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changeset 10:a35bda7ed678 draft default tip

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"
author ximgchess
date Thu, 07 Jul 2022 01:53:44 +0000
parents e67ad9795525
children
files hexrd_find_orientations.xml hexrd_fit_grains.xml macros.xml
diffstat 3 files changed, 129 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/hexrd_find_orientations.xml	Wed Feb 02 16:40:24 2022 +0000
+++ b/hexrd_find_orientations.xml	Thu Jul 07 01:53:44 2022 +0000
@@ -28,19 +28,24 @@
         <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
         <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
         <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
-        <data name="score_orientations" format="npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
-        <data name="accepted_orientations" format="tabular" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
+        <data name="score_orientations" format="hexrd.scored_orientations.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
+        <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
         <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
     </outputs>
     <tests>
+        <!-- Test-1 single_GE -->
         <test>
-            <param name="inputs" ftype="hexrd.images.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
+            <param name="analysis_name" value="ruby"/>
+            <param name="inputs" ftype="hexrd.images.npz" value="single_GE/RUBY_0000-fc_GE.npz,single_GE/RUBY_0001-fc_GE.npz,single_GE/RUBY_0002-fc_GE.npz,single_GE/RUBY_0003-fc_GE.npz,single_GE/RUBY_0004-fc_GE.npz,single_GE/RUBY_0005-fc_GE.npz"/>
             <conditional name="detector">
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
-            <param name="instrument" ftype="yaml" value="ge_detector.yml"/>
-            <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
+            <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
             <param name="active_material" value="ruby"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
             <section name="orientation_maps">
                 <param name="threshold" value="25"/>
                 <param name="bin_frames" value="1"/>
@@ -72,10 +77,62 @@
             </section>
             <output name="grains">
                 <assert_contents>
-                    <has_text text="6.6655" />
+                    <has_text text="6.670" />
                 </assert_contents>
             </output>
         </test>
+        <!-- Test-2 multiruby_dexelas -->
+        <test>
+            <param name="analysis_name" value="ruby"/>
+            <param name="inputs" ftype="hexrd.images.npz" value="multiruby_dexelas/mruby-0129_000004_ff1_000012-cachefile.npz,multiruby_dexelas/mruby-0129_000004_ff2_000012-cachefile.npz"/>
+            <conditional name="detector">
+                <param name="panel_assignment" value="infer_from_name"/>
+            </conditional>
+            <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
+            <param name="active_material" value="ruby"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
+            <section name="orientation_maps">
+                <param name="threshold" value="250"/>
+                <param name="bin_frames" value="1"/>
+                <param name="active_hkls" value="0,1,2,3,4,5"/>
+            </section>
+            <section name="search_options">
+                <conditional name="search">
+                    <param name="search_type" value="seed_search"/>
+                    <param name="hkl_seeds" value="0,1,2"/>
+                    <param name="fiber_step" value="0.5"/>
+                    <conditional name="params">
+                        <param name="method" value="blob_log"/>
+                            <param name="min_sigma" value="0.5"/>
+                            <param name="max_sigma" value="5.0"/>
+                            <param name="num_sigma" value="10"/>
+                            <param name="threshold" value="0.01"/>
+                            <param name="overlap" value="0.1"/>
+                    </conditional>
+                </conditional>
+            </section>
+            <section name="omega">
+                <param name="omega_tolerance" value="1.0"/>
+            </section>
+            <section name="eta">
+                <param name="eta_tolerance" value="1.0"/>
+                <param name="eta_mask" value="5.0"/>
+            </section>
+            <section name="clustering">
+                <param name="clustering_algorithm" value="dbscan"/>
+                <param name="clustering_radius" value="1.0"/>
+                <param name="clustering_completeness" value="0.85"/>
+            </section>
+            <output name="grains">
+                <assert_contents>
+                    <has_text text="6.94" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **HEXRD find-orientations**
--- a/hexrd_fit_grains.xml	Wed Feb 02 16:40:24 2022 +0000
+++ b/hexrd_fit_grains.xml	Thu Jul 07 01:53:44 2022 +0000
@@ -30,17 +30,22 @@
         </collection>
     </outputs>
     <tests>
+        <!-- Test-1 single_GE -->
         <test>
-            <param name="inputs" ftype="hexrd.iamges.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
+            <param name="analysis_name" value="ruby"/>
+            <param name="inputs" ftype="hexrd.images.npz" value="single_GE/RUBY_0000-fc_GE.npz,single_GE/RUBY_0001-fc_GE.npz,single_GE/RUBY_0002-fc_GE.npz,single_GE/RUBY_0003-fc_GE.npz,single_GE/RUBY_0004-fc_GE.npz,single_GE/RUBY_0005-fc_GE.npz"/>
             <conditional name="detector">
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
-            <param name="instrument" ftype="yaml" value="ge_detector.yml"/>
-            <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
+            <param name="instrument" ftype="hexrd.yml" value="single_GE/ge_detector.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="single_GE/materials.h5"/>
             <param name="active_material" value="ruby"/>
-            <param name="ome_map" ftype="hexrd.eta_ome.npz" value="analysis_ruby_eta-ome_maps.npz"/>
-            <param name="accepted_orientations" ftype="tabular" value="accepted_orientations_analysis_ruby.dat"/>
-            <param name="grains_estimate" ftype="tabular" value="grains.out"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
+            <param name="ome_map" ftype="hexrd.eta_ome.npz" value="single_GE/analysis_ruby_eta-ome_maps.npz"/>
+            <param name="accepted_orientations" ftype="hexrd.accepted_orientations" value="single_GE/accepted_orientations_analysis_ruby.dat"/>
+            <param name="grains_estimate" ftype="tabular" value="single_GE/grains_estimate.out"/>
             <param name="do_fit" value="true"/>
             <param name="npdiv" value="2"/>
             <param name="threshold" value="25"/>
@@ -49,19 +54,57 @@
                     <param name="tth" value="0.25"/>
                     <param name="eta" value="3.0"/>
                     <param name="omega" value="2.0"/>
-                    <param name="refit" value="1"/>
                 </repeat>
                 <repeat name="tolerance_lists">
                     <param name="tth" value="0.20"/>
                     <param name="eta" value="2.0"/>
                     <param name="omega" value="1.0"/>
-                    <param name="refit" value="1"/>
                 </repeat>
+                <param name="refit" value="1,1"/>
                 <param name="tth_max" value="14.25"/>
             </section>
             <output name="grains">
                 <assert_contents>
-                    <has_text text="6.6655" />
+                    <has_text text="6.69" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-2 multiruby_dexelas -->
+        <test>
+            <param name="analysis_name" value="ruby"/>
+            <param name="inputs" ftype="hexrd.images.npz" value="multiruby_dexelas/mruby-0129_000004_ff1_000012-cachefile.npz,multiruby_dexelas/mruby-0129_000004_ff2_000012-cachefile.npz"/>
+            <conditional name="detector">
+                <param name="panel_assignment" value="infer_from_name"/>
+            </conditional>
+            <param name="instrument" ftype="hexrd.yml" value="multiruby_dexelas/dexelas_id3a_20200130.yml"/>
+            <param name="material" ftype="hexrd.materials.h5" value="multiruby_dexelas/materials.h5"/>
+            <param name="active_material" value="ruby"/>
+            <param name="dmin" value="0.7"/>
+            <param name="tth_width" value="0.2"/>
+            <param name="min_sfac_ratio" value="0.05"/>
+            <param name="ome_map" ftype="hexrd.eta_ome.npz" value="multiruby_dexelas/mruby_monolithic_eta-ome_maps.npz"/>
+            <param name="accepted_orientations" ftype="hexrd.accepted_orientations" value="multiruby_dexelas/accepted_orientations_analysis_ruby.dat"/>
+            <param name="grains_estimate" ftype="tabular" value="multiruby_dexelas/grains_estimate.out"/>
+            <param name="do_fit" value="true"/>
+            <param name="npdiv" value="4"/>
+            <param name="threshold" value="25"/>
+            <section name="tolerance">
+                <repeat name="tolerance_lists">
+                    <param name="tth" value="0.25"/>
+                    <param name="eta" value="3.0"/>
+                    <param name="omega" value="2.0"/>
+                </repeat>
+                <repeat name="tolerance_lists">
+                    <param name="tth" value="0.20"/>
+                    <param name="eta" value="2.0"/>
+                    <param name="omega" value="1.0"/>
+                </repeat>
+                <param name="refit" value="3,1"/>
+                <param name="tth_max" value="true"/>
+            </section>
+            <output name="grains">
+                <assert_contents>
+                    <has_text text="0.98" />
                 </assert_contents>
             </output>
         </test>
--- a/macros.xml	Wed Feb 02 16:40:24 2022 +0000
+++ b/macros.xml	Thu Jul 07 01:53:44 2022 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.8.18</token>
+    <token name="@TOOL_VERSION@">0.8.19</token>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">21.09</token>
+    <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
@@ -60,6 +60,9 @@
     </token>
 
     <xml name="common_config" token_multiple_inputs="true" >
+        <param name="analysis_name" type="text" value="analysis" label="analysis name">
+            <validator type="empty_field" />
+        </param>
         <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
         <conditional name="detector">
             <param name="panel_assignment" type="select" label="Assign detector panel to images">
@@ -73,7 +76,7 @@
                 </param>
             </when>
         </conditional>
-        <param name="instrument" type="data" format="yaml" label="instrument"/>
+        <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
         <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
         <param name="active_material" type="select" label="active material name">
             <options>
@@ -101,7 +104,9 @@
     </token>
     <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
-ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') &&
+## hexrd looks for file named: accepted_orientations_{analysis_id}_{active_material}.dat
+#set $accepted_orientations_name = 'accepted_orientations_analysis_' + str($active_material) + '.dat'
+ln -s '$accepted_orientations' '$accepted_orientations_name' &&
 ##mkdir -p analysis &&
 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
 ]]>
@@ -301,7 +306,7 @@
     <xml name="fit_grains_config">
         <expand macro="common_config" token_multiple_inputs="true"/>
         <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
-        <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/>
+        <param name="accepted_orientations" type="data" format="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/>
         <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
         <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
         <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
@@ -313,7 +318,7 @@
                 <param name="omega" type="float" value="" min="0" label="omega"/>
             </repeat>
             <param name="refit" type="text" value="1" label="refit" help="float values separated by commas">
-                <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)*$</validator>
+                <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)+$</validator>
             </param>
             <conditional name="max_tth">
                 <param name="tth_max_value" type="select" label="Set tth_max">
@@ -345,7 +350,8 @@
 #set $tth = []
 #set $eta = []
 #set $omega = []
-#set $refit = '[' + str($tolerance.refit) + ']'
+## #set $refit_tol = str($tolerance.refit)
+## #set $refit = '[' + $refit_tol + ']'
 #for $tol in $tolerance.tolerance_lists
 #silent $tth.append(float($tol.tth))
 #silent $eta.append(float($tol.eta))
@@ -356,7 +362,7 @@
     eta: $eta
     omega: $omega
 
-  refit: $refit
+  refit: [${tolerance.refit}]
   #if $tolerance.max_tth.tth_max_value == 'entered':
   tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
   #else