# HG changeset patch
# User ximgchess
# Date 1605929688 0
# Node ID 72deb053b5a5f9ee0e59c003ed78ca110a8922c5
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 3e41869cdb6ad4c9a60a4b60dcf9bb4a40955cfa-dirty"
diff -r 000000000000 -r 72deb053b5a5 datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Sat Nov 21 03:34:48 2020 +0000
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diff -r 000000000000 -r 72deb053b5a5 hexrd_find_orientations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hexrd_find_orientations.xml Sat Nov 21 03:34:48 2020 +0000
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+ Process rotation image series to find grain orientations
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+ macros.xml
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diff -r 000000000000 -r 72deb053b5a5 hexrd_fit_grains.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hexrd_fit_grains.xml Sat Nov 21 03:34:48 2020 +0000
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+ Extracts G vectors, grain position and strain
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+ macros.xml
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diff -r 000000000000 -r 72deb053b5a5 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Nov 21 03:34:48 2020 +0000
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+ 0.8.0
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+ hexrd
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+ 10.1016/j.matchar.2020.110366
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+#import re
+#import yaml
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+#set global $img_panel_dict = dict()
+#if $detector.panel_assignment == 'panel_table'
+#set $fh = open(str($detector.image_panel_table),'r')
+#for $line in $fh:
+ #set $fields = $line.strip().split('\t')
+ #silent $img_panel_dict[$fields[0]] = $fields[1]
+#end for
+#end if
+#set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
+#def identifier_or_name($input1)
+ #if hasattr($input1, 'element_identifier')
+ #return $input1.element_identifier
+ #elif hasattr($input1, 'name')
+ #return $input1.name
+ #else
+ #return str($input1)
+ #end if
+#end def
+#def clean($name1)
+ #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz|hexrd|yml|dat|out)$','', $name1.split()[-1]))
+ #return $name_clean
+#end def
+#def ln_name($ds,$ext)
+ #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
+ #return $lname
+#end def
+#def get_panel($img_input):
+ #set $img_name = $identifier_or_name($img_input)
+ #if $img_panel_dict and $img_name in $img_panel_dict:
+ #return $img_panel_dict[$img_name]
+ #end if
+ #for $p in $panels:
+ #if $p in $img_name:
+ #return $p
+ #end if
+ #end for
+ #return $img_name
+#end def
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+ A 2-column table:image dataset name detector panel name
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+ ^\d(,\d)*$
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+ # fclusterdata; this is a fallback and won't work for large problems
+ algorithm: $clustering.clustering_algorithm
+ radius: $clustering.clustering_radius
+ completeness: $clustering.clustering_completeness
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+]]>
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+ ^\d(,\d)*$
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