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--- software:grainspotter [2018/06/23 10:47] – matthias
+++ software:grainspotter [2019/09/04 11:38] (current) – smerkel
@@ Line 1: / Line 1: @@
 ====== GrainSpotter ======
+GrainSpotter is a software which looks for grains in a 2D diffraction image. It was developed by S. Schmidt, Technical University of Denmark. See the publication for more information:
-GrainSpotter is a software which looks for grains in a 2D diffraction image.
+Søren Schmidt\\
+//GrainSpotter//: a fast and robust polycrystalline indexing algorithm\\
+J. Appl. Cryst. (2014). **47**, 276-284\\
+https://doi.org/10.1107/S1600576713030185
-To run it, you need a file with the ending //.ini//. When you perform a simulation with [[software:polyxsim|PolyXSim]], it should automatically create such a file. It usually looks like this:
+===== Installing GrainSpotter =====
-    spacegroup 136                       ! spacegroup [space group nr]
+==== Necessary Hardware and Software ====
-    !dsrange 0 4.2                       ! dsrange [min max], d-spacing range, multiple ranges can be specified
+First of all, you will need Linux, either as a separate harddrive (with lots of memory space) or as a virtual machine on your Windows/Apple computer. In case you are not familiar with Linux, ask your administrator for help and maybe do an online crash course to learn basic navigation and so on.
-    tthrange 0 25                        ! tthrange [min max], multiple ranges can be specified
-    etarange 0 360                       ! etarange [min max], multiple ranges can be specified
-    domega 0.5                           ! domega [stepsize] in omega, degrees
-    omegarange -28 28                    ! omegarange [min max] degrees, multiple ranges can be specified
-    filespecs g_vectors.gve grains.log   ! filespecs [gvecsfile grainsfile]
-    cuts 5 0.6 0.8                       ! cuts [min_measuments min_completeness min_uniqueness]
-    eulerstep 6                          ! eulerstep [stepsize] : angle step size in Euler space
-    uncertainties 0.1 0.2 .5    	       ! uncertainties [sigma_tth sigma_eta sigma_omega] in degrees
-    nsigmas 2                   	       ! nsigmas [Nsig] : maximal deviation in sigmas
-    !minfracg 0.2                        ! stop search when minfracg (0..1) of the gvectors have been assigned to grains
-    !Nhkls_in_indexing 15		       ! Nhkls_in_indexing [Nfamilies] : use first Nfamilies in indexing
-    random 10000                         ! use randomly chosen orientation seeds #trials
-    !positionfit                         ! fit the position of the grain
+==== Installation ====
+You have basically two options for getting GrainSpotter. One is with the help of Anaconda, or from the source.
-Explanations of the .ini file:\\
+=== Installation with Anaconta ===
-|...||
-|cut_first number|grain is chosen if there are at least this amount of peaks per grain|
+First of all, get yourself Anaconda: [[https://www.anaconda.com/download/#linux]]
-|cut_second number|grain is chosen if there are at least this fraction of the expected peaks present|
-|cut_third number|put in any number|
+Then go to the [[https://anaconda.org/|Anaconda Cloud]] with your browser and search the cloud for //grainspotter//. Then click on //Files// and download the Linux version. Unpack it to a directory of your choice.
+Go back to your browser and click on //Conda//. There is a short code which is necessary to install GrainSpotter. It should be something like ''conda install -c fable grainspotter''
+Copy the code to your Konsole and follow the installation instructions.
+=== Installation from the source code ===
+The installation requires a C compiler installed in your system.
+  - Download the GrainSpotter source code from [[https://sourceforge.net/p/fable/code/HEAD/tree/GrainSpotter/trunk/]],
+  - Move into the folder with GrainSpotter and type ''make'',
+  - Log-in as administrator (root) and type ''make install''.
+It should work out of the box.
+===== Running the software =====
+To run it, you need a file with the ending //.ini//. When you perform a simulation with [[software:polyxsim|PolyXSim]], it should automatically create such a file. For more information on how it should look like click [[fileformat:ini|here]].
+When you think your //.ini// file should be fine, it is time to "spot grains" (at least this is what the software should do according to its name). For this type the following to the Konsole:
+  grainspotter 'some_file_name'.ini
+  or
+  GrainSpotter.0.90 'some_file_name'.ini
+The algorithm produces a //.log// file, a //.spe// file and a //.gve// file.
+===== Manual =====
+There is a brief manual online at [[https://sourceforge.net/p/fable/code/HEAD/tree/GrainSpotter/trunk/doc/]].
+Otherwise, you should have a look at the following pages
+  * [[processing:indexing_with_grainspotter|Grain indexing with GrainSpotter]]
+  * [[processing:complex-multi-phase|In the works: indexing a complex dataset with many phases]]