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--- processing:compare-grain-orientations [2019/02/18 10:11]
127.0.0.1 external edit
+++ processing:compare-grain-orientations [2019/12/03 13:39] (current)
jeff [Usage]
@@ Line 22: / Line 22: @@
   file2                 second grain file, matched against the previous file
                         (gff or GrainSpotter output file, based on extension)
-optional arguments:
-  -h, --help            show this help message and exit
   -c {1,2,3,4,5,6,7}, --crystal_system {1,2,3,4,5,6,7}
                         Crystal system. Can be one of the following 1:
                         Triclinic 2: Monoclinic 3: Orthorhombic 4: Tetragonal
 : Trigonal 6: Hexagonal 7: Cubic
+optional arguments:
+  -h, --help            show this help message and exit
   -o OUTPUT_STEM, --output_stem OUTPUT_STEM
                         Stem for output files. Default is comp
@@ Line 118: / Line 117: @@
 In addition, the ''verbose'' option allows you to save a large file in which all grains from files 1 and 2 are compared to each other.
+===== Known issues =====
+==== Error: Found more than 1 pair for grain xy. Something is wrong ====
+Before it actually compares the two lists of grains, the script checks whether there are multiples within the same list (e.g. a certain grain appears more than once in the same list) and removes the multiple. So whenever the script finds a multiple in a later step it throws an error and stops because it assumes there must be something wrong.
+=== Cause of the issue ===
+However, this may actually happen, even if there is nothing wrong. Here is an example how this is possible:
+Let's assume our script considers grains identical if they have a misorientation of less than 2.0°. Going through the lists before the actual comparison throws out two lists of 100 grains each. Let's assume grain 44 and grain 66 of list A have a misorientation of 3.4°. This means they are not considered identical. Let's further assume there is a grain in list B (grain 20) which has a misorientation to grain 44 (list A) of 1.6° and also a misorientation of 1.9° to grain 66 (list A). This can actually happen if grain 20 lies roughly (or exactly) on the half-way rotation between grain 44 and 66.
+.7° is less than 2.0° so the script considers grain 20 (list A) and grain 44 (list B) identical. It also considers grain 20 (list A) and grain 66 (list B) identical. But at the beginning it considered grain 44 and grain 66 as NOT identical. The script is confused, throws the error ''Found more than 1 pair for grain 20. Something is wrong'' and stops.
+=== How to solve it ===
+Possibility 1: Delete the grain(s) with the issue from the list. (This is not a nice thing to do though.)
+Possibility 2: Decrease the maximum misorientation. (This is a better way.)\\
+The default value is 2.0°. Decrease it a bit and try again. In this example, decreasing it to 1.8° would already be enough:
+  * Grain 44 and grain 66 would still be considered not identical (misorientation = 3.4°).
+  * Grain 20 and grain 44 would still be considered identical (misorientation = 1.6°).
+  * But grain 20 and grain 66 would not be considered identical anymore because their misorientation of 1.9° is now above the threshold.
+During this process, you might lose other grains which were matching before but do not match anymore because of the decreased misorientation threshold.

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