Gwyddion user guide Petr Klapetek, David Necas,ˇ and Christopher Anderson This guide is a work in progress. ii Gwyddion user guide Copyright © 2004–2007, 2009–2011 Petr Klapetek, David Necas,ˇ 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 1.1 Motivation . .1 1.2 Licensing . .1 2 Installation 2 2.1 Linux/Unix Packages . .2 2.2 MS Windows Packages . .2 2.3 Build Dependencies . .3 2.4 Compilation on Linux/Unix . .4 Quick Instructions . .4 Source Unpacking . .4 Configuration . .5 Configuration tweaks . .5 Compilation . .6 Installation . .6 Running . .6 Deinstallation . .7 RPM Packages . .7 2.5 MacOSX.......................................................7 Preparation . .7 MacPorts . .7 Fink..........................................................8 Running . .8 2.6 Cross-Compiling for MS Windows . .8 Setup .........................................................9 Base MinGW32 Packages . .9 Wine .....................................................9 NSIS .....................................................9 Extra MinGW32 Packages . .9 Support scripts . 10 Compilation . 10 Running Under Wine . 10 2.7 Subversion Checkout, Development . 11 MSWindows ..................................................... 12 3 Getting Started 13 3.1 Main Window . 13 3.2 Data Browser . 14 Controlling the Browser . 14 Channels . 15 Graphs......................................................... 15 Spectra . 15 3.3 Managing Files . 15 File Loading . 16 File Merging . 16 File Saving . 16 Document History . 17 3.4 Data Window . 17 3.5 Graph Window . 18 3.6 Tools.......................................................... 18 iv Gwyddion user guide 3.7 False Color Mapping . 20 Color Range Tool . 20 Color Gradient Editor . 21 3.8 Presentations and Masks . 21 Presentations . 21 Masks......................................................... 21 Working with Masks . 22 Mask Editor Tool . 22 MarkWith....................................................... 23 3.9 Selections . 23 Selection Manager . 24 3.10 OpenGL 3D Data Display . 25 Basic Controls . 25 Full Controls . 25 Saving Images . 26 OpenGL Material Editor . 26 3.11 Single Point Spectra . 26 Point Spectroscopy Tool . 26 3.12 Metadata . 27 3.13 Raw Data File Import . 27 Information . 28 Data Format . 28 Presets . 29 3.14 Specific Data Import . 29 Graphics Formats . 29 Graph Curves . 29 XYZData....................................................... 29 3.15 Plug-ins . 30 4 Data Processing and Analysis 31 4.1 Basic Operations . 31 Basic 2D Data Operations . ..