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, 2009–2014 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 Uninstallation . .3 Registry keys . .3 Missing features . .3 Enabling pygwy . .3 2.3 Build Dependencies . .4 2.4 Compilation on Linux/Unix . .5 Quick Instructions . .5 Source Unpacking . .5 Configuration . .5 Configuration tweaks . .6 User’s tweaks . .6 Packager’s tweaks . .6 Developer’s tweaks . .7 Compilation . .7 Installation . .7 Running . .7 Deinstallation . .8 RPM Packages . .8 2.5 MacOSX.......................................................8 Preparation . .8 MacPorts . .8 Fink..........................................................9 Running . .9 2.6 Cross-Compiling for MS Windows . .9 Setup ......................................................... 10 Base MinGW Packages . 10 Gwyddion.net repository . 10 Wine ..................................................... 10 NSIS ..................................................... 10 Python . 11 Support scripts . 11 Compilation . 11 Running under Wine . 12 Cross-compilation of standalone modules . 12 2.7 Compiling on MS Windows using MinGW . 12 2.8 Subversion Checkout, Development . 12 MSWindows ..................................................... 13 3 Getting Started 14 3.1 Main Window . 14 3.2 Data Browser . 15 Controlling the Browser . 15 Channels . 16 iv Gwyddion user guide Graphs......................................................... 16 Spectra . 16 Volume ........................................................ 16 3.3 Managing Files . 16 File Loading . 17 File Merging . 17 File Saving . 17 Document History . 18 3.4 Data Window . 18 3.5 Graph Window . 19 3.6 Tools.......................................................... 19 3.7 False Color Mapping . 21 Color Range Tool . 21 Color Gradient Editor . 22 3.8 Presentations and Masks . 22 Presentations . 22 Masks......................................................... 22 Working with Masks . 23 Mask Editor Tool . 23 MarkWith....................................................... 24 3.9 Selections . 25 Selection Manager . 25 3.10 OpenGL 3D Data Display . 26 Basic Controls . 27 Full Controls . 27 Saving Images . 27 OpenGL Material Editor . 27 3.11 Single Point Spectra . 28 Point Spectroscopy Tool . 28 3.12 Volume Data . 28 3.13 Metadata . ..