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--- software:grainspotter [2018/07/06 15:06] – matthias
+++ software:grainspotter [2026/08/10 10:28] (current) – smerkel
@@ Line 13: / Line 13: @@
 ==== Installation ====
-You have basically two options for getting GrainSpotter. One is with the help of Anaconda, the other one I forgot. However, Anaconda is the more convenient one, anyway. So first of all, get yourself Anaconda: [[https://www.anaconda.com/download/#linux]]
+You have basically two options for getting GrainSpotter. One is with the help of Anaconda, or from the source.
-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.
+=== Installation with Anaconta ===
-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 this:
+First of all, get yourself Anaconda: [[https://www.anaconda.com/download/#linux]]
-    conda install -c fable grainspotter
+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.
-===== Running the software =====
+=== Installation from the source code ===
-==== The .ini file ====
+The installation requires a C compiler installed in your system.
-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:
+  - 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''.
-    spacegroup 136                       ! spacegroup [space group nr]
+It should work out of the box.
-    !dsrange 0 4.2                       ! dsrange [min max], d-spacing range, multiple ranges can be specified
-    tthrange 0 25                        ! tthrange [min max], multiple ranges can be specified
+On some machines, the compiling fails because of an undefined function ''my_atan'' in ''src/index/pseudodata.c''. In such case
-    etarange 0 360                       ! etarange [min max], multiple ranges can be specified
+  * open the code for ''src/index/pre_calculation.c''
-    domega 0.5                           ! domega [stepsize] in omega, degrees
+  * copy the code for the ''my_atan'' function, between lines 39 and 50
-    omegarange -28 28                    ! omegarange [min max] degrees, multiple ranges can be specified
+  * replace line 20 in ''src/index/pseudodata.c'' with the lines you copied just above
-    filespecs g_vectors.gve grains.log   ! filespecs [gvecsfile grainsfile]
+  * re-run the ''make''
-    cuts 5 0.6 0.8                       ! cuts [min_measuments min_completeness min_uniqueness]
+  * it should work.
-    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
+===== Running the software =====
-    !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
-You should adjust the .ini file for your specific purposes. Explanations of the .ini file are listed below.
+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]].
-|spacegroup|enter the space group number|
+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:
-|dsrange|...|
-|tthrange
-|cut_first number|grain is chosen if there are at least this amount of peaks per grain|
-|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|
-|
-|
-==== Running the simulation ====
+  grainspotter 'some_file_name'.ini
+  or
+  GrainSpotter.0.90 'some_file_name'.ini
-When you think your .ini file should be fine, you can start with the simulation. For this type the following to the Konsole:
+The algorithm produces a //.log// file, a //.spe// file and a //.gve// file.
-    grainspotter some_file_name.ini
+===== Manual =====
-If you didn't get your GrainSpotter from Anaconda but from somewhere else, the syntax is slightly different:
+There is a brief manual online at [[https://sourceforge.net/p/fable/code/HEAD/tree/GrainSpotter/trunk/doc/]].
-    GrainSpotter.0.90 some_file_name.ini
+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]]