Gwyddion user guide

Petr Klapetek, David Necas, and Christopher Anderson

This guide is a work in progress.

ii

Gwyddion user guide

Copyright 20042007, 20092014 Petr Klapetek, David Necas, Christopher Anderson

Permission is granted to copy, distribute and/or modify this document under the terms of either
The GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no
Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled
GNU Free Documentation License.
The GNU General Public License, Version 2 or any later version published by the Free Software Foundation. A copy of the
license is included in the section entitled GNU General Public License.

Contents

iii

Contents
1

Introduction
1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Licensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Installation
2.1 Linux/Unix Packages . . . . . . . . . . . .
2.2 MS Windows Packages . . . . . . . . . . .
Uninstallation . . . . . . . . . . . . . . . .
Registry keys . . . . . . . . . . . . . . . .
Enabling pygwy . . . . . . . . . . . . . . .
2.3 Build Dependencies . . . . . . . . . . . . .
2.4 Compilation on Linux/Unix . . . . . . . . .
Quick Instructions . . . . . . . . . . . . . .
Source Unpacking . . . . . . . . . . . . . .
Configuration . . . . . . . . . . . . . . . .
Configuration tweaks . . . . . . . . . . . .
Users tweaks . . . . . . . . . . . .
Packagers tweaks . . . . . . . . .
Developers tweaks . . . . . . . . .
Compilation . . . . . . . . . . . . . . . . .
Installation . . . . . . . . . . . . . . . . .
Running . . . . . . . . . . . . . . . . . . .
Deinstallation . . . . . . . . . . . . . . . .
RPM Packages . . . . . . . . . . . . . . .
2.5 Mac OS X . . . . . . . . . . . . . . . . . .
Preparation . . . . . . . . . . . . . . . . .
MacPorts . . . . . . . . . . . . . . . . . .
Fink . . . . . . . . . . . . . . . . . . . . .
Running . . . . . . . . . . . . . . . . . . .
2.6 Cross-Compiling for MS Windows . . . . .
Setup . . . . . . . . . . . . . . . . . . . .
Base MinGW Packages . . . . . . .
Gwyddion.net repository . . . . . .
Wine . . . . . . . . . . . . . . . .
NSIS . . . . . . . . . . . . . . . .
Python . . . . . . . . . . . . . . .
Support scripts . . . . . . . . . . .
Compilation . . . . . . . . . . . . . . . . .
Running under Wine . . . . . . . . . . . .
Cross-compilation of standalone modules .
2.7 Compiling on MS Windows using MinGW
2.8 Subversion Checkout, Development . . . .
MS Windows . . . . . . . . . . . . . . . .

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2
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13

Getting Started
3.1 Main Window . . . . . .
3.2 Data Browser . . . . . .
Controlling the Browser .
Channels . . . . . . . .
Graphs . . . . . . . . . .

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14
14
15
15
16
16

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1
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1

iv

Gwyddion user guide

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16
16
16
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21
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33

Data Processing and Analysis

4.1 Basic Operations . . . . . . . . . . . . . .
Basic 2D Data Operations . . . . . . . . .
Reading Values . . . . . . . . . . . . . . .
Read Value Tool . . . . . . . . . .
Inclinations . . . . . . . . . . . . .
Distance Tool . . . . . . . . . . .
Profile Extraction . . . . . . . . . . . . .
4.2 Interpolation . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . .
4.3 Data Leveling and Background Subtraction
Leveling . . . . . . . . . . . . . . . . . . .

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34
34
34
34
35
35
35
36
37
39
39
39

3.3

3.4
3.5
3.6
3.7

3.8

3.9
3.10

3.11
3.12
3.13
3.14
3.15

3.16

3.17
4

Spectra . . . . . . . . . .
Volume . . . . . . . . . .
Managing Files . . . . . .
File Loading . . . . . . . .
File Merging . . . . . . .
File Saving . . . . . . . .
Document History . . . . .
Data Window . . . . . . .
Graph Window . . . . . .
Tools . . . . . . . . . . . .
False Color Mapping . . .
Color Range Tool . . . .
Color Gradient Editor . . .
Presentations and Masks .
Presentations . . . . . . .
Masks . . . . . . . . . . .
Working with Masks . . .
Mask Editor Tool . . . .
Mark With . . . . . . . . .
Selections . . . . . . . . .
Selection Manager . . . .
OpenGL 3D Data Display
Basic Controls . . . . . . .
Full Controls . . . . . . .
Saving Images . . . . . . .
OpenGL Material Editor .
Single Point Spectra . . . .
Point Spectroscopy Tool .
Volume Data . . . . . . .
Metadata . . . . . . . . .
Logging . . . . . . . . . .
Disabling logging . . . . .
Raw Data File Import . . .
Information . . . . . . . .
Data Format . . . . . . . .
Presets . . . . . . . . . . .
Specific Data Import . . .
Graphics Formats . . . . .
Graph Curves . . . . . . .
XYZ Data . . . . . . . . .
Plug-ins . . . . . . . . . .

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Contents

4.4

4.5

4.6

4.7

4.8

4.9

v
Fix Zero and Zero Mean Value . . . . . .
Plane Level . . . . . . . . . . . . . . .
Three Point Leveling Tool . . . . . . .
Facet Level . . . . . . . . . . . . . . .
Level Rotate . . . . . . . . . . . . . . .
Background Subtraction . . . . . . . . . . . . .
Polynomial Background . . . . . . . .
Revolve Arc . . . . . . . . . . . . . . .
Median Level . . . . . . . . . . . . . . .
Fit Sphere . . . . . . . . . . . . . . . . .
Curvature . . . . . . . . . . . . . . . . . . . . .
Filters . . . . . . . . . . . . . . . . . . . . . . .
Basic Filters Tool . . . . . . . . . . . . . . . .
Convolution . . . . . . . . . . . . . . . . . . . .
Presentations . . . . . . . . . . . . . . . . . . .
Basic Operations . . . . . . . . . . . . . . . . .
Shading Presentation . . . . . . . . . . . . . . .
Gradient Detection Presentations . . . . . . . . .
Edge Detection Presentations . . . . . . . . . . .
Local Contrast . . . . . . . . . . . . . . . . . . .
Rank . . . . . . . . . . . . . . . . . . . . . . . .
Logscale . . . . . . . . . . . . . . . . . . . . . .
Data Edit and Correction . . . . . . . . . . . . .
Remove Spots Tool . . . . . . . . . . . . . . .
Remove Grains Tool . . . . . . . . . . . . . . .
Remove Scars . . . . . . . . . . . . . . . . . .
Mark Scars . . . . . . . . . . . . . . . . . . . .
Remove Data Under Mask . . . . . . . . . . . .
Fractal Correction . . . . . . . . . . . . . . . . .
Mask of Outliers . . . . . . . . . . . . . . . . .
Line Correction . . . . . . . . . . . . . . . . .
Path Leveling Tool . . . . . . . . . . . . . . . .
Unrotate . . . . . . . . . . . . . . . . . . . . .
Extended Data Edit . . . . . . . . . . . . . . . .
Drift Compensation . . . . . . . . . . . . . . . .
1D FFT Filter . . . . . . . . . . . . . . . . . . .
2D FFT Filter . . . . . . . . . . . . . . . . . . .
Affine Distortion . . . . . . . . . . . . . . . . .
Polynomial Distortion . . . . . . . . . . . . . . .
XY denoising . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . .
Statistical Analysis . . . . . . . . . . . . . . . .
Statistical Quantities Tool . . . . . . . . . . . .
Statistical Functions Tool . . . . . . . . . . . .
Height and Angle Distribution Functions
First-Order vs. Second-Order Quantities .
Autocorrelation Function . . . . . . . . .
Height-Height Correlation Function . . .
Power Spectral Density Function . . . . .
Minkowski Functionals . . . . . . . . . .
Row/Column Statistics Tool . . . . . . . . . . .
Two-Dimensional Slope Statistics . . . . . . . .
Facet Analysis . . . . . . . . . . . . . . . . . . .
One-Dimensional Roughness Parameters . . . . .

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59

vi

Gwyddion user guide

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86

Summaries and Tables

5.1 gwyddion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2 gwyddion-thumbnailer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.3 Keyboard Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

87
87
89
91

4.10

4.11
4.12

4.13
4.14

4.15

4.16

4.17

4.18

Roughness Amplitude Parameters . . . . .

Grain Analysis . . . . . . . . . . . . . . .
Watershed . . . . . . . . . . . . . . . . . .
Statistics . . . . . . . . . . . . . . . . . . .
Grain Statistics . . . . . . . . . . .
Grain Distributions . . . . . . . .
Grain Property Correlation . . . .
Grain Measurement Tool . . . . .
Grain Properties . . . . . . . . . . . . . . .
Grain Leveling . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . .
Fourier Transform . . . . . . . . . . . . . .
Wavelet Transform . . . . . . . . . . . . .
Discrete Wavelet Transform . . . . . . . .
Continuous Wavelet Transform . . . . . . .
References . . . . . . . . . . . . . . . . . .
Fractal Analysis . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . .
Tip Convolution Artefacts . . . . . . . . .
Obtaining the Tip Geometry . . . . . . . .
Tip Convolution and Surface Reconstruction
References . . . . . . . . . . . . . . . . . .
Multiple Data . . . . . . . . . . . . . . . .
Arithmetic . . . . . . . . . . . . . . . . . .
Detail Immersion . . . . . . . . . . . . . .
Merging . . . . . . . . . . . . . . . . . . .
Mutual Crop . . . . . . . . . . . . . . . . .
Cross-Correlation . . . . . . . . . . . . . .
Mask by Correlation . . . . . . . . . . . .
Neural network processing . . . . . . . . .
Training . . . . . . . . . . . . . . .
Application . . . . . . . . . . . . .
Graph Processing . . . . . . . . . . . . . .
Basic Operations . . . . . . . . . . . . . .
Graph Level . . . . . . . . . . . . . . . . .
Function Fitting . . . . . . . . . . . . . . .
Force-Distance Curve Fitting . . . . . . . .
Critical Dimension . . . . . . . . . . . . .
DOS spectrum . . . . . . . . . . . . . . . .
Synthetic Surfaces . . . . . . . . . . . . .
Spectral . . . . . . . . . . . . . . . . . . .
Objects . . . . . . . . . . . . . . . . . . .
Noise . . . . . . . . . . . . . . . . . . . .
Line Noise . . . . . . . . . . . . . . . . . .
Pattern . . . . . . . . . . . . . . . . . . . .
Calibration and uncertainties . . . . . . . .
Calibration data . . . . . . . . . . . . . .
Calibration data acquisition . . . . . . . . .
Calibration data application and further use

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Contents
5.4
5.5
5.6
5.7

Supported File Formats . .

High-Depth Image Formats
Expressions . . . . . . . .
Resources . . . . . . . . .
Gradients . . . . . . . . .
OpenGL Materials . . . .
Grain Values . . . . . . . .
Raw File Presets . . . . .
5.8 Toolbox Configuration . .
5.9 Format of Gwyddion Files
Byte Order . . . . . . . .
File Header . . . . . . . .
File Data . . . . . . . . . .
Object Layout . . . . . . .
Components . . . . . . . .
Data Types . . . . . . . .
Top-Level GwyContainer .
Channels . . . . . . . . .
Graphs . . . . . . . . . . .
Spectra . . . . . . . . . .
Volume data . . . . . . . .
Auxiliary Objects . . . . .
5.10 Simple Field Files . . . . .
Overall structure . . . . .
Magic line . . . . . . . . .
Text header . . . . . . . .
NUL padding . . . . . . .
Binary data . . . . . . . .
5.11 Simple XYZ Files . . . . .
Overall structure . . . . .
Magic line . . . . . . . . .
Text header . . . . . . . .
NUL padding . . . . . . .
Binary data . . . . . . . .
6

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Developing Gwyddion
113
API References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Bug reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

A GNU General Public License

A.1 Preamble . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
A.2 Terms And Conditions For Copying, Distribution And Modification
Section 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Section 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NO WARRANTY Section 11 . . . . . . . . . . . . . . . . . . . . .

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viii

Gwyddion user guide

Section 12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
A.3 How to Apply These Terms to Your New Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

B GNU Free Documentation License

B.1 Preamble . . . . . . . . . . . . . . . . . . . . . . . . . . .
B.2 Applicability And Definitions . . . . . . . . . . . . . . . . .
B.3 Verbatim Copying . . . . . . . . . . . . . . . . . . . . . . .
B.4 Copying In Quantity . . . . . . . . . . . . . . . . . . . . .
B.5 Modifications . . . . . . . . . . . . . . . . . . . . . . . . .
B.6 Combining Documents . . . . . . . . . . . . . . . . . . . .
B.7 Collections Of Documents . . . . . . . . . . . . . . . . . .
B.8 Aggregation With Independent Works . . . . . . . . . . . .
B.9 Translation . . . . . . . . . . . . . . . . . . . . . . . . . .
B.10 Termination . . . . . . . . . . . . . . . . . . . . . . . . . .
B.11 Future Revisions Of This License . . . . . . . . . . . . . .
B.12 ADDENDUM: How to use this License for your documents
7

Index

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1. Introduction

Chapter 1

Introduction
The latest version of this guide is available on-line at http://gwyddion.net/documentation/user-guide-en/. This guide is available
in several languages, namely English, French and Russian. All language versions are listed on-line at http://gwyddion.net/documentation/.

1.1

Motivation

Gwyddion is a modular program for SPM data analysis. Primarily it is supposed to be used for analysis of height fields obtained
by means of scanning probe microscopy techniques (AFM, MFM, STM, NSOM), but generally it can be used for any other
height field analysis or image analysis. Gwyddion is Free Software (and Open Source Software), covered by GNU General
Public License (GNU GPL).
The main idea behind Gwyddion development is to provide modular program for 2D data analysis that could be easily extended
by modules and plug-ins with no need of core recompilation. Moreover, the status of free software enables to provide source
codes to developers and users, which makes the further program improvement easier.
Gwyddion can be currently used with Linux/Unix (including Mac OS X) and Microsoft Windows operating systems. Both
families of systems can be used also for developement. For graphical interface, Gtk+ widget toolkit is used, therefore it can be
basically ported on any system that is supported by Gtk+.
Gwyddion core development is currently funded by Czech Metrology Institute. The project started as a part of the Nanomet
initiative (covered by Euromet) in August, 2004. It is supposed that more persons and institutions will participate on development.
Project is open for anyone. Welcome. . .

1.2

Licensing

Gwyddion is covered by GNU General Public License (GNU GPL). The full license text is also included as file COPYING in the
source distribution (MS Windows installers contain it as file COPYING.wri). In brief, this license means that:
You can freely use the program. You can freely make copies, modify and distribute them. You can download the program and
its source code from Gwyddion web pages and modify it as you want.
If you decide to distribute it, the modified code is still covered by the same license. In particular, you have to offer the source
code too.
The same holds for extensions, e.g. if you write an import module for a new file type or a new data analysis function it has to
be licensed under GNU GPL (if you distribute it).
However, it is also possible to execute third-party programs from Gwyddion and these do not necessarily have to be distributed
under the same license if they are not derived works of Gwyddion (which, admittedly, is not always easy to determine).
The main reasons, why the program is covered by this kind of license are here: first of all, this licensing policy enables us to
make modular program that can be easily developed by many persons from different institutions. Second, this license protects
the rights of developers that their code, here given to public, cannot be copied and used for closed proprietary products.

Gwyddion user guide

Chapter 2

Installation
Gwyddion source code and binaries can be downloaded from the download web page of the project, or alternatively from raw
SourceForge.net download page. The installation varies depending on the operating system and the various installation methods
will be described in the following sections.
Gwyddion needs or can utilise various software libraries, described in section Build Dependencies. If you install binary packages
you usually do not need to concern yourself with the required components as the packager has taken care of it and ensured that
all are present. However, it is important if you compile Gwyddion from source code.
To play with Gwyddion you might also want to download the sample Gwyddion files. They are in native Gwyddion format and
represent typical AFM data.

2.1

Linux/Unix Packages

Some GNU/Linux and Unix systems provide binary packages of Gwyddion. The download page of the project also tracks known
packages and packaging efforts. For instance, Debian, Ubuntu, Gentoo, openSuSE or FreeBSD offer Gwyddion packages. If
your operating system provides such a package and it is recent enough, install it using the standard means of the operating system.
Otherwise proceed with compilation from source code.
On Linux distributions using the RPM Package Manager, such as Fedora, openSuSE or Mandriva, you can also build a package
yourself from the source code, as described below.

2.2

MS Windows Packages

Note The packaging of MS Windows executables has changed substantially in version 2.23. So, if you upgrade from a pre-2.23
version to version 2.23 or newer, please read the description of the changes.

If you have already installed Gwyddion the installer asks if you want to replace the previous version.

The question what to do with the previous Gwyddion version.

You have three options:
Yes (replace) The already installed version will be replaced. This is the normal upgrade method.
No (keep) The already installed version will be ignored and the installation will proceed as a fresh one. Generally, this is a bad
idea as both versions will share settings and registry keys and if you uninstall one the other will be affected. In some cases,
though, you can find this option useful.
Cancel The installation will be aborted and the old version will be kept untouched.
In the following steps the installer reminds you of the software components included in the package and their licenses (that are
all Free Software), lets you change the installation directory and offers a choice of languages to use for the user interface.

2. Installation

Uninstallation
If you want to uninstall Gwyddion go to Start Control Panel Add or Remove Programs and choose Gwyddion. Note that
this is valid for Windows XP. The path to the Add/Remove window may be slightly different on other Windows OS.

Registry keys
The installer creates the following useful keys under HKEY_LOCAL_MACHINE\Software\Gwyddion\2.0:
InstallDir Installation directory, e.g. C:\Program Files\Gwyddion. Reading this key can be useful for determining
where to install extensions.
Version Full Gwyddion version as a string.
Locale Language of Gwyddion user interface chosen during the installation (more precisely, a locale specification that, among
other things, defines the language). You can modify it using regedit to choose another language as described below.
The list of available languages and corresponding Locale values include:
Locale

Language

cs_CZ.UTF-8
de_DE.UTF-8

Czech (Czech Republic)

German (Germany)

en_US.UTF-8

English (Unites States)

fr_FR.UTF-8

French (France)

it_IT.UTF-8

Italian (Italy)

ru_RU.UTF-8

Russian (Russia)

Enabling pygwy
The Python scripting interface, pygwy, is included in the installer, however, you need to install Python and PyGTK2 separately
to use Python scripting. This can be done either prior to Gwyddion installation or any time later. If Python and PyGTK2 is not
present pygwy simply does not register itself upon Gwyddion startup.
MS Windows Python installer can be obtained at http://python.org/download/releases/. Since pygwy requires Python 2 install
the latest Python 2.7 version, which will probably be python-2.7.3.msi.
Three packages are required for PyGTK2: PyGTK, PyCairo and PyGObject. Follow the corresponding download links for these
modules at http://www.pygtk.org/downloads.html to obtain the installers pygobject-2.28.3.win32-py2.7.msi, pyca
iro-1.8.10.win32-py2.7.msi, and pygtk-2.24.0.win32-py2.7.msi or possibly newer versions (if available).
Success has also been reported with the all-in-one installer pygtk-all-in-one-2.24.2.win32-py2.7.msi that contains everything. However, using the all-in-one installer means entire Gtk+ will be installed twice (into different locations).
Which bits of which installation will be used in pygwy is difficult to tell. Hence this method is not recommended.

2.3

Build Dependencies

The following table lists packages required to build Gwyddion from source code. If your operating system has separate development packages for libraries you need them too. The table does not include common software compilation prerequisites like the C
compiler or the make utility. Operating system specifics are described in following sections dedicated to building on particular
operating systems.
B UILD D EPENDENCIES
GTK+ 2.8.0 Required.
This includes the dependencies of GTK+ such as GLib, Pango or Cairo.
GLib 2.14.0 Required.
A bit newer version than strictly required by Gtk+ 2.8.

Gwyddion user guide

pkg-config 0.16 Required.

GtkGLExt 1.0 Optional.
Enables OpenGL 3D data views.
LibXML2 2.x Optional.
Enables import of SPML files.
FFTW3 3.0 (32bit), 3.1 (64bit), Unix only Optional.
Speeds up various integral transforms, power spectrum and correlation operations.
LibUnique 1.0 Optional.
Enables remote control based on D-BUS or whatever technology is currently in.
LibXmu, X11 only Optional.
Enables remote control on X11. This is a standard X Window System library and everyone having X probably has its
runtime files. However, since the modularisation of X in Xorg 7.0 it is distributed separately and therefore you might not
have its development files installed.
Zlib Optional.
Enables compression support in some file formats (Createc, NRRD).
Bzip2 Optional.
Enables compression support in some file formats (NRRD).
Minizip Optional.
Enables the import of some compressed formats (NanoObserver, NanoScanTech).
Libpng Optional.
Enables export of heightfields to 16bit greyscale PNG images and import of 16bit PNG images.
OpenEXR Optional.
Enables import and export of OpenEXR HDR images.
PyGTK2, including codegen Optional.
Enables pygwy, the Gwyddion Python scripting interface.
GtkSourceView Optional.
Enables syntax highlighting in the Python scripting console.
desktop-file-utils, Unix only Optional.
Enables basic desktop integration to Freedesktop-conforming environments, such as installation of Gwyddion to the menus
and file associations.
GConf2, Unix only Optional.
Enables better GNOME2 and XFce integration (up to XFce 4.6), in particular automatic generation of SPM file thumbnails
in Nautilus and Thunar. Newer versions of these desktop environments use different mechanisms.

2.4

Compilation on Linux/Unix

Gwyddion Unix build system is based on GNU autotools (autoconf, automake, libtool), like most of current Unix Free and Open
Source Software. If you have ever compiled software from source code, you very likely met autotools and already know how to
proceed. This section shall describe the compilation procedure in enough detail even for the uninitiated though. File INSTALL
in the top-level directory of the source tarball contains generic GNU autotools installation instructions.

2. Installation

Quick Instructions
If you know the drill:
tar -jxvf gwyddion-2.26.tar.xz
cd gwyddion-2.26
./configure
make install

Source Unpacking
Unpack the source code tarball with
tar -Jxvf gwyddion-2.26.tar.xz
replacing 2.26 with the actual version number. It will create directory gwyddion-2.26 (again, with the actual version number
in place of 2.26), cd to this directory. All other compilation actions will take place there.
If your operating system does not come with xz you might want to download gwyddion-2.26.tar.gz (compressed with
gzip) instead and unpack it with
tar -zxvf gwyddion-2.26.tar.gz
However, modern Unix and Unix-like systems come with both xz and gzip so, the considerably smaller gwyddion-2.26.
tar.xz should be normally the better choice.

Configuration
Run
./configure
to configure Gwyddion.
The configure shell script attempts to guess correct values for various system-dependent variables used during compilation.
It uses those values to create a Makefile in each directory of the package, a couple of header .h files containing systemdependent definitions and a few other system-dependent auxiliary files. Finally, it creates a shell script config.status that you
can run in the future to recreate the current configuration, and a file config.log. This file contains the details of the detection process and it is helpful to include it in compilation related bug reports. At the end, configure also prints a summary of
enabled/disabled optional features, including the reasons why features were disabled.
If configure reports missing required packages, install these packages and re-run it. The same applies to the case when configure
passes but you find you have not installed an optional package you want to compile Gwyddion with. It is possible a package is
not found or it is misdetected even if you have installed it, namely when it is installed into a non-standard directory. In this case
it is necessary to adjust certain environment variables to make configure able to find the packages:
PKG_CONFIG_PATH Most packages come with so called pkg-config files (.pc) that describe how programs should compile
and link with them. configure uses information from these files, therefore PKG_CONFIG_PATH must be set to list all
non-standard directories with relevant pkg-config files. To add for instance a GTK+ installation in /opt/gnome and a
FFTW3 installation in $HOME/opt/fftw3 one can do
PKG_CONFIG_PATH=/opt/gnome/lib/pkgconfig:$HOME/opt/fftw3/lib/pkgconfig
export PKG_CONFIG_PATH
PATH, LD_LIBRARY_PATH It may be necessary to adjust these variables to include non-standard directories with executables
and libraries of relevant packages, respectively.
CPPFLAGS, LDFLAGS It may be necessary to adjust these variables to include non-standard directories with header files and
libraries of packages that do not come with pkg-config files, for example for libTIFF in /usr/local one can set:

Gwyddion user guide

CPPFLAGS=-I/usr/local/include
export CPPFLAGS
LDFLAGS=-L/usr/local/lib
export LDFLAGS
Option --prefix of configure sets the base installation directory. Program components will be installed into its bin, lib,
share, etc. subdirectories (that will be created if they do not exist). More detailed control is possible with options specifying
particular subdirectories as --bindir, --libdir. The default prefix is /usr/local/bin, to install Gwyddion into your
home directory you may want to use for instance
./configure --prefix=$HOME/opt/gwyddion
If you install Gwyddion for personal use it is recommended to use a similar installation directory as no steps need to be performed
as root in this case.

Configuration tweaks
Optional features can be enabled/disabled with options such as --with-foo/--without-foo or --enable-foo/--dis
able-foo. For instance compilation with FFTW3 can be disabled with:
./configure --without-fftw3
By default all optional features are enabled if their prerequisites are found. A brief summary enabled and disabled optional
features is printed near the end of configure output.
The complete list of configure options and important variables can be obtained with:
./configure --help
Most of these options control inclusion/exclusion of optional features. Some interesting general options are explained below.
Users tweaks

Gwyddion comes with various desktop integration files defining MIME types, menu entries, file associations, thumbnailers, etc.
If you install Gwyddion to a system prefix they usually end up in the correct location. However, if you install it somewhere to
your home directory then these files need to be placed elsewhere, namely into certain dot-directories in your home.
This can be requested using --enable-home-installation option of configure. Note that using this option causes
installation of files outside the specified prefix.
Packagers tweaks

If Gwyddion is installed into a staging area for a subsequent packaging it is necessary to disable certain post-installation actions
that need to be done on the target system, not while packaging.
Updating of Freedesktop files can be disabled with --disable-desktop-file-update. Installation of GConf2 schemas
can be disabled with --disable-schemas-install. Usually, this does not have to be done explicitly as installations
into a staging area use non-empty DESTDIR (see installation). If DESTDIR is found to be non-empty the build system skips
post-installation actions automatically.
Developers tweaks

If you intend to patch or otherwise modify Gwyddion source code pass option --enable-maintainer-mode to configure
to enable various update and rebuild rules that are not used in plain compilation. Depending on the nature of the modifications,
some of the additional tools described in section Subversion Checkout, Development may be necessary.

Compilation
Run
make
and wait until Gwyddion is compiled. If configure finished without errors the compilation should pass too.
If you need to do unusual things to compile the package, please try to figure out how configure could detect whether and what
to do, and e-mail patches or instructions to the bug-report address so they can be considered for the next release.

2. Installation

Installation
Gwyddion has to be installed to be run, it is not possible to run it uninstalled.
Run
make install
to install Gwyddion to the target directory. If you install Gwyddion to a system directory you have to become root for running
this command. This is the only command that you might have to run as root during the installation. For example using sudo:
sudo make install
To install Gwyddion to a staging area, for example for packaging, set make DESTDIR variable to a prefix that will be prepended
to all target directories:
make install DESTDIR=/var/tmp/gwyddion-buildroot
Do not override individual directory variables as bindir, libdir.
If you do not install to a system directory, e.g. to a subdirectory of your home directory, you may need to adjust the following
variables during installation:
GCONF_SCHEMA_CONFIG_SOURCE location of GConf2 schemas
KDE4_MODULE_DIR location of KDE4 modules
Also, variable XDG_DATA_DIRS might need to be adjusted after installation to get full desktop integration.
If you install Gwyddion into /usr/local and get error message that libgwyapp.so.0 cannot be found your system
probably lacks standard library directories in the dynamic linker configuration. Notably, this happens on Ubuntu. Edit file /
etc/ld.so.conf and add the line
/usr/local/lib

there.

Running
Running Gwyddion does not normally require any additional setup.
The misfeatures of some desktop environments, however, may render Gwyddion unusable and need to be disabled. The hijacking
of program main menu in Unity makes most of Gwyddion menus inaccessible. It can be disabled by by unsetting UBUNTU_ME
NUPROXY while running Gwyddion:
UBUNTU_MENUPROXY= gwyddion

Deinstallation
Run
make uninstall
in the directory you previously compiled Gwyddion to remove it. If you have lost the source directory meanwhile you can try
to unpack, configure and build it exactly as before and then issue make uninstall, although this relies on your ability to
reproduce the build process.

RPM Packages
It is possible to build RPM packages on RPM-based GNU/Linux distributions directly from source code tarballs with
rpmbuild -tb gwyddion-2.26.tar.xz
where 2.26 is to be replaced with the actual version as above. This method was tested mainly on Fedora, openSuSE and Mandriva
and the RPM spec file contains some specific provisions for these systems. Specific support for other RPM-based systems can
be added on request.

Gwyddion user guide

2.5

Mac OS X

Much of the previous generic Unix/Linux installation section applies also to OS X. Therefore this section deals mainly with the
specifics of OS X installation, some of the steps listed here are explained in more detail in the generic Unix section.
Beside building everything on your own (good luck), at this time there are two ways to install Gwyddion:
using MacPorts (formerly Darwinports) and building from a Portfile.
using Fink and compiling Gwyddion the common Unix way,

Preparation
To install and run Gwyddion you need the Xcode Tools and X (SDK and App) installed. They where located on your CDs/DVDs. The Xcode Tools where located on the first DVD as XcodeTools.mpkg below Xcode Tools, the X11SDK is located as X11SDK.pkg below the Packages Folder within Xcode Tools. X11 is localed as X11User.pkg below System/
Installation/Packages even on the first DVD. If you have an CD Set the Discs may differ. The people from MacPorts recommending using the newest version of XCode. For further information look at the MacPorts Install Page. Also you
should have some experience using Terminal.app. All the commands in the the rest of this section are to be entered and run in
Terminal.app.
See installation dependencies section for an overview of required and optional packages to install prior to Gwyddion installation.
The following table summarises how they are called in the two software collections:
Package

Fink

MacPorts

Gtk+

gtk+2

gtk2

GtkGLExt

gtkglext1

gtkglext

FFTW3

fftw3

fftw-3

LibXML2

libxml2

libxml2

MacPorts
MacPorts is a Port based System for porting and installing Open Source/GNU software to OS X. Its based on using installation
files called Portfiles which where describing the steps to compile and install an application. So its far easy to port software to
OS X using MacPorts but every computer has to compile the application. Get and install MacPorts. After you installed MacPorts,
run
sudo port selfupdate
to update MacPorts to the latest version.
Usually installing ports with MacPorts is easy. But since X11 is not the native Desktop for OS X, things went a little worse.
So it is recommended to install an alternative X11 before installing Gwyddion. The recommended alternatives are XQuartz on
Leopard and the Port xorg-server on Tiger. After installing the suggested X11-System, Gwyddion can be then build and installed
simply by
sudo port install gwyddion
To install xorg-server (Tiger) simply type
sudo port install xorg-server
this is needed for the 3D view on tiger. After everything is done, you will find the StartUp-Icon below /Applications/
MacPorts.

2. Installation

Fink
Get and install Fink. After you installed Fink run
apt-get update
to update the database of available packages and install Gwyddion with
apt-get install gwyddion
To install Gwyddion from source code, for instance if you want to install a development version, you need to install the required
packages listed in the above table and then follow the generic Unix installation section instructions.

Running
On MacPorts you simply click on the StartUp-Icon and wait until Gwyddion appears. Using Fink or a self-compiled version you
should follow the steps below: Start X11.app and type in Terminal.app
export DISPLAY=":0"
Then run Gwyddion from the folder it was installed to. This is typically /usr/local/bin for Fink. So for example for Fink
run:
/usr/local/bin/gwyddion
You can also configure X11.app to run Gwyddion via: Locate X11.app in your dock, open the menu, choose Applications, choose
Customize from the next menu. Here you can choose add and enter the name (gwyddion for example) as Menu Name and the
complete path to gwyddion (e.g. /usr/local/bin/gwyddion) as Command. After this you can choose gwyddion from the X11
menu.

2.6

Cross-Compiling for MS Windows

Cross-compiling Gwyddion for MS Windows under Linux is quite similar to normal Unix compilation with certain additional
setup and extra steps. Although the process is quite smooth the initial setup may seem a bit complicated. If, in addition, you
are not familiar with the normal Unix compilation you might wish to start with that and attempt cross-compilation once you
familiarise yourself with the basic procedure.
These instructions describe compilation under Fedora using its MinGW cross-compilation support as this is what Gwyddion
developers use. In general, the instructions work on the current version of Fedora. Compilation on other versions and other
RedHat-based distributions (CentOS, Scientific Linux, . . . ) should be similar and relatively straightforward, possibly with some
tweaks. Building on, for instance, openSUSE will require modifications. Reports of success (or failure) of cross-compilation of
Gwyddion in other distributions and environments and namely improvements to these instructions are welcome.
Full cross-compilation has the following steps:
configuration for mingw64/mingw32,
compilation,
installation into a staging area,
creation of an installer using NSIS.
A script is available that automatically performs all the steps, as described below.

Setup
Before the first compilation you must set up the cross-compilation environment. This has to be done only once.

10

Gwyddion user guide

Base MinGW Packages

Run as root:
yum install mingw{32,64}-{gcc-c++,gtk2,libxml2,minizip}
to install the necessary mingw32 and mingw64 packages (several more packages will be installed as dependencies of those
explicitly given here).
Gwyddion.net repository

MinGW versions of a few packages used by Gwyddion are not available in Fedora yet. You can build them using the patches
and spec files at http://sourceforge.net/projects/gwyddion/files/mingw32-cross-compile/, however, it should be much easier to
just install them using yum. For this, download and install the gwyddion.net repository configuration package. The installation
makes available all the additional MinGW packages. After installing it you can run
yum install mingw32-{fftw,gtkglext,gtksourceview2}
Incidentally, the repository also contains a native Gwyddion package that you can install to use Gwyddion on Fedora; and a
package with cross-compiled Gwyddion libraries that can be used to cross-compile modules.
Wine

Wine is the MS Windows compatibility layer/emulator for Unix. It is used to run NSIS that creates the executable Gwyddion
Windows installer. Wine can also be used to run and test the cross-compiled Gwyddion, as described below.
Run
yum install wine
to install Wine.
NSIS

Nullsoft scriptable install system (NSIS) is used to create the Gwyddion installer. This is a MS Windows program, therefore, it
is installed under Wine. A cross-compiled version of NSIS might be available in the distribution but we have found the original
more reliable.
Download NSIS from its web page and run
wine nsis-2.46-setup.exe
replacing 2.46 with the actual version. Version 2.46 of NSIS is the oldest that has been tested.
Python

To compile pygwy you need to install Python into Wine. The steps are the same as if you just want to use pygwy, except that all
packages listed in Enabling pygwy need to be installed using msiexec:
wine
wine
wine
wine

msiexec
msiexec
msiexec
msiexec

/i
/i
/i
/i

python-2.7.3.msi
pygobject-2.28.3.win32-py2.7.msi
pycairo-1.8.10.win32-py2.7.msi
pygtk-2.24.0.win32-py2.7.msi

or similarly.
Support scripts

Support scripts and data are available in mingw32-cross-compile module in the Gwyddion subversion repository. Run
svn checkout http://svn.code.sf.net/p/gwyddion/code/trunk/mingw32-cross-compile

2. Installation

11

to check it out from the repository.

The most important tool you obtain is the cross-build-32 (or cross-build-64) script that automates all the cross-compilation
steps. Before you use it for the first time, review file setup32 that defines where various things are located (or setup64 for
the 64-bit target). The default contents looks as follows:
source_dir=$HOME/Projects/Gwyddion/gwyddion-mingw
mingw_prefix=/usr/i686-pc-mingw32/sys-root/mingw
target_prefix=$HOME/opt/gwyddion-mingw32
python_dir=$HOME/.wine/drive_c/Python27
nsis_compiler=C:\\Program\ Files\ \(x86\)\\NSIS\\makensis.exe

Variable source_dir specifies the location of the untarred or checked-out Gwyddion source code and it will likely need to
be adjusted. Variable target_prefix specifies the installation directory (staging area) for the cross-compiled Gwyddion.
The default value should be reasonable and you do not need to change it unless you want to. The remaining variables, mingw
32_prefix, nsis_compiler and python_dir, specify the location of MinGW files, NSIS compiler and Win32 Python,
respectively. They do not need to be changed from the default values under normal circumstances although NSIS can be installed
in either Program Files (x86) or Program Files by default depending on Wine configuration. Note setup is read
by shell so there must not be any spaces around =.

Compilation
The setup was tedious but it was worth it because the compilation is then extremely simple. Run
./cross-build-32
in mingw32-cross-compile directory to build Win32 insstaller. Thats all. If it succeeds an executable Gwyddion Windows
installer with bundled GTK+ and everything will be created in $target_prefix. Similarly, the Win64 installer is built just
with
./cross-build-64
Note the scripts run autogen.sh but do not clean the source code directory. You may wish to do that manually if you compile
Gwyddion repeatedly.
You can make a coffee meanwhile or study the cross-build script (it is actually quite short and clear).

Running under Wine

Compiled Gwyddion can be run under Wine. Assuming the default value of target_prefix:
wine ~/opt/gwyddion-mingw32/bin/gwyddion.exe
To run gwyddion.exe the dynamic linker must be able to find all the necessary DLLs. This is ensured in a somewhat crude
way by script copysysfiles that copies all necessary MinGW files from system to $target_prefix. Since copysysfiles is
executed by cross-build you normally do not need to execute it manually.
The second step that might be necessary is setting registry key
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\App Paths\gwyddion. exe
to point to gwyddion.exe and the value Path to point to the bin subdirectory.

Cross-compilation of standalone modules

Cross-compilation of standalone modules requires only Gwyddion headers and Win32 development libraries. While they can be
surely obtained by cross-compiling entire Gwyddion is it not necessary to do so. By compiling only the libraries you can avoid
the installation of various rarer Gwyddion dependencies. This can be achieved using the patch gwyddion-2.22-buildonly-libs.patch available among the build scripts.
But it gets even easier, the MinGW Gwyddion libraries are available as a RPM package mingw32-gwyddion-libs in the
gwyddion.net repository.
Once you have this package installed you can try cross-compilation of the sample standalone module threshold-example
that is available in the subversion repository (or as a tarball). See README therein for some more details.

12

2.7

Gwyddion user guide

Compiling on MS Windows using MinGW

Although the standard MS Windows executables are created using cross-compilation it is also possible to build Gwyddion on
MS Windows using the MinGW port of GNU tools to MS Windows. The standard MS Windows excutables also come with
almost all the optional features packaged the notable exception being Python scripting. Getting all these components work
in MS Windows requires additional effort. However, the most likely reason for compiling on MS Windows is to obtain all the
necessary files to develop and build standalone Gwyddion modules and for this purpose building all the optional components is
not necessary.
The procedure is essentially the same as the normal Unix compilation. Some MinGW-specific remarks follow.
It has been reported that the Gtk+ 2.24.10 bundle can be successfully used. After installing it, set in the MSYS shell
PKG_CONFIG=PATH-TO-GTK+/gtk+/bin/pkg-config.exe
where PATH-TO-GTK+ needs to be replaced with the actual Gtk+ installation directory.
To compile only the libraries, it may be useful to use the patch gwyddion-2.22-build-only-libs.patch described
in the cross-compilation section. In addition, it seems that the MinGW libintl redefines printf() to libintl_printf()
which it, however, does not provide. This leads to link failure of gwyddion.exe. This can be fixed by simply removing
include/libintl.h in the Gtk+ directory.

2.8

Subversion Checkout, Development

Gwyddion uses Subversion version control system for source code revision management. The organisation of the repository is
described on project web pages. For example the current head revision of the program itself can be checked out with
svn checkout http://svn.code.sf.net/p/gwyddion/code/trunk/gwyddion
The repository does not contain any generated files, no matter how exotic tools may be necessary to generate them. Therefore,
additional packages are required for building from a fresh checkout. There are also certain platform limitations. The additional
tools and packages required for development are essentially the same as for compilation from Subversion checkout. More
precisely, to build from a fresh checkout all the additional tools are necessary, whereas development may require only a subset
of them or even none, depending on the type and extent of the changes in the source code.
A DDITIONAL DEVELOPMENT BUILD DEPENDENCIES
GNU autoconf 2.60
GNU automake 1.11
GNU libtool 1.4
Python 2.2
Perl5
gtk-doc 1.12
GNU gettext 0.12, including development stuff
probably GNU versions of most tools: the compiler, binutils, . . .
After a fresh checkout, run ./autogen.sh with any arguments you would give to configure. Note it automatically adds
options --enable-maintainer-mode and --enable-gtk-doc to ensure the rules for creation and updates of various
files are active. Generally, you should always use --enable-maintainer-mode if you intend to change the program source
code in a non-trivial way.
On some systems, autogen.sh can fail even if you have sufficient versions of autotools installed. These systems do not install
general autoconf or automake commands, only versioned commands such as autoconf261 or automake19. This makes it particularly difficult to find for example automake 1.9 or newer with no limit on how newer it can be. Therefore, autogen.sh
does not attempt this at all. You can either create unversioned symbolic links to the versioned commands or run autogen.sh
as follows:
AUTOCONF=autoconf261 AUTOHEADER=autoheader261 ./autogen.sh You may need to set the

2. Installation

13

following variables: ACLOCAL, AUTOCONF, AUTOHEADER, AUTOM4TE, AUTOMAKE, LIBTOOLIZE. In addition, some operating systems may install autoconf macros in a place aclocal does not find them by default. This can be fixed by setting variable
ACLOCAL_FLAGS to give aclocal additional search paths:
ACLOCAL_FLAGS="-I /usr/local/share/aclocal"
./autogen.sh
It is often necessary to combine these adjustments. For instance on FreeBSD, where all tools are versioned, one typically invokes
(broken to lines for easier reading):
AUTOCONF=autoconf261 \
AUTOHEADER=autoheader261 \
AUTOM4TE=autom4te261 \
AUTOMAKE=automake19 \
ACLOCAL=aclocal19 \
ACLOCAL_FLAGS="-I /usr/local/share/aclocal" \
CPPFLAGS=-I/usr/local/include \
LDFLAGS=-L/usr/local/lib \
./autogen.sh --prefix=...
If autogen.sh passes you can compile the program as usual.

MS Windows
Since the standard method to create MS Windows executables is cross-compilation in Linux the recommended method to develop
for MS Windows is also to compile in Linux. This can be done either on a different physical computer using ssh or in a virtual
machine running on the same computer as the host MS Windows system. In both cases the Gwyddion build directory (and other
directories) can be shared between the Linux and MS Windows systems using either Samba or a shared directory mechanism
of the virtual machine and the compiled executables thus can be directly tested in MS Windows without having to transfer files
back and forth.

14

Gwyddion user guide

Chapter 3

Getting Started
This chapter introduces various basic concepts and terms, such as masks or selections, explains the organization of data in
Gwyddion and describes the user interface.
The descriptions are relatively thorough and some of the topics near the end of the chaper, such as raw file import or plug-ins,
might be considered advanced and not for everyday use. So, despite the name, it is not necessary to read this entire chapter to be
able to work with Gwyddion. The Gwyddion user interface is intuitive and much can be discovered by playing. The clarification
of the basic ideas and components provided here will hopefully ease the discoverying.
Tip Command Meta Tip of the Day displays data processing tips and highlights useful features that you might miss.

3.1

Main Window

The main window, also called toolbox, is one of the two Gwyddion windows that appear after program start (with no files given
to open), the other is the data browser. Closing the main window causes Gwyddion to exit.
The toolbox contains the set of Gwyddion menus and from several rows of buttons connected with common functions and tools.
The menus group the functions as follows:
File associates commands that are used for file loading and saving. Certain global commands (e. g. Exit) are located here too.
The history of recently opened files can be browsed with File Open Recent Document History.
Edit provides history manipulation commands (Undo, Redo) and editors of miscellaneous global resources, such as gradients
and materials for false color and 3D data representation or the default color used for data masking.
Data Process is built automatically from all data processing modules available in the Gwyddion module directory (depending
on the operating system). This menu together with Tools panel of buttons contain most of the commands you will need at
analyzing your SPM data. A subset of these functions is also available in Data Process button panel. These buttons serve
as shortcuts to commonly used functions from Data Process menu. All functions accessible from Data Process button
panel can be found in the menu too.
Graph is similar to Data Process, except it consists of graph functions. Graph processing includes function fitting, exporting
graph data etc. Button panel Graph again contains a subset of the commonly used functions from Graph menu.
Volume is similar to Data Process, except it consists of volume data functions.
Info contains commands that provide various auxiliary information about Gwyddion, such as program version or the list of
loaded modules and their functions.
Finally, you can find some rows of buttons in the main window. Buttons in View panel offer zooming functions (that are often
more easily invoked by keyboard shortcuts or just rezising the data window) and 3D data display. Panels Data Process and
Graph contain selected functions from Data Process and Graph menus as described above.
Panel Tools contains tools, i.e. functions that directly work with selections on data windows. These functions are accessible only
from this button panel.

3. Getting Started

15

Main window and a data window showing microchip surface (Gwyddion sample file chip.gwy).

3.2

Data Browser

Data browser is a window that displays the structure of currently focused file. It shows the content as represented in Gwyddion
which may differ somewhat from the organization in the original software.
Gwyddion supports an arbitrary number of two-dimensional data fields per file. Depending on the context, they are also often
called channels or height fields in this guide. The dimensions of channels in one file may differ and also the physical dimensions
and values can be arbitrary physical quantities.
In addition, one-dimensional data, represented as graphs, and single-point spectra can be present in the same file. The data
browser is a tool for browsing and managing all the available data in the file.

Data browser displaying several channels.

Controlling the Browser

Since the data browser always displays the structure of currently focused file, its contents change as you switch between different
windows, possibly showing data from different files. There is no difference between native Gwyddion files (.gwy) and other
files. Once a file is loaded its structure is shown as if it was a Gwyddion file.

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Gwyddion user guide

The data browser has three tabs, one for each type of data that can be present in the file:
Channels
Graphs
Spectra
Volume
Each list shows names of the data objects and some additional properties that depend on the specific data type. The names can
be edited after double-clicking on them.
Individual channels, graphs or spectra can be deleted, duplicated or extracted to new Gwyddion native file using the buttons at the
bottom of the browser. It is also possible to copy them to another file by dragging a data browser row to any window belonging
to the target file.
The close button in the top right corner of the data browser closes the current file, discarding all unsaved changes. A file is also
closed when all windows displaying data from this file are closed.
If the data browser is closed it can be recalled using the Meta Show Data Browser command.

Channels
The channel list shows channel thumbnails, check-boxes controlling whether the channel is visible (i.e. displayed in a window)
and channel names. Right to the name the presence of presentation, mask or calibration is indicated by the following letters:
M mask
P presentation
C calibration

Graphs
The graph list shows check-boxes controlling whether the graph is visible and graph names. Right to the name the number of
curves in the graph is displayed.

Spectra
The spectrum list shows the spectra name and the number of points in the set. Since single-point spectra are displayed and
operated on only in connection with a two-dimensional data using the spectroscopy tool, there is no check-box controlling the
visibility.

Volume
The volume data list shows the data name and the number of levels in the z direction, i.e. perpendicular to the section displayed
in the window.

3.3

Managing Files

Gwyddion uses its custom data format (.gwy) to store data. This format has the following important advantages:
Capability to store the complete state of the individual data, including masks, selections and other properties.
Arbitrary number of channels, graphs and spectrum sets, with arbitrary dimensions and units of both dimensions and values.
Double-precision representation of all data, preventing information loss due to rounding.
Therefore, we recommend to use this format for saving of processed files.
Other data file formats are handled with appropriate file loading and saving modules. Beside a large number of file formats used
in scanning probe microscopy, graphical file types (PNG, JPEG, TIFF, TARGA) and raw binary and text data can be imported
too. If your SPM data format is not supported by Gwyddion yet or it is loaded incorrectly, you are encouraged to write an import
module (if you can program) or contact the maintainers to help them improve the support.
The list of all supported file formats can be found in chapter Summaries and Tables.

3. Getting Started

17

File Loading
Files are opened using File Open. The file type is detected automatically, based solely on the file content. Since the same
extensions such as .img, .afm or .dat are used by many different SPM file types this approach is superior to relying on file
extensions.
The only exception is the import of various raw data, either two-dimensional or graph, that must be chosen explicitly in the file
open dialog. See sections Raw Data File Import for details of import of raw data and manual extraction of data from unsupported
formats and Specific Data Import for import of XYZ data, pixmap image data and graph data.
The list of files in the file open dialog can be limited to only files Gwyddion recognizes as loadable by enabling the Show
only loadable files option. The file type label then indicates the filtering by appending (filtered) to the end. This can be often
convenient, on the other hand it can slow down listing of directories with many files.

File open dialog with expanded file type options and channel preview. The small text above the preview shows the module used
to load the file (sis) and the number of channels (ch), graphs (gr) and single-point spectra (sps) in the file.

File Merging
File merging, performed by File Merge, is similar to normal file loading, except that the selected file (or files) is merged into
the current open file. In other words, channels, graphs and spectra, together with all their settings and properties are added to
those already present in the current file.

File Saving
Much of the previous paragraphs applies to file saving too. One of the main differences is the reliability of automatic file type
determination. While loading can and does examine the file contents, saving depends on file name and extension. Combined with
the large number of different file types using the same extension such as .img, .afm or .dat it leads to ambiguities. Select
the file type explicitly before saving if you are unsure.

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Gwyddion user guide

Since the only file type able to fully represent Gwyddion data structures is its native data format, saving to a .gwy file is the
only proper saving. Saving to other file formats essentially consists of exporting of a limited subset of the data, typically only the
active channel (without masks and presentations). Therefore it does not change the file name of the current file to the just saved
file name.
File Save as... can also be used to export channels to image formats. Just enter foo.png as the file name to export a PNG
image the current channel, similarly for other formats.

Document History
The history of recently opened files can be accessed with File Open Recent. The submenu contains the last 10 recently used
files for quick recalling, an extensive recent file history is accessed with the last item Document History.
Document history lists the files sorted by the last access time (the most recently accessed at the top), with previews and some
additional information about a selected channel. The function of the bottom row of buttons is following:
Prune Removes history entries of files that have been deleted or are no longer accessible for other reasons.
Close Closes the document history window.
Open Opens the selected file. This can be also achieved by activating the selected row, either by double-clicking or with the
keyboard.
The history can be searched/filtered by file name using the filter controls above the buttons. The filter is activated by pressing
Enter in the filter pattern entry. To display all history entries, clear the entry and activate it. The filter pattern is interpreted in
two ways:
If the pattern contains wildcards, i.e. * or ?, it is interpreted as file glob. This means ? represents a single arbitrary character,
* represents an arbitrary sequence of zero or more characters, and the file name has to precisely match the pattern. Note
directory separators (/ or \) are not treated specially, therefore in the pattern *.sis the initial * matches all leading directory
components. The pattern syntax is described in GPatternSpec documentation.
If the pattern does not contain any wildcards, it is directly searched as a part of the file name.
Search case sensitivity, controlled by option Case sensitive, is useful mainly on systems distinguishing letter case in file names,
such as Unix. On systems that do not distinguish the case themselves it is recommended to keep the setting on case insensitive.

3.4

Data Window

Two-dimensional data are presented in so called data windows. It is the main widget used for working with Gwyddion. The data
are presented as a field of false colors corresponding to heights. Color axis that represents mapping of colors to real height values
is on the right side of the data window.
The False color palette used to represent height data can be changed by clicking on the color axis with right mouse button (i.e.
invoking context menu) and selecting a palette from the list. Most frequently used palettes are available directly in the context
menu; however you can reach much more of the possible palettes using the More menu entry. Moreover, you can use the color
gradient editor to create your own palettes and select which palettes should be displayed in the short list.
There is a context menu available also for the data area. This menu consists of basic data and presentation operations. To reach
all the possible operations use Data process... menu at the Gwyddion main window, or use some of the tools available at the
Tools set of buttons at the Gwyddion main window.
The arrow in the upper left corner brings the aspect ratio switch menu. The data can be displayed either with pixels mapped with
1:1 aspect ratio to screen pixels (Pixelwise Square), or with physical dimensions mapped 1:1 onto the screen (Physically Square).
For instance a sample of size 11 m scanned with reduced slow axis resolution and having therefore 512128 pixels, can be
displayed either in 512128 or 512512 window.

3. Getting Started

19

Data window with all three available context menus shown.

3.5

Graph Window

Graph window is used for 1D data processing. They are created by appropriate tools or modules that extract graphs from height
field data. Currently, it is not possible to import standalone graphs into application as the main intent of Gwyddion is to provide
tools for analyzing height fields, not graphs.
Graph window consist of three tabs: the first two represent graphical and tabular views of the 1D data and the third one shows
a list of graph curves. Several tools connected with viewing 1D data are available directly in the graph window toolbar, namely
zoom buttons and logarithmic axis buttons. To reach all the possible operations use Graph menu in the Gwyddion main window.

A graph window with three profiles.

To edit curve presentation one can either click on the curve in the graph or activate (double-click) the corresponding row in
Curves. Individual curves can be deleted by selecting them in Curves and pressing Delete. It is also possible to copy individual
curves to other graphs by dragging their curve list rows onto them (provided the graphs are unit-wise compatible).
Clicking on a graph axis brings a dialog with axis properties and graph key properties can be edited after double-clicking on it.

3.6

Tools

Functions from Data Process menu and button panel either execute immediately or after asking for parameters and settings in a
dialog box. Tools, accessible from Tools button panel, work differently. Once selected, they remain active and always follow the

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Gwyddion user guide

current data window until one switches to another tool. In other words one can switch data windows freely while using a tool and
it always shows information from or operates on the current data. Tools also differ by working with selections, e.g. points, lines
or rectangles, on data windows. Nevertheless functionally they perform similar tasks as Data Process functions value reading,
leveling, statistics, correction, etc.
Tools can be launched only from Tools button panel located in the main window. Gwyddion includes these tools:
Read Value

Reads values at the position of mouse click.

Distance
Measures distances similarly to Read value this tool enables user to measure horizontal, vertical and Euclidean
distance and angle between points in the data field. In addition it displays the difference of data values between points.
Profile
Extracts profiles of the data field and puts them to separate graphs. These graphs can be further processed with
commands from the Graph menu.
Spectro

Views and extracts single point spectroscopy data.

Statistical Quantities
Computes basic statistical quantities (RMS, Ra, minimum, maximum, projected and surface area,
etc.) from a selection of full data field. It can also calculate them only on the masked area, or even combine these two
types of selection of area of interest.
Computes basic statistical functions (distribution of heights or slopes, autocorrelation function, power
Statistical Functions
spectrum density function, etc.) from a selection of full data field.
Row/Column Statistics
Somewhat complementary to 1D statistical functions, this tool plots characteristics such as mean,
median or surface length for each row (column).
Roughness

Evaluates standardized one-dimensional roughness parameters.

Levels data by plane obtained by clicking on three points within data window. The three values can be
Three Point Level
averaged over a small area around the selected point.
Path Level

Row leveling tool equalizing the height along a set of arbitrary straight lines.

Polynomial Line Level

Crop

Levels rows or columns by fitting and subtracting polynomials.

Cuts part of the data.

Mask Editor

Manual editing of masks: creation, exclusion, intersection, inversion, growing and shrinking, . . .

Grain Measurement

Measures individual grain parameters.

Grain Remover
Removes continuous parts of the mask by clicking on mask point and/or interpolates (removes) data under
a continuous part of mask.
Spot Remover
Manually removes spots. Select a point on a data window, mark an area to interpolate on the zoomed view
and remove the defect using chosen interpolation method.
Color Range
Stretches color range or changes false color mapping type. It enables the user to change the false color
representation range (by default from data minimum to data maximum).
Filter
Basic filters mean, median, conservative denoise, minimum, maximum and similar simple filters to reduce noise in
the data.
Selection Manager

Displays selections for a channel and copies them to other channels or files.

Tool dialogs can be closed (or more precisely hidden, as the current tool is still active even if its dialog is not visible), beside
activating the Hide button, by pressing Esc or clicking the tools button in the toolbox again.

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21

False Color Mapping

False color mapping is the basic two-dimensional data visualization method. The color gradient (also called palette) to use can
be selected after clicking on the false color map part of a data window with right mouse button.
This quick selection pop-up menu offers the list of preferred color gradients. In addition it allows to invoke the full color gradient
list by selecting More. Preferred gradients can be chosen by checking the corresponding check buttons in the full list or in the
gradient editor list. Selecting a row in the full list changes the gradient to the selected one, double-clicking (or pressing Enter)
also finishes selection and closes the list window. Gradients of known names can be quickly accessed by starting to type their
name. The default color gradient to use (when none is specified in the file) can be also set in the gradient editor.
More control over the way values are mapped to colors is possible with Color range tool.

A data window with the right-click color gradient pop up menu and the full color gradient list.

Color Range Tool

Color range tool is a special tool whose purpose is not to analyse or modify data, but to control the way values are mapped to
colors. It offers four basic color mapping types:
Full

Data values are mapped to colors linearly, the full data range corresponds to the full color range. This is the default
type (unless you have changed the default).

Fixed
Data values are mapped to colors linearly, a user-specified data range (which can be smaller or greater than the full
range) maps onto the full color range. Values outside this range are displayed with the edge colors. The range can be set
by several means:
by entering desired values numerically in the tool window,
by selecting a range on the height distribution graph in the tool window or
by selecting an area on the data window, the range is then set from the minimum to maximum of the data in this area
only.
If no range is manually set, fixed range type behaves identically to full range.
Note data processing operations often modify the value range and as the fixed range remains fixed as you set it, it can
result for instance in completely black data display. You may wish or have to update the range manually then, or to switch
to another mapping type.
Automatic
Data values are mapped to colors linearly, a heuristically determined subinterval of the full value range maps
onto the full color range. Values outside this subrange are again displayed with the edge colors.
Adaptive
The full data range corresponds to the full color range, however data values are mapped to colors non-linearly.
The mapping function is based on inverse cumulative height distribution, therefore flat areas generally get bigger slice of
the color gradient and smaller value variations can be seen on them than normally.
The false color map ruler on the right side of data windows does not display any ticks in this mode, only the minimum and
maximum value.

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A mapping type can be set to be default by checking the Default check button when it is active. Newly displayed data windows
then use this type, unless a channel explicitly specifies other type to use.
Saving data to .gwy file also saves all color mapping settings: mapping type, range and gradient. Gradient is however not
physically stored in the file, only referenced by name. In other words, color gradients of the same name are shared among files.

Color Gradient Editor

Color gradient editor can be invoked with Edit Color Gradients. It consists of a gradient list similar to the full gradient
selector, with an additional button panel, and the actual editor that can be invoked by double-clicking on a gradient you wish to
edit or by activating the Edit button. Renaming is possible. Only user-created color gradients can be edited or deleted, system
gradients installed with Gwyddion are immutable.
The last button in the gradient list control panel makes the currently selected gradient the default. It will be used for all newly
displayed data that do not specify any particular color gradient.
Two editing modes are available:
Points The color gradient is defined by a set of points and their associated colors. The points are represented by triangular
markers on the gradient displayed in the lower part of the editor window. Moving these markers moves the points, new
points can be added by clicking into an empty space, existing points can be removed by dragging them away from the
gradient.
Curve The color gradient is defined by red, green and blue curves. The curves are again segmented, but the segments of
individual curves do not need to coincide.

3.8

Presentations and Masks

Presentations
Presentations can be used to show the height field in another way than as a false color map of the heights, for instance with
shading or with highlighted edges. It is also possible to superimpose an arbitrary data field over another one as the presentation.
Note the superimposed presentation is really only a presentation, it is never used for calculations. In all data processing functions
or tools the results are always computed from the original underlying data. Since presentations can be computationaly intensive to
calculate, they are not automatically updated when the underlying data change. The various presentations available are described
in section Presentations.
The presence of presentation over the data is indicated by flag P in the data browser and also by the empty false color map ruler
on the right side of the data window that does not display any ticks nor the minimum and maximum value.

Masks
Masks are used for special areal selections, e.g. grains, defects or facets with certain orientation. Masks can have any shape and
within the data window and they are visualized by a color overlayed over the data. The mask color and opacity can be changed
in the right-click context menu of the data window.
Since grain marking is the most common use of masks, several functions that operate on marked areas are called grain functions,
e.g. Grain Statistics. Also, a contiguous part of mask is sometimes called grain in this guide. However, since a mask does not
bear any information how it was created all mask functions can be used with masks of any origin.

Visualization of masks and presentations. If you look from above they can be imagined to be stacked as in the picture.

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23

Both masks and presentations can be removed from the data by functions in the right-click menu of the data window, or with
keyboard shortcuts.

Data in default false color representation (left), with superimposed mask visualized with a red color (centre) and with shading
presentation (right).

Working with Masks

The mask-related functions can be divided into three main groups:
Creation Masks are created by various types of marking functions, namely grain marking functions (Mark by Threshold,
Mark by Watershed), defect marking functions (Mask of Outliers, Mark Scars) and feature marking functions (Mask by
Correlation, Facet Analysis, Certainty Map). In addition, some general mask editing functions provide means to create
masks from scratch.
Masks are also used to mark invalid pixels in files imported from formats that distinguish between valid and invalid pixels
since Gwyddion does not have a concept of invalid pixels.
Application In general, the mask-covered area is considered to be the area of interest, i.e. the area to operate on. This applies
namely to statistical functions such as the Statistical Quantities tool. Function Remove Data Under Mask replaces the data
under mask, while the Remove Grains tool can perform such replacement for individual grains. There are several functions
for the examination of grain properties, see section Grain Statistics.
Some functions ask whether to consider the area under mask included or excluded (or ignore the mask), namely leveling
functions. Such choice is offered only if a mask is present on the data.
Editing A few basic mask operations, such as inversion or complete removal, are available in Data Process Mask menu.
More advanced functions include the grain-oriented Remove Grains tool and Remove by Threshold that provide different
means to remove parts of the mask, as well as Mask Editor tool and Mark With focused on general mask editing.

Mask Editor Tool

The Mask Editor is the universal mask modification tool. It provides two groups of functions: editing of the mask by drawing
directly in the data window and global operations with the mask such as inversion or growing and shrinking.
The direct mask modification is controlled by the buttons in the Editor group. It can be done in two ways: by selecting geometrical
shapes that are subsequently filled or erased (using the Shapes option), and by freehand drawing operations using drawing tools
(option Drawing Tools).
Buttons in the Mode row select how the geometrical shape drawn in the data window will modify the mask:
Set

The mask is set to the drawn shape, discarding any mask already present.

Add
Subtract

The mask is extended by the drawn shape (if there is no mask yet a mask is created).
The drawn shape is cut out from the mask This function has no effect if there is no mask.

Intersect
The mask is set to the intersection of the drawn shape and the already present mask. This function has no effect
if there is no mask.
Buttons in the Shape row control which shape is drawn on the mask. The choices include rectangles, ellipses and thin lines.
Freehand drawing tools are selected by buttons in the Tool row:

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Pencil
Freehand drawing with a pencil of radius specified by parameter Radius. Note this may be slow on slow computers
and/or large data fields.
Freehand erasing with an eraser of radius specified by parameter Radius. Note this may be slow on slow computers
Eraser
and/or large data fields.
Fill

Bucket-filling of a contiguous unmasked area.

Unfill

Bucket-unfilling of a contiguous masked area.

The basic global operation with masks, i.e. inversion, removal and filling the entire data field area with a mask are available in
the Actions row. Additional operations include:
Grow
Extends the mask by Amount pixels on each side. More precisely, the mask is extended by one pixel on each side and
this is repeated Amount times.
Normally, growing does not distinguish between individual parts of the mask. Parts that grow so much that they touch
therefore merge. This can be prevented by Prevent grain merging by growing which makes individual parts of the mask
stop growing once there is only one-pixel space between them.
Reduces the mask by Amount pixels from each side. More precisely, the mask is reduced by one pixel from each
Shrink
side and this is repeated Amount times.
The reduction may or may not occur from the data field borders. This is controlled by the Shrink from border check box.
Fill Voids Makes the grains single-connected, i.e. without any holes, by filling the holes in grains.

Mark With
Data Process Mask Mark With
Mark With can create or modify masks using another mask or data of the same dimensions. The operations that can be applied
to the current mask are the same as in the Mask Editor tool: creation, union, subtraction and intersection. The source of the other
mask can be one of the following:
Mask This is the simplest case, a mask can be combined with another mask using the specified logical operations.
Data In the Data mode, another height field is used as the other mask source. The mask consists of pixels within a range of
heights, specified as relative values within the total range. To use pixels outside a certain range for the masking, set the
upper bound to a smaller value than the lower bound.
Presentation The Presentation mode differs from Data mode only in that a presentation is used instead of the data.
This is an exception to the rule stating that presentations are never used for further processing. Sometimes it can be useful
to mark, for instance, edges found on the data even though the corresponding presentation visualizes a quantity weird from
the physical point of view.

3.9

Selections

All interactive tools and some other processing methods allow to select geometrical shapes on data with mouse: points, lines,
rectangles, circles/ellipses. Existing selections can be similarly modified by dragging corners, endpoints, or complete selections.
When mouse cursor is moved near to an editable point of a selection, is changes its shape to indicate the possibility to edit this
point.
Each tool typically uses only one type of selection and when it is activated on a data window, it sets the selection mode to this
type. Selections of other types than currently displayed are remembered and they are recalled when a tool which uses them is
activated again. E.g. when you select several lines with Profile extraction tool, then switch to Statistical quantities (the lines
disappear) and select a rectangular area to calculate its statistical characteristics, and then switch back to Profile extraction, the
rectangle disappears and the lines appear again.
Tools that use the same type of selection e.g. both Statistical functions and Statistical quantities use rectangular selection
share it. To calculate height distribution of the same rectangle you have selected for statistical quantities, it is sufficient to switch
the tool.

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25

Data window with three selected lines, two horizontal and one vertical.
If you save data in Gwyddion native file format (.gwy), all selections are saved together with data and recalled the next time the
file is opened and appropriate tool chosen.
Pressing Shift during selection restricts the degrees of freedom of the shape, making it easier to draw shapes from a specific
subset. Specifically, pressing Shift restricts
rectangular selections to perfect squares,
elliptical selections to perfect circles,
directions of line selections to multiples of 15.

Selection Manager
The selection manager is a special tool that displays the list of all selections in a channel and enables to copy them to other
channels.
For each selection, the tool shows the name, which is how the selection is identified in the .gwy file; the selection type and the
number of objects (points, lines, rectangles, . . . ) selected. Usually, there is at most one selection of any type because they are
shared among the tools as described above. Neverthesless, sometimes there are special or private selections present as shown on
the following figure displaying two point-wise selections.

Selection Manager showing several selections present in the data.

Selection chosen in the list is displayed in the data window.
It is possible to delete individual selections by choosing them in the list and pressing Delete this is equivalent to clearing the
selection in the corresponding tool. The Clear button removes all selections.
However, the most interesting function of Selection Manager is selection copying. There are two ways to copy a selection to
another channel:
Dragging a row from the selection list onto a data window copies the selection to this data window.
Clicking the Distribute button copies the selection to all other channels in the file. Or, if to all files is enabled, to all channels
in all open files.

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Selections are copied only to channels with compatible lateral units. This means that a selection in a normal channel with meters
as the lateral units will not be distributed to a two-dimensional PSDF channel or a two-dimensional slope distribution.
If the physical dimensions of the target data are not sufficient to contain all the objects of the copied selection then only those
objects that fit are copied (this can also mean nothing is copied).

3.10

OpenGL 3D Data Display

Three-dimensional OpenGL display of the current data window can be invoked with the button with symbol of cube in View
button row of main window.
This feature is optional, i.e. it can be disabled at compile time. It can also happen that while Gwyddion is capable of 3D data
display your system does not support it. In both cases an attempt to invoke 3D view gives an error message explaining which of
the two cases occured. In the former case you have to ask the producers of Gwyddion executables to build them with 3D support
or build Gwyddion yourself from source code. If it is the latter case, refer to your operating system guide on how to enable
OpenGL 3D capabilities.
The 3D window has two possible forms: with basic and expanded controls. It starts with basic controls only, this form is
displayed on the following figure. It can be switched to the expanded form (and back) with an expander button in the upper right
corner. Clicking on the view with right mouse button brings a quick color gradient/GL material selector.

Three-dimensional OpenGL data display window with basic controls.

Basic Controls
Basic 3D window contains interaction mode controls at the right side of the view. By default, dragging the view with mouse
rotates it horizontally and vertically. All possible modes are listed below:
Rotation this is the default. Dragging the view horizontally rotates it around z-axis, vertical drag rotates it around horizontal
axis parallel with the plane of view.
Scale dragging the view right and down enlarges it, drag in the opposite direction makes it smaller.
Z-scale dragging the view up (down) increases (decreases) the z-scale, making the hills and valleys more or less pronounced.
Light rotation this possibility is available only in lighting visualization mode. Dragging the view changes position of light
source similarly to rotation of data in normal rotation mode.
The basic controls also include an image export button.
When basic controls are shown it is possible to switch between the modes using keys R (rotation), S (scale), V (value scale) and
L (light rotation).

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Full Controls
In expanded controls the mode buttons are located in top row, however their function does not change. In addition, there are
several tabs with options below them:
Basic controls to set rotations and scales numerically and to switch on and off axes, axis labels, and perspective projection.
Light & Material visualization settings. Gwyddion 3D view has two basic visualization modes: gradient, in which the data
are simply colored with a false color scale exactly like in normal 2D view; and material, in which the data are presented as an
OpenGL material rendered according to light position. This tab also contains controls to set light position numerically.
Labels fine tuning of sizes, positions, and other properties of axis labels.

Saving Images
The 3D view can be saved into a bitmap image with the Save button. The output is currently always a PNG (Portable Network
Graphics) image with exactly the same size and contents as displayed on the screen. Entering a different file extensions than .
png still produces an image in PNG format, albeit with a confusing extension.
Note due to the peculiarities of certain operating systems, graphics drivers and windowing environments, artefacts may sometimes
appear on the exported image in parts corresponding to obscured parts of the 3D view. If you encounter this problem, make sure
the 3D view is not obscured by other windows during the image export.

OpenGL Material Editor

OpenGL material editor can be invoked with Edit GL Materials. The controls in the material list are the same as in the color
gradient editor list and the material management works identically. The actual editor is of course different. It allows to edit four
quantities defining the material:
ambient color ka, (where = red, green, blue), controlling the reflection of ambient light that is assumed coming uniformly
from all directions,
diffuse color kd, , describing the diffuse reflection which is independent on the direction of incident light and whose apparent
brightness is independent of the viewing angle,
specular color ks, , controlling the specular reflection with reflected light intensity dependent on the angle between the observing direction and the direction of light that would be reflected by an ideal mirror with the same normal, and
shininess s, a numeric exponent determining how much the specular reflection resembles an ideal mirror, smaller values mean
rougher surfaces, higher values mean smoother surfaces.
If we denote L the normal vector pointing from the observed surface point to the light source, V the normal vector to the observer,
N the normal vector to the surface and R the normal vector in the direction of ideal mirror reflection, the observed light intensity
in OpenGL lighting model can be expressed as
I = ka, Ia, + kd, Id, (N L) + ks, Is, (R V)s
where Ia, , Id, and Is, are the ambient, diffuse and specular light source intensities, respectively.

3.11

Single Point Spectra

Gwyddion currently offers some basic visualization and extraction means for single point spectroscopy data (we will generally
refer to any curves measured in or otherwise attached to individual points of the sample as to spectra here). If spectra import
is supported for a file type, they will appear in the Spectra tab of the data browser. Standalone spectra files can be added to the
two-dimensional data using file merging.

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Point Spectroscopy Tool

The primary spectra visualization and extraction tool is the Point spectroscopy tool. It displays a list of measurement points and
shows their positions on the data window. Individual curves can be selected either in the list or by selecting the corresponding
crosses on the data window. If the file contains more than one spectrum set, one can choose among them by selecting the desired
one in the Spectra tab list of the data browser.
The Apply button then extracts the selected set of curves into a graph that can be further analysed by graph functions, such as
force-distance curve fitting.

A data window with measurement points displayed and the point spectroscopy tool showing curves from three selected points.

3.12

Volume Data

Volume data are three-dimensional data representing, for instance, grid spectroscopy (spectra in each image point) or time
evolution of the image. So, depending on the point of view, they can be imagined as either a stack of identically-sized images or
as a set of curves forming a regular grid (image).
Gwyddion currently offers some basic visualization and extraction tools in the Volume menu. Volume data windows, as shown
in the following figure, provide the most basic visualisation of volume data: an preview image, representing one plane of the
volume data or other associated two-dimensional data. The x and x coordinates of the image correspond to the x and x coordinates
of the volume data; the z coordinates can be imagined as orthogonal to the screen.

A volume data window displaying the associated two-dimensional preview data.

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29

Button Change Preview near the top of the window can be used to change the preview image. The preview can either be calculated
as a summary quantity characterising data along the invisible z direction (minimum, maximum, mean, . . . ), chosen as a section
of the volume data, alternatively just any two-dimensional data of the same dimensions can be shown as the preview.

3.13

Metadata

Auxiliary information and values describing certain data and the conditions it was measured on are called metadata in Gwyddion.
They may include the SPM mode, tip bias, scanning frequency, measurement date and time or user comments.
Metadata are always per-channel. The metadata for the current channel or volume data can be displayed with Metadata Browser
command in the right-click context menu (in version 2.32 or newer) or using Meta Metadata Browser (in older versions). The
browser lists all available metadata as Name, Value pairs. It also enables to modify and delete values or add new ones. It is
possible to export all metadata of a channel to a text file with Export button.
The level of metadata support differs widely between file formats. For file formats that are well documented and/or allow to
import all metainformation generically lots of auxiliary data including obscure hardware settings can be listed. On the other hand
it is possible that no metadata is imported from your files, for example when they contain no auxiliary data or it is not known
how to read it.

Metadata browser showing the metadata of a Nanoscope file.

3.14

Logging

Gwyddion records data modification operations for each channel or volume data in so-called log. When data are saved to a .
gwy file, the log is saved along with them. The log can be displayed by selecting the View Log command in the right-click
context menu of the channel or volume data window. This is useful for recalling later what corrections you applied, how a mask
or presentation was created, etc. It should be noted that the logs are informational; they are neither intended nor suitable for
auditing purposes.
The log view is live: if you keep it open you can see individual data processing operations appearing there as you perform them.
A simple log example is shown in the following figure. For each operation, the type, name, parameters and time are recorded.
The type can be for instance file import, data processing function or tool application. The function names correspond to those
shown in the module browser (Meta Module Browser), where they are listed in Registered functions for each module; or in
the on-line module browser. The parameter list represents the settings of the function at the time it was used. Since the log is
only informative, the parameters may or may not allow a precise reconstruction of the operation. For typical simple operations,
they should be sufficient. In the case of complex or interactive operations involving multiple channels, the log entry may not be
detailed enough. The time is recorded in the local time zone when the operation is performed; it is not recalculated when you
send the files around the world and display elsewhere.

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Log viewer showing a simple data processing operation log for a channel, starting with file import from an SPM vendor format
and continuing with the application of data processing functions, tools and undo.
The entire log can be exported to a text file using the Export button. It not possible to modify the log entries as that would defeat
the purpose of logging somehow, but you can clear the entire log with Clear.

Disabling logging
In some circumstances, you may wish to store or publish .gwy files without logs. Therefore, logging is controllable on several
levels:
It can be enabled and disabled globally using Edit Logging Enabled. When logging is disabled no new log entries are added.
Existing logs are not removed though and you can still view them. They are also still saved to .gwy files.
The log for a specific channel or volume data can be cleared with button Clear in the viewer.
All logs in the current file can be removed using File Remove All Logs. As with any other file modification, the file needs
to be saved afterwards for the log removal to have any effect on the on-disk file. And, of course, if logging is enabled and you
start modifying the data, new logs will be created and the new data operations recorded in them.

3.15

Raw Data File Import

Both raw ASCII and binary data files and files in unsupported formats can be imported with rawfile module with some effort.
Raw data import can be explicitly invoked by selecting Raw data files type in the file open dialog. It can be also set to appear
automatically when you try to open a file in an unknown format. This is controlled in the raw file dialog by option Automatically
offer raw data import of unknown files.

Information
Its first tab, Information, allows to set basic file information:
Horizontal size, Vertical size Horizontal and vertical data resolution (number of samples).
Square sample Fixes horizontal and vertical resolution to the same value.
Width, Height Physical sample dimensions.
Identical measure Keeps the ratio between physical dimension and number of samples equal for horizontal and vertical direction, that is the data has square pixels.
Z-scale (per sample unit) The factor to multiply raw data with to get physical values.

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Data Format
On the second tab, Data Format, particular data format can be chosen. There are two independent possibilities: Text data and
Binary data.
Text files are assumed to be organized by lines, each line containing a one data row, data being represented by integers or floating
point numbers in standard notation. Following options are available:
Start from line The line data starts at, that is the number of lines to ignore from file start. All types of end-of-line markers (Unix,
MS-DOS, Macintosh) are recognized.
Each row skip The number of fields to ignore at the begining of each line.
Field delimiter, Other delimiter If delimiter is Any whitespace, then any nonzero number of whitespace characters counts as
field delimiter. If a whitespace character is selected, the delimiter must be this character. Otherwise field are separated by
specified character or string and all whitespace around delimiters is ignored.
Decimal separator is comma By default, floating point numbers are assumed to use decimal point. This option changes it to
comma.
Following options are available for binary files:
Binary data You can either select one of predefined standard data formats, or User defined to specify a format with odd number
of bits per sample or other peculiarities.
Byte swap pattern How bytes in samples are swapped. This option is only available for predefined formats larger than one byte.
Its bits correspond to groups of bytes to swap: if the j-th bit is set, adjacent groups of 2 j bits are swapped.
For example, value 3 means sample will be divided into couples (bit 1) of bytes and adjacent couples of bytes swapped,
and then divided into single bytes (bit 0) and adjacent bytes swapped. The net effect is reversal of byte order in groups
of four bytes. More generally, if you want to reverse byte order in groups of size 2 j , which is the common case, use byte
swap pattern j 1.
Start at offset Offset in file, in bytes, the data starts at.
Sample size Size of one sample in bits for user defined formats. E.g., if you have a file with only 4 bits per sample, type 4 here.
For predefined formats, their sample size is displayed, but it is not modifiable.
After each sample skip The number of bits to skip after each sample.
Usually, samples are adjacent to each other in the file. But sometimes there are unused bits or bytes between them, that
can be specified with this option. Note for predefined types the value must be a multiple of 8 (i.e., only whole bytes can be
skipped).
After each row skip The number of bits to skip after each sample in addition to bits skipped after each sample.
Usually, rows are adjacent to each other in the file. But sometimes there are unused bits or bytes between them, that can
be specified with this option. Note for predefined types the value must be a multiple of 8 (i.e., only whole bytes can be
skipped).
Reverse bits in bytes Whether the order of bits in each byte should be reversed.
Reverse bits in samples Whether the order bits in each sample should be reversed for user defined samples.
Samples are signed Whether samples are to be interpreted as signed numbers (as opposed to unsigned). For predefined formats,
their signedness is displayed, but it is not modifiable.

Presets
Import settings can be saved as presets that allow to easily import the same file or the same file type later.
Button Store saves current import settings under the name in Preset name field. Rename renames currently selected preset to
specified name, Delete deletes selected preset, and Load replaced current import setting with selected preset.

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Specific Data Import

Import of several other types of data is not automatic and it requires human intervention.

Graphics Formats
Importing data from image formats such as PNG, TIFF, JPEG or BMP is similar to import from raw/unknown file formats, only
simpler.
It is simpler because the file structure is known and the file format is automatically detected. Hence the file type does need to be
selected explicitly. However, the data interpretation is still unknown and must be specified manually. The Pixmap import dialog
therefore resembles the Information tab of raw data import, requiring you to set the physical dimensions and value scale.
Note the physical dimensions suggested there are not obtained from the file, they are simply the last values used. Some SPM data
format are based on an image format (typically, TIFF is used as the base) and contain the information about physical scales and
units, albeit stored in a manufacturer-specific way. In this case a separate import module can be written for this particular format
to load the files automatically with correctly scaled values.
See the reference section High-Depth Image Formats for the details of support for high-depth images and the possibility of using
them for data representations.

Graph Curves
Simple two-column text files containing curve data can be imported as graph curves. In some cases, these files are recognized
automatically. They can also be explicitly selected as ASCII graph curve files in the file open dialog, causing the import module
to try harder to load the file as a graph data.
The import dialog shows a preview of the graph and permits to set the units and labels.

XYZ Data
Three-column text files containing XYZ data are imported by selecting the XYZ data files file type. Again, they can be recognized
automatically but requesting this format explicitly makes the module to try harder to load the file as XYZ data.
Since Gwyddion only works with data in a regular grid irregular XYZ data must be interpolated to a regular grid upon import. In
fact, the XYZ data import module serves two different purposes:
loading of data in a regular grid that were just saved as XYZ data if the data is found to be in a regular grind only a very
simple import dialog is presented where you can set the units because the import is straightforward;
regularization and interpolation of irregular XYZ data this case is much less straightforward and the rest of this section will
discuss the options you have and some of the pitfalls.
The import dialog permits to set the basic parameters as the regularized data resolution and range and lateral and value units.
However, the most important option is Interpolation type:
Round This interpolation is analogous to the Round interpolation for regular grids. The interpolated value in a point in the plane
equals to the value of the nearest point in the XYZ point set. This means the Voronoi triangulation is performed and each
Voronoi cell is filled with the value of the nearest point.
Linear This interpolation is analogous to the Linear interpolation for regular grids. The interpolated value in a point is calculated
from the three vertices of the Delaunay triangulation triangle containing the point. As the tree vertices uniquely determine
a plane in the space, the value in the point is defined by this plane.
Field The value in a point is the weighted average of all the XYZ point set where the weight is proportional to the inverse fourth
power of the mutual distance. Since all XYZ data points are considered for the calculation of each interpolated point this
method can be very slow.
The former two interpolation types are based on Delaunay/Voronoi triangulation which is not well-defined for point sets where
more than two points lie on a line or more than three lie on a circle. If this happens the triangulation fails and the import module
displays an error message.
The values outside the convex hull of the XYZ point set in the plane are influenced by Exterior type:

3. Getting Started

33

Border The point set is not amended in any way and the values on the convex hull simply extend to the infinity.
Mirror The point set is amended by points reflected about the bounding box sides.
Periodic The point set is amended by periodically repeated points from around the opposite side of bounding box.

Delaunay triangulation displayed on linear (left), round (centre) and field (right) interpolation of a irregular set of points.

3.17

Plug-ins

Plug-ins are external programs that can be executed by Gwyddion to either perform some operation on the data or to read or
write data in a third-party file format. In general, plug-ins are programs that can register themself within Gwyddion (for example
printing something on standard output) to enable Gwyddion to create plugin menu choice and can be used for data processing
(or IO operation).
Generally it is preferable to extend Gwyddion functionality by modules, because modules are dynamic libraries linked directly
to Gwyddion at run-time allowing much more versatile interaction with the application, and they are also faster (for the same
reason). For example, plug-ins generally cannot make use of existing Gwyddion data processing functions and cannot modify
data in-place, a new window is always created for the result. Programming of modules is also no harder than programming of
plug-ins, maybe it is even easier (assuming you know C).

Warning The plug-in mechanism is deprecated. It will remain supported in Gwyddion 2.x, however, it will not be extended or improved. The recommended method to extend Gwyddion by routines in another language is to use language
bindings, at this moment a Python interface is available. The recommended method to run third-party programs is to
write a small specialized C module that knows how to communicate with these programs.

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Chapter 4

Data Processing and Analysis

The number and breadth of data manipulation and analysis functions is one of the Gwyddion main strengths. The description of
their principles and applications is the purpose of this chapter, with focus on the explanation of how they work and what they
calculate or perform. Elements of their user interface are also occasionaly described where it seems useful, nevertheless, it is
assumed the reader is familiar with the basic organization of data and controls in Gwyddion, as described in the previous chapter.

4.1

Basic Operations

Value-reading and basic geometrical operations represent the core of any data processing program. Gwyddion offers a wide set of
functions for data scaling, rotation, resampling or profile extraction. This section describes these simple but essential functions.

Basic 2D Data Operations

Within basic modules it is possible to perform the following operations with 2D data field:
Resample the data to chosen dimensions or scale using selected interpolation method by Data Process Basic Operations
Scale
Crop the data using the Crop tool either in place or putting the result to a new channel (with option Create new channel). With
Keep lateral offsets option enabled, the top left corner coordinates of the resulting image correspond to the top left corner of
the selection, otherwise the top left corner coordinates are set to (0, 0).
Extend the data with Data Process Basic Operations Extend. Extending is essentially the opposite of cropping. Of
course, adding more real data around the image borders is only possible by measuring more data. So this function offers,
instead, several simple artificial extension methods such as mirrored and unmirrored periodic continuation or repetition of
boundary values.
Rotate data by 90 degrees or by user-specified amount using some of the rotate functions: Data Process Basic Operations
Rotate Clockwise, Rotate Anticlockwise or Rotate.
Flip the data horizontally (i.e. about the vertical axis) and vertically (i.e. about the horizontal axis) with Data Process Basic
Operations Flip Horizontally and Flip Vertically, respectively.
Flip the data about the centre (i.e. about both axes) with Data Process Basic Operations Flip Both.
Invert the data values using the Invert Value function: Data Process Basic Operations Invert Value. The values are
inverted about the mean value which keeps the mean value unchanged.
Limit the data range by cutting values outside a specified range by Data Process Basic Operations Limit Range. The
range can be set numerically or taken from the false color map range previously set using the Color range tool and it is also
possible to cut off outliers farther than a chosen multiple of RMS from the mean value.
Upsample the data to make pixels square with Data Process Basic Operations Square Samples. Most scans have pixels
with 1:1 aspect ratio, therefore this function has no effect on them.
Tilt the data by specified gradient or angle using Data Process Basic Operations Tilt.
Change physical dimensions, units or value scales and also lateral offsets using Data Process Basic operations Dimensions
and Units. This is useful to correct raw data that have been imported with wrong physical scales or as a simple manual recalibration of dimensions and values.

Reading Values
The simplest value reading method is to place the mouse cursor over the point you want to read value of. The coordinates and/or
value is then displayed in the data window or graph window status bar.

4. Data Processing and Analysis

35

Read Value Tool

Tool Read Value offers more value reading possibilities: it displays coordinates and values of the last point of the data window
the mouse button was pressed. It can average the value from a circular neighbourhood around the selected point, this is controlled
by option Averaging radius. When the radius is 1, the value of a single pixel is displayed (as the simplest method does). Button
Set Zero shifts the surface to make the current z the new zero level.
Read Value can also display the inclination of the local facet. Averaging radius again determines the radius of the area to use for
the plane fit.
Inclinations

In all Gwyddion tools, facet and plane inclinations are displayed as the spherical angles ( , ) of the plane normal vector.
Angle is the angle between the upward direction and the normal, this means that = 0 for horizontal facets and it increases
with the slope. It is always positive.
Angle is the counter-clockwise measured angle between axis x and the projection of the normal to the xy plane, as displayed
on the following figure. For facets it means corresponds to the downward direction of the facet.

Surface facet (displayed blue) orientation measured as the counterclockwise angle from x-axis to the projection of facet normal
vector n to xy plane.
Distance Tool

Distances and differences can be measured with the Distance tool. It displays the horizontal (x), vertical (y) and total planar
(R) distances; the azimuth (measured identically to inclination ) and the endpoint value difference z for a set of lines selected
on the data.
The distances can be copied to the clipboard or saved to a text file using the buttons below the list.

Distance tool with three selected lines.

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Profile Extraction
The profile extraction tool can be accessed from the toolbox. You can use mouse to draw several profiles in the image and they
can be further moved and adjusted. The dialog includes a live profile graph preview. Profiles can be of different thickness
which means that more neighbour data perpendicular to profile direction are used for evaluation of one profile point for thicker
profiles. This can be very useful for noise suppression while measuring regular objects.
After profiles are chosen, they can be extracted to graphs (separate or grouped in one Graph window) that can be further analysed
using Graph functions.

Profile tool with three extracted profiles and expanded options.

The profile curve is constructed from data sampled at regular intervals along the selected line. Values in points that do not lie
exactly at pixel centres (which normally occurs for oblique lines) are interpolated using the chosen interpolation mode. Unless
an explicit number of samples to take is set using the Fix res. option, the number of samples corresponds to the line length in
pixels. This means that for purely horizontal or purely vertical lines no interpolation occurs.

4. Data Processing and Analysis

37

Natural resolution prole

Round interpolation, natural resolution

9

z [nm]

8
7
6
5
4
3
Round interpolation, high resolution
9

High resolution prole

z [nm]

8
7
6
5
4
3
Key interpolation, high resolution
9

z [nm]

8
7
6
5
4
3
0

10

12

14

16

18

20

x [nm]

Illustration of data sampling in profile extraction for oblique lines. The figures on the left show the points along the line where the
values are read for natural and very high resolution. The graphs on the right show the extracted values. Comparison of the natural
and high resolution profiles taken with Round interpolation reveals that indeed natural-resolution curve points form a subset of
the high-resolution points. The influence of the interpolation method on values taken in non-grid positions is demonstrated by
the lower two graphs, comparing Round and Key interpolation at high resolution.

4.2

Interpolation

Most geometrical transformations, such as rotation, scaling or drift compensation utilize or depend on data interpolation. Also
some other operations, e.g. profile extraction, can work with values between individual pixels and hence involve interpolation.
Since SPM data are relatively coarsely sampled compared to measured details (full images are typically only a few hundred
pixels in width and height), the interpolation method used can become critical for proper quantitative analysis of data properties.
Gwyddion implements several interpolation methods [1] and the user can choose which method to use for most of the modules
using interpolation.
Here, we describe the principles and properties of one-dimensional interpolation methods. All implemented two-dimensional
interpolation methods are separable and thus simply composed of the corresponding one-dimensional methods. The following
interpolation method are currently available:
Round Round interpolation (also called nearest neighbourhood interpolation) is the simplest method it just takes rounded
value of the expected position and finds therefore the closest data value at integer position. Its polynomial degree is 0,
regularity C1 and order 1.
Linear Linear interpolation is a linear interpolation between the two closest data values. The value z at point of relative position
x is obtained as
z = (1 x)z0 + xz1
where z0 and z1 are values at the preceding and following points, respectively. Its polynomial degree is 1, regularity C0
and order 2. It is identical to the second-order B-spline.
Key Key interpolation (more precisely Keys interpolation with a = 1/2 which has the highest interpolation order) makes use
also of values in the before-preceding and after-following points z1 and z2 , respectively. In other words it has support of
length 4. The value is then obtained as
z = w1 z1 + w0 z0 + w1 z1 + w2 z2

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where


w1 = 12 + (1 2x )x x
w0 = 1 + ( 52 + 32 x)x2


w1 = 12 + (2 32 x)x x
w2 = ( 12 + 2x )x2
are the interpolation weights. Keys interpolation degree is 3, regularity C1 and order 3.

Schaum Schaum interpolation (more precisely fourth-order Schaum) has also support of length 4. The interpolation weights are
w1 = 61 x(x 1)(x 2)
w0 = 12 (x2 1)(x 2)
w1 = 12 x(x + 1)(x 2)
w2 = 16 x(x2 1)
Its polynomial degree is 3, regularity C0 and order 4.
NNA Nearest neighbour approximation is again calculated from the closest four data values but unlike all others it is not
piecewise-polynomial. The interpolation weights are

wk =

1
rk4
2

1
4
j=1 r j

for k = 1, 0, 1, 2, where r1 = 1 + x, r0 = x, r1 = 1 x, r2 = 2 x. Its order is 1.

B-spline The weights are
w1 = 16 (1 x)3
w0 = 23 x2 (1 2x )


w1 = 16 + 12 x 1 + x(1 x)
w2 = 16 x3
However, they are not used with directly function values as above, but with interpolation coefficients calculated from
function values [1]. Its polynomial degree is 3, regularity C2 and order 4.
O-MOMS The weights are
4
11
1
x
21 + 21 + ( 2 6 )x x


1
x
w0 = 13
21 + 14 + (1 + 2 )x x


4
w1 = 21
+ 37 + ( 12 2x )x x
1
+ 61 x2 )x
w2 = ( 42

w1 =

However, they are not used directly with function values as above, but with interpolation coefficients calculated from
function values [1]. Its polynomial degree is 3, regularity C0 and order 4.

Illustration of the available interpolation types (the original pixels are obvious on the result of Round interpolation). All images
have identical false color map ranges.

4. Data Processing and Analysis

39

References
[1] P. Thvenaz, T. Blu, M. Unser: Interpolation revisited. IEEE Transactions on medical imaging, Volume 10, Number 7, July
2000, 739

4.3

Data Leveling and Background Subtraction

Leveling
The data obtained from SPM microscopes are very often not leveled at all; the microscope directly outputs raw data values
computed from piezoscanner voltage, strain gauge, interferometer or other detection system values. This way of exporting data
enables the user to choose his/her own method of leveling data.
The choice of leveling method should be based on your SPM system configuration. Basically, for systems with independent
scanner(s) for each axis, plane leveling should be sufficient. For systems with scanner(s) moving in all three axes (tube scanners)
2nd order polynomial leveling should be used.
Of course, you can use higher order leveling for any data, however, this can supress real features on the surface (namely waviness
of the surface) and therefore alter the statistical functions and quantities evaluated from the surface.
Fix Zero and Zero Mean Value

Data Process Level Fix Zero

Data Process Level Zero Mean Value
The simplest modules that are connected with data leveling are Fix Zero and Zero Mean Value that simply set the average height
of the data to put the minimum to zero (Fix Zero) or mean value to zero (Zero Mean Value).
Plane Level

Data Process Level Plane Level

Plane leveling is usually one of the first functions applied to raw SPM data. The plane is computed from all the image points and
is subtracted from the data.
If a mask is present plane leveling offers to use the data under mask for the plane fitting, exclude the data under mask or ignore
the mask and use the entire data.
Tip You can quickly apply plane leveling by simply right-clicking on the image window and selecting Level.

Three Point Leveling Tool

The Three Point Leveling tool can be used for leveling very complicated surface structures. The user can simply mark three
points in the image that should be at the same level, and then click Apply. The plane is computed from these three points and is
subtracted from the data.
Facet Level

Data Process Level Facet Level

Facet Level levels data by subtracting a plane similarly to the standard Plane Level function. However, the plane is determined
differently: it makes facets of the surface as horizontal as possible. Thus for surfaces with flat horizontal areas it leads to much
better results than the standard Plane Level especially if large objects are present.
On the other hand, it is not suitable for some types of surface. These includes random surfaces, data with considerable fine noise
and non-topographic images as the method does not work well if the typical lateral dimensions and heights differ by many
orders.
Similarly to Plane Level, Facet Level can include or exclude the data under mask. This choice is offered only if a mask is present.
Finding the orientation of the facets is an iterative process that works as follows. First, the variation of local normals is determined:
1 N
2 = n2i
N i=1

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where ni is the vector of local facet normal (see inclination coordinates) in the i-th pixel. Then the prevalent normal is estimated
as


N
n2i
ni exp c 2
i=1
n= N


n2i
exp
c

2
i=1
where c = 1/20 is a constant. Subsequently, the plane corresponding to the prevalent normal n is subtracted and these three steps
are repeated until the process converges. The gaussian weighting factors serve to pick a single set of similar local facet normals
and converge to their mean direction. Without these factors, the procedure would obviously converge in one step to the overall
mean normal and hence would be completely equivalent to plain plane leveling.

Facet Level example: (a) uncorrected, sloping data; (b) data leveled by standard plane fitting (Plane Level); (c) data leveled by
Facet Level.
Level Rotate

Data Process Level Level Rotate

Level Rotate behaves similarly to Plane Level, however it does not simply subtract the fitted plane from the data. Instead, this
module takes the fitted plane parameters and rotates the image data by a calculated amount to make it lie in a plane. So unlike
Plane Level, this module should therefore preserve angle data in the image.

Background Subtraction
Gwyddion has several special modules for background subtraction. All allow you to extract the subtracted background to a
separate data window.
Tip For finer control, you can use any of Gwyddions filtering tools on an image, and then use the Data Arithmetic module to
subtract the results from your original image.

Polynomial Background

Data Process Level Polynomial Background

Fits data by a polynomial of the given order and subtracts this polynomial. In the Independent degree mode the horizontal and
vertical polynomial orders can be generally set separately, i.e. the fitted polynomial is
m

a j,k x j yk

j=0 k=0

where m and n are the selected horizontal and vertical polynomial degrees, respectively. In the Limited total degree mode the
fitted polynomial is
a j,k x j yk
j+kn

where n is the selected total polynomial degree.

Similarly to Plane Level, polynomial background subtraction can include or exclude the data under mask. This choice is offered
only if a mask is present.

4. Data Processing and Analysis

41

Revolve Arc

Data Process Level Revolve Arc

Revolves virtual arc of given radius horizontally or vertically over (or under) the data. The envelope of this arc is treated as a
background, resulting in removal of features larger than the arc radius (approximately).
Median Level

Data Process Level Median Level

Filters data with a median filter using a large kernel and treats the result as background. Only features smaller than approximately
the kernel size will be kept.
Note This method can be very slow.

Fit Sphere

Data Process Level Fit sphere

Fits part of sphere surface on the data. Sphere orientation (i.e. centre position) and initial fit values can be preset before fitting.
Marquardt-Levenberg fitting routine is used to calculate the result.

Curvature
Data Process Level Curvature
The global surface curvature parameters are calculated by fitting a quadratic polynomial and finding its main axes. Positive signs
of the curvature radii correspond to a concave (cup-like) surface, whereas negative signs to convex (cap-like) surface, mixed
signs mean a saddle-like surface.
Beside the parameter table, it is possible to set the line selection on the data to the fitted quadratic surface axes and/or directly
read profiles along them. The zero of the abscissa is placed to the intersection of the axes.
Similarly to the background subtraction functions, if a mask is present on the data the module offers to include or exclude the
data under mask.

Curvature dialog screenshot showing the strong deflection of a glass plate with a thin film with compressive internal stress.

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4.4

Gwyddion user guide

Filters

Basic Filters Tool

The Basic Filters tool lets you apply several simple filters to your image. This can be very useful for data denoising; however, the
real measured data will get altered in the process, so great care should be taken not to destroy important features of the image.
Mean filter takes the mean value of neighbourhood of the filtered value as the value.
Median filter takes the median value of neighbourhood of the filtered value as the value.
Conservative denoise filter checks whether the value is not extreme within the neighbourhood. If yes, filter substitutes the
value by of the next highest (lowest) value.
Kuwahara filter is an edge-preserving smoothing filter.
Minimum filter also known as erode filter, replaces values by minimum found in neighbourhood.
Maximum filter also known as dilate filter, replaces values by maximum found in neighbourhood.
Dechecker filter a smoothing filter specially designed to remove checker pattern from the image while preserving other
details. It is a convolution filter with kernel

0
1/144 1/72 1/144
0
1/9
1/18 1/144
1/144 1/18

1/9
7/9
1/9
1/72
wdechecker = 1/72

1/144 1/18
1/9
1/18 1/144
0
1/144 1/72 1/144
0
Gaussian filter a smoothing filter, the size parameter determines the FWHM (full width at half maximum) of the Gaussian.
The relation between FWHM and is

FWHM = 2 2 ln 2 2.35482
Tip By default, these filters will be applied to the entire image. However, you can apply a filter to a specific region within your
image by selecting it with the mouse. This can be useful for correcting badly measured areas within a good image. To apply a
filter to the entire image again, just click once anywhere within the image window.

Moreover, there are more denoising functions in Gwyddion, for example DWT denoising and FFT filtering. For details see
section Extended Data Edit.
If you need to only suppress some values in the SPM data that are obviously wrong, you can also try the Mask of Outliers module
and the Remove Data Under Mask module. For details see section Data Edit.

Screenshot of filter tool with median filter applied to a rectangular selection

4. Data Processing and Analysis

43

Convolution
Data Process Integral Transforms Convolution Filter
Convolutions with arbitrary kernels up to 9 9 can be performed with the Convolution Filter module.
The Divisor entry represents a common factor all the coefficients are divided before applying the filter. This allows to use
denormalized coefficients that are often nicer numbers. The normalization can be also calculated automatically when automatic
is checked. When the sum of the coefficients is nonzero, it makes the filter sum-preserving, i.e. it the factor normalizes the sum
of coefficients to unity. When the sum of the coefficients is zero, the automatic factor is simply let equal to 1.
Since many filters used in practice exhibit various types of symmetry, the coefficients can be automatically completed according
to the selected symmetry type (odd, even). Note the completion is performed on pressing Enter in the coefficient entry.
In a fresh installation only a sample Identity filter is present (which is not particularly useful as it does nothing). This filter cannot
be modified, to create a new filter use the New button on the Presets page.

4.5

Presentations

Presentation modules do not modify the data, instead, they output their results into a separate layer displayed on top of the
original data. The other data processing modules and tools will still operate on the underlying data. To remove a presentation,
right-click on the data window, and select Remove Presentation.

Basic Operations
The Data Process Presentation menu contains a few basic presentation operations:
Attach Presentation Attaches another data field as a presentation to the current data. Note that this useful option can be particularly confusing while evaluating anything from the data as all the computed values are evaluated from the underlying data
(not from the presentation, even if it looks like the data).
Remove Presentation Removes presentation from the current data window. This is an alternative to the right-click data window
menu.
Extract Presentation Extracts presentation from the current data window to a new channel in the same file. In this way one
can get presentation data for further processing. Note, however, the extracted data have no absolute scale information as
presentation often help to visualize certain features, but the produced values are hard or impossible to assign any physical
meaning to. Hence the value range of the new channel is always [0, 1].

Presentation examples: (a) original data, (b) shading, (c) vertical Prewitt gradient, (d) Canny edge detection, (e) local nonlinearity edge detection, (f) local contrast improvement.

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Gwyddion user guide

Shading Presentation
Data Process Presentation Shading
Simple and very useful way of seeing data as illuminated from some direction. The direction can be set by user. It is also
possible to mix the shaded and original images for presentational purposes. Of course, the resulting image is meaningless from
the physical point of view.

Gradient Detection Presentations

Data Process Presentation Gradient
Sobel horizontal and vertical gradient filter and Prewitt horizontal and vertical gradient filter create similar images as shading,
however, they output data as a result of convolution of data with relatively standardized kernel. Thus, they can be used for further
presentation processing for example. The kernels for horizontal filters are listed below, vertical kernels differ only by reflection
about main diagonal.

1/3 0 1/3
1/4 0 1/4
wPrewitt = 1/3 0 1/3 , wSobel = 1/2 0 1/2
1/3 0 1/3
1/4 0 1/4

Edge Detection Presentations

Data Process Presentation Edge Detection
One is often interested in the visualization of the discontinuities present in the image, particularly in discontinuities in the value
(zeroth order) and discontinuities in the derivative (first order). Although the methods of location of both are commonly referred
to as edge detection methods, these are actually quite different, therefore we will refer to the former as to step detection and to
the latter as to edge detection. Methods for the detection of more specific features, e.g. corners, are commonly used too, these
methods usually are of order zero.
The order of a discontinuity detection method can be easily seen on its output as edge detection methods produce typical double
edge lines at value discontinuities as is illustrated in the following figure. While the positions of the upper and lower edge in an
ideal step coincide, real-world data tend to actually contain two distinct edges as is illustrated in the picture. In addition, finding
two edges on a value step, even an ideally sharp one, is often an inherent feature of edge detection methods.

Edge
Step

Edge

Step versus edge in one dimension.

The following step and edge detection functions are available in Gwyddion (the later ones are somewhat experimental, on the
other hand they usually give better results than the well-known algorithms):
Canny Canny edge detector is a well-known step detector that can be used to extract the image of sharp value discontinuities
in the data as thin single-pixel lines.
Laplacian of Gaussians Laplacian presents a simple convolution with the following kernel (that is the limit of discrete Laplacian of Gaussians filter for 0):

0 1/4 0
wlaplace = 1/4 1 1/4
0 1/4 0
Zero Crossing Zero crossing step detection marks lines where the result of Laplacian of Gaussians filter changes sign, i.e.
crosses zero. The FWHM (full width half maximum) of the Gaussians determines the level of details covered. Threshold
enables to exclude sign changes with too small absolute value of the neighbour pixels, filtering out fine noise. Note,
however, that for non-zero threshold the edge lines may become discontinuous.

4. Data Processing and Analysis

45

Step A step detection algorithm providing a good resolution, i.e. sharp discontinuity lines, and a good dynamic range while
being relatively insensitive to noise. The principle is quite simple: it visualizes the square root of the difference between
the 2/3 and 1/3 quantiles of the data values in a circular neighbourhood of radius 2.5 pixels centered around the sample.
RMS This step detector visualizes areas with high local value variation. The root mean square of deviations from the mean
value of a circular neighbourhood of radius 2.5 pixels centered around each sample is calculated and displayed.
RMS Edge This function essentially postprocesses RMS output with a filter similar to Laplacian to emphasize boundaries of
areas with high local value variation. Despite the name it is still a step detector.
Local Non-Linearity An edge detector which visualizes areas that are locally very non-planar. It fits a plane through a circular
neighbourhood of radius 2.5 pixels centered around each sample and then it calculates residual sum of squares of this
fit reduced to plane slope, i.e. divided by 1 + b2x + b2y where bx and by are the plane coefficients in x and y directions,
respectively. The square root is then displayed.
Inclination Visualizes the angle of local plane inclination. Technically this function belongs among step detectors, however,
the accentuation of steps in its output is not very strong and it is more intended for easy visual comparison of different
slopes present in the image.

Comparison of step and edge detection methods on several interesting, or typical example data. Canny and Zero crossing are
step detectors that produce one pixel wide edge lines, Step and Inclination are step detectors with continuous output, Local
nonlinearity is an edge detector the edge detection can be easily observed on the second and third row. Note zero crossing is
tunable, it parameters were chosen to produce reasonable output in each example.

Local Contrast
Data Process Presentation Local Contrast
A method to visualize features in areas with low and high value variation at the same time. This is achieved by calculation of
local value range, or variation, around each data sample and stretching it to equalize this variation over all data.

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Rank
Data Process Presentation Rank
An alternative local contrast enhancement method. It is an equalising high-pass filter, somewhat complementary to the median
filter. Each pixel value is transformed to its rank among all values from a certain neihbourhood. The neighbourhood radius can
be specified as Kernel size.
The net effect is that all local maxima are equalised to the same maximum value, all local minima to the same minimum value,
and values that are neither maxima nor minima are transformed to the range between based on their rank. Since the output of the
filter with radius r can contain at most (r + 1/2)2 different values (approximately), the filter also leads to value discretisation,
especially for small kernel sizes.

Logscale
Data Process Presentation Logscale
Logarithmic scale is used for false colors data presentation.

4.6

Data Edit and Correction

There are several modules that enable direct or indirect editing of the SPM data. In principal, most of the data processing
modules change the data in one way or another. However, in this section we would like to describe the modules and tools that
are specifically designed to correct local defects in an image. The functions below remove bad data from an image, and then
fill it in using an interpolation algorithm.

Remove Spots Tool

The Remove Spots tool can be used for removing very small parts of the image that are considered a scanning error, dust particle
or anything else that should not be present in the data. Note that doing so can dramatically alter the resulting statistical parameters
of the surface, so be sure not to remove things that are really present on the surface.
While using this tool you can pick up position of the spot to magnify its neighbourhood in the tool window. Then, in the tool
window, select a rectangle around the area that should be removed. You can then select one of several interpolation methods for
creating data in place of the former spot:
Hyperbolic flatten - uses information from selected area boundaries to interpolate the information inside area.
Pseudo-Laplace and Laplace solver - solves Laplace equation to calculate data inside area; the boundary is treated as virtual
source.
Fractal correction - uses whole image to determine fractal dimension. Then tries to create randomly rough data that have the
same fractal dimension and put them into the area.
Clicking Apply will execute the selected algorithm.
Note Spot removal will only work for regions of size 64 64 pixels or smaller. To remove larger regions, create a mask using
the Mask Editor tool, then use Data Process Correct Data Remove Data Under Mask.

Remove Grains Tool

This simple tool removes manually selected connected parts of mask or interpolates the data under them, or possibly both. The
part of mask to remove is selected by clicking on it with left mouse button.

Remove Scars
Data Process Correct Data Remove Scars
Scars (or stripes, strokes) are parts of the image that are corrupted by a very common scanning error: local fault of the closed
loop. Line defects are usually parallel to the fast scanning axis in the image. This function will automatically find and remove
these scars, using neighbourhood lines to fill-in the gaps. The method is run with the last settings used in Mark Scars.

4. Data Processing and Analysis

47

Mark Scars
Data Process Correct Data Mark Scars
Similarly, the Mark Scars module can create a mask of the points treated as scars. Unlike Remove Scars which directly
interpolates the located defects, this module lets you interactively set several parameters which can fine-tune the scar selection
process:
Maximum width only scars that are as thin or thinner than this value (in pixels) will be marked.
Minimum length only scars that are as long or longer than this value (in pixels) will be marked.
Hard threshold the minimum difference of the value from the neighbouring upper and lower lines to be considered a defect.
The units are relative to image RMS.
Soft threshold values differing at least this much do not form defects themselves, but they are attached to defects obtained
from the hard threshold if they touch one.
Positive, Negative, Both the type of defects to remove. Positive means defects with outlying values above the normal values
(peaks), negative means defects with outlying values below the normal values (holes).
After clicking Ok the new scar mask will be applied to the image. Other modules or tools can then be run to edit this data.

Scars marking and removal example: (a) original data with defects, (b) data with marked deffects, (c) corrected data.

Remove Data Under Mask

Data Process Correct Data Remove Data Under Mask
This function substitutes the data under the mask by the solution of solving the Laplacian equation. The data values around the
masked areas define the boundary conditions. The solution is calculated iteratively and it can take some time to converge.

Fractal Correction
Data Process Correct Data Fractal Correction
The Fractal Correction module, like the Remove Data Under Mask module, replaces data under the mask. However, it uses a
different algorithm to come up with the new data: The fractal dimension of the whole image is first computed, and then the areas
under the mask are substituted by a randomly rough surface having the same fractal dimension. The root mean square value of
the height irregularities (roughness) is not changed by using this module.
Note This calculation can take some time, so please be patient.

Warning Running this module on data that do not have fractal properties can cause really unrealistic results and is
strictly not recommended.

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Mask of Outliers
Data Process Correct Data Mask of Outliers
This module creates mask of areas in the data that not pass the 3 criterion. All the values above and below this confidence
interval are marked in mask and can be edited or processed by other modules afterwards.

Line Correction
Profiles taken in the fast scanning axis (usually x-axis) can be mutually shifted by some amount or have slightly different slopes.
The basic line correction functions deal with this type of discrepancy. Several functions can be used: The Polynomial and Path
level tools and then several procedures under Data Process Correct Data menu.
The Polynomial tool fits each horizontal or vertical line by a polynomial up to the third order and then subtracts the fitted
polynomial a very frequently used function in basic processing of raw SPM data. It also permits to exclude or include selected
area from the fit. The inclusion or exclusion only applies to the lines interseting the selected area. Other lines are always fitted
using all data values.
Line correction functions in Correct Data perform only horizontal line corrections, therefore one has to rotate the image to
perform column-wise correction. They include:
Match Line Correction,
Median Line Correction,
Modus Line Correction, and
Median Difference Line Correction,
Step Line Correction.
The first three are very similar, they all align rows of the data field to minimize some quantity. As the names indicate, Median Line
Correction matches line medians while Modus Line Correction attempts to match line (pseudo)modus. Match Line Correction
minimizes certain line difference function that gives more weight to flat areas and less weight to areas with large slopes. The
effect of all three functions is often very similar, although some can be more suitable for certain type of data than others.
Tip Median line correction supports masking. If a mask is present it offers to use the data under mask for the leveling, exclude
the data under mask or ignore the mask and use the entire data.

Function Median Difference Line Correction shifts the lines so that the median of differences (between vertical neighbour pixels)
becomes zero, instead of the difference of medians. Therefore it better preserves large features while it is more sensitive to
completely bogus lines.
Function Step Line Correction differs from the others. It attempts to identify misaligned segments within the rows and correct
the height of each such segment individually. Therefore it is often able to correct data with discontinuities in the middle of a row.
This function is rather experimental and the exact way it works can be subject of futher changes.

Path Leveling Tool

The Path Leveling tool can be used to correct the heights in an arbitrary subset of rows in complicated images.
First, one selects a number of straight lines on the data. The intersections of these lines with the rows then form a set of points in
each row that is used for leveling. The rows are moved up or down to minimize the difference between the heights of the points
of adjacent rows. Rows that are not intersected by any line are not moved (relatively to neighbouring rows).

4. Data Processing and Analysis

49

Path Level example: (a) uncorrected data with steps that the automated method may fail to correct, two suitable leveling lines are
selected; (b) the result of Path Level application with line width 5.

Unrotate
Data Process Correct Data Unrotate
Unrotate can automatically make principal directions in an image parallel with horizontal and/or vertical image edges. For that
to work, the data need to have some principal directions, therefore it is most useful for scans of artifical and possibly crystallic
structures.
The rotation necessary to straighten the image displayed as Correction is calculated from peaks in angular slope distribution
assuming a prevalent type of structure, or symmetry. The symmetry can be estimated automatically too, but it is possible to select
a particular symmetry type manually and let the module calculate only corresponding rotation correction. Note if you assume a
structure type that does not match the actual structure, the calculated rotation is rarely meaningful.
It is recommended to level (or facet-level) the data first as overall slope can skew the calculated rotations.

Parallel

Triangular

Square

Rhombic

Hexagonal

Orientations of prevalent directions corresponding to Unrotate symmetry types.

The assumed structure type can be set with Assume selector. Following choices are possible:
Detected Automatically detected symmetry type, displayed above as Detected.
Parallel Parallel lines, one prevalent direction.
Triangular Triangular symmetry, three prevalent directions (unilateral) by 120 degrees.
Square Square symmetry, two prevalent directions oriented approximately along image sides.
Rhombic Rhombic symmetry, two prevalent directions oriented approximately along diagonals. The only difference from
Square is the preferred diagonal orientation (as opposed to parallel with sides).
Hexagonal Hexagonal symmetry, three prevalent directions (bilateral) by 120 degrees.

4.7

Extended Data Edit

This section presents extended modules designed for editing (correcting) SPM data. Using simple data editing tools presented in
chapter Data Edit and Correction it is possible to correct many local scanning defects that can be found on SPM images. There
are also many error sources within SPM methods that lead to global errors, like low frequencies modulated on the data or data
drift in the slow scanning axis.

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Drift Compensation
Data Process Correct Data Compensate Drift
Compensate Drift calculates and/or corrects drift in the fast scanning axis (horizontal). This adverse effect can be caused by
thermal effects or insufficient mechanical rigidity of the measuring device.
The drift graph, which is one of possible outputs, represents the horizontal shift of individual rows compared to a reference row
(which could be in principle chosen arbitrarily, in practice the zero shift is chosen to minimize the amount of data sticking out of
the image after compensation), with the row y-coordinate on the abscissa.
The drift is determined in two steps:
1. A mutual horizontal offset is estimated for each couple of rows not more distant than Search range. It is estimated as the
offset value giving the maximum mutual correlation of the two rows. Thus a set of local row drift estimations is obtained
(together with the maximum correlation scores providing an estimate of their actual similarity).
2. Global offsets are calculated from the local ones. At present the method is very simple as it seems sufficient in most
cases: local drift derivatives are fitted for each row onto the local drift estimations and the global drift is then obtained by
integration (i.e. summing the local drifts).
Option Exclude linear skew subtracts the linear term from the calculated drift, it can be useful when the image is anisotropic and
its features are supposed to be oriented in a direction not paralled to the image sides.

Drift correction example: (a) original data exhibiting strong drift in the fast scan axis, (b) corrected data, (c) calculated drift
graph.

1D FFT Filter
Data Process Correct Data 1D FFT Filtering
One excellent way of removing frequency based of noise from an image is to use Fourier filtering. First, the Fourier transform
of the image is calculated. Next, a filter is applied to this transform. Finally, the inverse transform is applied to obtain a filtered
image. Gwyddion uses the Fast Fourier Transform (or FFT) to make this intensive calculation much faster.
Within the 1D FFT filter the frequencies that should be removed from spectrum (suppress type: null) or suppressed to value of
neighbouring frequencies (suppress type: suppress) can be selected by marking appropriate areas in the power spectrum graph.
The selection can be inverted easily using the Filter type choice. 1D FFT filter can be used both for horizontal and vertical
direction.

2D FFT Filter
Data Process Correct Data 2D FFT Filtering
2D FFT filter acts similarly as the 1D variant (see above) but using 2D FFT transform. Therefore, the spatial frequencies that
should be filtered must be selected in 2D using mask editor. As the frequencies are related to center of the image (corresponding
to zero frequency), the mask can be snapped to the center (coordinate system origin) while being edited. There are also different
display and output modes that are self-explanatory image or FFT coefficients can be outputted by module (or both).

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51

Affine Distortion
Data Process Correct Data Affine Distortion
Affine distortion in the horizontal plane caused by thermal drift is common for instance in STM. If the image contains a regular
structure, for instance an atomic lattice of known parameters, the distortion can be easily corrected using this function.
The affine distortion correction requires to first select the distorted lattice in the image. This is done by moving the lattice
selection on the preview with mouse until it matches the regular features present in the image. For images of periodic lattices, it
is usually easier to select the lattice in the autocorrelation function image (2D ACF). Also, only a rough match needs to be found
manually in this case. Button Refine refines the selected lattice vectors to the nearest maxima in autocorrelation function with
subpixel precision.
The correct lengths of the lattice vectors a1 and a2 and the angle between them, entered to the dialog, determine the affine
transformation to perform. A few common lattice types (such as HOPG surface) are offered predefined, but it is possible to enter
arbitrary lengths and angle.

(a)

(b)

(c)

Affine correction example: (a) original image exhibiting an affine distortion, (b) correction dialog with the lattice selected on the
two-dimensional autocorrelation, (c) corrected image.
It should be noted that the correction method described above causes all lateral scale information in the image to be lost because
the new lateral scale is fully determined by the correct lattice vectors. This is usually the best option for STM images of known
atomic lattices, however, for a general skew or affine correction it can be impractical. Therefore, the dialog offers three different
scaling choices:
Exactly as specified Lattice vectors in the corrected image will have the specified lengths and angle between them. Scale
information of the original image is discarded completely.
Preserve area Lattice vectors in the corrected image will have the specified ratio of lengths and angle between them. However,
the overall scale is calculated as to make the affine transformation area-preserving.
Preserve X scale Lattice vectors in the corrected image will have the specified ratio of lengths and angle between them. However, the overall scale is calculated as to make the affine transformation preserve the original x-axis scale. This is somewhat
analogous to the scale treatment in Drift compensation.

Polynomial Distortion
Data Process Correct Data Polynomial Distortion
General distortion in the horizontal plane can be compensated, or created, with Polynomial distortion. It performs transforms
that can be expressed as
xold = Px (xnew , ynew ),
yold = Py (xnew , ynew ),
where Px and Py are polynomials up to the third total order with user-defined coefficients. Note the direction of the coordinate
transform the reverse direction would not guarantee an unambiguous mapping.
The polynomial coefficients are entered as scale-free, i.e. as if the coordinate ranges were always [0, 1]. If Instant updates are
enabled, pressing Enter in a coefficient entry (or just leaving moving keyboard focus elsewhere) updates the preview.

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XY denoising
Data Process Multidata XY denoise
Calculates denoised image on the basis of two measurements of the same area one performed in x direction and one in y
direction (and rotated back to be aligned the same way as the x direction one). It is based on work of E. Anguiano and M. Aguilar
(see [1]). Module performs FFT of both images, combines information from both images in reciprocal space, and then performs
backward FFT in order to get denoised image. It is useful namely for large scars and fast scanning axis stripes removal.

XY denoise procedure simulation: A) original data, B) simulated measurement in x axis, C) simulated measurement in y axis,
D) denoised image.

References
[1] E. Anguiano and M. Aguilar, Ultramicroscopy, 76 (1999) 47

4. Data Processing and Analysis

4.8

53

Statistical Analysis

While analyzing randomly rough surfaces we often need a statistical approach to determine some set of representative quantities.
Within Gwyddion, there are several ways of doing this. In this section we will explain the various statistical tools and modules
offered in Gwyddion, and also present the basic equations which were used to develop the algorithms they utilize.
Scanning probe microscopy data are usually represented as a two-dimensional data field of size N M, where N and M are the
number of rows and columns of the data field, respectively. The real area of the field is denoted as Lx Ly where Lx and Ly are the
dimensions along the respective axes. The sampling interval (distance between two adjacent points within the scan) is denoted
. We assume that the sampling interval is the same in both the x and y direction and that the surface height at a given point (x, y)
can be described by a random function (x, y) that has given statistical properties.
Note that the AFM data are usually collected as line scans along the x axis that are concatenated together to form the twodimensional image. Therefore, the scanning speed in the x direction is considerably higher than the scanning speed in the y
direction. As a result, the statistical properties of AFM data are usually collected along the x profiles as these are less affected by
low frequency noise and thermal drift of the sample.

Statistical Quantities Tool

Statistical quantities include basic properties of the height values distribution, including its variance, skewness and kurtosis. The
quantities accessible within Gwyddion by means of the Statistical Quantities tool are as follows:
Mean value, minimum, maximum and median.
RMS value of the height irregularities: this quantity is computed from data variance.
Grain-wise RMS value which differs from the ordinary RMS only if masking is used. The mean value is then determined
for each grain (contiguous part of mask or inverted mask, depending on masking type) separately and the variance is then
calculated from these per-grain mean values.
Ra value of the height irregularities: this quantity is similar to RMS value with the only difference in exponent (power) within
the data variance sum. As for the RMS this exponent is q = 2, the Ra value is computed with exponent q = 1 and absolute
values of the data (zero mean).
Height distribution skewness: computed from 3rd central moment of data values.
Height distribution kurtosis: computed from 4th central moment of data values.
Projected surface area and surface area: computed by simple triangulation.
Mean inclination of facets in area: computed by averaging normalized facet direction vectors.
Tip By default, the Statistical Quantities tool will display figures based on the entire image. If you would like to analyze a certain
region within the image, simply click and drag a rectangle around it. The tool window will update with new numbers based on
this new region. If you want you see the stats for the entire image again, just click once within the data window and the tool will
reset.

More precisely, RMS ( ), skewness (1 ), and kurtosis (2 ) are computed from central moments of i-th order i according to the
following formulas:
3
4
1/2
= 2 , 1 = 3/2 , 2 = 2 3
2
2
The surface area is estimated by the following method. Let zi for i = 1, 2, 3, 4 denote values in four neighbour points (pixel
centres), and hx and hy pixel dimensions along corresponding axes. If an additional point is placed in the centre of the rectangle
which corresponds to the common corner of the four pixels (using the mean value of the pixels), four triangles are formed and
the surface area can be approximated by summing their areas. This leads to the following formulas for the area of one triangle
(top) and the surface area of one pixel (bottom):
s
 


hx hy
z1 + z2 2z 2
z1 z2 2
A12 =
1+
+
4
hx
hy
A = A12 + A23 + A34 + A41

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The method is now well-defined for inner pixels of the region. Each value participates on eight triangles, two with each of the
four neighbour values. Half of each of these triangles lies in one pixel, the other half in the other pixel. By counting in the area
that lies inside each pixel, the total area is defined also for grains and masked areas. It remains to define it for boundary pixels of
the whole data field. We do this by virtually extending the data field with a copy of the border row of pixels on each side for the
purpose of surface area calculation, thus making all pixels of interest inner.

Surface area calculation triangulation scheme (left). Application of the triangulation scheme to a three-pixel masked area (right),
e.g. a grain. The small circles represent pixel-center vertices zi , thin dashed lines stand for pixel boundaries while thick lines
symbolize the triangulation. The surface area estimate equals to the area covered by the mask (grey) in this scheme.

Statistical Functions Tool

One-dimensional statistical functions can be accessed by using the Statistical Functions tool. Within the tool window, you
can select which function to evaluate using the selection box on the left labeled Output Type. The graph preview will update
automatically. You can select in which direction to evaluate (horizontal or vertical), but as stated above, we recommend using the
fast scanning axis direction. You can also select which interpolation method to use. When you are finished, click Apply to close
the tool window and output a new graph window containing the statistical data.
Tip Similar to the Statistical Quantities tool, this tool evaluates for the entire image by default, but you can select a sub-region
to analyze if you wish.

Height and Angle Distribution Functions

The simplest statistical functions are the height and slope distribution functions. These can be computed as non-cumulative (i.e.
densities) or cumulative. These functions are computed as normalized histograms of the height or slope (obtained as derivatives
in the selected direction horizontal or vertical) values. In other words, the quantity on the abscissa in angle distribution is the
tangent of the angle, not the angle itself.
The normalization of the densities (p) (where p is the corresponding quantity, height or slope) is such that
Z

(p) dp = 1

Evidently, the scale of the values is then independent on the number of data points and the number of histogram buckets. The
cumulative distributions are integrals of the densities and they have values from interval [0, 1].
First-Order vs. Second-Order Quantities

The height and slope distribution quantities belong to the first-order statistical quantities, describing only the statistical properties
of the individual points. However, for the complete description of the surface properties it is necessary to study higher order
functions. Usually, second-order statistical quantities observing mutual relationship of two points on the surface are employed.
These functions are namely the autocorrelation function, the height-height correlation function, and the power spectral density
function. A description of each of these follows:

4. Data Processing and Analysis

55

Autocorrelation Function

The autocorrelation function is given by

ZZ

G(x , y ) =

z1 z2 w(z1 , z2 , x , y ) dz1 dz2

1
S S

ZZ

= lim

(x1 , y1 ) (x1 + x , y1 + y ) dx1 dy1

where z1 and z2 are the values of heights at points (x1 , y1 ), (x2 , y2 ); furthermore, x = x1 x2 and y = y1 y2 . The function
w(z1 , z2 , x , y ) denotes the two-dimensional probability density of the random function (x, y) corresponding to points (x1 , y1 ),
(x2 , y2 ), and the distance between these points .
From the discrete AFM data one can evaluate this function as
G(m, n) =

Nn Mm
1
zk+m,l+n zk,l
(N n)(M m) l=1
k=1

where m = x /x, n = y /y. The function can thus be evaluated in a discrete set of values of x and y separated by the sampling
intervals x and y, respectively. The two-dimensional autocorrelation function can be calculated with Data Process Statistics
2D Autocorrelation.
For AFM measurements, we usually evaluate the one-dimensional autocorrelation function based only on profiles along the fast
scanning axis. It can therefore be evaluated from the discrete AFM data values as
Gx (m) = G(m, 0) =

N Mm
1

zk+m,l zk,l
N(M m) l=1 k=1

The one-dimensional autocorrelation function is often assumed to have the form of a Gaussian, i.e. it can be given by the
following relation
Gx (x ) = 2 exp(x2 /T 2 )
where denotes the root mean square deviation of the heights and T denotes the autocorrelation length.
For the exponential autocorrelation function we have the following relation
Gx (x ) = 2 exp(x /T )
450
evaluated ACF
gaussian ACF t

400
350

G [nm2]

300
250
200
150
100
50
0
-50
0

500

1000

1500

2000

2500

x[nm]

Autocorrelation function obtained for simulated Gaussian randomly rough surface (i.e. with a Gaussian autocorrelation function)
with 20 nm and T 300 nm.
We can also introduce the radial ACF Gr (), i.e. angularly averaged two-dimensional ACF, which of course contains the same
information as the one-dimensional ACF for isotropic surfaces:
Z 2

Gr () =

W ( cos , sin ) d
0

Note For optical measurements (e. g. spectroscopic reflectometry, ellipsometry) the Gaussian autocorrelation function is
usually expected to be in good agreement with the surface properties. However, some articles related with surface growth and
oxidation usually assume that the exponential form is closer to the reality.

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Height-Height Correlation Function

The difference between the height-height correlation function and the autocorrelation function is very small. As with the autocorrelation function, we sum the multiplication of two different values. For the autocorrelation function, these values represented
the different distances between points. For the height-height correlation function, we instead use the power of difference between
the points.
For AFM measurements, we usually evaluate the one-dimensional height-height correlation function based only on profiles along
the fast scanning axis. It can therefore be evaluated from the discrete AFM data values as
Hx (x ) =

N Mm
1
(zn+m,l zn,l )2
N(M m) l=1
n=1

where m = x /x. The function thus can be evaluated in a discrete set of values of x separated by the sampling interval x.
The one-dimensional height-height correlation function is often assumed to be Gaussian, i.e. given by the following relation

 2 

Hx (x ) = 2 2 1 exp x2
T
where denotes the root mean square deviation of the heights and T denotes the autocorrelation length.
For the exponential height-height correlation function we have the following relation
h
 i
x
Hx (x ) = 2 2 1 exp
T
In the following figure the height-height correlation function obtained for a simulated Gaussian surface is plotted. It is fitted
using the formula shown above. The resulting values of and T obtained by fitting the HHCF are practically the same as for the
ACF.
900
800
700
H [nm2]

600
500
400
300
200
evaluated HHCF
gaussian HHCF t

100
0
0

500

1000

1500

2000

2500

x[nm]

Height-height correlation function obtained for simulated Gaussian randomly rough surface with 20 nm and T 300 nm.
Power Spectral Density Function

The two-dimensional power spectral density function can be written in terms of the Fourier transform of the autocorrelation
function
ZZ
1
G(x , y ) ei(Kx x +Ky y ) dx dy
W (Kx , Ky ) =
4
Similarly to the autocorrelation function, we also usually evaluate the one-dimensional power spectral density function which is
given by the equation
Z

W1 (Kx ) =

W (Kx , Ky ) dKy

This function can be evaluated by means of the Fast Fourier Transform as follows:
W1 (Kx ) =

2
NMh

|Pj (Kx )|2

j=0

4. Data Processing and Analysis

57

where Pj (Kx ) is the Fourier coefficient of the j-th row, i.e.

h
Pj (Kx ) =
2

zk j exp(iKx kh)
k=0

If we choose the Gaussian ACF, the corresponding Gaussian relation for the PSDF is
2T
W1 (Kx ) = exp(Kx2 T 2 /4)
2
For the surface with exponential ACF we have
W1 (Kx ) =

2T
1
1 + Kx2 T 2

In the following figure the resulting PSDF and its fit for the same surface as used in the ACF and HHCF fitting are plotted. We
can see that the function can be again fitted by Gaussian PSDF. The resulting values of and T were practically same as those
from the HHCF and ACF fit.
40000
evaluated PSDF
gaussian PSDF t

35000

W1[nm3]

30000
25000
20000
15000
10000
5000
0
0

10

15

20

25

30

35

Kx[m-1]

PSDF obtained for data simulated with Gaussian autocorrelation function.

We can also introduce the radial PSDF Wr (K), i.e. angularly integrated two-dimensional PSDF, which of course contains the
same information as the one-dimensional PSDF for isotropic rough surfaces:
Z 2

Wr (K) =

W (K cos , K sin ) K d
0

For a surface with Gaussian ACF this function is expressed as

Wr (K) =

2T
KT exp(K 2 T 2 /4)
2

while for exponential-ACF surface as

Wr (K) = 2 T

KT
(1 + K 2 T 2 )3/2

Tip Within Gwyddion you can fit all statistical functions presented here by their Gaussian and exponential forms. To do this, fist
click Apply within the Statistical Functions tool window. This will create a new graph window. With this new window selected,
click on Graph Fit Graph.

Minkowski Functionals

The Minkowski functionals are used to describe global geometric characteristics of structures. Two-dimensional discrete variants
of volume V , surface S and connectivity (Euler-Poincar Characteristic) are calculated according to the following formulas:
V=

Nwhite
,
N

S=

Nbound
,
N

Cwhite Cblack
N

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Here N denotes the total number of pixels, Nwhite denotes the number of white pixels, that is pixels above the threshold. Pixels
below the threshold are referred to as black. Symbol Nbound denotes the number of white-black pixel boundaries. Finally, Cwhite
and Cblack denote the number of continuous sets of white and black pixels respectively.
For an image with continuous set of values the functionals are parametrized by the height threshold value that divides white
pixels from black, that is they can be viewed as functions of this parameter. And these functions V ( ), S( ) and ( ) are
plotted.

Row/Column Statistics Tool

This tool calculates numeric characteristics of each row or column and plots them as a function of its position. This makes it kind
of complementary to Statistical Functions tool. Available quantities include:
Mean value, minimum, maximum and median.
RMS value of the height irregularities computed from data variance Rq .
Skewness and kurtosis of the height distribution.
Surface line length. It is estimated as the total length of the straight segments joining data values in the row (column).
Overall slope, i.e. the tangent of the mean line fitted through the row (column).
Tangent of 0 . This is a characteristics of the steepnes of local slopes, closely related to the behaviour of autocorrelation and
height-height correlation functions at zero. For discrete values it is calculated as follows:
tan2 0 =

N1
1
(zi zi1 )2
2
(N 1)h i=1

Standard roughness parameters Ra, Rz, Rt.

In addition to the graph displaying the values for individual rows/columns, the mean value and standard deviation of the selected
quantity is calculated from the set of individual row/column values.

Two-Dimensional Slope Statistics

Several functions in Data Process Statistics operate on two-dimensional slope (derivative) statistics.
Slope Distribution calculates a plain two-dimensional distribution of derivatives, that is the horizontal and vertical coordinate on
the resulting data field is the horizontal and vertical derivative, respectively. The slopes can be calculated as central derivatives
(one-side on the borders of the image) or, if Use local plane fitting is enabled, by fitting a local plane through the neighbourhood
of each point and using its gradient. Slope Distribution has also another mode operation called Per-angle graph, in which it
plots the distribution of r2 over where we introduced polar coordinates (r, ) in the plane of derivatives. The relation between
the derivative Cartesian coordinates of the two-dimensional slope distribution and the facet inclination angles are given by the
following formula:




dz dz
dz dz
= atan hypot
,
, = atan2
,
dx dy
dy dx
Angle Distribution function is a visualization tool that does not calculate a distribution in the strict sense. For each derivative v
the circle of points satisfying
2r . v = r2
is drawn. The number of points on the circle is given by Number of steps.

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59

Facet Analysis
Data Process Statistics Facet Analysis
Facet analysis enables to interactively study orientations of facets occuring in the data and mark facets of specific orientations on
the image. The left view displays data with preview of marked facets. The right smaller view, called facet view below, displays
two-dimensional slope distribution.
The centre of facet view always correspond to zero inclination (horizontal facets), slope in x-direction increases towards left and
right border and slope in y-direction increases towards top and bottom borders. The exact coordinate system is a bit complex and
it adapts to the range of slopes in the particular data displayed.
Facet plane size controls the size (radius) of plane locally fitted in each point to determine the local inclination. The special value
0 stands for no plane fitting, the local inclination is determined from symmetric x and y derivatives in each point. The choice
of neighbourhood size is crucial for meaningful results: it must be smaller than the features one is interested in to avoid their
smoothing, on the other hand it has to be large enough to suppress noise present in the image.

Illustration of the influence of fitted plane size on the distribution of a scan of a delaminated DLC surface with considerable fine
noise. One can see the distribution is completely obscured by the noise at small plane sizes. The neighbourhood sizes are: (a) 0,
(b) 2, (c) 4, (d) 7. The angle and false color mappings are full-scale for each particular image, i.e. they vary among them.
Both facet view and data view allow to select a point with mouse and read corresponding facet normal inclination value and
direction under Normal. When you select a point on data view, the facet view selection is updated to show inclination in this
point.
Button Find Maximum sets facet view selection to slope distribution maximum (the initial selection position).
Button Mark updates the mask of areas with slope similar to the selected slope. More precisely, of areas with slope within
Tolerance from the selected slope. The facet view then displays the set of slopes corresponding to marked points (note the set of
selected slopes may not look circular on facet view, but this is only due to selected projection). Average inclination of all points
in selected range of slopes is displayed under Mean Normal.

4.9

One-Dimensional Roughness Parameters

Standardized one-dimensional roughness parameters can be evaluated with the roughness tool.
The one-dimensional texture is split into waviness (the low-frequency components defining the overall shape) and roughness (the
high-frequency components) at the cut-off frequency. This frequency is specified in the units of the Nyquist frequency, that is
value 1.0 corresponds to the Nyquist frequency.
In the following formulas we assume the mean value of r j is zero, i.e. it holds
r j = z j z

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Roughness Amplitude Parameters

Roughness Average Ra Standards: ASME B46.1-1995, ASME B46.1-1985, ISO 4287-1997, ISO 4287/1-1997.
Arithmetical mean deviation. The average deviation of all points roughness profile from a mean line over the evaluation
length
1 N
Ra = |r j |
N j=1
An older means of specifying a range for Ra is RHR. This is a symbol on a drawing specifying a minimum and maximum
value for Ra .
Root Mean Square Roughness Rq Standards: ASME B46.1-1995, ISO 4287-1997, ISO 4287/1-1997.
The average of the measured height deviations taken within the evaluation length and measured from the mean line
v
u N
u1
Rq = t r2j
N j=1
Maximum Height of the Profile Rt Standards: ASME B46.1-1995, ISO 4287-1997.
Maximum peak-to-peak-valley height. The absolute value between the highest and lowest peaks

 


 

Rt =  min r j  +  max r j 
1 jN
1 jN
Maximum Profile Valley Depth Rv , Rm Standards: ASME B46.1-1995, ASME B46.1-1985, ISO 4287-1997, ISO 4287/11997.
Lowest valley. There is the depth of the deepest valley in the roughness profile over the evaluation length





Rv =  min r j 
1 jN

Maximum Profile Peak Height Rp Standards: ASME B46.1-1995, ASME B46.1-1985, ISO 4287-1997, ISO 4287/1-1997.
Highest peak. There is the height of the highest peak in the roughness profile over the evaluation length





Rp =  max r j 
1 jN

Average Maximum Height of the Profile Rtm Standards: ASME B46.1-1995, ISO 4287-1997.
Mean peak-to-valley roughness. It is determined by the difference between the highest peak ant the lowest valley within
multiple samples in the evaluation length
Rtm = Rvm + Rpm
where Rvm and Rpm are defined below.
For profile data it is based on five sample lengths (m = 5). The number of samples corresponds with the ISO standard.
Average Maximum Profile Valley Depth Rvm Standards: ISO 4287-1997.
The mean valley depth based on one peak per sampling length. The single deepest valley is found in five sampling lengths
(m = 5) and then averaged
1 m
Rvm = Rvi
m i=1
where


Rvi = min r j 

for

(i 1)

N
N
< j<i
m
m

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61

Average Maximum Profile Peak Height Rpm Standards: ISO 4287-1997.

The mean peak height based on one peak per sampling length. The single highest peak is found in five sampling lengths
(m = 5) and then averaged
1 m
Rpm = Rpi
m i=1
where


Rpi = max r j 

for

(i 1)

N
N
< j<i
m
m

Base roughness depth R3z Standards: ISO 4287-1997.

The distance between the third highest peak and the third lowest valley. A peak is a portion of the surface above the mean
line crossings.
Base roughness profile depth R3zISO Standards: ISO 4287-1997.
The height of the third highest peak from the third lowest valley per sampling length. The base roughness depth is found
in five sampling lengths and then averaged.
Ten-point height Rz Standards: ISO 4287-1997
The average absolute value of the five highest peaks and the five lowest valleys over the evaluation length.
Average peak-to-valley profile roughness RzISO Standards: ISO 4287-1997.
The average peak-to-valley roughness based on one peak and one valley per sampling length. The single largest deviation
is found in five sampling lengths and then averaged. It is identical to Rtm .
The Amplitude Distribution Function ADF Standards: ISO 4287-1997.
The amplitude distribution function is a probability function that gives the probability that a profile of the surface has a
certain height z at any position x.
The Bearing Ratio Curve BRC Standards: ISO 4287-1997.
The Bearing Ratio Curve is related to the ADF, it is the corresponding cumulative probability distribution and sees much
greater use in surface finish. The bearing ratio curve is the integral (from the top down) of the ADF.
Skewness Rsk Standards: ISO 4287-1997.
Skewness is a parameter that describes the shape of the ADF. Skewness is a simple measure of the asymmetry of the ADF,
or, equivalently, it measures the symmetry of the variation of a profile about its mean line
Rsk =

1
NR3q

r3j

j=1

Kurtosis Rku Standards: ISO 4287-1997.

Kurtosis is the ADF shape parameter considered. Kurtosis relates to the uniformity of the ADF or, equivalently, to the
spikiness of the profile.
1 N 4
Rku =
rj
NR4q j=1

4.10

Grain Analysis

There are several grain-related algorithms implemented in Gwyddion. First of all, simple thresholding algorithms can be used
(height, slope or curvature thresholding). These procedures can be very efficient namely within particle analysis (to mark particles
located on flat surface).
Thresholding methods can be accessed within Gwyddion as Data Process Grains Mark by Threshold. Height, slope and
curvature thresholding is implemented within this module. The results of each individual thresholding methods can be merged
together using several operators.
The automated Otsus thresholding method is available as Data Process Grains Mark by Otsus. This method classifies
the data values into two classes, minimising the intra-class variances within both. It is most suitable for images that contain two
relatively well defined value levels.

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Another grain marking function, Data Process Grains Mark by Edge Detection, is based on edge detection (local curvature).
The image is processed with a difference-of-Gaussians filter of a given size and thresholding is then performed on this filtered
image instead of the original.
Similarly, the grains can be removed from the mask using Data Process Grains Remove Grains menu choice. Maximum
height and/or size thresholding methods can be used to eliminate false grains occurred by noise or some dust particles, for
example. You can use also interactive grain removal tool for doing this manually.
This function can also remove all grains that touch image sides which is useful if such grains are considered incomplete and must
be excluded from analysis.

Watershed
For more complicated data structures the effectiveness of thresholding algorithms can be very poor. For these data a watershed
algorithm can be used more effectively for grain or particle marking.
The watershed algorithm is usually employed for local minima determination and image segmentation in image processing. As
the problem of determining the grain positions can be understood as the problem of finding local extremes on the surface this
algorithm can be used also for purposes of grain segmentation or marking. For convenience in the following we will treat the
data inverted in the z direction while describing the algorithm (i.e. the grain tops are forming local minima in the following text).
We applied two stages of the grain analysis (see [1]):
1. Grain location phase: At each point of the inverted surface the virtual water drop was placed (amount of water is controlled
by parameter Drop size). In the case that the drop was not already in a local minimum it followed the steepest descent path
to minimize its potential energy. As soon as the drop reached any local minimum it stopped here and rested on the surface.
In this way it filled the local minimum partially by its volume (see figure below and its caption). This process was repeated
several times (parameter Number of steps). As the result a system of lakes of different sizes filling the inverted surface
depressions was obtained. Then the area of each of the lakes was evaluated and the smallest lakes are removed under
assumption that they were formed in the local minima originated by noise (all lakes smaller than parameter Threshold are
removed). The larger lakes were used to identify the positions of the grains for segmentation in the next step. In this way
the noise in the AFM data was eliminated. As a result
2. Segmentation phase: The grains found in the step 1 were marked (each one by a different number). The water drops
continued in falling to the surface and filling the local minima (amount of water is controlled by parameter Drop size).
Total number of steps of sphlashing a drop at every surface position is controlled by parameter Number of steps. As the
grains were already identified and marked after the first step, the next five situations could happen as soon as the drop
reached a local minimum.
(a) The drop reached the place previously marked as a concrete grain. In this case the drop was merged with the grain, i.
e. it was marked as a part of the same grain.
(b) The drop reached the place where no grain was found but a concrete grain was found in the closest neighbourhood of
the drop. In this case the drop was merged with the grain again.
(c) The drop reached the place where no grain was found and no grain was found even in the closest neighbourhood of
the drop. In that case the drop was not marked at all.
(d) The drop reached the place where no grain was found but more than one concrete grain was found in the closest
neighbourhood (e. g. two different grains were found in the neighbourhood). In this case the drop was marked as the
grain boundary.
(e) The drop reached the place marked as grain boundary. In this case the drop was marked as the grain boundary too.
In this way we can identify the grain positions and then determine the volume occupied by each grain separately. If features of
interest are valleys rather than grains (hills), parameter Invert height can be used.

4. Data Processing and Analysis

63

Image of grain-like surface structure (a) and corresponding results of height thresholding (b), curvature thresholding (c), and
watershed (d) algorithm. Within watershed algorithm it is possible to segment image even further.

Statistics
Grain properties can be studied using several functions. The simplest of them is Grain Statistics
Grain Statistics

Data Process Grains Statistics

This function calculates the total number of marked grains, their total projected area, both as an absolute value and as a fraction
of total data field area, total grain volumes, total length of grain boundaries and the mean area and equivalent square size of one
grain. The mean size is calculated by averaging the equivalent square sides so its square is not, in general, equal to the mean
area.
Overall characteristics of the marked area can be also obtained with Statistical Quantities tool when its Use mask option is
switched on. By inverting the mask the same information can be obtained also for the non-grain area.
Grain Distributions

Data Process Grains Distributions

Grain Distributions is the most powerful and complex tool. It has two basic modes of operation: graph plotting and raw data
export. In graph plotting mode selected characteristics of individual grains are calculated, gathered and summary graphs showing
their distributions are plotted.
Raw data export is useful for experts who need for example to correlate properties of individual grains. In this mode selected grain
characteristics are calculated and dumped to a text file table where each row corresponds to one grain and columns correspond
to requested quantities. The order of the colums is the same as the relative order of the quantities in the dialog; all values are
written in base SI units, as is usual in Gwyddion.
Grain Property Correlation

Data Process Grains Correlate

Grain correlation plots a graph of one selected graph quantity as the function of another grain quantity, visualizing correlations
between them.

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Grain Measurement Tool

The grain measurement tool is the interactive method to obtain the same information about individual grains as Grain Distributions in raw mode. After selecting a grain on the data window with mouse, all the available quantities are displayed in the tool
window.
Beside physical characteristics this tool also displays the grain number. Grain numbers corresponds to row numbers (counting
from 1) in files exported by Grain Distributions.

Grain Properties
Grain Distributions and Grain measurement tool can calculate the following grain properties:
Value-related properties
Minimum, the minimum value (height) occuring inside the grain.
Maximum, the maximum value (height) occuring inside the grain.
Mean, the mean of all values occuring inside the grain, that is the mean grain height.
Median the median of all values occuring inside the grain, that is the median grain height.
Minimum on boundary, the minimum value (height) occuring on the inner grain boundary. This means within the set of
pixels that lie inside the grain but at least one of their neighbours lies outside.
Maximum on boundary, the maximum value (height) occuring on the inner grain boundary, defined similarly to the
minimum.
Area-related properties
Projected area, the projected (flat) area of the grain.
Equivalent square side, the side of the square with the same projected area as the grain.
Equivalent disc radius, the radius of the disc with the same projected area as the grain.
Surface area, the surface area of the grain, see statistical quantities section for description of the surface area estimation
method.
Area of convex hull, the projected area of grain convex hull. The convex hull area is slightly larger than the grain area
even for grains that appear to be fairly convex due to pixelization of the mask. The only grains with exactly the same
area as their convex hulls are perfectly rectangular grains.
Boundary-related properties
Projected boundary length, the length of the grain boundary projected to the horizontal plane (that is not taken on the
real three-dimensional surface). The method of boundary length estimation is described below.
Minimum bounding size, the minimum dimension of the grain in the horizontal plane. It can be visualized as the
minimum width of a gap in the horizontal plane the grain could pass through.
Minimum bounding direction, the direction of the gap from the previous item. If the grain exhibits a symmetry that
makes several directions to qualify, an arbitrary direction is chosen.
Maximum bounding size, the maximum dimension of the grain in the horizontal plane. It can be visualized as the
maximum width of a gap in the horizontal plane the grain could fill up.
Maximum bounding direction, the direction of the gap from the previous item. If the grain exhibits a symmetry that
makes several directions to qualify, an arbitrary direction is chosen.
Maximum inscribed disc radius, the radius of maximum disc that fits inside the grain. The entire full disc must fit, not
just its boundary circle, which matters for grains with voids within. You can use Mask Editor tool to fill voids in grains
to get rid of voids.
Maximum inscribed disc center x position, the horizontal coordinate of center of the maximum inscribed disc. More
precisely, of one such disc if it is not unique.
Maximum inscribed disc center y position, the vertical coordinate of center of the maximum inscribed disc. More
precisely, of one such disc if it is not unique but of the same as in the previous item.
Minimum circumcircle radius, the radius of minimum circle that contains the grain.

4. Data Processing and Analysis

65

Minimum circumcircle center x position, the horizontal coordinate of center of the minimum circumcircle.
Minimum circumcircle center y position, the vertical coordinate of center of the minimum circumcircle.
Mean radius, the mean distance from grain center of mass to its boundary. This quantity is mostly meaningful only for
convex or nearly-convex grains.
Volume-related properties
Zero basis, the volume between grain surface and the plane z = 0. Values below zero form negative volumes. The zero
level must be set to a reasonable value (often Fix Zero is sufficient) for the results to make sense, which is also the
advantage of this method: one can use basis plane of his choice.
Grain minimum basis, the volume between grain surface and the plane z = zmin , where zmin is the minimum value (height)
occuring in the grain. This method accounts for grain surrounding but it typically underestimates the volume, especially
for small grains.
Laplacian backround basis, the volume between grain surface and the basis surface formed by laplacian interpolation
of surrounding values. In other words, this is the volume that would disappear after using Remove Data Under Mask or
Grain Remover tool with Laplacian interpolation on the grain. This is the most sophisticated method, on the other hand
it is the hardest to develop intuition for.
Position-related properties
Center x position, the horizontal coordinate of the grain center. Since the grain area is defined as the area covered by the
corresponding mask pixels, the center of a single-pixel grain has half-integer coordinates, not integer ones. Data field
origin offset (if any) is taken into account.
Center y position, the vertical coordinate of the grain center. See above for the interpretation.
Slope-related properties
Inclination , the deviation of the normal to the mean plane from the z-axis, see inclinations for details.
Inclination , the azimuth of the slope, as defined in inclinations.
Curvature-related properties
Curvature center x, the horizontal position of the center of the quadratic surface fitted to the grain surface.
Curvature center y, the vertical position of the center of the quadratic surface fitted to the grain surface.
Curvature center z, the value at the center of the quadratic surface fitted to the grain surface. Note this is the value at the
fitted surface, not at the real grain surface.
Curvature 1, the smaller curvature (i.e. the inverse of the curvature radius) at the center.
Curvature 2, the larger curvature (i.e. the inverse of the curvature radius) at the center.
Curvature angle 1, the direction corresponding to Curvature 1.
Curvature angle 2, the direction corresponding to Curvature 2.

D min

D max
min
max

Maximum and minimum bounding dimensions and angles of a grain.

The grain boundary length is estimated by summing estimated contributions of each four-pixel configuration on the boundary.
The contributions are displayed on the following figure for each type of configuration, where hx and hy are pixel dimension along
corresponding axes and h is the length of the pixel diagonal:
q
h = h2x + h2y

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The contributions correspond one-to-one to lengths of segments of the boundary of a polygon approximating the grain shape.
The construction of the equivalent polygonal shape can also be seen in the figure.

(a)

(b1)

(b2)

(c)

(d)

(e)

L = 6 + 62

grain

polygonal shape

length

Contributions of pixel configurations to the estimated boundary length (top). Grey squares represent pixels inside the grain, white
squares represent outside pixels. The estimated contribution of each configuration is: (a) h/2, (b1), (b2) h, (c) hy , (d) hx , (e) h/2.
Cases (b1) and (b2) differ only in the visualization of the polygonal shape segments, the estimated boundary lengths are identical.
The bottom part of the figure illustrates how the segments join to form the polygon.
The grain volume is, after subtracting the basis, estimated as the volume of exactly the same body whose upper surface is used
for surface area calculation. Note for the volume between vertices this is equivalent to the classic two-dimensional trapezoid
integration method. However, we calculate the volume under a mask centered on vertices, therefore their contribution to the
integral is distributed differently as shown in the following figure.

Contributions of individual pixels to the volume of single pixel (grey).

Curvature-related properties of individual grains are calculated identically to the global curvature calculated by Curvature. See
its description for some discussion.

Ri
(xi, yi)

Re
(xe, ye)

Maximum inscribed disc and minimum circumcircle of a grain.

Inscribed discs and circumcircles of grains can be visualized using Data Process Grains Select Inscribed Discs and Data
Process Grains Select Exscribed Circles. These functions create circular selections representing the corresponding disc or
circle for each grain that can be subsequently displayed using Selection Manager tool.

Grain Leveling
Grains can be aligned vertically using Data Process Grains Level Grains. This function vertically shifts each grain to
make a certain height-related quantity of all grains equal. Typically, the grain minimum values are aligned but other choices are
possible.
Data between grains are also vertically shifted. The shifts are interpolated from the grain shifts using the Laplace equation,
leading to a smooth transition of the shifts between the grains (though with no regard to other possible surface features).

4. Data Processing and Analysis

67

References
[1] Petr Klapetek, Ivan Ohldal, Daniel Franta, Alberto Montaigne-Ramil, Alberta Bonanni, David Stifter, Helmut Sitter: Acta
Physica Slovaca, 3 (223-230), 2003

4.11

Fourier Transform

Two-dimensional Fourier transform can be accessed using Data Process Integral Transforms 2D FFT which implements
the Fast Fourier Transform (FFT). Fourier transform decomposes signal into its harmonic components, it is therefore useful while
studying spectral frequencies present in the SPM data.
The 2D FFT module provides several types of output:
Modulus absolute value of the complex Fourier coefficient, proportional to the square root of the power spectrum density
function (PSDF).
Phase phase of the complex coefficient (rarely used).
Real real part of the complex coefficient.
Imaginary imaginary part of the complex coefficient.
and some of their combinations for convenience.
Radial sections of the two-dimensional PSDF can be conveniently obtained with Data Process Statistics PSDF Section.
Several other functions producing spectral densities are described in section Statistical Analysis. It is also possible to filter
images in the frequency domain using one-dimensional or two-dimensional FFT filters.
Note that the Fourier transform treats data as being infinite, thus implying some cyclic boundary conditions. As the real data do
not have these properties, it is necessary to use some windowing function to suppress the data at the edgest of the image. If you
do not do this, FFT treats data as being windowed by rectangular windowing function which has really bad Fourier image thus
leading to corruption of the Fourier spectrum.
Gwyddion offers several windowing functions. Most of them are formed by some sine and cosine functions that damp data correctly at the edges. In the following windowing formula table the independent variable x is from interval [0, 1] which corresponds
to the normalized abscissa; for simplicity variable = 2x is used in some formulas. The available windowing types include:
Name

Formula

None

Rect

0.5 at edge points, 1 everywhere else

Hann

wHann (x) = 0.5 0.5 cos

Hamming

wHamming (x) = 0.54 0.46 cos

Blackmann

wBlackmann (x) = 0.42 0.5 cos + 0.08 cos 2

Lanczos
Welch

wLanczos (x) = sinc (2x 1)

wWelch (x) = 4x(1 x)

Nutall

wNutall (x) = 0.355768 0.487396 cos + 0.144232 cos 2 0.012604 cos 3

Flat-top

wflattop (x) = 0.25 0.4825 cos + 0.3225 cos 2 0.097 cos 3 + 0.008 cos 4
p


I0 4x(1 x)
wKaiser, (x) =
, where I0 is the modified Bessel function of zeroth order and is a parameter
I0 ()

Kaiser

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1.2

Hann
Hamming
Blackmann
Lanzcos
Welch
Nuttall
Flat-top
Kaiser-2.5

1.0
0.8
0.6
0.4
0.2
0.0
-0.2
0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Windowing functions: Hann, Hamming, Blackmann, Lanczos, Welch, Nutall, Flat-top, Kaiser 2.5.
100

Hann
Hamming
Blackmann
Lanzcos
Welch
Nuttall
Flat-top
Kaiser-2.5

10-1
10-2
10-3
10-4
10-5
10-6
10-7
10-8
10-9
-1

-0.8

-0.6

-0.4

-0.2

0.2

0.4

0.6

0.8

Envelopes of windowing functions frequency responses: Hann, Hamming, Blackmann, Lanczos, Welch, Nutall, Flat-top, Kaiser
2.5.
Fourier transforms of data with sizes that are not factorable into small prime factors can be very slow and many programs only
implement FFT of arrays with dimensions that are powers of two.
In Gwyddion, however, the Fourier transform can be applied to data fields and lines of arbitrary dimensions, with no data
resampling involved (at least since version 2.8). Fourier transforms are calculated either using the famous FFTW library or, if it
is not available, using Gwyddion built-in routines that are slower but can also handle transforms of arbitrary size.
Nevertheless, if the data size is not factorable into small prime factors the transform is still considerably slower. Hence it is
preferable to transform data fields of nice sizes.

4.12

Wavelet Transform

The wavelet transform is similar to the Fourier transform (or much more to the windowed Fourier transform) with a completely
different merit function. The main difference is this: Fourier transform decomposes the signal into sines and cosines, i.e. the
functions localized in Fourier space; in contrary the wavelet transform uses functions that are localized in both the real and
Fourier space. Generally, the wavelet transform can be expressed by the following equation:
Z

F(a, b) =

f (x) (a,b)
(x) dx

where the * is the complex conjugate symbol and function is some function. This function can be chosen arbitrarily provided
that obeys certain rules.
As it is seen, the Wavelet transform is in fact an infinite set of various transforms, depending on the merit function used for its
computation. This is the main reason, why we can hear the term wavelet transform in very different situations and applications.
There are also many ways how to sort the types of the wavelet transforms. Here we show only the division based on the wavelet
orthogonality. We can use orthogonal wavelets for discrete wavelet transform development and non-orthogonal wavelets for
continuous wavelet transform development. These two transforms have the following properties:
1. The discrete wavelet transform returns a data vector of the same length as the input is. Usually, even in this vector
many data are almost zero. This corresponds to the fact that it decomposes into a set of wavelets (functions) that are
orthogonal to its translations and scaling. Therefore we decompose such a signal to a same or lower number of the wavelet
coefficient spectrum as is the number of signal data points. Such a wavelet spectrum is very good for signal processing and
compression, for example, as we get no redundant information here.

4. Data Processing and Analysis

69

2. The continuous wavelet transform in contrary returns an array one dimension larger thatn the input data. For a 1D data we
obtain an image of the time-frequency plane. We can easily see the signal frequencies evolution during the duration of the
signal and compare the spectrum with other signals spectra. As here is used the non-orthogonal set of wavelets, data are
correlated highly, so big redundancy is seen here. This helps to see the results in a more humane form.
For more details on wavelet transform see any of the thousands of wavelet resources on the Web, or for example [1].
Within Gwyddion data processing library, both these transforms are implemented and the modules using wavelet transforms can
be accessed within Data Process Integral Transforms menu.

Discrete Wavelet Transform

The discrete wavelet transform (DWT) is an implementation of the wavelet transform using a discrete set of the wavelet scales
and translations obeying some defined rules. In other words, this transform decomposes the signal into mutually orthogonal set
of wavelets, which is the main difference from the continuous wavelet transform (CWT), or its implementation for the discrete
time series sometimes called discrete-time continuous wavelet transform (DT-CWT).
The wavelet can be constructed from a scaling function which describes its scaling properties. The restriction that the scaling
functions must be orthogonal to its discrete translations implies some mathematical conditions on them which are mentioned
everywhere, e.g. the dilation equation

(x) =

ak (Sx k)

k=

where S is a scaling factor (usually chosen as 2). Moreover, the area between the function must be normalized and scaling
function must be ortogonal to its integer translations, i.e.
Z

(x) (x + l) dx = 0,l

After introducing some more conditions (as the restrictions above does not produce unique solution) we can obtain results of all
these equations, i.e. the finite set of coefficients ak that define the scaling function and also the wavelet. The wavelet is obtained
from the scaling function as N where N is an even integer. The set of wavelets then forms an orthonormal basis which we use to
decompose the signal. Note that usually only few of the coefficients ak are nonzero, which simplifies the calculations.
In the following figure, some wavelet scaling functions and wavelets are plotted. The most known family of orthonormal wavelets
is the family of Daubechies. Her wavelets are usually denominated by the number of nonzero coefficients ak , so we usually talk
about Daubechies 4, Daubechies 6, etc. wavelets. Roughly said, with the increasing number of wavelet coeficients the functions
become smoother. See the comparison of wavelets Daubechies 4 and 20 below. Another mentioned wavelet is the simplest one,
the Haar wavelet, which uses a box function as the scaling function.
Scaling function and wavelet

Fourier coecient amplitudes

1.5

1.0

1.0

scaling function
wavelet

0.8

0.5

0.6

0.0
0.4

-0.5

0.2

-1.0
-1.5
-0.2

0.0
0

0.2

0.4

0.6

0.8

1.2

0.5

1.5

2.5

3.5

Haar scaling function and wavelet (left) and their frequency content (right).

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Scaling function and wavelet

Fourier coecient amplitudes

1.5

1.0

1.0

scaling function
wavelet

0.8

0.5
0.0

0.6

-0.5

0.4

-1.0
0.2

-1.5
-2.0

0.0
0

0.5

1.5

2.5

0.5

1.5

2.5

3.5

Daubechies 4 scaling function and wavelet (left) and their frequency content (right).
Scaling function and wavelet

Fourier coecient amplitudes

1.2
1.0
0.8
0.6
0.4
0.2
0.0
-0.2
-0.4
-0.6
-0.8
-1.0

1.0
scaling function
wavelet

0.8
0.6
0.4
0.2
0.0
0

10

12

14

16

18

20

0.5

1.5

2.5

3.5

Daubechies 20 scaling function and wavelet (left) and their frequency content (right).
There are several types of implementation of the DWT algorithm. The oldest and most known one is the Mallat (pyramidal)
algorithm. In this algorithm two filters smoothing and non-smoothing one are constructed from the wavelet coefficients and
those filters are recurrently used to obtain data for all the scales. If the total number of data D = 2N is used and the signal length
is L, first D/2 data at scale L/2N1 are computed, then (D/2)/2 data at scale L/2N2 , . . . up to finally obtaining 2 data at scale
L/2. The result of this algorithm is an array of the same length as the input one, where the data are usually sorted from the largest
scales to the smallest ones.
Within Gwyddion the pyramidal algorithm is used for computing the discrete wavelet transform. Discrete wavelet transform in
2D can be accessed using DWT module.
Discrete wavelet transform can be used for easy and fast denoising of a noisy signal. If we take only a limited number of highest
coefficients of the discrete wavelet transform spectrum, and we perform an inverse transform (with the same wavelet basis) we can
obtain more or less denoised signal. There are several ways how to choose the coefficients that will be kept. Within Gwyddion,
the universal thresholding, scale adaptive thresholding [2] and scale and space adaptive thresholding [3] is implemented. For
threshold determination within these methods we first determine the noise variance guess given by
=

Median |Yi j |
0.6745

where Yi j corresponds to all the coefficients of the highest scale subband of the decomposition (where most of the noise is
assumed to be present). Alternatively, the noise variance can be obtained in an independent way, for example from the AFM
signal variance while not scanning. For the highest frequency subband (universal thresholding) or for each subband (for scale
adaptive thresholding) or for each pixel neighbourhood within subband (for scale and space adaptive thresholding) the variance
is computed as
1 n
Y2 = 2 Yi2j
n i, j=1
Treshold value is finally computed as
T ( X ) = 2 / X
where
X =

max(Y2 2 , 0)

When threshold for given scale is known, we can remove all the coefficients smaller than threshold value (hard thresholding) or
we can lower the absolute value of these coefficients by threshold value (soft thresholding).
DWT denoising can be accessed with Data Process Integral Transforms DWT Denoise.

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Continuous Wavelet Transform

Continuous wavelet transform (CWT) is an implementation of the wavelet transform using arbitrary scales and almost arbitrary
wavelets. The wavelets used are not orthogonal and the data obtained by this transform are highly correlated. For the discrete
time series we can use this transform as well, with the limitation that the smallest wavelet translations must be equal to the data
sampling. This is sometimes called Discrete Time Continuous Wavelet Transform (DT-CWT) and it is the most used way of
computing CWT in real applications.
In principle the continuous wavelet transform works by using directly the definition of the wavelet transform, i.e. we are computing a convolution of the signal with the scaled wavelet. For each scale we obtain by this way an array of the same length N
as the signal has. By using M arbitrarily chosen scales we obtain a field N M that represents the time-frequency plane directly.
The algorithm used for this computation can be based on a direct convolution or on a convolution by means of multiplication in
Fourier space (this is sometimes called Fast Wavelet Transform).
The choice of the wavelet that is used for time-frequency decomposition is the most important thing. By this choice we can
influence the time and frequency resolution of the result. We cannot change the main features of WT by this way (low frequencies
have good frequency and bad time resolution; high frequencies have good time and bad frequency resolution), but we can
somehow increase the total frequency of total time resolution. This is directly proportional to the width of the used wavelet
in real and Fourier space. If we use the Morlet wavelet for example (real part damped cosine function) we can expect high
frequency resolution as such a wavelet is very well localized in frequencies. In contrary, using Derivative of Gaussian (DOG)
wavelet will result in good time localization, but poor one in frequencies.
CWT is implemented in the CWT module that can be accessed with Data Process Integral Transforms CWT.

References
[1] A. Bultheel: Bull. Belg. Math. Soc.: (1995) 2
[2] S. G. Chang, B. Yu, M. Vetterli: IEEE Trans. Image Processing, (2000) 9 p. 1532
[3] S. G. Chang, B. Yu, M. Vetterli: IEEE Trans. Image Processing, (2000) 9 p. 1522

4.13

Fractal Analysis

In practice objects exhibiting random properties are encountered. It is often assumed that these objects exhibit the self-affine
properties in a certain range of scales. Self-affinity is a generalization of self-similarity which is the basic property of most
of the deterministic fractals. A part of self-affine object is similar to whole object after anisotropic scaling. Many randomly
rough surfaces are assumed to belong to the random objects that exhibit the self-affine properties and they are treated self-affine
statistical fractals. Of course, these surfaces can be studied using atomic force microscopy (AFM). The results of the fractal
analysis of the self-affine random surfaces using AFM are often used to classify these surfaces prepared by various technological
procedures [1,2,3,4].
Within Gwyddion, there are different methods of fractal analysis implemented within Data Process Statistics Fractal analysis.
Cube counting method [1,2] is derived directly from a definition of box-counting fractal dimension. The algorithm is based
on the following steps: a cubic lattice with lattice constant l is superimposed on the z-expanded surface. Initially l is set at
X/2 (where X is length of edge of the surface), resulting in a lattice of 2 2 2 = 8 cubes. Then N(l) is the number of
all cubes that contain at least one pixel of the image. The lattice constant l is then reduced stepwise by factor of 2 and the
process repeated until l equals to the distance between two adjacent pixels. The slope of a plot of log N(l) versus log 1/l
gives the fractal dimension Df directly.
Triangulation method [1] is very similar to cube counting method and is also based directly on the box-counting fractal
dimension definition. The method works as follows: a grid of unit dimension l is placed on the surface. This defines the
location of the vertices of a number of triangles. When, for example, l = X/4, the surface is covered by 32 triangles of
different areas inclined at various angles with respect to the xy plane. The areas of all triangles are calculated and summed
to obtain an approximation of the surface area S(l) corresponding to l. The grid size is then decreased by successive factor
of 2, as before, and the process continues until l corresponds to distance between two adjacent pixel points. The slope of a
plot of S(l) versus log 1/l then corresponds to Df 2.
Variance method [3,4] is based on the scale dependence of the variance of fractional Brownian motion. In practice, in the
variance method one divides the full surface into equal-sized squared boxes, and the variance (power of RMS value of
heights), is calculated for a particular box size. Fractal dimension is evaluated from the slope of a least-square regression
line fit to the data points in log-log plot of variance as Df = 3 /2.

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Power spectrum method [3,4,5] is based on the power spectrum dependence of fractional Brownian motion. In the power
spectrum method, every line height profiles that forms the image is Fourier transformed and the power spectrum evaluated
and then all these power spectra are averaged. Fractal dimension is evaluated from the slope of a least-square regression
line fit to the data points in log-log plot of power spectrum as Df = 7/2 /2.
The axes in Fractal Dimension graphs always show already logarithmed quantities, therefore the linear dependencies mentioned
above correspond to straight lines there. The measure of the axes should be treated as arbitrary.
Note, that results of different methods differ. This fact is caused by systematic error of different fractal analysis approaches.

Fractal Dimension dialog.

Moreover, the results of the fractal analysis can be influenced strongly by the tip convolution. We recommend therefore to check
the certainty map before fractal analysis. In cases when the surface is influenced a lot by tip imaging, the results of the fractal
analysis can be misrepresented strongly.
Note, that algorithms that can be used within the fractal analysis module are also used in Fractal Correction module and Fractal
Correction option of Remove Spots tool.

References
[1] C. Douketis, Z. Wang, T. L. Haslett, M. Moskovits: Fractal character of cold-deposited silver films determined by lowtemperature scanning tunneling microscopy. Physical Review B, Volume 51, Number 16, 15 April 1995, 51
[2] W. Zahn, A. Zsch: The dependence of fractal dimension on measuring conditions of scanning probe microscopy. Fresenius
J Analen Chem (1999) 365: 168-172
[3] A. Van Put, A. Vertes, D. Wegrzynek, B. Treiger, R. Van Grieken: Quantitative characterization of individual particle surfaces
by fractal analysis of scanning electron microscope images. Fresenius J Analen Chem (1994) 350: 440-447
[4] A. Mannelquist, N. Almquist, S. Fredriksson: Influence of tip geometry on fractal analysis of atomic force microscopy
images. Appl. Phys. A 66,1998, 891-895
[5] W. Zahn, A. Zsch: Characterization of thin film surfaces by fractal geometry. Fresenius J Anal Chem (1997) 358: 119-121

4.14

Tip Convolution Artefacts

Tip convolution artefact is one of the most important error sources in SPM. As the SPM tip is never ideal (like delta function) we
often observe a certain degree of image distortion due to this effect. We can even see some SPM tips imaged on the surface scan
while sharp features are present on the surface.

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Images of ZnSe surface measured with four different SPM tips (more or less broken ones).
We can fortunately simulate and/or correct the tip effects using algorithms of dilation and/or erosion, respectively. These algorithms were published by Villarubia (see [1]).

Obtaining the Tip Geometry

For studying the tip influence on the data we need to know tip geometry first. In general, the geometry of the SPM tip can be
determined in these ways:
1. use manufacturers specifications (tip geometry, apex radius and angle)
2. use scanning electron microscope of other independent technique to determine tip properties
3. use known tip characterizer sample (with steep edges)
4. use blind tip estimation algorithm together with tip characterizers or other suitable samples
Within Gwyddion, we can use the first and the last approach of the mentioned ones. Using tip modelling (Data Process Tip
Model Tip) most of the tips with simple geometries can be simulated. This way of tip geometry specification can be very
efficient namely when we need to check only certainty map of perform tip convolution simulation.
To obtain more detailed (and more realistic) tip structure blind tip estimation algorithm can be used (Data Process Tip Blind
Estimation).
Blind tip estimation algorithm is an extension of the well-known fact that on some surface data we can see images of certain parts
of tip directly. The algorithm iterates over all the surface data and at each point tries to refine each tip point according to steepest
slope in the direction between concrete tip point and tip apex.
We can use two modification of this algorithm within Gwyddion: partial tip estimation that uses only limited number of highest
points on the image and full tip estimation that uses full image (and is much slower therefore). Within Gwyddion tip estimation
module we can use also partial tip estimation results as starting point for full estimation. This should improve the full tip
estimation algorithm speed.

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SPM tips obtained from data of previous figure using blind estimation algorithm.

Tip Convolution and Surface Reconstruction

When we know tip geometry, we can use tip convolution (dilation) algorithm to simulate data acquisition process. For doing this
use Dilation module (Data Process Tip Dilation). This can be in particular useful when working with data being result of
some numerical modelling (see e.g. [2]).
Note this algorithm (as well as the following two) requires compatible scan and tip data, i.e. the physical dimensions of a scan
pixel and of a tip image pixels have to be equal. This relation is automatically guaranteed for tips obtained by blind estimate
when used on the same data (or data with an identical measure). If you obtained the tip image by other means, you may need to
resample it.

Simulated fractal surface before (left) and after (right) tip convolution.
The opposite of the tip convolution is surface reconstruction (erosion) that can be used to correct partially the tip influence on
image data. For doing this, use Surface Reconstruction function (Data Process Tip Surface Reconstruction). Of course, the
data corresponding to points in image not touched by tip (e. g. pores) cannot be reconstructed as there is no information about
these points.

Original and reconstructed image of ZnSe imaged by broken SPM tip.

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As it can be seen, the most problematic parts of SPM image are data points where tip did not touch the surface in a single point,
but in multiple points. There is a loss of information in these points. Certainty map algorithm can mark points where surface was
probably touched in a single point.

Certainty map obtained from standard grating. Note that the modelled tip parameters were taken from datasheet here for illustration purposes. (left) sample, (right) sample with marked certainty map.
Certainty map algorithm can be therefore used to mark data in the SPM image that are corrupted by tip convolution in an
irreversible way. For SPM data analysis on surfaces with large slopes it is important to check always presence of these points.
Within Gwyddion you can use Certainty Map function for creating these maps (Data Process Tip Certainty Map).

References
[1] J. S. Villarubia, J. Res. Natl. Inst. Stand. Technol. 102 (1997) 425.
[2] P. Klapetek, I. Ohldal, Ultramicroscopy, 94 (19-29), 2003

4.15

Multiple Data

Arithmetic
Data Process Multidata Arithmetic
Data Arithmetic module enables to perform arbitrary point-wise operations on a single data field or on the corresponding points
of several data fields (currently up to eight). And although it is not its primary function it can be also used as a calculator
with immediate expression evaluation if a plain numerical expression is entered. The expression syntax is described in section
Expressions.
The expression can contain the following variables representing values from the individual input data fields:
Variable

Description

d1, . . . , d8

Data value at the pixel. The value is in base physical units, e.g. for height of 233 nm, the value of d1 is
2.33e-7.

m1, . . . , m8

Mask value at the pixel. The mask value is either 0 (for unmasked pixels) or 1 (for masked pixels). The
mask variables can be used also if no mask is present; the value is then 0 for all pixels.

bx1, . . . , bx8

Horizontal derivative at the pixel. Again, the value is in physical units. The derivative is calculated as
standard symmetrical derivative, except in edge pixels where one-side derivative is taken.

by1, . . . , by8

Vertical derivative at the pixel, defined similarly to the horizontal derivative.

Horizontal coordinate of the pixel (in real units). It is the same in all fields due to the compatibility requirement (see below).

Vertical coordinate of the pixel (in real units). It is the same in all fields due to the compatibility requirement
(see below).

In addition, the constant is available and can be typed either as or pi.

All data fields that appear in the expression have to be compatible. This means their dimensions (both pixel and physical) have to

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be identical. Other data fields, i.e. those not actually entering the expression, are irrelevant. The result is always put into a newly
created data field in the current file (which may be different from the files of all operands).
Since the evaluator does not automatically infer the correct physical units of the result the units have to be explicitly specified.
This can be done by two means: either by selecting a data field that has the same value units as the result should have, or by
choosing option Specify units and typing the units manually.
The following table lists several simple expression examples:
Expression

Meaning

-d1

Value inversion. The result is very similar to Invert Value, except that Invert Value reflects about
the mean value while here we simply change all values to negative.

(d1 - d2)2

Squared difference between two data fields.

d1 + m1*1e-8

Modification of values under mask. Specifically, the value 10-8 is added to all masked pixels.

d1*m3 + d2*(1-m3)

Combination of two data fields. Pixels are taken either from data field 1 or 2, depending on the
mask on field 3.

In the calculator mode the expression is immediately evaluated as it is typed and the result is displayed below Expression entry.
No special action is necessary to switch between data field expressions and calculator: expressions containing only numeric
quantities are immediately evaluated, expressions referring to data fields are used to calculate a new data field. The preview
showing the result of an operation with fields is not immediately updated as you type; you can update it either by clicking Update
or just pressing Enter in the expression entry.

Detail Immersion
Data Process Multidata Immerse
Immerse insets a detailed, high-resolution image into a larger image. The image the function was run on forms the large, base
image.
The detail can be positioned manually on the large image with mouse. Button Improve can then be used to find the exact
coordinates in the neighbourhood of the current position that give the maximum correlation between the detail and the large
image. Or the best-match position can be searched through the whole image with Locate.
It should be noted that correlation search is insensitive to value scales and offsets, therefore the automated matching is based
solely on data features, absolute heights play no role.
Result Sampling controls the size and resolution of the result image:
Upsample large image The resolution of the result is determined by the resolution of the inset detail. Therefore the large image
is scaled up.
Downsample detail The resolution of the result is determined by the resolution of the large image. The detail is downsampled.
Detail Leveling selects the transform of the z values of the detail:
None No z value adjustment is performed.
Mean value All values of the detail image are shifted by a constant to make its mean value match the mean value of the
corresponding area of the large image.

Merging
Data Process Multidata Merge
Images that form parts of a larger image can be merged together with Merge. The image the function was run on corresponds to
the base image, the image selected with Merge with represents the second operand. The side of the base image the second one
will be attached to is controlled with Put second operand selector.
If the images match perfectly, they can be simply placed side by side with no adjustments. This behaviour is selected by option
None of alignment control Align second operand.

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However, usually adjustments are necessary. Option Correlation selects automated alignment by correlation-based search of the
best match. The search is performed both in the direction parallel to the attaching side and in the perpendicular direction. If a
parallel shift is present, the result is expanded to contain both images fully (with undefined data filled with a background value).
Option Boundary treatment is useful only for the latter case of imperfectly aligned images. It controls the treatment of overlapping
areas in the source images:
First operand Values in overlapping areas are taken from the first, base image.
Second operand Values in overlapping areas are taken from the second image.
Smooth A smooth transition between the first and the second image is made through the overlapping area by using a weighted
average with a suitable weighting function.

Mutual Crop
Data Process Multidata Mutual Crop
Two slightly different images of the same area (for example, before and after some treatment) can be croped to intersecting area
(or non-intersecting parts can be removed) with this module.
Intersecting part is determined by correlation of larger image with center area of smaller image. Images resolution (pixels per
linear unit) should be equal.
The only parameter now is Select second operand - correlation between it and current image will be calculated and both data
fields will be cropped to remove non-intersecting near-border parts.

Cross-Correlation
Data Process Multidata Cross-correlation
This module finds local correlations between details on two different images. As an ideal output, the shift of every pixel on the
first image as seen on the second image is returned. This can be used for determining local changes on the surface while imaged
twice (shifts can be for example due to some sample deformation or microscope malfunction).
For every pixel on the first operand (actual window), the module takes its neighbourhood and searches for the best correlation
in the second operand within defined area. The position of the correlation maximum is used to set up the value of shift for the
mentioned pixel on the first operand.
Second operand Image to be used for comparison with the first operand - base image.
Search size Used to set the area whera algorithm will search for the local neighbourhood (on the second operand). Should be
larger than window size. Increase this size if there are big differences between the compared images.
Window size Used to set the local neighbourhood size (on the first operand). Should be smaller than search size. Increasing
this value can improve the module functionality, but it will surely slow down the computation.
Output type Determines the output (pixel shift) format.
Add low score threshold mask For some pixels (with not very pronounced neighbourhood) the correlation scores can be small
everywhere, but the algorithm anyway picks some maximum value from the scores. To see these pixels and possibly
remove them from any further considerations you can let the module to set mask of low-score pixel shifts that have larger
probability to be not accurately determined.

Mask by Correlation
Data Process Multidata Mask by Correlation
This module searches for a given correlation pattern within the actual image. The resulting pattern position is marked as a mask
in the data window.
Correlation kernel Image to be found on the base image.
Output type There are several possibilities what to output: local correlation maxima (single points), masks of kernel size for
each correlation maximum (good for presentation purposes), or simply the correlation score.
Correlation method Algorithm for computing correlation can be selected here.
Threshold Threshold for determining whether the local maximum will be treated as correlation kernel found here.

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Neural network processing

Neural network processing can be used to calculate one kind of data from another even if the formula or relation between them is
not explicitly known. The relation is built into the network implicitly by a process called training which employs pairs of known
input and output data, usually called model and signal. In this process, the network is optimised to reproduce as well as possible
the signal from model. A trained network can then be used to process model data for which the output signal is not available and
obtain usually somewhat approximately what the signal would look like. Another possible application is the approximation
of data processing methods that are exact but very time-consuming. In this case the signal is the output of the exact method and
the network is trained to reproduce that.
Since training and application are two disparate steps they are present as two different functions in Gwyddion.
Training

Data Process Multidata Neural Network Training

The main functions that control the training process are contained in tab Training:
Model Model data, i.e. input for training. Multiple models can be chosen sequentially for training (with corresponding signals).
Signal Signal data for training, i.e. the output the trained network should produce. The signal data field must be compatible with
model field, i.e. it must have the same pixel and physical dimensions.
Training steps Number of training steps to perform when Train is pressed. Each step consists of one pass through the entire
signal data. It is possible to set the number of training steps to zero; no training pass is performed then but the model is
still evaluated with the network and you can observe the result.
Train Starts training. This is a relatively slow process, especially if the data and/or window size are large.
Reinitialize Reinitializes the neural network to an untrained state. More precisely, this means neuron weights are set to random
numbers.
Masking Mode It is possible to train the network only on a subset of the signal, specified by a mask on the signal data. (Masking
of model would be meaningless due to the window size.)
Neural network parameters can be modified in tab Parameters. Changing either the window dimensions or the number of hidden
nodes means the network is reinitialized (as if you pressed Reinitialize).
Window width Horizontal size of the window. The input data for the network consists of an area around the model pixel, called
window. The window is centered on the pixel so, odd sizes are usually preferred.
Window height Vertical size of the window.
Hidden nodes Number of nodes in the hidden layer of the neural network. More nodes can lead to more capable network, on
the other hand, it means slower training and application. Typically, this number is small compared to the number of pixels
in the window.
Power of source XY The power in which the model lateral dimensions units should appear in the signal. This is only used when
the network is applied.
Power of source Z The power in which the model height units should appear in the signal. This is only used when the network
is applied.
Fixed units Fixed units of the result. They are combined with the other units parameters so if you want result units that are
independent of input units you have to set both powers to 0. This is only used when the network is applied.
Trained neural network can be saved, loaded to be retrained on different data, etc. The network list management is similar to raw
file presets.
In addition to the networks in the list, there is one more unnamed network and that of the network currently in training. When
you load a network the network in training becomes a copy of the loaded network. Training then does not change the named
networks; to save the network after training (under existing or new name) you must explicitly use Store.

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Application

Data Process Multidata Apply Neural Network

Application of a trained neural network is simple: just choose one from the list and press OK. The unnamed network currently
in training is also present in the list under the label In training.
Since neural networks process and produce normalised data, it does not perserve proportionality well, especially if the scale of
training model differs considerably from the scale of real inputs. If the output is expected to scale with input you can enable
option Scale proportionally to input that scales the output with the inverse ratio of actual and training input data ranges.

4.16

Graph Processing

Many of the Gwyddion data processing modules produce graph as an output. Graphs can be exported into text files or further
analyzed within Gwyddion by several graph processing modules. These modules can be found in the Graph menu in the Gwyddion main window. Note that the number of graph modules is quite limited now and consists of basic modules for doing things
that are very frequent within SPM data analysis. For more analytical tools you can use your favorite graph processing program.
In this section the graph modules present in Gwyddion are briefly presented.

Basic Operations
First of all zooming and data reading functions are available directly in the graph window:
Logarithmic axes horizontal and vertical axes can be switched between linear and logarithmic using the logscale buttons.
Switching to logarithmic scale is possible only for positive values (either on abscissa or ordinate).
Zoom in and zoom out after selecting zoom in simply draw the area that should be zoomed by mouse. Zoom out restores the
state where all data can be seen.
Measure distances enables user to select several points within the graph and displays their distances and angles between
them.

Graph Level
Graph level is a very simple module that currently performs linear fit of each graph curve and subtracts the fitted linear functions
from them.

Function Fitting
The curve fitting is designed namely for fitting of statistical functions used in roughness parameters evaluation. Therefore most
of the available functions are currently various statistical functions of surfaces with Gaussian or exponential autocorrelation
functions. Nevertheless it also offers a handful of common general-purpose functions.
Within the fitting module you can select the area that should be fitted (with mouse or numerically), try some initial parameters,
or let the module to guess them, and then fit the data using Marquardt-Levenberg algorithm.
As the result you obtain the fitted curve and the set of its parameters. The fit report can be saved into a file using Save button.
Pressing OK button adds the fitted curve to the graph, if this is not desirable, quit the dialog with Cancel.

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Curve fitting module dialog

Force-Distance Curve Fitting

The module for fitting of force-distance curves is very similar to the general curve fitting module, it is just specialized for forcedistance curves. Currently, the module serves for fitting jump-in part of force-distance curve (representing attractive forces) using
different models:
van der Waals force between semisphere and half-space
van der Waals force between pyramide and half-space
van der Waals force between truncated pyramide and half-space
van der Waals force between sphere and half-space
van der Waals force between two spheres
van der Waals force between cone and half-space
van der Waals force between cylinder and half-space
van der Waals force between paraboloid and half-space
Note that the curve being fitted must be a real force-distance curve, not a displacement-distance or sensor-distance curve. Recalculation of cantilever deflection into force should be done before calling this module.
Also note that for small cantilever spring constants the amount of usable data in attractive region is limited by effect of jumping
into contact.

Critical Dimension
Critical dimension module can be used to fit some typical objects that are often found while analyzing profiles extracted from
microchips and related surfaces. These objects are located in the graph and their properties are evaluated.
The user interface of this module is practically the same as of the graph fit module.

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Critical dimension module dialog.

DOS spectrum
DOS spectrum module intended to obtain Density-of-States spectra from I-V STM spectroscopy. It calculates
 
 dI 
 dU 
 I  (U)
U 
and plots it as graph.

4.17

Synthetic Surfaces

Beside functions for analysis of measured data, Gwyddion provides several generators of artificial surfaces that can be used for
testing or simulations also outside Gwyddion.
All the surface generators share a certain set of parameters, determining the dimensions and scales of the created surface and
the random number generator controls. These parameters are described below, the parameters specific to each generator are
described in the corresponding subsections.
Image parameters:
Horizontal, Vertical size The horizontal and vertical resolution of the generated surface in pixels.
Square image This option, when enabled, forces the horizontal and vertical resolution to be identical.
Width, Height The horizontal and vertical physical dimensions of the generated surface in selected units. Note square pixels
are assumed so, changing one causes the other to be recalculated.
Dimension, Value units Units of the lateral dimensions (Width, Height) and of the values (heights). The units chosen here also
determine the units of non-dimensionless parameters of the individual generators.
Take Dimensions from Current Channel Clicking this button fills all the above parameters according to the current channel.
Note that while the units of values are updated, the value scale is defined by generator-specific parameters that might not
be directly derivable from the statistical properties of the current channel. Hence these parameters are not recalculated.
Replace the current channel This option has two effects. First, it causes the dimensions and scales to be automatically set to
those of the current channel. Second, it makes the generated surface replace the current channel instead of creating a new
channel.
Start from the current channel This option has two effects. First, it causes the dimensions and scales to be automatically set
to those of the current channel. Second, it makes the generator to start from the surface contained in the current channel
and modify it instead of starting from a flat surface. Note this does not affect whether the result actually goes to the current
channel or a new channel is created.

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Random generator controls:

Random seed The random number generator seed. Choosing the same parameters and resolutions and the same random seed
leads to the same surface, even on different computers. Different seeds lead to different surfaces with the same overall
characteristics given by the generator parameters.
New Replaces the seed with a random number.
Randomize Enabling this option makes the seed to be chosen randomly every time the generator is run. This permits to
conveniently re-run the generator with a new seed simply by pressing Ctrl-F (see keyboard shortcuts).

Spectral
Spectral synthesis module creates randomly rough surfaces by constructing the Fourier transform of the surface according to
specified parameters and then performing the inverse Fourier transform to obtain the real surface. The generated surfaces are
periodic (i.e. perfectly tilable).
The Fourier image parameters define the shape of the PSDF, i.e. the Fourier coefficient modulus, the phases are chosen randomly.
At present, all generated surfaces are isotropic, i.e. the PSDF is radially symmetric.
RMS The root mean square value of the heights (or of the differences from the mean plane which, however, always is the z = 0
plane). Button Like Current Channel sets the RMS value to those of the current channel.
Minimum, maximum frequency The minimum and maximum spatial frequency. Increasing the minimum frequency leads to
flattening of the image, i.e. to removal of large features. Decreasing the maximum frequency limits the sharpness of the
features.
Enable Gaussian multiplier Enables the multiplication of the Fourier coefficients by a Gaussian function that in the real space
corresponds to the convolution with a Gaussian.
Enable Lorentzian multiplier Enables the multiplication of the Fourier coefficients by a function proportional to 1/(1 +
k2 T 2 )3/4 , where T is the autocorrelation length. So, the factor itself is not actually Lorentzian but it corresponds to
Lorentzian one-dimensional power spectrum density which in turn corresponds to exponential autocorrelation function
(see section Statistical Analysis for the discussion of autocorrelation functions). This factor decreases relatively slowly so
the finite resolution plays usually a larger role than in the case of Gaussian.
Autocorrelation length The autocorrelation length of the Gaussian or Lorentzian factors (see section Statistical Analysis for
the discussion of autocorrelation functions).
Enable power multiplier Enables multiplication of Fourier coefficients by factor proportional to 1/k p , where k is the spatial
frequency and p is the power. This permits to generate various fractal surfaces.
Power The power p.

Artificial surfaces generated by spectral synthesis: a narrow range of spatial frequencies (left), Gaussian random surface (centre)
and a fractal surface generated with power multiplier and p equal to 1.5 (right).

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83

Objects
The object placement method permits to create random surfaces composed of features of a specific shape. The algorithm is
simple: the given number of objects is placed on random positions at the surface. For each object placed, the new heights are
changed to max(z, z0 + h), where z is the current height at a specific pixel, h is the height of the object at this pixel (assuming a
zero basis) and z0 is the current minimum height over the basis of the object being placed. The algorithm considers the horizontal
plane to be filled with identical copies of the surface, hence, the generated surfaces are also periodic (i.e. perfectly tilable).
Shape The shape (type) of placed objects. At present the possibilities include half-spheres, boxes, pyramids, tetrahedrons and
some more weird shapes.
Coverage The average number of times an object covers a pixel on the image. Coverage value of 1 means the surface would be
exactly once covered by the objects assuming that they covered it uniformly. Larger values mean more layers of objects
and slower image generation.
Size The lateral object size, usually the side of a containing square.
Aspect Ratio The ratio between the x and y dimensions of an object with respect to some default proportions.
Changing the aspect ratio does not always imply mere geometrical scaling, e.g. objects called nuggets change between
half-spheres and rods when the ratio is changed.
Height A quantity proportional to the height of the object, normally the height of the highest point.
Checking Scales with size makes unperturbed heights to scale proportionally with object size. Otherwise the height is
independent on size.
Button Like Current Channel sets the height value to a value based on the RMS of the current channel.
Orientation The rotation of objects with respect to some base orientation, measured counterclockwise.
Truncate The shapes can be truncated at a certain height, enabling creation of truncated cones, pyramids, etc. The truncation
height is given as a proportion to the total object height. Unity means the shape is not truncated, zero would mean complete
removal of the object.
Each parameter can be randomized for individual objects, this is controlled by Variance. For multiplicative quantities (all except
orientation and truncation), the distribution is log-normal with the RMS value of the logarithmed quantity given by Variance.

Artificial surfaces generated by object placement: spheres of varied size (left), narrow thatches of varied direction (centre),
nuggets of varied aspect ratio (right).

Noise
Random uncorrelated point noise is generated independently in each pixel. Several distributions are available.
Distribution The distribution of the noise value. The possibilities include Gaussian, exponential, uniform and triangular distributions.
Direction The noise can be generated as symmetrical or one-sided. The mean value of the distribution of a symmetrical noise
is zero, i.e. the mean value of data does not change when a symmetrical noise is added. One-sided noise only increases (if
positive) or decreases (if negative) the data values.
RMS Root mean square value of the noise distribution. More precisely, it is the RMS of the corresponding symmetrical
distribution in the case the distribution is one-sided.

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Line Noise
Line noise represents noise with non-negligible duration that leads to typical steps or scars (also called strokes) in the direction of
the fast scanning axis. Parameters Distribution, Direction and RMS have the same meaning as in Point noise. Other parameters
control the lateral characteristics of the noise.
Two basic line defect types are available: steps and scars. Steps represent abrupt changes in the value that continue to the end of
the scan (or until another step occurs). Scars are changes of the value with a finite duration, i.e. the values return to the original
level after some time.
Steps have the following parameters:
Density Average number of defects per scan line, including any dead time (as determined by parameter Within line).
Within line Fraction of the time to scan one line that corresponds to actual data acquisition. The rest of time is a dead time.
Value 1 means there is no dead time, i.e. all steps occur within the image. Value 0 means the data acquisition time is
negligible to the total line scan time, consequently, steps only occur between lines.
Cumulative For cumulative steps the random step value is always added to the current value offset; for non-cumulative steps
the new value offset is directly equal to the random step value.
Scars have the following parameters:
Coverage The fraction of the the image covered by defect if they did not overlap. Since the defect may overlap coverage value
of 1.0 does not mean the image is covered completely.
Length Scar length in pixels.
Variance Variance of the scar length, see Objects for description of variances.

Different types of line noise added to an artificial pyramidal surface: unmodified surface (left); with relatively unfrequent noncumulative steps (centre); with scars of mean length of 16 px and high coverage (right).

Pattern
Regular geometrical patterns represent surfaces often encountered in microscopy as standards or testing samples such as ridges,
steps or holes. Each type of pattern has its own set of geometrical parameters determining the shape and dimensions of various
part of the pattern. Each parameter has a variance control, similar to Object synthesis, that permits to make the pattern irregular
in some aspects.
The placement of the pattern in the horizontal plane is controlled by parameters in tab Placement, common to all pattern types:
Orientation The rotation of the pattern with respect to some base orientation, measured counterclockwise.
This tab also contains the deformation parameters. While enabling the variation of geometrical parameters makes the generated surface somewhat irregular the shape of its features is maintained. Deformation is a complementary method to introduce
irregularity, specifically by distorting the pattern in the xy plane. It has two parameters:
Amplitude The magnitude of the lateral deformation. It is a relative numerical quantity essentially determining how far the
deformation can reach.

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85

Lateral scale The characteristic size of the deformations. It describes not how far the features are moved but how sharply or
slowly the deformation itself changes within the horizontal plane.

Artificial pattern surfaces: sharp steps oriented at 30 deg, deformed with a deformation with a large autocorrelation length (left);
non-uniformly spaced ridges with moderate slopes between the top and bottom planes, deformed with a deformation with a small
autocorrelation length (right).

4.18

Calibration and uncertainties

Calibration data
Calibration data can be used to provide correction of measured data or perform uncertainty calculations. Generally, calibration
data can be of different types and different levels of complexity. For most of the cases user acquires error in each axis, e. g. using
a calibrated standard. This value can be used for data correction. Similarly, the value of uncertainty is mostly determined for
each axis from calibrated standard certificate and from measurement process uncertainty budget.
In more complex cases, calibration data can be determined locally. Scanner error cannot always be described by only three
parameters (one for each axis) and its uncertainty is not necessarily the same in whole range. For precise measurements it is
therefore practical to determine local errors and namely local uncertainties that can be used for further calculations. By "local"
we mean here uncertainties that are related to certain location in the complete volume that can be reached by the scanner.
To obtain local errors and uncertainties, one can use a calibration standard again or use a more complex instrument, like interferometer for scanning stage calibration. This is usually done in metrology institutes.
In Gwyddion, there is a set of tools helping local uncertainty processing. Primary calibration data, related to a scanning stage, can
be determined or loaded. They can be assigned to a certain SPM measurement data creating a set of calibrations. These are used
automatically in tools and modules where uncertainty propagation calculation can be performed in order to provide measurement
uncertainty.

Calibration data acquisition

Data Process Calibration 3D calibration
Calibration data can be acquired in the following ways:
The module 3D calibration Create... can be used for creating simplest primary calibration data - based only on knowledge
of xyz errors and uncertainties and on scanner volume geometry. We also need to specify calibration name. Primary calibration
data will be accessible under this name module for its data application to SPM measurements.
Using 3D calibration Get simple error map... module, we can determine primary xyz calibration data from a set of calibration
grating measurements. Here we need to provide several measurements of calibration grating for different z-levels of the scanner.
This forms several cross-sections of the full scanner volume. Providing single grating detail, nominal grating pitch and assuming
that the grating planarity and orthogonality is much higher than that of scanning stage we can determine primary calibration data
on the basis of correlation. Note that this way of calibrating a microscope is only very approximate and its use for metrology
purposes is very limited. However, it can provide a lot of useful information about our scanner properties if we are unable to
perform more complex analysis.
Finally, using 3D calibration Load from file... we can load any primary 3D calibration data determined by an external device,
like set of interferometers. Data should be a plain text file containing number of calibration sets and sets (x, y, z, x_err, y_err,
z_err, x_unc, y_unc, z_unc).

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Calibration data application and further use

Data Process Calibration 3D calibration
Primary calibration data obtained in previous steps are related to a scanning stage, not to concrete SPM measurements. We can
use primary calibration data for different measurements. To use primary calibration data for our measured data processing, we
need to apply them first. Using module 3D calibration Apply to data... we can review and select calibration data applied on
our height field measurements. After applying calibration data a set of calibration datafields is created and attached to selected
data. A C character appears in data browser as a sign of data with attached calibration. Note that the calibration attached to
SPM measurement is no more related with primary calibration data (that were used for its creation).
When there is calibration attached to data, data reading and statistical quantities evaluation modules and tools recognize it
automatically. Measurement uncertainty is then added to the measurement results. Uncertainty is calculated using uncertainty
propagation law.

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Chapter 5

Summaries and Tables

This chapter provides the reference for various formats, syntaxes and command options that you might find helpful. Most are
related to advanced use of Gwyddion, except perhaps the table of common keyboard shortcuts and table of supported file formats.

5.1

gwyddion

gwyddion SPM data visualization and analysis

Synopsis
gwyddion [OPTION ...] [FILE ...]

Description
Gwyddion is a graphical SPM (Scanning Probe Microscope) data visualization and analysis program, using Gtk+.

Options
The program accepts all standard Gtk+, Gdk, and GtkGLExt options like --display or --sync. Please see documentation
of these packages for description of toolkit options.
The behaviour of the remote-control options --remote-* is undefined when more than one instance of Gwyddion is running
on the display. They can choose an arbitrary instance to communicate to.
If a directory is given as FILE argument the program opens a file chooser in this directory.
Gwyddion options:
--help Prints a brief help and terminates.
--version Prints version information and terminates.
--no-splash Disables splash screen on program startup.
--remote-new Opens files given on the command line in an already running instance of Gwyddion on the display. Runs a
new instance if none is running.
This is probably the most useful remote control option. File type associations are usually installed to run Gwyddion with
this option.
--remote-existing Opens files given on the command line in an already running instance of Gwyddion on the display.
Fails if none is running.
This is useful if you want to handle the case of Gwyddion not running differently than by starting it.
--remote-query Succeeds if an instance of Gwyddion is already running on the display and prints its instance identifier.
Fails if none is running.
The instance identifier depends on the remote control backend in use. In some cases it is useful as a global window
identifier, in some it is not. With libXmu this option prints the X11 Window, on Win32 HWND is printed, while with
LibUnique the startup id is printed.
--check Instead of running the user interface and opening FILE s, it loads the files, performs a sanity check on them (printing
errors to standard error output) and terminates.

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--disable-gl Disables OpenGL entirely, including any checks whether it is available. This option, of course, has any effect
only if Gwyddion was built with OpenGL support and one of the most visible effects is that 3D view becomes unavailable.
However, you may find it useful if you encounter a system so broken that even checking for OpenGL capabilities leads to
X server errors.
--log-to-file Redirects messages from GLib, Gtk+, Gwyddion, etc. to ~/.gwyddion/gwyddion.log or file given
in GWYDDION_LOGFILE environment variable. This option is most useful on Unix as on Win32 messages are redirected
to a file by default.
--no-log-to-file Prevents redirection of messages from GLib, Gtk+, Gwyddion, etc. to a file. This is most useful on
Win32 (where messages are redirected to a file by default) provided that stdout and stderr go somewhere you can see them.
--debug-objects Prints list of objects created during run time, with creation and desctruction times or reference counts
on program exit. Useful only for developers.
--startup-time Prints wall-clock time taken by various startup (and shutdown) tasks. Useful only for developers and
people going to complain about too slow startup.

Environment
On Linux/Unix, following environment variables can be used to override compiled-in installation paths (MS Windows version
always looks to directories relative to path where it was installed). Note they are intended to override system installation paths
therefore they are not path lists, they can contain only a single path.
GWYDDION_DATADIR Base data directory where resources (color gradients, OpenGL materials, . . . ) were installed. Gwyddion looks into its gwyddion subdirectory for resources.
When it is unset, it defaults to compiled-in value of ${datadir} which is usually /usr/local/share.
GWYDDION_LIBDIR Base library directory where modules were installed. Gwyddion looks into its gwyddion/modules
subdirectory for modules.
When it is unset, it defaults to compiled-in value of ${libdir} which is usually /usr/local/lib or /usr/local/
lib64.
GWYDDION_LIBEXECDIR Base lib-exec directory where plug-ins were installed. Gwyddion looks into its gwyddion/
plugins subdirectory for plug-ins.
When it is unset, it defaults to compiled-in value of ${libexecdir} which is usually /usr/local/libexec.
GWYDDION_LOCALEDIR Locale data directory where message catalogs (translations) were installed.
When it is unset, it defaults to compiled-in value of ${datadir}/locale which is usually /usr/local/share/
locale.
Other variables that influence Gwyddion run-time behaviour include GLib+ variables and Gtk+ variables and some Gwyddionspecific variables:
GWYDDION_LOGFILE Name of file to redirect log messages to. On MS Windows, messages are always sent to a file as
working with the terminal is cumbersome there. The default log file location, gwyddion.log in users Documents
and Settings, can be overridden with GWYDDION_LOGFILE. On Unix, messages go to the terminal by default and this
environment variable has effect only if --log-to-file is given.

Files
~/.gwyddion/settings Saved user settings and tool states. Do not edit while Gwyddion is running, it will overwrite it
at exit.
~/.gwyddion/glmaterials, ~/.gwyddion/gradients, ... User directories with various resources (OpenGL materials, color gradients, ...).
$GWYDDION_DATADIR/gwyddion/glmaterials, $GWYDDION_DATADIR/gwyddion/gradients ... The same for
system-wide resources.

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89

~/.gwyddion/pixmaps Directory to place user icons to. This is mainly useful for installation of modules to home.
$GWYDDION_DATADIR/gwyddion/pixmaps, The same for system-wide icons.
~/.gwyddion/modules Directory to place user modules to. They should be placed into file, graph, process,
layer, and tools subdirectories according to their kind, though this is more a convention than anything else.
$GWYDDION_LIBDIR/gwyddion/modules, The same for system-wide modules.
~/.gwyddion/plugins Directory to place user plug-ins to. They should be placed into file and process subdirectories according to their kind.
$GWYDDION_LIBEXECDIR/gwyddion/plugins, The same for system-wide plug-ins.
~/.gwyddion/pygwy Directory to place user python modules or scripts to.

See also
gwyddion-thumbnailer(1), gxsm(1)

5.2

gwyddion-thumbnailer

gwyddion-thumbnailer Creates thumbnails of SPM data files

Synopsis
gwyddion-thumbnailer --version | --help
gwyddion-thumbnailer [OPTION ...] MODE [ARGUMENT ...]

Description
Gwyddion-thumbnailer creates thumbnails of SPM (Scanning Probe Microscope) image files. Depending on the mode of operation, described below, the thumbnails are written to conform to various desktop standards so that they can be displayed in
nautilus(1), thunar(1) and similar file managers.
Gwyddion-thumbnailer loads and renders files using gwyddion(1), libraries and modules, therefore, it can create thumbnails of
all file formats supported by your Gwyddion installation. This also means it inherits Gwyddion settings, e.g. the default false
color gradient, and that it is influenced by the same environment variables as Gwyddion.

Informative Options
--help Prints a brief help and terminates.
--version Prints version information and terminates.

Thumbnailing Options
--update Writes the thumbnail only if it does not exist yet or does not seem to be up-to-date. By default, gwyddionthumbnailer overwrites existing thumbnails with fresh ones even if they seem up to date.

Mode
Three thumbnailing modes are available: gnome2, tms and kde4; and one special mode: check. They are described below.

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Gnome 2
gwyddion-thumbnailer [OPTION ...] gnome2 MAX-SIZE INPUT-FILE OUTPUT-FILE
In gnome2 mode, gwyddion-thumbnailer creates PNG thumbnails according to the Gnome thumbnailer specification. Using the
convention from this specification, it should be run
gwyddion-thumbnailer gnome2 %s %i %o

Gwyddion installs the corresponding GConf schemas and enables thumbnailers for all file types it supports by default, so usually
this should Just Work and should not need to be set up manually.
The thumbnails created in gnome2 more are identical as in tms mode, including all the PNG auxiliary chunks (provided that
the same MAX-SIZE as in tms mode is specified, of course).

TMS
gwyddion-thumbnailer [OPTION ...] tms MAX-SIZE INPUT-FILE
In tms mode, gwyddion-thumbnailer creates PNG thumbnails according to the Thumbnail Managing Standard. Argument MAXSIZE must be 128 or normal (both meaning 128 pixels) or 256 or large (both meaning 256 pixels).
Output file name is not given as it is prescribed by the TMS. The thumbnail is placed to the directory for normal or large
thumbnails according to given MAX-SIZE .
This mode can also be useful for manual batch-creation of thumbnails. For instance, to create them for all *.afm files in
directory scans and its subdirectories, you can run
find scans -type f -name *.afm -print0 \\
| xargs -0 -n 1 gwyddion-thumbnailer --update tms normal

And then go make yourself a coffee because this will take some time.

KDE 4
gwyddion-thumbnailer kde4 MAX-SIZE INPUT-FILE
In kde4 mode, gwyddion-thumbnailer creates PNG thumbnails that are intended to be consumed by gwythumbcreator KDE
module. The thumbnail, again identical as in the other modes, is written to the standard output.
Do not use this mode from the command line. It is documented for completness, however, the protocol between gwythumbcreator
and gwyddion-thumbnailer must be considered private and it can change at any time.

Check
gwyddion-thumbnailer check INPUT-FILE
The check mode does not serve for thumbnail creation. Instead, gwyddion-thumbnailer prints information about available
thumbnails of INPUT-FILE and cached failures to produce a thumbnail by individual applications, as described by the TMS.
If the normal-sized thumbnail exists and is up to date, the large version does not exist and there is one cached failure from
gnome-thumbnail-factory, the output can be for instance:
File:
INPUT-FILE
URI:
file:///home/me/Pictures/naughty/broken-tip3/INPUT-FILE
Normal: /home/me/.thumbnails/normal/MD5.png
status: OK
Large: /home/me/.thumbnails/large/MD5.png
status: Thumbnail does not exist or stat() fails on it.
Failed: /home/me/.thumbnails/fail/gnome-thumbnail-factory/MD5.png
URI is the canonical URI of the input file, MD5 stands for the hex representation of MD5 sum of the URI, as described by the
TMS. If there are no cached failures, no Failed lines are printed.
This function can be used to check thumbnails of any kind, not necessarily created by gwyddion or gwyddion-thumbnailer. In
future, it might be reported as an error if the thumbnail does not contain Gwyddion-specific information though.

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91

See also
gwyddion(1),

5.3

Keyboard Shortcuts

Shortcut

Menu equivalent

Context

Action

Ctrl-Q

File Quit

toolbox, data window, 3D

window, graph window, tool
window

Quit Gwyddion.

Ctrl-O

File Open

toolbox, data window, 3D

window, graph window, tool
window

Open a data file.

Ctrl-S

File Save

Ctrl-Shift-S

File Save As

toolbox,
window,
window
toolbox,
window,
window

Save current data (you will be

prompted for a file name if
none is associated yet).
Save current data under a different name. The file name associated with the data changes
to the new name.

Ctrl-Shift-M

File Merge

toolbox, data window, 3D

window, graph window, tool
window

Merge data from a file to the

current file.

Ctrl-H

File Open Recent Document History

toolbox, data window, 3D

window, graph window, tool
window

Open the document history

browser (or bring it forward if
it is already displayed).

Ctrl-Z

Edit Undo

toolbox, data window, 3D

window, graph window, tool
window

Undo the last processing step

applied on current data.

Ctrl-Y

Edit Redo

toolbox, data window, 3D

window, graph window, tool
window

Redo the last processing step

applied on current data.

Ctrl-K

Edit Remove Mask

toolbox, data window, 3D

window, graph window, tool
windows

Remove mask from current

data window.

Ctrl-Shift-K

Edit Remove Presentation

toolbox, data window, 3D

window, graph window, tool
windows

Remove presentation from

current data window.

Ctrl-Shift-B

Metadata Browser (in the context menu)

image or volume data window

Show metadata browser for

the data.

image or volume data window

Zoom current data window in.

image or volume data window

Zoom current data window in.

image or volume data window

Zoom current data window

out.

image or volume data window

Zoom current data window

1:1.

toolbox, data window, 3D

window, graph window, tool
windows

Repeat last data processing

function with the last used
parameters, on current data.
Normally the operation is repeated silently, but if the processing step cannot be carried
out without a human interaction, a dialog is shown.

Ctrl-F

Data Process Repeat Last

data window, 3D
graph window, tool
data window, 3D
graph window, tool

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Shortcut

Menu equivalent

Context

Action

Ctrl-Shift-F

Data Process Re-Show Last

toolbox, data window, 3D

window, graph window, tool
windows

Re-show parameter dialog of

the last data processing function. If the operation has no
parameters to set, it is performed immediately.

You can assign your own keyboard shortcuts to all functions in the menus and it is also possible to invoke tools with keyboard
shortcuts.
To change the keyboard shortcut of a menu item simply select the item using the mouse or arrow keys, press the key combination
you want to assing to it and it will be immediately assigned. The shortcut must be either a special key, e.g. F3, or a key
combination including modifiers, e.g. Ctrl-Shift-D. It is not possible to assign bare keys such as Q.
To prevent inadvertent modification of shortcuts, they can be changed only if Edit Keyboard Shortcuts is enabled. Modifications are disabled by default which is also the recommended setting during normal use.
All keyboard shortucts are stored in file ui/accel_map in the users directory, which usually means ~/.gwyddion (Unix)
or Documents and Settings\gwyddion (MS Windows). Assigning shortcuts to tools can be only done by editing this
file. Each line corresponds to an action that can be invoked with a shortcut. For instance the Mask Editor tools line is by default:
; (gtk_accel_path "<tool>/GwyToolMaskEditor" "")

Semicolons represents comments, i.e. lines starting with a semicolon are inactive. Hence, to assign the combo Ctrl-Shift-E to
the Mask Editor tool, remove the semicolon to make the line active and fill the desired shortcut in the empty quotes:
(gtk_accel_path "<tool>/GwyToolMaskEditor" "<Control><Shift>e")

5.4

Supported File Formats

File Format

Extensions

Module

Read

Write

SPS

Volume

AIST-NT

.aist

aistfile

Yes

Alicona Imaging AL3D data

.al3d

alicona

Yes

Ambios AMB

.amb

ambfile

Yes

Anfatec

.par, .int

anfatec

Yes

A.P.E. Research DAX

.dax

apedaxfile

Yes

A.P.E. Research DAT

.dat

apefile

Yes

Text matrix of data values

.txt

asciiexport

Yes

Assing AFM

.afm

assing-afm

Yes

Yes

Attocube Systems ASC

.asc

attocube

Yes

Image Metrology BCR, BCRF

.bcr, .bcrf

bcrfile

Yes

Burleigh BII

.bii

burleigh_bii

Yes

Burleigh IMG v2.1

.img

burleigh

Yes

Burleigh exported data

.txt, .bin

burleigh_exp

Yes

Code V interferogram data

.int

codevfile

Yes

Createc DAT

.dat

createc

Yes

Benyuan CSM

.csm

csmfile

Yes

Digital Micrograph DM3 TEM

data

.dm3

dm3file

Yes

DME Rasterscope

.img

dmefile

Yes

Gwyddion dumb dump data

.dump

dumbfile

Yes

ECS

.img

ecsfile

Yes

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File Format

Extensions

Module

Read

Write

SPS

Volume

Nanosurf EZD, NID

.ezd, .nid

ezdfile

Yes

DME GDEF

.gdf

gdeffile

Yes

Gwyddion Simple Field

.gsf

gsffile

Yes

Yes

Gwyddion native data

.gwy

gwyfile

Yes

Yes

Yes

Yes

Gwyddion XYZ data

.gxyzf

gxyzffile

Yesa

Psi HDF4

.hdf

hdf4file

Yes

Hitachi AFM

.afm

hitachi-afm

Yes

Hitachi S-3700 and S-4800

SEM data

.txt, +, image

hitachi-sem

Yes

WaveMetrics
wave v5

.ibw

igorfile

Yes

.sdf

intematix

Yes

IGOR

binary

Intematix SDF
ISO 28600:2011 SPM data
transfer format

.spm

iso28600

Yes

Yes

Limitedb

JEOL

.tif

jeol

Yes

JPK Instruments

.jpk

jpkscan

Yes

Olympus LEXT 4000

.lext

lextfile

Yes

FEI Magellan SEM images

.tif

magellan

Yes

MapVue

.map

mapvue

Yes

Zygo MetroPro DAT

.dat

metropro

Yes

MicroProf TXT

.txt

microprof

Yes

MicroProf FRT

.frt

microprof

Yes

DME MIF

.mif

miffile

Yes

Molecular Imaging MI

.mi

mifile

Yes

Limitedb

Aarhus MUL

.mul

mulfile

Yes

Nanoeducator

.mspm, .stm, .spm

nanoeducator

Yes

Yes

Nanomagnetics NMI

.nmi

nanomagnetics

Yes

Nanonics NAN

.nan

nanonics

Yes

Nanonis SXM

.sxm

nanonis

Yes

NanoObserver

.nao

nanoobserver

Yes

Nanoscan XML

.xml

nanoscan

Yes

NanoScanTech

.nstdat

nanoscantech

Yes

Yes

Yes
Yes

Veeco Nanoscope III

.001, .002, etc.

nanoscope

Yes

Limitedb

Veeco Nanoscope II

.001, .002, etc.

nanoscope-ii

Yes

Nanotop SPM

.spm

nanotop

Yes

GSXM NetCDF

.nc

netcdf

Yes

Yesd

Nearly raw raster data (NRRD)

.nrrd

nrrdfile

Yesc

NT-MDT

.mdt

nt-mdt

Yes

Yes

Yes

NT-MDT old MDA

.sxml, .dat

oldmda

Yes

Yes

Olympus LEXT 3000

.ols

ols

Yes

Omicron SCALA

.par, .tf*, .tb*, .sf*, .sb*

omicron

Yes

Yes

Omicron flat format

.*_flat

omicronflat

Yes

Omicron MATRIX

.mtrx

omicronmatrix

Yes

Wyko OPD

.opd

opdfile

Yes

Wyko ASCII

.asc

opdfile

Yes

Pixmap images

.png, .jpeg, .tiff, .tga, .pnm,

.bmp

pixmap

Yese

Yesf

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Gwyddion user guide

File Format

Extensions

Module

Read

Write

SPS

Volume

Nanosurf PLT

.plt

pltfile

Yes

Pacific Nanotechnology PNI

.pni

pnifile

Yes

Park Systems

.tiff .tif

psia

Yes

SymPhoTime TTTR v2.0 data

.pt3

pt3file

Yes

Quesant AFM

.afm

quesant

Yes

Raw text files

any

rawfile

Yes

Raw binary files

any

rawfile

Yes

Graph text data (raw)

any

rawgraph

Yesg

XYZ data

.xyz, .dat

rawxyz

Yesa

Limitedb

Limitedb

RHK Instruments SM3

RHK Instruments SM4

.sm3
.sm4

rhk-sm3
rhk-sm4

Yes
Yes

RHK Instruments SM2

.sm2

rhk-spm32

Yes

Limitedb

Automation and Robotics Dual

Lens Mapper

.mcr, .mct, .mce

robotics

Yes

S94 STM files

.s94

s94file

Yes

Surfstand Surface Data File

.sdf

sdfile

Yes

Yes

Micromap SDFA

.sdfa

sdfile

Yes

Seiko SII

.xqb, .xqd, .xqt, .xqp

seiko

Yes

Sensofar PLu v2000

.plu

sensofar

Yes

Sensolytics DAT

.dat

sensolytics

Yes

Shimadzu

.sph, .spp, .001, .002, etc.

shimadzu

Yes

Shimadzu ASCII

.txt

shimadzu

Yes

IonScope SICM

.img

sicmfile

Yes

Surface Imaging Systems

.sis

sis

Yes

SPIP ASCII

.asc

spip-asc

Yes

Thermicroscopes SPMLab R4R7

.tfr, .ffr, etc.

spmlab

Yes

Thermicroscopes
floating point

.flt

spmlabf

Yes

SPML (Scanning Probe Microscopy Markup Language)

.xml

spml

Yes

Omicron STMPRG

tp*, ta*

stmprg

Yes

Molecular Imaging STP

.stp

stpfile

Yes

Surf

.sur

surffile

Yes

Tescan MIRA SEM images

.tif

tescan

Yes

FEI Tecnai imaging and analysis (former Emispec) data

.ser

tiaser

Yes

Yes

Yes

Unisoku

.hdr, .dat

unisoku

Yes

SPMLab

VTK structured grid file

.vtk

vtkfile

Yes

WITec Project data

.wip

wipfile

Yes

Yes

Yes

WITec ASCII export

.dat

witec-asc

Yes

WITec

.wit

witfile

Yes

WSF ASCII data

.wsf

wsffile

Yes

Nanotec WSxM

.tom .stp

wsxmfile

Yes

Carl Zeiss SEM scans

.tif

zeiss

Yes

Zemax grid sag data

.dat

zemax

Yes

OpenEXR images

.exr

hdrimage.cc

Yes

Yes

5. Summaries and Tables

95

XYZ data are interpolated to a regular grid upon import.

Spectra curves are imported as graphs, positional information is lost.

Not all variants are implemented.

Data are exported in a fixed attached native-endian float point format.

Import support relies on Gdk-Pixbuf and hence may vary among systems.

Usually lossy, intended for presentational purposes. 16bit grayscale export is possible to PNG, TIFF and PNM.

At present, only simple two-column data, imported as graph curves, are supported.

5.5

High-Depth Image Formats

Gwyddion can export data to 16bit greyscale PNG, PNM and TIFF images and to OpenEXR images with half, float and 32bit
data types. In case of 16bit images the full data range is always stretched to the full greyscale range; OpenEXR export permits to
specify the value scaling factor.
When data are exported to a high-depth image additional information is stored to the file to enable automated loading back
to Gwyddion without having to specify the dimensions and scales manually. By storing this additional information to image
files you create in other programs, you can also make them directly loadable to Gwyddion with correct dimensions and scales.
The information is organised as key-value pairs, stored using individual format-specific means for each format, described in the
following table.
Format

Method

PNG

tEXt chunks

OpenEXR

named attributes

PNM

header comments of the form #key:value

Most keys are identical to those used in Gwyddion Simple Fields, except for the added Gwy:: prefix, so see also GSF description
for more details. Floating point values are stored directly if the format permits it (OpenEXR), otherwise a text representation of
the number is used (in the C format). The keys are listed below.
Key

Type

Meaning

Gwy::XReal

floating point

Horizontal size in physical units (given by XYUnits), a positive floating point number.

Gwy::YReal

floating point

Vertical size in physical units (given by XYUnits), a positive floating point number.

Gwy::XOffset

floating point

Horizontal offset in physical units (given by XYUnits).

Gwy::YOffset

floating point

Vertical offset in physical units (given by XYUnits).

Gwy::ZScale

floating point

Value scaling factor. Image data are to be multiplied by this factor to obtain physical
values. This parameter is usually used with limited-range floating point formats such as
half. For integer data, Gwy::ZMin and Gwy::ZMax is usually used.

Gwy::ZMin

floating point

Gwy::ZMax

floating point

Value in physical units corresponding to the minimum value representable in the image
(normally 0).
Value in physical units corresponding to the maximum value representable in the image.

Gwy::XYUnits

string

Lateral units, i.e. units of physical sizes and offsets.

Gwy::ZUnits

string

Value units, i.e. units of data values.

Gwy::Title

string

Data/channel title.

In case of PNG, the scaling information is also stored in the standard sCAL and pCAL chunks (with linear scaling formula).
Conversely, if these chunks are present (and the Gwyddion-specific are absent) the information from them is used in import. See
the PNG specifiation for the chunk description.

96

5.6

Gwyddion user guide

Expressions

Expressions used in Data Arithmetic module, grain quantity formulas and in graph function fitting have syntax similar to common
programming languages.
All numbers are real (floating point), number literals use standard notation. Examples of valid numbers: 1, .707, 2.661, 8.
2e-34.
Function, constant, and variable names start with a letter and continue with zero or more letters, numbers, or underscores.
Examples of valid identifiers: pow10 (a function), Pi (a constant), d2_2 (a variable).
The precedence of operations is summarized in following table.
Operation

Associativity

Examples

parentheses

N.A.

(x)

function call and unary operators

right to left

-sqrt 3

power operator

right to left

216

multiplication, division, and modulo operators

left to right

addition and subtraction operators

left to right

9/2 * 8
3 -4 + 5

Note -32 is 9, that is (-3)2, like in bc, but unlike in Perl or Python.
Available operators and functions are listed in following table.

5. Summaries and Tables

Operator

Meaning

+ (unary)

no op

- (unary)

negative value

~
+ (binary)

negative value (equivalent to -)

addition

- (binary)

subtraction

*
/

multiplication

floating point modulo

power

abs

absolute value

floor

rounding down to nearest integer

ceil

rounding up to nearest integer

sqrt

square root

cbrt

cubic root

sin

sine function

cos

cosine function

tan

tangent function

asin

arc sine function

acos

arc cosine function

atan

arc tangent function

exp

base-e exponential function

ln

base-e logarithm function

log

base-e logarithm function

pow10

base-10 exponential function

log10

base-10 logarithm function

sinh

hyperbolic sine function

cosh

hyperbolic cosine function

tanh

hyperbolic tangent function

asinh

inverse hyperbolic sine function

acosh
atanh

inverse hyperbolic cosine function

inverse hyperbolic tangent function

pow

power function, pow(x,y) equals to xy

min

minimum of two values

max

maximum of two values

97

division

mod

floating point modulo, mod(x,y) equals to x % y

hypot

Euclidean distance function, hypot(x,y) equals to sqrt(x2+y2)

atan2

arc tangent function of two variables

Beside that, there are a few peculiarities that may make typing simple expression easier:
Multiplication signs are optional, you can use spaces instead (or nothing, in some cases). E.g., 3/4 Pi and 5(4+3)(2+1)
are valid expressions. However, 3a is not a valid expression, 3e-4 always means 0.0003, not 3*e -4.
There is no difference between function calls and unary operators, so parentheses can be often omitted. E.g, sqrt 5 and
hypot hypot 3,4,5 are valid expression. The latter can be parenthesized as follows: hypot(hypot(3,4),5).
Note however, function calls have higher priority than any other operator, thus sin Pi/2 is the same as (sin Pi)/2, not
as sin(Pi/2).
If in doubt, write out expressions in full form.

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Gwyddion user guide

5.7

Resources

Various bits of data, e.g. false color maps or raw file import presets, are stored in standalone files that are collectively called
resource files. Gwyddion looks for resources in two different locations: system and user-specific.
System resources are installed along with the program and they are not modifiable. Typically, they are located under a directory
such as /usr/share/gwyddion (Unix), Program Files\Gwyddion (MS Windows) or other directory determined by
GWYDDION_DATADIR.
User resources are located in a users directory, this usually means under ~/.gwyddion (Unix) or Documents and Sett
ings\gwyddion (MS Windows).
All resource files are simple text files that can be easily examined and modified by text editors or sent to other users (if they
are copied or created manually Gwyddion needs to be restarted to notice them). In most cases only characters of the ASCII can
appear in the files. If international text can appear there it must be in the UTF-8 encoding. Numerical values are represented in
the standard POSIX format, i.e. with decimal point, independently on what decimal separator is usual in the users language.
Resources are organized in subdirectories according to their kind, e.g. color gradients reside in the subdirectory gradients.
The name of the file determines the resource name gradient Gray is found in file gradients/Gray. Modules can define
their own resource types; the types described here are the most important types but the list may not be comprehensive.
Every resource file has the same structure. It starts with a line identifying the resource type:
Gwyddion resource GwyGradient

where GwyGradient is the type name in the type system (which is quite a low-level detail but so it is), followed by named
parameters in the form
name value

and resource data. Some resource types may contain only named parameters, other may contain only data.

Gradients
Gradients, i.e. false color maps, reside in directory gradients, they are identified by GwyGradient and contain only data.
They can be edited in the application using the gradient editor.
The gradient data consists of rows corresponding to individual points in the gradient:
position red green blue alpha

The position determines where the color defined by red , green, blue and alpha components is placed in the interval [0, 1]
where 0 corresponds to the gradient start, 1 corresponds to the end. The color is interpolated linearly between the specified
points.
The positions must form an increasing sequence from 0 to 1 (i.e. the minimum number of color points is two). The range of the
color components is also [0, 1]. Note the alpha value, corresponding to opacity, is unused and must be given as 1 (fully opaque).
For instance, the standard gradient Red going from black (0 0 0) to red (1 0 0) to white (1 1 1) is defined as follows:
Gwyddion resource GwyGradient
0.0 0 0 0 1
0.5 1 0 0 1
1.0 1 1 1 1

OpenGL Materials
OpenGL materials reside in directory glmaterials, they are identified by GwyGLMaterial and contain only data. They can
be edited in the application using the OpenGL material editor.
The material data consists of four RGBA lines, similar to gradients that correspond in to the four OpenGL material components
in the following order:
1. ambient,

5. Summaries and Tables

99

2. diffuse,
3. specular,
4. emission.
See section OpenGL Material Editor for explanation of the components. They are followed by a line containing the shininess,
again as a number from the interval [0, 1].
Note the emission component, while read and written by Gwyddion, is presently unused by the 3D view. It is recommended to
set it to 0 0 0 1, i.e. black.
For instance, the standard material Red-Rubber with very dark red ambient color, grayish diffuse reflection, red specular reflection
and low shininess is defined as follows:
Gwyddion resource GwyGLMaterial
0.05 0.0 0.0 1.0
0.5 0.4 0.4 1.0
0.7 0.04 0.04 1.0
0.0 0.0 0.0 1.0
.078125

Grain Values
Grain values reside in directory grainvalues, they are identified by GwyGrainValue and contain only named parameters.
They can be used to define additional grain quantities, derived from the built-in quantities, that appear under User group in grain
analysis functions. At the time of writing this, there is no editor in the application, new quantities must be created manually.
The named parameters are summarized in the following table:
Parameter

Required

Type

Description

symbol

required

identifier

Identifier to use in other expressions (but see below). It must be a valid identifier of ASCII letters, numbers and underscores, starting with a letter.

expression

required

free-form

Formula for calculation of this quantity from other grain quantities. The general expression syntax is described in section Expressions.

symbol_markup

optional

free-form

Fancy symbol that can include Greek letters or subscripts and superscripts
expressed with the Pango markup language. It is used for presentation in the
application so, while it is optional, it is recommended to at least define it
identically to symbol.

power_xy

optional

integer

The power in which the lateral dimensions appear in the quantity. For instance, this is 1 for grain dimensions, 2 for areas and volumes. The default
value is 0.

power_z

optional

integer

The power in which the height dimension appears in the quantity. For instance, this is 1 for values and volumes, 0 for dimensions and areas. The
default value is 0.

same_units

optional

0 or 1

Given as 1 if the quantity makes sense only for lateral and height dimensions being the same physical quantities. For instance, this is required for the
surface area. The default is 0.

is_angle

optional

0 or 1

Given as 1 if the quantity is an angle. The expression should calculate angles

in radians. However, if is_angle is set Gwyddion knowns the value can be
converted to degrees for presentation. The default is 0.

At present, user-defined grain quantities cannot depend on other user-defined grain quantities to avoid circular dependencies. The
built-in grain quantities are listed below:

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Gwyddion user guide

Symbol

Group

Name

x_c

Position

Center x position

y_c

Position

Center y position

z_min
z_max

Value
Value

Minimum value
Maximum value

z_m

Value

Mean value

z_med

Value

Median value

b_min

Value

Minimum value on boundary

b_max

Value

Maximum value on boundary

A_0

Area

Projected area

A_s

Area

Surface area

a_eq

Area

Equivalent square side

r_eq

Area

Equivalent disc radius

A_h

Area

Area above half-height

A_c

Area

Area of convex hull

V_0

Volume

Zero basis volume

V_min

Volume

Grain minimum basis volume

V_L

Volume

Laplacian background basis volume

L_b0

Boundary

Projected boundary length

D_min

Boundary

Minimum bounding size

phi_min

Boundary

Minimum bounding direction

D_max

Boundary

Maximum bounding size

phi_max

Boundary

Maximum bounding direction

R_i

Boundary

Maximum inscribed disc radius

x_i

Boundary

Maximum inscribed disc center x position

y_i

Boundary

Maximum inscribed disc center y position

R_e

Boundary

Minimum circumcircle radius

x_e

Boundary

Minimum circumcircle center x position

y_e

Boundary

Minimum circumcircle center y position

R_m

Boundary

Mean radius

theta
phi

Slope
Slope

Inclination
Inclination

x_0

Curvature

Curvature center x position

y_0

Curvature

Curvature center y position

z_0

Curvature

Curvature center z value

kappa_1

Curvature

Curvature 1

kappa_2

Curvature

Curvature 2

phi_1

Curvature

Curvature angle 1

phi_2

Curvature

Curvature angle 2

For instance, a new grain value Height, measuring the grain height as the difference between the maximum and minimum value,
can be defined as follows:
Gwyddion resource GwyGrainValue
symbol dz
symbol_markup z
power_xy 0
power_z 1
expression z_max - z_min

5. Summaries and Tables

101

Raw File Presets

Raw file presents reside in directory rawfile, they are identified by GwyRawFilePreset and contain only named parameters.
They are normally created and edited by the preset editor in the raw file import module.
The named parameters in the resource files correspond closely to the parameters in the user interface explained in detail in section
Raw Data File Import. Hence, they will be described only briefly here.
Parameter

Type

Description

xres, yres

integer

horizontal and vertical size

xreal, yreal

number

physical dimensions, in units given by xyexponent and xyunit

xyexponent

multiple of 3

power of 10 to multiply xreal and yreal with

xyunit

string

base units of xreal and yreal, e.g. "m"

zscale

number

unit step in values

zexponent

multiple of 3

power of 10 to multiply zscale with

zunit

string

base units of zscale

format

0 or 1

0 means binary, 1 means text

builtin (binary)

integer

built-in data format id, see below

offset (binary)

integer

data offset in file, in bytes

size (binary)

integer

data value size, in bits

skip (binary)

integer

number of bits to skip after each value

rowskip (binary)

integer

number of additional bits to skip after each row

sign (binary)

0 or 1

0 means unsigned, 1 means signed

revsample (binary)

0 or 1

1 means reverse bits in values

revbyte (binary)

0 or 1

1 means reverse bits in bytes

byteswap (binary)

integer

byte swap pattern

lineoffset (text)

integer

lines to skip before starting to read the data

skipfields (text)

integer

fields to skip at the start of each line

delimiter (text)

string

field delimiter, empty string means arbitrary whitespace

decomma (text)

0 or 1

1 if decimal separator is comma, 0 for dot

Note the choice of a built-in binary format, i.e. nonzero builtin, implies the binary format to some extent. This means the
options size, revbyte and sign are ignored as they are used only for detailed specification of user formats. The available
formats are listed in the following table:
Type

Description

user-specified

signed 8bit integer

unsigned 8bit integer

signed 16bit integer

unsigned 16bit integer

signed 32bit integer

unsigned 32bit integer

IEEE float

IEEE double

signed 64bit integer

10

unsigned 64bit integer

5.8

Toolbox Configuration

The lower part of the toolbox containing the buttons for functions and tools can be customised by editing file ui/toolbox.
xml. Similarly to custom keyboard shortcuts, the file should be placed in the users directory, which usually means ~/.gwyd

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dion (Unix) or Documents and Settings\gwyddion (MS Windows). A good starting point for customisation is the
default ui/toolbox.xml file installed with Gwyddion under share/gwyddion.
The number buttons in a row is controlled by the width attribute of the top level element toolbox. To change it to five just
change the begining of the file to
<toolbox width=5>

Expandable and collapsable groups of buttons such as Data Process or Tools are created with tag group. You can create as many
or as few groups as you want. Functions of different kinds can placed in one group if you wish. Each group must be identified
with a unique id attribute which is, among other things, used to remember which group was collapsed and which expanded. The
attribute title determines the title:
<group id=proc title=Data Process>

Individual buttons are created with elements item:

<item type=proc function=edge_step icon=gwy_edge/>

Each item must have the type attribute, defining the function type. Unless the type is empty it must also have a function
attribute defining the specific function. Function names can be located in the module browser (Meta Module Browser), where
they are listed in Registered functions for each module; or in the on-line module browser. The available function types are listed
in the following table:
Type name

Function kind

empty

Empty placeholder that can be used for separation or row alignment.

builtin

A built-in function, which includes zooming in and out and 3D view activation. There are exacly four: disp
lay_3d, zoom_in, zoom_out and zoom_1_1.

proc

A two-dimensional data (image) processing function. It has prefix proc:: in the module browser.

graph

A graph function. It has prefix graph:: in the module browser.

volume

A volume data function. It has prefix volume:: in the module browser.

tool

A tool. It has prefix tool:: in the module browser.

The button icon is specified using the icon attribute. Some module functions have icons predefined (so you do not have to
specify it) but not all have because the number of available functions is huge. A Gwyddion stock icon can be used or possibly a
Gtk+ stock icon. Note Gwyddion icon names have words separated with underscores while Gtk+ icon names use dashes.
If you cannot choose from the provided set of icons it is also possible to draw your own icon and put it to ~/.gwyddion/
pixmaps (or its equivalent on other systems), using the same naming convention as Gwyddion icons. It may be useful to start
from the GIMP XCF source images for the icons since they contain individual pieces that can be mixed and matched. If you
draw a nice icon you are of course encouraged to submit it for inclusion in Gwyddion.
Since tools are accessible only from the toolbox, not listing a tool in ui/toolbox.xml renders it unavailable. Therefore, a
special empty item
<item type=tool/>

can be used to place all tools that have not been explicitly placed yet to the corresponding position (in a pretty much arbitrary
order).

5.9

Format of Gwyddion Files

Gwyddion native data files consists of a tree-like structure of serialized objects. Generally, these objects can be of various kind
and contain other embedded objects (hence the tree-like structure). It can be instructive to play with gwydump, a simple file
structure visualizer available in on the projects web, for a while and examine the contents of various files.
First of all, we will describe physical file structure without regard to possible interpretation of contained data.

5. Summaries and Tables

103

Byte Order
All data is stored in little-endian (also known as LSB or Intel) byte order.

File Header
The file header consists of four bytes (magic number) with the values of ASCII characters GWYP.
This is the new file format, an older version of file format with magic header GWYO also exists. It will not be discussed here.

File Data
The rest of the file consists of a serialized GwyContainer object that contains all the data. It is stored exactly the same way as
any other object, that is as described in the next section.

Object Layout
An object consists of three parts (in the following order):
Type name, stored as a NUL-terminated string of ASCII characters. This is the type name in GObject type system.
Serialized data size, stored as an unsigned 32bit integer. It does not include the size of the type name and the size of self.
Component list. Components are named parts of object data, each of particular data type: an atomic type, an array of atomic
types, or again an object. They are stored in no particular order.

Components
Each component consists of three parts (in the following order):
Name, stored as a NUL-terminated string.
Type, stored as a single unsigned byte (character). The table of possible component types is presented below.
Data, stored as whatever is appropriate for a particular type.

Data Types
Available atomic data types are listed in following table:
Type

Character

Note

boolean

Stored as a byte, zero is false, nonzero (normally 1) is true

character

32bit integer

64bit integer

double

finite IEEE 754 double precision floating point number, i.e. files must not contain infinities and
not-a-numbers

string

NUL-terminated

object

Serialized object as described above

Each atomic type except boolean has its array counterpart. The type character of array types is the same as of the corresponding
atomic type, except it is uppercase. Arrays are stored as unsigned 32bit array length (the number of items), followed by the item
values. Array data types are listed in following table:

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Gwyddion user guide

Type

Character

Note

array of characters

Not NUL-terminated

array of 32bit integers

array of 64bit integers

array of doubles

Q
D

array of strings

array of objects

Uppercase Oh, not zero

Top-Level GwyContainer
The names (keys) of data objects in a GwyContainer representing a Gwyddion file strongly resemble UNIX file names, i.e. they
have the form of /-separated paths and form a sort of tree-like structure. For instance the title of the first channel, numbered 0, is
stored under the key /0/data/title. Note some data or information is found under keys that do not seem logical; the reason
is usually historical.
The following sections describe the organisation of interesting data and information in the GwyContainer. The list is not necessarily complete. However, since all data items in the file specify consistently their name, type and size in bytes it is always
possible to skip unknown data types or data you are not interested in and extract only the desired data items.

Channels
The following table summarises the common keys of channel-related data in the top-level container for channel number 0. For
other channels, the number 0 has to be replaced with the corresponding channel number. Note that channels are often numbered
sequentially, starting from 0, however, they can have any numbers and the set of channels numbers does not have to be contiguous.
Key

Type

Meaning

/0/data

GwyDataField

Channel data.

/0/data/title

string

Channel title, as shown in the data browser.

/0/data/visible

boolean

Whether the channel should be displayed in a window when the file

is loaded.

/0/base/palette

string

Name of the false color gradient used to display the channel.

/0/base/range-type

32bit integer

False color mapping type (as set by the Color range tool), the value
is from GwyLayerBasicRangeType enum.

/0/base/min

double

Minimum value for user-set display range.

/0/base/max

double

Maximum value for user-set display range.

/0/mask

GwyDataField

Mask data. The pixel dimensions of this data field must match those
of the channel data.

/0/mask/red

double

Red component of the mask color.

/0/mask/green

double

Green component of the mask color.

/0/mask/blue

double

Blue component of the mask color.

/0/mask/alpha

double

Alpha (opacity) component of the mask color.

/0/show

GwyDataField

Presentation data. The pixel dimensions of this data field must

match those of the channel data.

/0/meta

GwyContainer

Channel metadata. The keys are directly the names as displayed in

the metadata browser and the string values are the values.

/0/data/log

GwyStringList

Channel log as a list of string log entries. They have the format
type::function(param=value, ...)@time.

/0/select/foo

a GwySelection subclass

Selection data. Each kind of selection has (usually) a different object type and is stored under a different name; the specific name foo
is the same as shown in the selection manager.

5. Summaries and Tables

105

Channels are represented as GwyDataField objects. The components of a GwyDataField are summarised in the following table:
Component

Type

Meaning

xres

32bit integer

Horizontal size in pixels.

yres

32bit integer

Vertical size in pixels.

xreal

double

Horizontal dimension in physical units.

yreal

double

Vertical dimension in physical units.

xoff

double

Horizontal offset of the top-left corner in physical units. It usually occurs only if nonzero.

yoff

double

Vertical offset of the top-left corner in physical units. It usually occurs only if non-zero.

si_unit_xy

GwySIUnit

Unit of lateral dimensions.

si_unit_z

GwySIUnit

Unit of data values.

data

array of doubles

Field data, stored as a flat array of size xresyres, from top to bottom and from left
to right.

Graphs
The following table summarises the common keys of graph-related data in the top-level container for graph number 1. For other
graphs, the number 1 has to be replaced with the corresponding graph number. Note that graphs are often numbered sequentially,
starting from 1, however, they can have any numbers positive and the set of graph numbers does not have to be contiguous. The
number 0 in the prefix of graph keys is a historical relic that does not mean anything and it is always 0.
Key

Type

Meaning

/0/graph/graph/1

GwyGraphModel

Graph model object data.

/0/graph/graph/1/visible

boolean

Whether the graph should be displayed in a window when the file

is loaded.

Graphs are represented as GwyGraphModel objects. The components of a GwyGraphModel are summarised in the following
table:
Component

Type

Meaning

curves

array of GwyGraphCurveModels

Individual graph curves.

title

string

Graph title as displayed in the data browser.

x_unit

GwySIUnit

Unit of the abscissa.

y_unit

GwySIUnit

Unit of the ordinate.

top_label

string

Label on the top axis.

bottom_label

string

Label on the bottom axis.

left_label

string

Label on the left axis.

right_label

string

Label on the right axis.

x_is_logarithmic

boolean

Whether the abscissa has a logarithmic scale.

y_is_logarithmic

boolean

Whether the ordinate has a logarithmic scale.

x_min
x_min_set

double
boolean

User-set minimum value of the abscissa.

Whether user-set minimum value of the abscissa
should be used (otherwise the range is determined automatically).

x_max

double

User-set maximum value of the abscissa.

x_max_set

boolean

Whether user-set maximum value of the abscissa

should be used (otherwise the range is determined automatically).

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Component

Type

Meaning

y_min

double

User-set minimum value of the ordinate.

y_min_set

boolean

Whether user-set minimum value of the ordinate

should be used (otherwise the range is determined automatically).

y_max

double

User-set maximum value of the ordinate.

y_max_set

boolean

Whether user-set maximum value of the ordinate

should be used (otherwise the range is determined automatically).

grid-type

32bit integer

Type of grid shown. The value is from GwyGraphGridType enum.

label.has_frame

boolean

Whether the graph key has a frame.

label.frame_thickness

32bit integer

Width of graph key frame.

label.reverse

boolean

Whether to reverse the graph key.

label.visible

boolean

Whether the graph key is visible.

label.position

32bit integer

The position (corner) where the graph key is places.

The value is from GwyGraphLabelPosition enum.

Graph curves are represented as GwyGraphCurveModel objects. The components of a GwyGraphCurveModel are summarised
in the following table:
Component

Type

Meaning

xdata

array of doubles

Abscissa points. The number of point must match ydata.

ydata

array of doubles

Ordinate points. The number of point must match xdata.

description

string

Curve description (name).

type

32bit integer

Curve mode (points, lines, etc.) The value is from GwyGraphCurveType enum.

color.red

double

Red component of the curve color.

color.green

double

Green component of the curve color.

color.blue

double

Blue component of the curve color.

point_type

32bit integer

Type of symbols representing data points. The value is from GwyGraphPointType

enum.

point_size

32bit integer

Size of symbols representing data points.

line_type

32bit integer

Type of lines connecting data points. The value is from GwyGraphLineType enum.

line_size

32bit integer

Width of lines connecting data points.

Spectra
The following table summarises the common keys of spectra-related data in the top-level container for spectra set number 0.
For other spectra, the number 0 has to be replaced with the corresponding spectra set number. Note that spectra sets are often
numbered sequentially, starting from 0, however, they can have any numbers and the set of spectra set numbers does not have to
be contiguous.
Key

Type

Meaning

/sps/0

GwySpectra

Spectra data.

Sets of spectra of one kind are represented as GwySpectra objects. The components of a GwySpectra are summarised in the
following table:

5. Summaries and Tables

107

Component

Type

Meaning

title

string

Spectra title as displayed in the data browser.

si_unit_xy

GwySIUnit

Unit of spectrum position coordinates.

coords

array of doubles

Coordinates of points where the spectra were taken, in physical units. Each spectrum takes two items: for the horizontal and vertical coordinate. The number of
coordinates must match the number of curves in data.

data

array of GwyDataLines

Individual spectra curves.

selected

array of 32bit integers

Indices of selected spectra curves.

Individual curves in spectra are represented as GwyDataLine objects. The components of a GwyDataLine are summarised in the
following table:
Component

Type

Meaning

res

32bit integer

Number of data points.

real

double

Length in physical units.

off

double

Offset of the begining in physical units. It usually occurs only if non-zero.

si_unit_x

GwySIUnit

Unit of abscissa.

si_unit_y

GwySIUnit

Unit of data values.

data

array of doubles

Line data, stored as an array of res, from left to right.

Volume data
The following table summarises the common keys of volume-related data in the top-level container for volume data number 0.
For other volume data, the number 0 has to be replaced with the corresponding volume data number. Note that volume data are
often numbered sequentially, starting from 0, however, they can have any numbers and the set of volume data numbers does not
have to be contiguous.
Key

Type

Meaning

/brick/0

GwyBrick

Volume data.

/brick/0/preview

GwyDataField

Two-dimensional data shown when the volume data is displayed in a

window.

/brick/0/title

string

Volume data title, as shown in the data browser.

/brick/0/visible

boolean

Whether the volume data should be displayed in a window when the

file is loaded.

/brick/0/preview/palette

string

Name of the false color gradient used to display the preview data.

/brick/0/meta

GwyContainer

Volume data metadata. The keys are directly the names as displayed
in the metadata browser and the string values are the values.

/brick/0/log

GwyStringList

Volume data log as a list of string log entries. They have the format
type::function(param=value, ...)@time.

Volume data are represented as GwyBrick objects. The components of a GwyBrick are summarised in the following table:
Component

Type

Meaning

xres

32bit integer

Horizontal size in pixels.

yres

32bit integer

Vertical size in pixels.

zres

32bit integer

Depth (number of levels) in pixels.

xreal

double

Horizontal dimension in physical units.

yreal

double

Vertical dimension in physical units.

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Component

Type

Meaning

zreal

double

Depthwise dimension in physical units.

xoff

double

Horizontal offset of the top-left corner in physical units. It usually occurs only if non-zero.

yoff

double

Vertical offset of the top-left corner in physical units. It usually occurs only if non-zero.

zoff

double

Depthwise offset of the top-left corner in physical units. It usually occurs only if non-zero.

si_unit_x

GwySIUnit

Unit of horizontal lateral dimensions.

si_unit_y

GwySIUnit

Unit of vertical lateral dimensions.

si_unit_z

GwySIUnit

Unit of depthwise dimensions.

si_unit_w

GwySIUnit

Unit of data values.

data

array of doubles

Field data, stored as a flat array of size xresyreszres, from the zeroth to the last
plane, top to bottom and from left to right.

Auxiliary Objects
The components of a GwySIUnit are summarised in the following table:
Component

Type

Meaning

unitstr

string

Textual representation of the unit, e.g. "A" or "m-1" (as base SI unit, prefixes are ignored).

The components of a GwySelection are summarised in the following table. Some selection types can have other data members;
refer to the documentation of specific selection classes for how to interpret the data.
Component

Type

Meaning

max

32bit integer

Maximum number of objects the selection can hold (this is the number set by gwy_sele
ction_set_max_objects()).

data

array of doubles

Selection data. The number of items that form one selection object is determined by the
selection type.

The components of a GwyStringList are summarised in the following table. Note if GwyStringLists are used to represent logs,
the strings have a specific structure described above.

5.10

Component

Type

Meaning

strings

array of strings

List of string items.

Simple Field Files

The Gwyddion native file format captures all the information and state Gwyddion needs to save and consequently it is quite
complex. Often it is not practical to save files in .gwy format in custom programs and scripts creating input for Gwyddion.
The Gwyddion Simple Field file format (.gsf) can be used in these situations instead. It is a single-channel format for 2D data
that was designed to be easy and efficient to read and write, with human-readable header, reasonably expressive, and avoiding
instrument or application specific fields (though it can optionally bear them).
GSF can be read and written by Gwyddion version 2.20 or later.

Overall structure
A GSF file consists of four parts, in the following order:
magic line Files begin with a magic line identifying the file type.

5. Summaries and Tables

109

text header The header consists of lines of the form

name = value

defining individual parameters.

NUL padding The header is terminated by one to four NUL bytes, aligning the data start to a multiple of 4.
binary data Binary data is in 32bit floating-point format.

Magic line
GSF files start with the line
Gwyddion Simple Field 1.0

terminated by a linefeed character (\n, ASCII 0x0a).

Text header
Each header line has the form
name = value

where any whitespace before the name, around the equal sign and at the end of value is ignored. Field names are case-sensitive
and follow the usual rules for identifiers in programming languages.
Similarly to the magic line, the lines in the text header are terminated by a linefeed character as is usual on Unix. This means
the header must be read and written in binary mode to ensure preservation of end-of-line characters on other systems (and not
changing the header size e.g. by LF CRLF transformation).
Any non-ASCII characters, that can occur for example in the channel title, are represented in UTF-8 encoding. The NUL
character may not occur in the header.
Header fields:
Name

Type

Value

XRes

Mandatory

The horizontal size in pixels, a positive integer.

YRes

Mandatory

The vertical size in pixels, a positive integer.

XReal

Optional

Horizontal size in physical units (given by XYUnits), a positive floating point number. It defaults
to 1.0 if not given.

YReal

Optional

Vertical size in physical units (given by XYUnits), a positive floating point number. It defaults to
1.0 if not given.

XOffset

Optional

Horizontal offset in physical units (given by XYUnits), a floating point number. It defaults to 0.0
if not given.

YOffset

Optional

Vertical offset in physical units (given by XYUnits), a floating point number. It defaults to 0.0 if
not given.

Title

Optional

Data/channel title. It has no default, applications might display Unknown or something similar
if not given.

XYUnits

Optional

Lateral units, i.e. units of physical sizes and offsets. They must be given as base units, that is m
or A with no power-of-10 prefix (Gwyddion could deal with it but it might present a problem for
other software). The default is no units. This means in SPM data, you normally wish to specify
XYUnits as m because the lateral dimensions are in metres.

ZUnits

Optional

Value units, i.e. units of data values. See XYUnits above for details.

Floating point numbers can be in the scientific format, e.g. 1.23e-4. They are represented in the standard C/POSIX locale, i.e.
decimal dot is used (not comma or other separators).

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The header may contain other fields beside those listed above. Gwyddion will load them into metadata. Common informational
fields can include Comment, Date or Direction.
Fields may occur in any order, nevertheless, it is recommended to start with mandatory fields, continue with optional fields and
put custom fields last.
A simple header example (also including the magic line):
Gwyddion Simple Field 1.0
XRes = 400
YRes = 400
XReal = 5e-05
YReal = 5e-05
XYUnits = m
ZUnits = V
Title = ADC2

NUL padding
The text header is followed by one to four NUL (\0, ASCII 0x00) bytes that (a) terminate it and (b) align the data start to an
offset from the begining of file that is a multiple of 4. More precisely, denoting N the total length of the magic line and the text
header, the data starts at the nearest multiple of 4 larger than N.
This padding to a multiple of 4 ensures aligned memory access when mapping the file directly to memory. The number of NUL
bytes is uniquely determined by the remainder of the length modulo four (N mod 4):
Remainder

Number of padding NULs

2
3

2
1

Binary data
Data values are stored as IEEE 32bit single-precision floating point numbers, in little-endian (LSB, or Intel) byte order. Values
are stored by row, from top to bottom, and in each row from left to right.
The physical units of these values are ZUnits.
The size of the image data is exactly 4*XRes*YRes bytes and there is no data after it in the file.

5.11

Simple XYZ Files

Although Gwyddion does work with general XYZ data and raw XYZ data are interpolated to a grid upon import, need has arisen
for a file format similar in spirit to Gwyddion simple field (.gsf) but representing the data in XYZ format. Such file format, called
Gwyddion XYZ Field (.gxyzf), is described in this section.
It should be noted that Z simply stands for the ordinate here. Z values in the file may be actual Z coordinates (heights) but they
may also be currents, voltages, etc.
GXYZF can be written by Gwyddion version 2.31 or later. They can also be read since this version, although the regularisation
to a grid may be somewhat crude.

Overall structure
A GXYZF file consists of four parts, in the following order:
magic line Files begin with a magic line identifying the file type.
text header The header consists of lines of the form

5. Summaries and Tables

111

name = value

defining individual parameters.

NUL padding The header is terminated by one to eight NUL bytes, aligning the data start to a multiple of 8.
binary data Binary data is in 64bit floating-point format.

Magic line
gxyzf files start with the line
Gwyddion XYZ Field 1.0

terminated by a linefeed character (\n, ASCII 0x0a).

Text header
Each header line has the form
name = value

where any whitespace before the name, around the equal sign and at the end of value is ignored. Field names are case-sensitive
and follow the usual rules for identifiers in programming languages.
Similarly to the magic line, the lines in the text header are terminated by a linefeed character as is usual on Unix. This means
the header must be read and written in binary mode to ensure preservation of end-of-line characters on other systems (and not
changing the header size e.g. by LF CRLF transformation).
Any non-ASCII characters, that can occur for example in channel titles, are represented in UTF-8 encoding. The NUL character
may not occur in the header.
Header fields:
Name

Type

Value

NChannels

Mandatory

Number of value (Z) channels, a positive integer. The values stored for each point
include also coordinates X and Y but they are not counted into NChannels.

NPoints

Mandatory

Number data points in the file.

XYUnits

Optional

Lateral units, i.e. units of X and Y values. They must be given as base units, that
is m or A with no power-of-10 prefix (Gwyddion could deal with it but it might
present a problem for other software). The default is no units. This means in SPM
data, you normally wish to specify XYUnits as m because the lateral dimensions
are in metres.

ZUnits1, ZUnits2, . . .

Optional

Value units, i.e. units of data values for individual channels. Channels are numbered from 1 to NChannels. See XYUnits above for details.

Title1, Title2, . . .

Optional

Titles of individual channels. Channels are numbered from 1 to NChannels.

Titles have no default, applications might display Unknown or something similar
if not given.

XRes

Optional

Hint specifying the preferred horizontal size in pixels if the data are regularised to
a grid, a positive integer. Readers are not required to honour it and may interpolate
data to grids of different dimensions.

YRes

Optional

Hint specifying the preferred vertical size in pixels if the data are regularised to a
grid, a positive integer. Readers are not required to honour it and may interpolate
data to grids of different dimensions.

The header may contain other fields beside those listed above. Gwyddion will load them into metadata. Common informational
fields can include Comment, Date or Direction.

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Gwyddion user guide

Fields may occur in any order, nevertheless, it is recommended to start with mandatory fields, continue with optional fields and
put custom fields last.
A simple header example of a two-channel file (also including the magic line):
Gwyddion XYZ Field 1.0
NChannels = 2
NPoints = 457884
XYUnits = m
ZUnits1 = m
ZUnits2 = V
Title1 = Height
Title2 = ADC2

NUL padding
The text header is followed by one to eight NUL (\0, ASCII 0x00) bytes that (a) terminate it and (b) align the data start to an
offset from the begining of file that is a multiple of 8. More precisely, denoting N the total length of the magic line and the text
header, the data starts at the nearest multiple of 8 larger than N.
This padding to a multiple of 8 ensures aligned memory access when mapping the file directly to memory. The number of NUL
bytes is uniquely determined by the remainder of the length modulo eight (N mod 8):
Remainder

Number of padding NULs

4
5

4
3

Binary data
Data values are stored as IEEE 64bit double-precision floating point numbers, in little-endian (LSB, or Intel) byte order. Points
are stored in arbitrary order. Each point is stored as a block of NChannels+2 values: X, Y and then all ordinate values, in the
channel order.
The physical units of the values are given by XYUnits for X and Y and then ZUnits1, ZUnits2, . . . for the ordinate values.
The size of the data is exactly 8*NPoints*(NChannels+2) bytes and there is no data after it in the file.

6. Developing Gwyddion

113

Chapter 6

Developing Gwyddion
You are encouraged to become a developer of Gwyddion.
If you want to become developer, we recommend you to start with some simple modules (see module tutorial), to see how the
application works. If you write a module or plug-in, you are encouraged to share it here with other Gwyddion users. Let us know,
so that we can link your modules or plug-ins to these pages or even include in it Gwyddion. You dont have to limit yourself to
modules or plug-ins of course, but they should be easier to start with.

API References
There are many functions that can help you while developing your module. See API reference at Documentation section of the
project web.

Bug reports
We will be very happy if you send us bug reports if you find errors in Gwyddion. For doing this, please, specify as much as
possible the situation that led to error, operating system and Gwyddion version used. You can also send us the SPM data that
were being processed when the problem was found, this is necessary namely for reporting bugs related to file loading and saving.
The preferred bug reporting method is to send an e-mail to [email protected].

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Appendix A

GNU General Public License

A.1

Preamble

The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General
Public License is intended to guarantee your freedom to share and change free software - to make sure the software is free for
all its users. This General Public License applies to most of the Free Software Foundations software and to any other program
whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General
Public License instead.) You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure
that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source
code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know
you can do these things.
To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the
rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights
that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so
they know their rights.
We protect your rights with two steps:
1. copyright the software, and
2. offer you this license which gives you legal permission to copy, distribute and/or modify the software.
Also, for each authors protection and ours, we want to make certain that everyone understands that there is no warranty for this
free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is
not the original, so that any problems introduced by others will not reflect on the original authors reputations.
Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free
program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear
that any patent must be licensed for everyones free use or not licensed at all.
The precise terms and conditions for copying, distribution and modification follow.

A.2

Terms And Conditions For Copying, Distribution And Modification

Section 0
This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The Program, below, refers to any such program or work, and a work
based on the Program means either the Program or any derivative work under copyright law: that is to say, a work containing the
Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation
is included without limitation in the term modification.) Each licensee is addressed as you.
Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act
of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based
on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program
does.

A. GNU General Public License

115

Section 1
You may copy and distribute verbatim copies of the Programs source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact
all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy
of this License along with the Program.
You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange
for a fee.

Section 2
You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy
and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
1. You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change.
2. You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or
any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.
3. If the modified program normally reads commands interactively when run, you must cause it, when started running for
such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright
notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute
the program under these conditions, and telling the user how to view a copy of this License.
Exception:
If the Program itself is interactive but does not normally print such an announcement, your work based on the Program
is not required to print an announcement.)

These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to
those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which
is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other
licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is
to exercise the right to control the distribution of derivative or collective works based on the Program.
In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program)
on a volume of a storage or distribution medium does not bring the other work under the scope of this License.

Section 3
You may copy and distribute the Program (or a work based on it, under Section 2 in object code or executable form under the
terms of Sections 1 and 2 above provided that you also do one of the following:
1. Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms
of Sections 1 and 2 above on a medium customarily used for software interchange; or,
2. Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost
of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
3. Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative
is allowed only for noncommercial distribution and only if you received the program in object code or executable form
with such an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for making modifications to it. For an executable work,
complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the
scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed

116

Gwyddion user guide

need not include anything that is normally distributed (in either source or binary form) with the major components (compiler,
kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent
access to copy the source code from the same place counts as distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.

Section 4
You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this
License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated
so long as such parties remain in full compliance.

Section 5
You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify
or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore,
by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to
do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.

Section 6
Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from
the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any
further restrictions on the recipients exercise of the rights granted herein. You are not responsible for enforcing compliance by
third parties to this License.

Section 7
If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent
issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this
License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your
obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at
all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies
directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from
distribution of the Program.
If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is
intended to apply and the section as a whole is intended to apply in other circumstances.
It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity
of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which
is implemented by public license practices. Many people have made generous contributions to the wide range of software
distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or
she is willing to distribute software through any other system and a licensee cannot impose that choice.
This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.

Section 8
If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License may add an explicit geographical distribution limitation
excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this
License incorporates the limitation as if written in the body of this License.

A. GNU General Public License

117

Section 9
The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such
new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to
it and any later version, you have the option of following the terms and conditions either of that version or of any later version
published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose
any version ever published by the Free Software Foundation.

Section 10
If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the
author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software
Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status
of all derivatives of our free software and of promoting the sharing and reuse of software generally.

NO WARRANTY Section 11
BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO
THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

Section 12
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT
HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED
ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT
LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR
THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH
HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS

A.3

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to
make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least the copyright line and a pointer to where the full notice is
found.
<one line to give the programs name and a brief idea of what it does.>
Copyright (C) <year>
<name of author>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA

118

Gwyddion user guide

Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author Gnomovision
comes with ABSOLUTELY NO WARRANTY; for details type show w.
This is free software, and you are welcome to redistribute it under
certain conditions; type show c for details.

The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course,
the commands you use may be called something other than show w and show c; they could even be mouse-clicks or menu
items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your school, if any, to sign a copyright disclaimer for the
program, if necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
program Gnomovision (which makes passes at compilers) written
by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want
to do, use the GNU Library General Public License instead of this License.

B. GNU Free Documentation License

119

Appendix B

GNU Free Documentation License

B.1

Preamble

The purpose of this License is to make a manual, textbook, or other functional and useful document free in the sense of
freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially
or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while
not being considered responsible for modifications made by others.
This License is a kind of copyleft, which means that derivative works of the document must themselves be free in the same
sense. It complements the GNU General Public License, which is a copyleft license designed for free software.
We have designed this License in order to use it for manuals for free software, because free software needs free documentation:
a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to
software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book.
We recommend this License principally for works whose purpose is instruction or reference.

B.2

Applicability And Definitions

This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it
can be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration,
to use that work under the conditions stated herein. The Document, below, refers to any such manual or work. Any member
of the public is a licensee, and is addressed as you. You accept the license if you copy, modify or distribute the work in a way
requiring permission under copyright law.
A Modified Version of the Document means any work containing the Document or a portion of it, either copied verbatim, or
with modifications and/or translated into another language.
A Secondary Section is a named appendix or a front-matter section of the Document that deals exclusively with the relationship
of the publishers or authors of the Document to the Documents overall subject (or to related matters) and contains nothing that
could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section
may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related
matters, or of legal, commercial, philosophical, ethical or political position regarding them.
The Invariant Sections are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the
notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then
it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not
identify any Invariant Sections then there are none.
The Cover Texts are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that
says that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may
be at most 25 words.
A Transparent copy of the Document means a machine-readable copy, represented in a format whose specification is available
to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed
of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text
formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise
Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification
by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not
Transparent is called Opaque.
Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input
format, SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for
human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary
formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing

120

Gwyddion user guide

tools are not generally available, and the machine-generated HTML, PostScript or PDF produced by some word processors for
output purposes only.
The Title Page means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the
material this License requires to appear in the title page. For works in formats which do not have any title page as such, Title
Page means the text near the most prominent appearance of the works title, preceding the beginning of the body of the text.
A section Entitled XYZ means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in
parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned
below, such as Acknowledgements, Dedications, Endorsements, or History.) To Preserve the Title of such a section
when you modify the Document means that it remains a section Entitled XYZ according to this definition.
The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These
Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any
other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.

B.3

Verbatim Copying

You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License,
the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that
you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the
reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies.
If you distribute a large enough number of copies you must also follow the conditions in section 3.
You may also lend copies, under the same conditions stated above, and you may publicly display copies.

B.4

Copying In Quantity

If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than
100, and the Documents license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly,
all these Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also
clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the
title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the
covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other
respects.
If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably)
on the actual cover, and continue the rest onto adjacent pages.
If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machinereadable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from
which the general network-using public has access to download using public-standard network protocols a complete Transparent
copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you
begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated
location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of
that edition to the public.
It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of
copies, to give them a chance to provide you with an updated version of the Document.

B.5

Modifications

You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that
you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus
licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these
things in the Modified Version:
GNU FDL M ODIFICATION C ONDITIONS
A. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous
versions (which should, if there were any, be listed in the History section of the Document). You may use the same title as
a previous version if the original publisher of that version gives permission.

B. GNU Free Documentation License

121

B. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the
Modified Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has
fewer than five), unless they release you from this requirement.
C. State on the Title page the name of the publisher of the Modified Version, as the publisher.
D. Preserve all the copyright notices of the Document.
E. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices.
F. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version
under the terms of this License, in the form shown in the Addendum below.
G. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Documents license
notice.
H. Include an unaltered copy of this License.
I. Preserve the section Entitled History, Preserve its Title, and add to it an item stating at least the title, year, new authors,
and publisher of the Modified Version as given on the Title Page. If there is no section Entitled History in the Document,
create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item
describing the Modified Version as stated in the previous sentence.
J. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and
likewise the network locations given in the Document for previous versions it was based on. These may be placed in the
History section. You may omit a network location for a work that was published at least four years before the Document
itself, or if the original publisher of the version it refers to gives permission.
K. For any section Entitled Acknowledgements or Dedications, Preserve the Title of the section, and preserve in the
section all the substance and tone of each of the contributor acknowledgements and/or dedications given therein.
L. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the
equivalent are not considered part of the section titles.
M. Delete any section Entitled Endorsements. Such a section may not be included in the Modified Version.
N. Do not retitle any existing section to be Entitled Endorsements or to conflict in title with any Invariant Section.
O. Preserve any Warranty Disclaimers.
If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no
material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add
their titles to the list of Invariant Sections in the Modified Versions license notice. These titles must be distinct from any other
section titles.
You may add a section Entitled Endorsements, provided it contains nothing but endorsements of your Modified Version by
various partiesfor example, statements of peer review or that the text has been approved by an organization as the authoritative
definition of a standard.
You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the
end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may
be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover,
previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but
you may replace the old one, on explicit permission from the previous publisher that added the old one.
The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to
assert or imply endorsement of any Modified Version.

122

B.6

Gwyddion user guide

Combining Documents

You may combine the Document with other documents released under this License, under the terms defined in section 4 above
for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents,
unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their
Warranty Disclaimers.
The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with
a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such
section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or
else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the
combined work.
In the combination, you must combine any sections Entitled History in the various original documents, forming one section
Entitled History; likewise combine any sections Entitled Acknowledgements, and any sections Entitled Dedications. You
must delete all sections Entitled Endorsements.

B.7

Collections Of Documents

You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you
follow the rules of this License for verbatim copying of each of the documents in all other respects.
You may extract a single document from such a collection, and distribute it individually under this License, provided you insert
a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of
that document.

B.8

Aggregation With Independent Works

A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of
a storage or distribution medium, is called an aggregate if the copyright resulting from the compilation is not used to limit the
legal rights of the compilations users beyond what the individual works permit. When the Document is included in an aggregate,
this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.
If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half
of the entire aggregate, the Documents Cover Texts may be placed on covers that bracket the Document within the aggregate,
or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that
bracket the whole aggregate.

B.9

Translation

Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section
4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include
translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a
translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also
include the original English version of this License and the original versions of those notices and disclaimers. In case of a
disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will
prevail.
If a section in the Document is Entitled Acknowledgements, Dedications, or History, the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.

B.10

Termination

You may not copy, modify, sublicense, or distribute the Document except as expressly provided for under this License. Any
other attempt to copy, modify, sublicense or distribute the Document is void, and will automatically terminate your rights under
this License. However, parties who have received copies, or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.

B. GNU Free Documentation License

B.11

123

Future Revisions Of This License

The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time.
Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
See http://www.gnu.org/copyleft/.
Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered
version of this License or any later version applies to it, you have the option of following the terms and conditions either of
that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the
Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the
Free Software Foundation.

B.12

ADDENDUM: How to use this License for your documents

To use this License in a document you have written, include a copy of the License in the document and put the following copyright
and license notices just after the title page:
S AMPLE I NVARIANT S ECTIONS LIST
Copyright (c) YEAR YOUR NAME. Permission is granted to copy, distribute and/or modify this document under
the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software
Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is
included in the section entitled GNU Free Documentation License.
If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the with...Texts. line with this:
S AMPLE I NVARIANT S ECTIONS LIST
with the Invariant Sections being LIST THEIR TITLES, with the Front-Cover Texts being LIST, and with the BackCover Texts being LIST.
If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit
the situation.
If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your
choice of free software license, such as the GNU General Public License, to permit their use in free software.

124

Gwyddion user guide

Chapter 7

Index
_
3D
choosing default material, 27
data display, 26
material editing, 27
A
angle distribution
1D, 54
2D, 58
angle measurement, 35
arithmetic on data, 75
aspect ratio, 18
resampling to square pixels, 34
autocorrelation function
one-dimensional, 55
radial, 55
two-dimensional, 55
B
background subtraction, 40
boundary length calculation, 65
C
Canny
edge detection, 44
checker pattern removal filter, 42
color
mapping, 21
color map
choosing default, 22
editing, 22
conservative denoise filter, 42
correlation search, 77
critical dimension, 80
cropping, 34
cross-correlation, 77
curvature, 41
D
data browser, 15
dechecker filter, 42
defect correction, 46
detail image immersion, 76
dilation filter, 42
distance measurement, 35
Distance tool, 35
distortion in xy plane
affine, 51
polynomial, 51
DOS spectrum, 81
drift compensation, 50

E
edge detection, 44
erosion filter, 42
extending, 34
F
facet analysis, 59
facet leveling, 39
file, 17, 18, 92
flipping
horizontally, 34
vertically, 34
Fourier transform, 67
1D filtering, 50
2D filtering, 50
fractal dimension, 71
fractal interpolation, 47
function fitting, 79
G
gaussian filter, 42
gradient filters, 44
grain leveling, 66
grain marking, 61
edge-based, 61
threshold, 61
Otsus method, 61
watershed, 62
H
height distribution, 54
height-height correlation function, 56
I
inclination
calculation, 35
reading on data, 35
interpolation, 37
of data under mask, 47
J
joining images, 76
K
Keyboard shortcuts
custom, 92
standard, 91
Kuwahara filter, 42
L
Laplacian of Gaussians, 44
leveling
along paths, 48

B. GNU Free Documentation License

mean plane subtraction, 39
three-point, 39
to align facets horizontally, 39
line correction, 48
local contrast improvement, 45
local nonlinearity edge detection, 45
local rank transform, 46
logarithmic scale, 46
M
mask, 22
maximum
filter, 42
of a data area, 53
of a grain, 64
of a row/column, 58
on a grain boundary, 64
mean
filter, 42
of a data area, 53
of a grain, 64
of a row/column, 58
median
background removal, 41
filter, 42
of a data area, 53
of a grain, 64
of a row/column, 58
merging images, 76
minimum
filter, 42
of a data area, 53
of a grain, 64
of a row/column, 58
on a grain boundary, 64
Minkowski functionals, 57
mutual crop of two images, 77
N
neural network, 78
application, 79
training, 78
number of grains, 63
O
outliers correction, 48
P
path leveling, 48
plane leveling, 39
polynomial background, 40
power spectral density function
one-dimensional, 56
radial, 57
section, 67
presentation, 22, 43
Prewitt filter, 44
profile extraction, 36
R

125
Read Value tool, 35
remove non-intersecting areas, 77
resampling, 34
rms
edge detection, 45
of a data area, 53
of a row/column, 58
rms edge edge detection, 45
rotation
by arbitary angle, 34
by multiple of 90, 34
rotation correction, 49
rotation leveling, 40
roughness
ISO parameters, 59
Row/Column Statistics tool, 58
S
scaling, 34
scars correction, 46
shading, 44
slope distribution (2D), 58
slope measurement, 35
Sobel filter, 44
spectra, 27
sphere fitting, 41
Statistical Functions tool, 54
Statistical Quantities tool, 53
step detection, 44
strokes correction, 46
surface area calculation, 53
T
three-point leveling, 39
tilt, 34
tip
certainty map, 75
convolution, 74
deconvolution, 74
modelling, 73
Toolbox, 14, 19, 101
U
unrotate, 49
V
value inversion, 34
volume calculation, 66
volume data, 28
W
wavelet transform, 68
continuous, 71
discrete, 69
X
xy denoising, 52
XYZ data, 32
Z
zero crossing edge detection, 44