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--- examples:gs_loop_multiphase [2023/12/10 11:49] – smerkel
+++ examples:gs_loop_multiphase [2023/12/10 14:19] (current) – smerkel
@@ Line 12: / Line 12: @@
 This script requires
-  * one g-vector file per phase, experimental g-vectors should be identical for all phases, but the list of computed theoretical g-vectors depends on the unit cell (see [[processing:complex-multi-phase|In the works: indexing a complex dataset with many phases]]),
+  * one g-vector file per phase, experimental g-vectors should be identical for all phases, but the list of computed theoretical g-vectors depends on the unit cell (see [[processing:complex-multi-phase|Indexing a complex dataset with many phases]]),
   * some basic information on each phase (space group number, etc) and experiment wavelength,
   * to update the GrainSpotter parameters (tthrange, etarange, domega, omegarange, etc)*
@@ Line 21: / Line 21: @@
 The number of times to run GrainSpotter, number of parameters to try, etc, is not limited. In some cases, with have run GrainSpotter up to 100 times, with 100000 random trials at each run. This is a test for 10 million configurations.
+What it will do
+  - Create a folder for the indexing (Indexing-1, and then -2, etc if you request the loop to be run multiple times),
+  - Make a copy of the starting GVE file,
+  - Run the GrainSpotter iterations, saving a GrainSpotter output file for each iteration, and removing assigned experimental g-vectors from the GVE file (for all phases)
+  - Merge the indexed grains into a master ''merge-XXX-grains.log'' for each phase,
+  - Extract a list of Euler angles for those grains into ''merge-XXX-grains-euler.txt'' so you can plot the orientations of the indexed grains,
+  - Saving list of indexed g-vectors for each phase,
+  - Save the list of remaining g-vectors,
+  - Provide some indexing statistics using the script described in the section on how to [[evaluation:evaluate_indexing_statistics|evaluate your indexing performance]]
 ===== The loop =====
-You wanted it?! Here is the source code for the loop above
+You wanted it?! Here is the source code for the loop above.
+If you find that this script is useful for you, please cite one of the relevant [[http://timeless.texture.rocks/publications/ |TIMEleSS publications]] for which this script was slowly developped:
+  * One of the 2 Ledoux et al (2023) publications on olivine and wadsleyite,
+  * Gay et al (2023) on transformation microsctructures in pyrolite
+  * Upcoming (I hope) Gay et al publication on pyrolite deformation.
 <code bash gsLoop-NPhases.sh>
 #!/bin/bash
+#
+# This is part of the TIMEleSS tools
+# http://timeless.texture.rocks/
+#
+# Copyright (C) S. Merkel, Universite de Lille, France
+#
+# 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.
+#
+# Please cite one of the relevant TIMEleSS publications if you find that was of any use
+#
 # Number of phases