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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 944c00504583f201b006fb01f7e19fd98fca4a29"
author ximgchess
date Wed, 05 Jan 2022 14:14:56 +0000
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-1:000000000000 0:3316ac4fd07b
1 <macros>
2 <token name="@TOOL_VERSION@">0.8.12</token>
3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">21.09</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
8 <yield/>
9 </requirements>
10 </xml>
11 <xml name="citations">
12 <citations>
13 <citation type="doi">10.1016/j.matchar.2020.110366</citation>
14 <yield />
15 </citations>
16 </xml>
17
18 <token name="@CMD_IMPORTS@">
19 #import re
20 #import yaml
21
22 #set global $img_panel_dict = dict()
23 #if $detector.panel_assignment == 'panel_table'
24 #set $fh = open(str($detector.image_panel_table),'r')
25 #for $line in $fh:
26 #set $fields = $line.strip().split('\t')
27 #silent $img_panel_dict[$fields[0]] = $fields[1]
28 #end for
29 #end if
30 #set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
31 #def identifier_or_name($input1)
32 #if hasattr($input1, 'element_identifier')
33 #return $input1.element_identifier
34 #elif hasattr($input1, 'name')
35 #return $input1.name
36 #else
37 #return str($input1)
38 #end if
39 #end def
40 #def clean($name1)
41 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz|hexrd|yml|dat|out)$','', $name1.split()[-1]))
42 #return $name_clean
43 #end def
44 #def ln_name($ds,$ext)
45 #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
46 #return $lname
47 #end def
48 #def get_panel($img_input):
49 #set $img_name = $identifier_or_name($img_input)
50 #if $img_panel_dict and $img_name in $img_panel_dict:
51 #return $img_panel_dict[$img_name]
52 #end if
53 #for $p in $panels:
54 #if $p in $img_name:
55 #return $p
56 #end if
57 #end for
58 #return $img_name
59 #end def
60 </token>
61
62 <xml name="common_config" token_multiple_inputs="true" >
63 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
64 <conditional name="detector">
65 <param name="panel_assignment" type="select" label="Assign detector panel to images">
66 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
67 <option value="panel_table">Input a table with image panels assignments</option>
68 </param>
69 <when value="infer_from_name"/>
70 <when value="panel_table">
71 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
72 <help>A 2-column table:image dataset name detector panel name</help>
73 </param>
74 </when>
75 </conditional>
76 <param name="instrument" type="data" format="yaml" label="instrument"/>
77 <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
78 <param name="active_material" type="select" label="active material name">
79 <options>
80 <filter type="data_meta" ref="material" key="materials"/>
81 </options>
82 </param>
83 <param name="dmin" type="float" value="1.0" min="0" max="10" optional="true" label="dmin angstroms" help="used to figure out the maximum sampling for g-vectors default 1.0"/>
84 <param name="tth_width" type="float" value="0.25" min="0" max="10" optional="true" label="tth tolerance in degrees" help="tth_width default 0.25 "/>
85 <param name="min_sfac_ratio" type="float" value="" min="0" max="1" optional="true" label="min percentage of max to exclude" help="min_sfac_ratio min percentage of max |F|^2 to exclude; default None"/>
86 <!--
87 <param name="active_material" type="text" value="" label="active material name">
88 <validator type="empty_field" />
89 </param>
90 -->
91 </xml>
92
93 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
94 mkdir -p imageseries &&
95 ln -s '$material' $ln_name($material,'h5') &&
96 ln -s '$instrument' $ln_name($instrument,'yml') &&
97 #for $input in $inputs
98 ln -s '$input' imageseries/$ln_name($input,'npz') &&
99 #end for
100 ]]>
101 </token>
102 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
103 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
104 ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') &&
105 ##mkdir -p analysis &&
106 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
107 ]]>
108 </token>
109
110 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token>
111
112 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
113 #slurp
114 #set instrument_file = $ln_name($instrument,'yml')
115 analysis_name: analysis
116
117 multiprocessing: -1
118
119 material:
120 definitions: $ln_name($material,'h5')
121 active: $active_material
122 #if $dmin
123 dmin: $dmin # defaults to 1.0 angstrom
124 #end if
125 #if $tth_width
126 tth_width: $tth_width # defaults to 0.25 degrees
127 #end if
128 #if $min_sfac_ratio
129 min_sfac_ratio: $min_sfac_ratio # min percentage of max |F|^2 to exclude; default None
130 #end if
131
132 image_series:
133 format: frame-cache
134 data:
135 #for $input in $inputs
136 - file: imageseries/$ln_name($input,'npz')
137 args: {}
138 panel: $get_panel($input) # must match detector key
139 #end for
140
141 instrument: $instrument_file
142
143 ]]></token>
144
145 <xml name="find_orientations_config">
146 <expand macro="common_config" token_multiple_inputs="true" />
147 <section name="orientation_maps" title="Orientation Maps" expanded="true">
148 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
149 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
150 <!-- active_hkls should be able to be optional="true" -->
151 <param name="active_hkls" type="text" value="" label="active hkl planes">
152 <help>commas separated list of planes, e.g.: 0,1,2,3,4,5</help>
153 <validator type="regex" message="plane indeces separated by commas">^\d(,\d)*$</validator>
154 </param>
155 </section>
156 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
157 <section name="search_options" title="Search Options" expanded="true">
158 <conditional name="search">
159 <param name="search_type" type="select" label="Specify Search">
160 <option value="seed_search" selected="true">use seed search</option>
161 <option value="use_quaternion_grid">use quaternion grid</option>
162 </param>
163 <when value="seed_search">
164 <!-- hkl_seeds should be able to be optional="true" -->
165 <param name="hkl_seeds" type="text" value="" label="hkl seeds">
166 <help>commas separated list of planes, e.g.: 0,1,2 (subset of active hkl planes)</help>
167 <validator type="regex" message="">^\d(,\d)*$</validator>
168 </param>
169 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
170 <conditional name="params">
171 <param name="method" type="select" label="Method">
172 <option value="label" selected="true">label</option>
173 <option value="blob_dog">blob_dog</option>
174 <option value="blob_log">blob_log</option>
175 </param>
176 <when value="label">
177 <param name="filter_radius" type="integer" value="1" min="1" label="label filter radius"/>
178 <param name="threshold" type="integer" value="1" min="1" label="label threshold"/>
179 </when>
180 <when value="blob_dog">
181 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_dog min_sigma"/>
182 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_dog max_sigma"/>
183 <param name="sigma_ratio" type="float" value="1.6" min="0" max="10" label="blob_dog sigma_ratio"/>
184 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_dog threshold"/>
185 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_dog overlap"/>
186 </when>
187 <when value="blob_log">
188 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_log min_sigma"/>
189 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_log max_sigma"/>
190 <param name="num_sigma" type="integer" value="10" min="0" max="20" label="blob_log num_sigma"/>
191 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_log threshold"/>
192 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_log overlap"/>
193 </when>
194 </conditional>
195 </when>
196 <when value="use_quaternion_grid">
197 <param name="quaternion_grid" type="data" format="npz" label="quaterion grid file"/>
198 </when>
199 </conditional>
200 </section>
201 <section name="omega" title="Omega" expanded="true">
202 <param name="omega_tolerance" type="float" value="1.0" min="0" max="10.0" label="omega tolerance"/>
203 </section>
204 <section name="eta" title="eta" expanded="true">
205 <param name="eta_tolerance" type="float" value="1.0" min="0" max="10.0" label="eta tolerance"/>
206 <param name="eta_mask" type="float" value="5.0" min="0" max="10.0" label="eta mask"/>
207 </section>
208 <section name="clustering" title="Clustering" expanded="true">
209 <param name="clustering_algorithm" type="select" label="Clustering algorithm">
210 <option value="dbscan" selected="true">dbscan</option>
211 <option value="sph-dbscan">sph-dbscan</option>
212 <option value="ort-dbscan">ort-dbscan</option>
213 <option value="fclusterdata">fclusterdata (won't work for large problems)</option>
214 </param>
215 <param name="clustering_radius" type="float" value="1.0" min="0" max="10" label="clustering radius"/>
216 <param name="clustering_completeness" type="float" value="0.85" min="0" max="1" label="clustering completeness threshold"/>
217 </section>
218 <!--
219 -->
220 </xml>
221
222 <token name="@FIND_ORIENTATIONS_YML@"><![CDATA[@COMMON_YML@
223
224 #set active_hkls = 'all'
225 #if $orientation_maps.active_hkls:
226 #set active_hkls = '[' + str($orientation_maps.active_hkls) + ']'
227 #end if
228 find_orientations:
229 orientation_maps:
230 # A file name must be specified. If it doesn't exist, one will be created
231 file: null
232
233 threshold: $orientation_maps.threshold
234 bin_frames: $orientation_maps.bin_frames # defaults to 1
235
236 # "all", or a list of hkl orders used to find orientations
237 # defaults to all orders listed in the material definition
238 active_hkls: $active_hkls
239
240 # either search full quaternion grid, or seed search based on sparse
241 # orientation maps. For input search space:
242 #
243 # use_quaternion_grid: some/file/name
244 #
245 # otherwise defaults to seeded search
246 #if $search_options.search.search_type == 'use_quaternion_grid'
247 use_quaternion_grid:
248 #elif $search_options.search.search_type == 'seed_search'
249 #set hkl_seeds = '[' + str($search_options.search.hkl_seeds) + ']'
250 seed_search: # this section is ignored if use_quaternion_grid is defined
251 hkl_seeds: $hkl_seeds # hkls ids to use, must be defined for seeded search
252 fiber_step: $search_options.search.fiber_step # degrees, defaults to ome tolerance
253 # Method selection:
254 # Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
255 # Each has its own parameter names, examples below.
256 #
257 method:
258 #if $search_options.search.params.method == 'label'
259 label:
260 filter_radius: $search_options.search.params.filter_radius
261 threshold: $search_options.search.params.threshold
262 #elif $search_options.search.params.method == 'blob_dog'
263 blob_dog:
264 min_sigma: $search_options.search.params.min_sigma
265 max_sigma: $search_options.search.params.max_sigma
266 sigma_ratio: $search_options.search.params.sigma_ratio
267 threshold: $search_options.search.params.threshold
268 overlap: $search_options.search.params.overlap
269 #elif $search_options.search.params.method == 'blob_log'
270 blob_log:
271 min_sigma: $search_options.search.params.min_sigma
272 max_sigma: $search_options.search.params.max_sigma
273 num_sigma: $search_options.search.params.num_sigma
274 threshold: $search_options.search.params.threshold
275 overlap: $search_options.search.params.overlap
276 #end if
277 # this is the on-map threshold using in the scoring
278 # defaults to 1
279 #end if
280 threshold: $on_map_threshold
281
282 omega:
283 tolerance: $omega.omega_tolerance # in degrees, defaults to 2x ome step
284
285 eta:
286 tolerance: $eta.eta_tolerance # in degrees, defaults to 2x ome step
287 mask: $eta.eta_mask # degrees, mask angles close to ome rotation axis, defaults to 5
288
289 clustering:
290 # algorithm choices are
291 # sph-dbscan
292 # ort-dbscn
293 # dbscan <default>
294 # fclusterdata; this is a fallback and won't work for large problems
295 algorithm: $clustering.clustering_algorithm
296 radius: $clustering.clustering_radius
297 completeness: $clustering.clustering_completeness
298
299 ]]></token>
300
301 <xml name="fit_grains_config">
302 <expand macro="common_config" token_multiple_inputs="true"/>
303 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
304 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/>
305 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
306 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
307 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
308 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
309 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
310 <repeat name="tolerance_lists" title="Tolerance values" min="1">
311 <param name="tth" type="float" value="" min="0" label="tth"/>
312 <param name="eta" type="float" value="" min="0" label="eta"/>
313 <param name="omega" type="float" value="" min="0" label="omega"/>
314 </repeat>
315 <param name="refit" type="text" value="1" label="refit">
316 <validator type="regex" message="">^\d(,\d)*$</validator>
317 </param>
318 <conditional name="max_tth">
319 <param name="tth_max_value" type="select" label="Set tth_max">
320 <option value="true" selected="true">true</option>
321 <option value="false">false</option>
322 <option value="entered">enter value</option>
323 </param>
324 <when value="true"/>
325 <when value="false"/>
326 <when value="entered">
327 <param name="tth_max" type="float" value="14.25" label="tth_max"/>
328 </when>
329 </conditional>
330 </section>
331 </xml>
332
333 <token name="@FIT_GRAINS_YML@"><![CDATA[@COMMON_YML@
334 find_orientations:
335 orientation_maps:
336 # A file name must be specified. If it doesn't exist, one will be created
337 file: $ln_name($ome_map,'npz')
338
339 fit_grains:
340 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
341 # estimate: null
342 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
343 threshold: $threshold
344
345 #set $tth = []
346 #set $eta = []
347 #set $omega = []
348 #set refit = '[' + str($tolerance.refit) + ']'
349 #for $tol in $tolerance.tolerance_lists
350 #silent $tth.append(float($tol.tth))
351 #silent $eta.append(float($tol.eta))
352 #silent $omega.append(float($tol.omega))
353 #end for
354 tolerance:
355 tth: $tth # tolerance lists must be identical length
356 eta: $eta
357 omega: $omega
358
359 refit: $refit
360 #if $tolerance.max_tth.tth_max_value == 'entered':
361 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
362 #else
363 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
364 #end if
365 ]]></token>
366 <token name="@HEXRD_HELP@"><![CDATA[
367 HEXRD_ provides analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
368
369 .. _HEXRD: https://github.com/HEXRD/hexrd
370 ]]></token>
371
372 <token name="@COMMON_INPUTS_HELP@"><![CDATA[
373
374 **INPUTS**
375
376 - imageseries - Detector image files converted to sparse matrix compressed numpy arrays.
377 - instrument - A yaml file that decribes the instrument
378 - materials.hexrd - A "pickled" hexrd Materials object that desscribes the sample material
379 ]]></token>
380 <token name="@FIT_GRAIN_INPUTS_HELP@"><![CDATA[@COMMON_INPUTS_HELP@
381 - analysis eta-ome_maps.npz from find_orientations
382 - accepted_orientations from find_orientations
383
384 ]]></token>
385
386 <token name="@COMMON_OUTPUTS_HELP@"><![CDATA[
387
388 **OUTPUTS**
389
390 - config yaml - parameter for hexrd
391 - log - the hexrd logging output
392 - grains.out
393 ]]></token>
394 <token name="@FIND_ORIENTATIONS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
395 - analysis eta-ome_maps.npz *(used as input for hexrd fit-grains)*
396 - analysis accepted_orientations_analysis.dat *(used as input for hexrd fit-grains)*
397 - analysis scored_orientations_analysis.npz
398 ]]></token>
399 <token name="@FIT_GRAINS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
400 - Collection of spots.out
401 ]]></token>
402
403
404 </macros>