] dialog box.

File name/result list

From [Common Options...] From [IR Options...]

Figure 3.75 [Data Comparison Settings] dialog box

Files for comparison Sets the comparison file.

[Spectrum files] Selects the spectrum reference file for comparison. Files other than
spectrum files with the extension (.jws) cannot be opened, In the CFR
version, only reviewed and approved jws files can be specified.
[Folder] Selects the folder in which reference spectrum files in jws format are
saved. All of the spectra in the selected folder are compared. The
results are displayed in descending matching order in the file
name/result list. In the CFR version, only reviewed and approved jws
files can be specified.

98
 [Library file] Selects the spectrum file in a library file created using the [SSP-4000
Spectra Search] program. In the CFR version, this function is not
available.
<Browse...> Selects the folder name and path for the saved spectrum files.
<Delete> Deletes the selected comparison spectrum file in the file name/result
list when [Spectrum files] is selected.
[Specify comparison Enabled when [Spectrum files] is selected.
range]
<Range...> Displays the dialog box in Fig. 3.76.

Figure 3.76 [Comparison Range Settings] dialog box

[Select full range] Compares the spectra using the measurement

wavelength range. Deselecting this check box
enables the comparison wavelength range to
be entered.
[Start], [End] Displays the wavelength range for comparing
the spectra. To set the wavelength range, drag
the vertical bars on the graph.
<Add> Registers a new wavelength range.
<Delete> Deletes the selected wavelength range.
<OK> Applies the changes to the [Comparison
Range Settings] settings and closes the dialog
box.
<Cancel> Closes the dialog box without applying any
changes to the [Comparison Range Settings]
settings.

Algorithm Selects the comparison algorithm.

Options: Euclidean Distance, 1st Derivative Euclidean Distance,
Correlation Coefficient, 1st Derivative Correlation
Coefficient, Absolute Value, 1st Derivative Absolute Value,
Least Squares, 1st Derivative Least Squares

99
<Threshold...> Sets the pass or fail criteria (Fig. 3.77).

Figure 3.77 [Threshold Settings] dialog box

[Evaluate] Selects whether to perform a pass/fail

evaluation.
[Threshold] Sets the criteria for passing values.
[Notation for data with Specifies the string to be displayed when
higher value] the value is higher than the threshold.
[Notation for data with Specifies the string to be displayed when
lower value] the value is lower than the threshold.
<OK> Applies the changes to the [Threshold
Settings] settings and closes the dialog
box.
<Cancel> Closes the dialog box without applying
any changes to the [Threshold Settings]
settings.
[Y-axis Normalize Selects the normalization method when the spectrum is compared.
method] Options:
[Normalized at max point of std spectrum]
Normalizes the scale for each spectrum at the x-axis value where
the maximum intensity is obtained for the comparison spectrum. Use
this option when the data is obtained using an IR or Raman
spectrometer.
[Normalized at maximum intensity point]
Select if the maximum intensity in either the target or comparison
spectrum is negative. Normalizes the scale for each spectrum at the
x-axis value which gives the absolute maximum intensity.
[Not normalized]
Do not normalize the target and comparison spectra. Use this option
when the data is obtained using a UV/Vis spectrophotometer or
spectrofluorometer.

Note: If [Data Comparison...] is selected from [IR Options],

[Y-axis Normalize method] is not displayed (right pane

100
 in Fig. 3.75) but the calculation method [Normalized at
max point of std spectrum] is automatically applied.

[Score normalize]/ Enabled when [Euclidean Distance] or [1st Derivative Euclidean

[Normalize] Distance] is selected for [Algorithm]. The closer the value is to 1, the
higher the similarity to the comparison file is. If [Data Comparison] is in
[IR Options...], this option name is [Normalize]. The equation is as
follows,
200 S
I I: score after normalization
200
S: score calculated by the algorithm
<OK> Performs the comparison calculation using the defined parameters
and closes the dialog box. The results are attached to the original
spectrum file as metadata and the file must be saved for the results to
be retained.
<Cancel> Closes the [Data Comparison] dialog box.

Separated layout Overlaid layout Overlaid layout

(normalized) (no normalization)
Figure 3.78 Print preview window

Selects the items to print (see Fig. 3.74). In the CFR version, Managers or
Analysts authority is required to select print items.
Specifies the paper margins in inches or millimeters (Section 3.2.11, Fig. 3.17). In
the CFR version, Managers or Analysts authority is required to specify margins.
Specifies the font for the title, information and data (Section 3.2.11, Fig. 3.18). In
the CFR version, Managers or Analysts authority is required to specify fonts.
Prints the data. “Unsigned” will be watermarked on the printed page when no
creation signature is assigned to the analysis data.
<Close> Closes the [Print Preview] window.

101
 Figure 3.79 [Print Items] dialog box

[Title] Prints the title. Enter a desired title in the text box.
[Detailed information] Prints information about the data such as the creation date or start
and end wavelengths.
[Measurement Prints measurement information such as the creation date,
information] instrument name, accessory name and measurement parameters.
[Comments] Prints the sample name, comment, user name, workgroup name
(only for CFR version), division and company names.
[Legends] Prints the legends.
[Results] Prints the spectrum comparison results for the comparison file.
When [Folder] or [Library file] is selected in Fig. 3.75, the results for
comparison with the single file selected in the results display field in
Fig. 3.75 are printed.
Spectrum Selects the layout options for spectra.
[Separate] Tiles two spectra horizontally.
[Overlay] Overlays two spectra.
[Normalize] Normalizes two spectra and overlays them.
<OK> Applies the changes to the [Print Items] dialog box and closes the
dialog box.
<Cancel> Closes the dialog box without changing any settings in the [Print
Items] dialog box.

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3.6 [Window] Menu
Determines the layout of Views.

[Cascade] Cascades all open Views.

[Tile Horizontally] Tiles all open Views horizontally.
[Tile Vertically] Tiles all open Views vertically.
[Arrange Icons] Arranges the minimized View icons.
[Close All] Closes all Views. If any spectral data has been changed or if the data
is new, a message is displayed which asks if you wish to save the
data before closing (Fig. 3.80). Click the <Yes> button to save the
data before closing. Click the <No> button to close the View without
saving. Click the <Cancel> button to cancel closing the View.

Figure 3.80 Save message

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3.7 [Other] Menu
Customizes toolbars, specifies the View and print style options, and sets the number of
decimal places in the View.
3.7.1 [Customize Toolbar...]
Customizes the [Data Processing] toolbar (Fig. 3.81).

Figure 3.81 [Customize Toolbar] dialog box

[Available toolbar buttons] Displays the tool buttons that can be added to the toolbar.
[Current toolbar buttons] Displays the tool buttons displayed in the toolbar.
[Add ] Adds the selected button from [Available toolbar buttons] to
[Current toolbar buttons].
[ Remove] Deletes the selected button from [Current toolbar buttons] and
moves it to [Available toolbar buttons].
<Close> Closes the dialog box.
[Reset] Restores the toolbar settings to their default settings.
[Move Up], [Move Down] Moves the active button in [Current toolbar buttons] upwards
or downwards.

104
3.7.2 [Options...]
Changes the View and print style options (Fig. 3.82). The settings are applied to subsequently
opened data.
3.7.2.1 [View] tab

Figure 3.82 [View] tab in [Options] dialog box

[Apply view settings to all Select to apply the parameter settings in the [Patterns], [Fonts],
spectra] and [Gridlines] dialog boxes from the [View] menu to all open
Views.
[Apply scale settings to all Select to apply the parameter settings in the [Scales] dialog box
views] from the [View] menu to all open Views.
[Automatically scale Select to use the y-axis auto-scaling function when opening or
display range when a overlaying spectra in a View.
spectrum is opened or
overlaid]
Default for wavenumber Select the default setting for the wavenumber axis. Select:
axis [1:1]: for a constant wavenumber interval.
[2:1]: for an expanded scale from 2000 cm-1 and below, values
above 2000 cm-1 will be compressed 2:1 compared to data
displayed below 2000 cm-1.
[4:1]: for an expanded scale from 2000 cm-1 and below, values
above 2000 cm-1 will be compressed 4:1 compared to data
displayed below 2000 cm-1.
[2000 cm-1]: displays a solid line at 2000 cm-1. Available when
[2:1] or [4:1] is selected.
y-axis auto scale Allows customization of the settings used for the y-axis auto
scale.

105
[Standard] Fits the y-axis scale to the maximum and minimum values
displayed in the View.
[User defined]
[Upper and lower Automatically calculates the y-axis scale with a specified
margins] proportion of blank space above and below the maximum and
minimum values displayed in the View. Settings range from 0 to
20%.
[Number of decimal Specifies the number of significant figures to be used for the
places for y-axis label] y-axis label. Settings range from 2 to 6 significant figures. The
y-axis label is always rounded up.
[Peak Unit Indicators] Shows or hides the units for the x- and y- axes when peak
detection is performed. When [OFF] is selected, units are not
displayed. Even when [ON] is selected, units are not displayed if
they are non-dimensional (Abs, Int, SB, or %T).

3.7.2.2 [Print] tab

Figure 3.83 [Print] tab in [Options] dialog box

[Prompt the user to type title Prompts to enter a title for the printout before printing.
before printing]
[Print histories for data Prints the data processing histories and page ID when
processing] [Print...] command in the [File] menu is selected. If the
printouts have multiple pages, they are uniquely
numbered.
Print format
[Standard form] Selects to print using the standard format.
[Fixed form] Selects to print using the fixed format.

106
 [User form] Selects to print using a template file created in JASCO
Canvas. Click the <Browse...> button and designate the
JASCO canvas template file to be used.
Legends
[Always] Selects to always print a legend with the spectra.
[Never] Selects to never print a legend with spectra.
[Only when printing multiple Selects to print a legend with spectra only when multiple
data] data are displayed.
<OK> Applies the settings and closes the dialog box.
<Cancel> Closes the dialog box without applying any changes to the
settings.

3.7.2.3 [Data Processing] tab

Note: This tab is displayed only when the non-CFR version is used.

Figure 3.84 [Data processing] tab in [Options] dialog box

[Auto save after data Select to automatically assign a file name to the measured
processing] data and save the file in the specified folder after data
processing.
[Folder] Displays the path and folder name for the save destination.
<Browse...> Browses to the drive and folder for saving the data.
[File name] Selects the file name format to be used when automatically
saving. The file format is Standard Files (*. jws). The file
name is automatically assigned to the measured data
using the format selected in the [File name] drop-down list.
[Date-No.]: Sets [Date] + [3-digit serial number] as the file

107
 name. The date and serial number are
connected with a hyphen “-”.
[Sample-No.]: Sets [Sample name] + [3-digit serial
number] as the file name. [Sample name] is
the name entered in the [Information] tab.
[Comment-No.]: Sets [Comment] + [3-digit serial number]
as the file name. [Comment] is the comment
entered in the [Information] tab.
[Sample-Comment-No.]: Sets [Sample name] + [Comment]
+ [3-digit serial number] as the file name.
[Sample name] and [Comment] are the name
and comment entered in the [Information] tab,
respectively.
[String-No.]: Sets [String] + [3-digit serial number] as the
file name. Type the character string in the
[String] text box below.
[String] Enters a character string when [String-No.] is selected for
[File name] (maximum 30 single-byte characters).
[Data name display format] Selects the naming format for the processed data.
[Standard]: Names the processed data “Memory-x”, where
x is a number.
[Add “*” for each data processing]: Appends an asterisk “*”
to the data name after each processing step.
For example, if the original data name is
“Polystyrene.jws”, and the data is processed
once, it becomes “Polystyrene.jws*”. If it is
again processed, it becomes
“Polystyrene.jws**”.
[Add processing menus for each processing]: Appends the
name of each data processing step to the
original data name. For example, if baseline
correction and smoothing are performed on
“Polystyrene.jws”, the data name becomes
“Polystyrene.jws-[Baseline
Correction]-[Smoothing]”.

Note 1: If [Data name display format] is changed when there are some processed data
in the window, the processed data names are automatically displayed in the
new format.
Note 2: If processed data named using the asterisk format or the process-name format
is saved and later reopened for further processing, additional asterisks or
process names will be appended.
Note 3: Unsaved data that is transferred from a measurement program or imported is
always displayed as “Memory-x”, regardless of the selected [Data name

108
 display format]. Once this data is processed, the new name depends on [Data
name display format].
Note 4: If [Auto save after data processing] is selected, [Data name display format]
cannot be selected.

[Display the default file name in Select to enter a default file name in the [Save As] dialog
the [Save] dialog] box, using the format specified in [File name].
[File name] Select the format of the file name to be assigned when
automatically saving.
[Date-No.]: Sets [Date] + [3-digit serial number] as the file
name. The date and serial number are
connected with a hyphen “-”.
[Sample-No.]: Sets [Sample name] + [3-digit serial
number] as the file name. [Sample name] is
the name entered in the [Information] tab.
[Comment-No.]: Sets [Comment] + [3 digit serial number]
as the file name. [Comment] is the comment
entered in the [Information] tab.
[Sample-Comment-No.]: Sets [Sample name] + [Comment]
+ [3-digit serial number] as the file name.
[Sample name] and [Comment] are the name
and comment entered in the [Information] tab,
respectively.
[String-No.]: Sets [String] + [3-digit serial number] as the
file name. Type the character string in the
[String] text box below.
[Source-file name-No.]: Sets [Original file name] + [3-digit
serial number] as the file name. The original
file name and serial number are connected
with a hyphen “-”. If the original file name is
“Memory-x”, where x is a number, the new file
name will be “Memory-x-y, where y is a 3-digit
number.
[Source file name-String.]: Sets [Original file name] +
[String] as the file name. Type the character
string in the [String] text box below. If the
original file name is “Memory-x”, where x is a
number), the new file name will be
“Memory-x-String”.
[String-source file name]: Sets [String] + [Source file name]
as the file name. Type the character string in
the [String] text box below. If the original file
name is “Memory-x”, where x is a number, the
new file name will be “String-Memory-x”.

109
[String] Enters a character string when [String-No.], [Source file
name-String.] or [String-source file name] is selected for
[File name] (maximum 30 single-byte characters).
<OK> Click to apply the settings and close the dialog box.
<Cancel> Click to close the dialog box without applying any changes
to the settings.

Note 1: Even if [Display the default file name in the [Save] dialog] is selected, if
[Standard] is selected for [Data name display format], irrespective of the format
specified for [File name], “Memory-x”, where x is the number displayed in the
View title, is entered in the [Save As] dialog box.
Note 2: If [Auto save after data processing] is selected, [Display the default file name in
the [Save] dialog] cannot be selected.

3.7.3 [Decimal Places...]

Sets the display format for the vertical and horizontal axes (Fig. 3.85). The format set here will
be reflected in the numeric value field for each item in the status bar, the [Processing]-[Peak
Processing] submenu and the [View Offset] dialog box (see Sections 3.5.3 and 3.1.4.6,
respectively).

Figure 3.85 [Decimal Places] dialog box

[Item] Selects the units of the vertical and horizontal axis for which the format is
to be set.
[Decimal places] Selects the decimal places for the units selected in the [Item] drop-down
list.
<OK> Applies the format settings and closes the dialog box.
<Cancel> Closes the dialog box without applying any changes to the format
settings.

Note: The View format is set with [View]-[Styles] (Refer to Section 3.4.9).

110
3.8 [Help] Menu
3.8.1 [Contents]
Displays the help window with the contents tab selected.

3.8.2 [Search Topic]

Displays the help window with the index tab selected.

3.8.3 [About...]
Displays version information for the [Spectra Analysis] program.

Figure 3.86 [About Spectra Manager] dialog box

111
4. Appendix

4.1 JCAMP-DX Format Files

The JCAMP-DX file format allows data conversion between various computers and media.
This format was created by JCAMP (Joint Committee of Atomic and Molecular Physical Data)1).
The JCAMP-DX format offers the following advantages:
Format file data can be easily transferred between large computers, multi-purpose laboratory
computers, common data processing systems, workstations, and personal computers.
Because JCAMP-DX files are text files, the data can be viewed or edited using various
commercially available editors.
In addition to spectra, peak tables and three-dimensional data can be handled.
The Spectra Analysis software can save measured and calculated data in the JCAMP-DX
format. Data saved in this format can be manipulated using the Grams data processing
program or the Sadtler reference program; among others. Although JCAMP-DX has several
formats, only the FT-IR format is explained here. The following explanation requires some
knowledge of ASCII code. A sample of JASCO's JCAMP-DX obtained using a JASCO FT-IR is
given below as an example.

##TITLE= Sample name JCAMP-DX files always start with the ##TITLE= line.
##JCAMP-DX= 4.24 JCAMP-DX version
##DATA TYPE= INFRARED SPECTRUM Designation for IR spectrum.
##ORIGIN= JASCO Always JASCO.
##OWNER= xxxxxx Contents entered in [Organization] in [Comment Edit]
##DATE= 96/08/17 Measurement date
##TIME= 13:33:46
##SPECTROMETER/DATA SYSTEM
##RESOLUTION=
##DELTAX= 1.92905045 Interval between data points (units in ##XUNITS=)
##XUNITS= 1/CM Units of horizontal axis
##YUNITS= TRANSMITTANCE Units of vertical axis (attribute)
##XFACTOR= 1.0000 Actual value is obtained by multiplying value
in ##XYDATA= by this factor.
##YFACTOR= 0.00001
##FIRSTX= 370.3777 First value for x-axis of ##XYDATA= (actual value)
##LASTX= 4627.7920 Last value for x-axis of ##XYDATA= (actual value)
##NPOINTS= 2208 Number of data points
##FIRSTY= 74.58664 Y-axis value corresponding to ##FIRSTX= (actual value)
##MAXY= 91.44050 Maximum value of y-axis (actual value)
##MINY= 0.46792 Minimum value of y-axis (actual value)
##XYDATA= (X++(Y..Y)) Data are written from this point on
370.3777 7458664 7164965 6797073 6463581 6262086 6216446 6313309 6520278
385.8191 6759706 6993072 7203347 7370707 7518471 7794603 7953664

112
------(all data not shown)
4608.5015 8470810 8478381 8484588 8489256 8495972 8500248 8504088 4623.9341
8505672 85807172 8509182
##END= JCAMP-DX files always end with the ##END=.

4.1.1 JCAMP-DX File Structure

4.1.1.1 Labeled-Data-Records (LDRs)
Labeled Data Records (LDRs) consist of a data label (described later) and data. LDRs start
with the ## data label flag and end with the next data label flag.

4.1.1.2 Lines
One line can contain up to 80 characters. The terminator for a line is CR-LF. LDRs can include
several lines. Therefore, CR-LF does not necessarily designate the end of an LDR.

4.1.1.3 Data labels

A data label clarifies an LDR. Several labels are defined in the above example and further
details are provided in Section 4.1.2. Data labels include the reserved labels defined by
JCAMP as well as user defined labels that can record any information input by the user. The
JASCO Spectra Analysis software does not employ user-defined labels.

4.1.1.4 Blocks
A block is a set of LDRs starting with ##TITLE= and ending with ##END=. A single JCAMP-DX
file can contain multiple blocks (the Spectra Analysis software only responds to a one-block
format).

4.1.2 Reserved Labels

Only JCAMP-DX reserved labels that the Spectra Analysis software can use are described
here. Reserved labels that start with ##, and multiple labels cannot be placed on one line.

(1) ##TITLE=
All JCAMP-DX files begin with the LDR ##TITLE=. Spectra Analysis data files use the
contents of the “Sample name” field as the ##TITLE=.
(2) ##JCAMP-DX= 4.24
This LDR always follows ##TITLE=, and indicates the version of the file format.
(3) ##DATA TYPE=
Defines the data format of the block. The ##DATA TYPE= includes ULTRAVIOLET
SPECTRUM, FLUORESCENCE SPECTRUM, RAMAN SPECTRUM, INFRARED PEAK

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 TABLE, INFRARED INTERFEROGRAM, and INFRARED TRANSFORMED
SPECTRUM.
(4) ##ORIGIN=

Name and address of the file creator. This is always JASCO.

(5) ##OWNER=
Name of the owner of the spectrum. Here, the content entered is described in the
“Organization” field of a Spectra Analysis data file.
(6) ##DATE=, ##TIME=
The date (yy/mm/dd) and time (hh:mm:ss) when the spectrum was measured.

(7) ##SPECTROMETER/DATA SYSTEM=

Describes the measurement system and data processing system. This reflects the
instrument used to record the spectral data and the Spectra Manager version.
(8) ##RESOLUTION=
(9) ##DELTAX=
Interval between data points. The unit is ##XUNITS=. In the case of data subjected to
zero filling, the unit differs based on the value of ##RESOLUTION=, as mentioned
earlier.
(10) ##XUNITS=
Unit (attribute) of the horizontal axis. ##XUNITS= is always 1/CM (cm-1) because Spectra
Manager cannot save an interferogram as a JCAMP-DX file. Other ##XUNITS= include
MICROMETERS, NANOMETERS and SECONDS.
(11) ##YUNITS=
Unit of the vertical axis. Spectra Manager supports the following units (units enclosed by
parentheses are as named in Spectra Manager). TRANSMITTANCE (%T),
REFLECTANCE (%R), ABSORBANCE (ABS), KUBELKA-MUNK (KM) and
ARBITRARY UNITS (other y-axis labels).
(12) ##XFACTOR=, ##YFACTOR=
Multiplying the data of ##XYDATA= by this factor gives the actual value.
(13) ##FIRSTX=, ##LASTX=
The first value and the last value (actual value) of the horizontal axis of ##XYDATA=.
(14) ##NPOINTS=
Number of data points of ##XYDATA=.
(15) ##FIRSTY=

The value of the vertical axis (actual value) corresponding to ##FIRSTX.

(16) ##MAXY=, ##MINY=
The maximum and minimum values (actual values) of the vertical axis.

114
(17) ##XYDATA=
Data starts here. Indicates that (X++(Y..Y)) is the data format and that the first datum in
each row is the X-axis datum and that the remaining data on the row until the CR-LF are
Y-axis data.
In the examples above, the data 370.3777, 385.8101,... represent wavenumbers. Here,
7458664 indicates the data at 370.3777 cm-1 and 7164965 indicates the data at
(370.3777 + ##DELTAX) cm-1. (The actual value can be obtained by multiplying the
y-axis data by ##YFACTOR=.)
JCAMP-DX defines other data formats, but Spectra Manager is only compatible with this
data format.
(18) ##END=
All JCAMP-DX blocks terminate with ##END=.

4.1.3 User-defined Labels

In addition to the labels reserved by JCAMP-DX, users can create new labels. These labels are
called user-defined labels. User-defined labels start with a $. Spectra Manager CFR cannot
output user-defined labels.

4.1.4 Adding Comments

(1) ##=
Comments starting with this label can occupy any number of lines up to the next ## data
label flag.

(2) $$
Comments starting with $$ can be placed anywhere on a line. This type of comment can
only continue to the end of the line and does not designate the end of the LDR.

Reference literature
1) R.S. McDonald, P.A. Wilks Jr., Appl. Spectrosc. 42, 151 (1988).

115
4.2 Smoothing Methods
Smoothing is used to eliminate noise components from a spectrum in order to improve the
signal-to-noise ratio. It is important that the optimum method is selected for a given waveform
because smoothing may distort spectrum analyte bands. The [Spectra Analysis] program has
the following four types of smoothing methods. All are based on the moving averaging method,
in which appropriate weights are assigned to the data point of interest and surrounding points.

1. Simple moving average method

This method is used when the spectrum bandwidth is wide, that is, when the signal component
is sufficiently smooth compared with the noise. The simple moving average method uses a
rectangular function as a weighting function and produces a large smoothing effect; however, a
significant amount of signal distortion can also occur.

2. Savitzky-Golay method
This method can be used to eliminate noise from most spectra. It uses the weighting algorithm
outlined by Savitzky and Golay1). The weighting function changes depending on the data width
(convolution width) setting used for smoothing.

3. Adaptive smoothing method

This method is convenient for eliminating noise from sharp spectra, such as gas phase spectra.
The spectrum is distorted only slightly in the peak area and the smoothing effect can be
enhanced in the baseline area by choosing weighting coefficients based on the noise variance
and local signal variance.

4. Binomial method
In this smoothing method, the weighting is calculated using binomial coefficients2). Compared
with the Savitzky-Golay method, the binomial method has a number of advantages, such as no
distortion over the entire waveform, no phase (peak position) shift, and a short processing
time.

Reference literature
1) A. Savitzky, M. Golay, Anal. Chem. 36, 1627 (1964).
2) P. Marchand, L. Marmet, Rev. Sci. Instrum. 54, 1034 (1983).

116
4.2.1 Moving Average Method

The operating principle of the moving average method is based on a convolution calculation,
similar to that for an analog filter. The output y(t) of an analog filter is expressed by the
following equation representing convolution of the input signal x(t) and the filter impulse
response h(t).
y (t ) x( ) h(t )d h( ) x(t )d
In the moving average method, the input signal is expressed by n discrete values x(i) (where i
= 1, 2,..., n), and the smoothed value y(i) is determined as shown below by using a weighting
function, w(j), consisting of N (=2m +1) discrete points (where, j = -m,...-1, 0, 1,..., m).
m
1
y (i) w( j ) x(i j) :i m 1, m 2,..., n m (1)
W j m
m
W w( j )
j m
(2)

where W is a normalization constant.

4.2.2 Simple Moving Average Method

This is the simplest smoothing method and uses a rectangular function as a weighting function.
For a rectangle with a width of N = 2m + 1, the operation is described by the following
expression, which is derived by setting n equation (2):
m
1
y (i) x(i j) :i m 1, m 2,..., n m
N j m

117
4.2.3 Savitzky-Golay Method
This is a method of fitting the measured spectrum to a polynomial curve, based on the least
squares error criterion in the neighborhood of each sample point. The type of weighting
function varies with the order of the polynomial. A detailed table of values (weighting
coefficients) for each discrete point of this weighting function was first reported by Savitzky and
Golay. Thus, the smoothing operation can be carried out simply by performing a convolution
using the coefficient table below.

Discrete point No. 25 23 21 19 17 15 13 11 9 7 5

-12 -253
-11 -138 -42
-10 -33 -21 -171
-9 62 -2 -76 -136
-8 147 15 9 -51 -21
-7 222 30 84 24 -6 -78
-6 287 43 149 89 7 -13 -11
-5 342 54 204 144 18 42 0 -36
-4 387 63 249 189 27 87 9 9 -21
-3 422 70 284 224 34 122 16 44 14 -2
-2 447 75 309 249 39 147 21 69 39 3 -3
-1 462 78 324 264 42 162 24 84 54 6 12
0 467 79 329 269 43 167 25 89 59 7 17
1 462 78 324 264 42 162 24 84 54 6 12
2 447 75 309 249 39 147 21 69 39 3 -3
3 422 70 284 224 34 122 16 44 14 -2
4 387 63 249 189 27 87 9 9 -21
5 342 54 204 144 18 42 0 -36
6 287 43 149 89 7 -13 -11
7 222 30 84 24 -6 -78
8 147 15 9 -51 -21
9 62 -2 -76 -136
10 -33 -21 -171
11 -138 -42
12 -253
Normalization 5175 805 3059 2261 323 1105 143 429 231 21 35
coefficient

The coefficients in this table were obtained by fitting to quadratic and cubic polynomials. The
following figure shows the principle of smoothing using seven discrete points.

118
 Secondary
adaption range
Smoothed point
y(i)=c

Y(i)=a(j-i)2+(j-i)+c

Measurement points x(k)

Weighting function W(j)

In this example, it is assumed that within the range i-m to i+m (number of points is 2m+1) about
a given data point i (seven points in the above figure), the measured spectrum y(j) can be
expressed by the following quadratic polynomial:
y ( j ) a ( j i ) 2 b( j i ) c :j m i,..., 1 i, i,1 i,..., m i

Here, the coefficients a, b and c are determined by minimizing the sum of the squared errors
between the polynomial and the measured data points, given by:
m i
{x( j ) y ( j )}2
j m i

The smoothed value y(i) at the center point i of the quadratic function is then given by c. The
coefficient table contains the weighting coefficients used to determine the coefficient c.
Therefore, the smoothed value y(i) at point i is calculated using the (2m+1) measurement
values x(j) and the coefficients w(j) (J= -m,..., -1, 0, 1,..., m) from the table as follows:
m
1
y (i) x(i j ) w( j )
W j m
m
W w( j )
j m

119
4.2.4 Adaptive Smoothing Method
It is assumed that the measured data curve spectrum x(i) can be expressed as the sum of a
signal component s(i) and a noise component n(i):
x (i ) s (i ) n (i )

It is also assumed that n(i) is random static noise (i.e., noise that does not change with time)
having an average value of zero and a variance , and that the signal is also static within a short
period of time. The estimated value of the signal that satisfies the least squares error criterion
2
is denoted by sˆ(i ) That is, sˆ(i ) is the value that minimizes E sˆ(i ) s (i ) and is expressed
as:
2 2
(i)
sˆ(i) x
2
n
x(i) x (i) x (i)
(i)
x

x (i ) E x (i )
2 2
x E x(i ) x (i)

(Strictly speaking, E {} represents an aggregate average, but here it is given as a local average
that varies with time.)
2 2
(i )
The noise variance n is obtained from actual measurements. x is determined by a
simple moving average with a constant width N, and the estimated value of the true signal
2
(i )
component can be obtained by calculating the variance dispersion x of the measured
data curve within this width.

120
4.2.5 Binomial Method
This is a moving average method that is very simple to implement and produces no rippling
effects after smoothing. Smoothing is performed by repeatedly applying the following equation
a designated number of times:
1
y (i) ( x(i 1) 2 x(i) x(i 1))
4

The table below gives the coefficients calculated using the weighting function w(j)) and the
normalization constant W for different cycle numbers. In contrast to the Savitzky-Golay method
based on the polynomial approximation, in this method the weighting coefficients cannot be
negative. Thus, no rippling occurs in the neighborhood of abrupt changes.

Discrete point 12 11 10 9 8 7 6 5 4 3 2 1
No.
-12 1
-11 24 1
-10 276 22 1
-9 2024 231 20 1
-8 10626 1540 190 18 1
-7 42504 7315 1140 153 16 1
-6 134596 26334 4845 816 120 14 1
-5 346104 74613 15504 3060 560 91 12 1
-4 735471 170544 38760 8568 1820 364 66 10 1
-3 1307504 319770 77520 18564 4368 1001 220 45 8 1
-2 1961256 497420 125970 31824 8008 2002 495 120 28 6 1
-1 2496144 646646 167960 43758 11440 3003 792 210 56 15 4 1
0 2704156 705432 184756 48620 12870 3432 924 252 70 20 6 2
1 2496144 646646 167960 43758 11440 3003 792 210 56 15 4 1
2 1961256 497420 125970 31824 8008 2002 495 120 28 6 1
3 1307504 319770 77520 18564 4368 1001 220 45 8 1
4 735471 170544 38760 8568 1820 364 66 10 1
5 346104 74613 15504 3060 560 91 12 1
6 134596 26334 4845 816 120 14 1
7 42504 7315 1140 153 16 1
8 10626 1540 190 18 1
9 2024 231 20 1
10 276 22 1
11 24 1
12 1
Normalization 1677721 4194304 1048576 262144 65536 16384 4096 1024 256 64 16 4
constant 6

121
4.3 Self-deconvolution Method
The Fourier self-deconvolution method is used to precisely distinguish the peak positions of
individual bands in measured spectra containing multiple bands with the same width. The
following conditions apply when using this method.
(1) The program assumes that the spectral band shapes are Lorentzian.
(2) After processing, only the peak position of each band is meaningful. The reason for this
is that vertical axis information is sacrificed in order to elucidate horizontal axis
information.
(3) The program cannot be applied to measured spectra consisting of bands with different
widths. If the half width at half maximum of a band is σ' and that of the deconvolution filter
is σ, excessive deconvolution will occur when σ > σ' and insufficient deconvolution will
occur when σ < σ'.
(4) The signal-to-noise ratio of the measured spectrum will be reduced after processing
because, as with differential operations, the deconvolution filter emphasizes high
frequencies.

Principles
The program is an improved version of both the FSD (Fourier self-deconvolution)1) method
proposed by Kauppinen et al. and the FIRO (finite impulse response operator)2) method
formulated by Jones and Shimokoshi. Since both methods can be explained based on the FSD
principles, only the FSD method will be described here.

If the real spectrum is given by E ( ) , the measured spectrum M ( ) is generally distorted by

the instrument function G( ) of the measurement system. If the system is linear, the following
equation applies:
M ( ) G( ) * E ( ) (1)
where the * symbol expresses a convolution integral. If I M ( x ) and I E ( x ) are taken to be the
inverse Fourier transforms of M ( ) and E( ) , respectively, the equation becomes
1
I E ( x) 1
I M ( x) (2)
F G( )
1
where F G ( ) is the inverse Fourier transform of G( ) . In other words, this gives the ideal
inverse filter in the interferogram region. This filter is extremely sensitive to noise, so an
apodization function D( x , L ) is introduced into equation (2) to cut the high-frequency noise
using the FSD method
D( x , L)
I E ( x) I M ( x)
F 1 G( )
(3)
where L is the frequency to be eliminated.
The instrument function G( ) is assumed to be Lorentzian with a half width at half maximum σ.
Therefore, equation (3) becomes

122
 D( x , L)
I E ( x) I M ( x)
exp x
(4)
By taking the Fourier transform of equation (4), the deconvoluted profile E( ) can be obtained
as
D( x , L)
E( ) F I M ( x)
exp x
(5)
These are the principles of the FSD method.
Equation (5) can be converted as follows:
D( x , L)
E( ) F * M( )
exp x
(6)
exp x
The FIRO method involves expanding the term in equation (6) in the spectrum
region for various types of apodization functions D( x , L ) .
In this program, in order to reduce the calculation time, an algorithm that combines the FSD
and FIRO methods is used. The deconvolution filter that is ultimately used on the spectrum has
the following form:
D( x , L)
F * D ( , FL)
exp x

where D( x , L ) and D ( , FL) are taken to be Bessel functions, and L and FL are taken to be
automatically determined values.

Reference literature
1) Appl. Spectrosc. 35, 271 (1981).
2) Appl. Spectrosc. 37, 59 (1983).

123
4.4 Kubelka-Munk Transform (K-M Transform)
The Kubelka-Munk equation expresses the relationship between the diffuse reflectance and
the absorption/scattering coefficient. In JASCO [Spectra Manager], the function that
transforms the reflectance to the extinction/diffusion coefficient using the Kubelka-Munk
equation is called the “K-M Transform”. After this transform has been applied, the vertical data
axis is K/M.

4.4.1 Principle of K-M Transform

The interaction between light and a diffusely reflecting sample is considered to be as follows.
The surface and interior of the sample consist of many fine particles. When light is incident on
the sample, it is repeatedly transmitted, absorbed, or reflected by the fine particles as it enters
the sample. Figure 1 illustrates this process for a single particle layer with a thickness dx at an
arbitrary depth x in the sample. Assuming K to be the extinction coefficient and S to be the
diffusion coefficient, and taking the direction of the light into consideration, equations (1a) and
(1b) express the variation of the transmitted light intensity i and reflected light intensity j.
di (K S )i dx Sj dx (1a )
dj (K S ) j dx Si dx (1b )
Kidx is the attenuation due to absorption of light beam i, Sidx is its attenuation due to scattering,
Kjdx is the attenuation due to absorption of light beam j, and Sjdx is its attenuation due to
scattering.

Kubelka and Munk solved the above differential equations and expanded them to include the
measured quantity as a parameter. The Kubelka-Munk equation is expressed as follows:

K (1 R ) 2
(2)
S 2R
R : R represents the reflectance for a sample thick enough for the effect of the base to be
negligible.

j
dx
x

Figure 4.1 Repeated transmission, absorption and reflection of light incident on a sample

124
4.5 Kramers-Kronig Transform (K-K Transform)
The Kramers-Kronig transform calculates the wavelength dispersion of the refractive index n
and extinction coefficient k from the specular reflectance spectrum of a sample.

4.5.1 Principle of the Kramers-Kronig Transform

In the following, normal incidence is considered. The reflected amplitude r and energy R can
be expressed by the following equations:

1 (n ik )
r r exp(i ) (1)
1 (n ik )

2 (n 1) 2 k2
R r (2)
(n 1) 2 k2
Here, is the phase difference upon reflection.
The refractive index n and extinction coefficient k can be expressed using the following
equations:
1 R
n (3)
1 R 2 R cos

2 R sin
k (4)
1 R 2 R cos
The following Kramers-Kronig relation is applied to calculate the phase difference.
'
2 ln R '
P '2 2
d (5)
0

The integral in equation (5) contains a pole, and several methods exist to perform the
integration.

125
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2967-5, Ishikawa-machi, Hachioji-shi
TOKYO, JAPAN

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