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annotate macros.xml @ 0:72deb053b5a5 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 3e41869cdb6ad4c9a60a4b60dcf9bb4a40955cfa-dirty"
author ximgchess
date Sat, 21 Nov 2020 03:34:48 +0000
parents
children a0be4e3aa66d
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.8.0</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <xml name="citations">
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10 <citations>
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11 <citation type="doi">10.1016/j.matchar.2020.110366</citation>
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12 <yield />
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13 </citations>
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14 </xml>
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15
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16 <token name="@CMD_IMPORTS@">
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17 #import re
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18 #import yaml
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19
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20 #set global $img_panel_dict = dict()
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21 #if $detector.panel_assignment == 'panel_table'
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22 #set $fh = open(str($detector.image_panel_table),'r')
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23 #for $line in $fh:
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24 #set $fields = $line.strip().split('\t')
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25 #silent $img_panel_dict[$fields[0]] = $fields[1]
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26 #end for
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27 #end if
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28 #set global $panels = $yaml.safe_load(open(str($instrument),'r'))['detectors'].keys()
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29 #def identifier_or_name($input1)
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30 #if hasattr($input1, 'element_identifier')
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31 #return $input1.element_identifier
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32 #elif hasattr($input1, 'name')
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33 #return $input1.name
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34 #else
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35 #return str($input1)
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36 #end if
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37 #end def
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38 #def clean($name1)
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39 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](npz|hexrd|yml|dat|out)$','', $name1.split()[-1]))
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40 #return $name_clean
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41 #end def
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42 #def ln_name($ds,$ext)
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43 #set $lname = "%s.%s" % ($clean($identifier_or_name($ds)),$ext)
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44 #return $lname
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45 #end def
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46 #def get_panel($img_input):
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47 #set $img_name = $identifier_or_name($img_input)
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48 #if $img_panel_dict and $img_name in $img_panel_dict:
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49 #return $img_panel_dict[$img_name]
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50 #end if
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51 #for $p in $panels:
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52 #if $p in $img_name:
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53 #return $p
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54 #end if
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55 #end for
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56 #return $img_name
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57 #end def
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58 </token>
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59
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60 <xml name="common_config" token_multiple_inputs="true" >
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61 <param name="inputs" type="data" format="hexrd.npz" multiple="true" label="Image series frame-cache"/>
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62 <conditional name="detector">
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63 <param name="panel_assignment" type="select" label="Assign detector panel to images">
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64 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
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65 <option value="panel_table">Input a table with image panels assignments</option>
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66 </param>
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67 <when value="infer_from_name"/>
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68 <when value="panel_table">
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69 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
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70 <help>A 2-column table:image dataset name detector panel name</help>
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71 </param>
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72 </when>
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73 </conditional>
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74 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
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75 <param name="material" type="data" format="material.hexrd" label="material"/>
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76 <param name="active_material" type="text" value="" label="active material name">
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77 <validator type="empty_field" />
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78 </param>
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79 </xml>
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80
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81 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
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82 mkdir -p imageseries &&
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83 ln -s '$material' $ln_name($material,'hexrd') &&
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84 ln -s '$instrument' $ln_name($instrument,'yml') &&
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85 #for $input in $inputs
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86 ln -s '$input' imageseries/$ln_name($input,'npz') &&
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87 #end for
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88 ]]>
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89 </token>
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90 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
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91 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
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92 ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') &&
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93 ##mkdir -p analysis &&
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94 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
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95 ]]>
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96 </token>
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97
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98 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token>
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99
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100 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
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101 analysis_name: analysis
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102
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103 multiprocessing: -1
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104
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105 material:
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106 definitions: $ln_name($material,'hexrd')
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107 active: $active_material
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108
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109 instrument: $ln_name($instrument,'yml')
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110
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111 image_series:
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112 format: frame-cache
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113 data:
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114 #for $input in $inputs
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115 - file: imageseries/$ln_name($input,'npz')
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116 args: {}
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117 panel: $get_panel($input) # must match detector key
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118 #end for
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119
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120 ]]></token>
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121
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122 <xml name="find_orientations_config">
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123 <expand macro="common_config" token_multiple_inputs="true" />
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124 <section name="orientation_maps" title="Orientation Maps" expanded="true">
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125 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
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126 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
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127 <param name="active_hkls" type="text" value="" optional="true" label="active hkls">
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128 <validator type="regex" message="">^\d(,\d)*$</validator>
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129 </param>
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130 </section>
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131 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
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132 <section name="search_options" title="Search Options" expanded="true">
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133 <conditional name="search">
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134 <param name="search_type" type="select" label="Specify Search">
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135 <option value="seed_search" selected="true">use seed search</option>
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136 <option value="use_quaternion_grid">use quaternion grid</option>
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137 </param>
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138 <when value="seed_search">
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139 <param name="hkl_seeds" type="text" value="" optional="true" label="hkl seeds">
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140 <validator type="regex" message="">^\d(,\d)*$</validator>
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141 </param>
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142 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
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143 <conditional name="params">
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144 <param name="method" type="select" label="Method">
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145 <option value="label" selected="true">label</option>
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146 <option value="blob_dog">blob_dog</option>
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147 <option value="blob_log">blob_log</option>
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148 </param>
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149 <when value="label">
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150 <param name="filter_radius" type="integer" value="1" min="1" label="label filter radius"/>
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151 <param name="threshold" type="integer" value="1" min="1" label="label threshold"/>
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152 </when>
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153 <when value="blob_dog">
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154 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_dog min_sigma"/>
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155 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_dog max_sigma"/>
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156 <param name="sigma_ratio" type="float" value="1.6" min="0" max="10" label="blob_dog sigma_ratio"/>
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157 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_dog threshold"/>
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158 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_dog overlap"/>
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159 </when>
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160 <when value="blob_log">
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161 <param name="min_sigma" type="float" value="0.5" min="0" max="10" label="blob_log min_sigma"/>
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162 <param name="max_sigma" type="float" value="5.0" min="0" max="10" label="blob_log max_sigma"/>
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163 <param name="num_sigma" type="integer" value="10" min="0" max="20" label="blob_log num_sigma"/>
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164 <param name="threshold" type="float" value="0.01" min="0" max="1.0" label="blob_log threshold"/>
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165 <param name="overlap" type="float" value="0.1" min="0" max="1.0" label="blob_log overlap"/>
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166 </when>
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167 </conditional>
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168 </when>
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169 <when value="use_quaternion_grid">
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170 <param name="quaternion_grid" type="data" format="hexrd.npz" label="quaterion grid file"/>
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171 </when>
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172 </conditional>
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173 </section>
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174 <section name="omega" title="Omega" expanded="true">
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175 <param name="omega_tolerance" type="float" value="1.0" min="0" max="10.0" label="omega tolerance"/>
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176 </section>
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177 <section name="eta" title="eta" expanded="true">
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178 <param name="eta_tolerance" type="float" value="1.0" min="0" max="10.0" label="eta tolerance"/>
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179 <param name="eta_mask" type="float" value="5.0" min="0" max="10.0" label="eta mask"/>
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180 </section>
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181 <section name="clustering" title="Clustering" expanded="true">
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182 <param name="clustering_algorithm" type="select" label="Clustering algorithm">
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183 <option value="dbscan" selected="true">dbscan</option>
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184 <option value="sph-dbscan">sph-dbscan</option>
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185 <option value="ort-dbscan">ort-dbscan</option>
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186 <option value="fclusterdata">fclusterdata (won't work for large problems)</option>
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187 </param>
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188 <param name="clustering_radius" type="float" value="1.0" min="0" max="10" label="clustering radius"/>
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189 <param name="clustering_completeness" type="float" value="0.85" min="0" max="1" label="clustering completeness threshold"/>
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190 </section>
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191 <!--
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192 -->
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193 </xml>
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194
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195 <token name="@FIND_ORIENTATIONS_YML@"><![CDATA[@COMMON_YML@
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196
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197 #set active_hkls = 'all'
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198 #if $orientation_maps.active_hkls:
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199 #set active_hkls = '[' + str($orientation_maps.active_hkls) + ']'
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200 #end if
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201 find_orientations:
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202 orientation_maps:
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203 # A file name must be specified. If it doesn't exist, one will be created
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204 file: null
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205
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206 threshold: $orientation_maps.threshold
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207 bin_frames: $orientation_maps.bin_frames # defaults to 1
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208
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209 # "all", or a list of hkl orders used to find orientations
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210 # defaults to all orders listed in the material definition
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211 active_hkls: $active_hkls
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212
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213 # either search full quaternion grid, or seed search based on sparse
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214 # orientation maps. For input search space:
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215 #
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216 # use_quaternion_grid: some/file/name
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217 #
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218 # otherwise defaults to seeded search
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219 #if $search_options.search.search_type == 'use_quaternion_grid'
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220 use_quaternion_grid:
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221 #elif $search_options.search.search_type == 'seed_search'
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222 #set hkl_seeds = '[' + str($search_options.search.hkl_seeds) + ']'
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223 seed_search: # this section is ignored if use_quaternion_grid is defined
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224 hkl_seeds: $hkl_seeds # hkls ids to use, must be defined for seeded search
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225 fiber_step: $search_options.search.fiber_step # degrees, defaults to ome tolerance
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226 # Method selection:
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227 # Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
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228 # Each has its own parameter names, examples below.
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229 #
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230 method:
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231 #if $search_options.search.params.method == 'label'
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232 label:
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233 filter_radius: $search_options.search.params.filter_radius
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234 threshold: $search_options.search.params.threshold
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235 #elif $search_options.search.params.method == 'blob_dog'
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236 blob_dog:
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237 min_sigma: $search_options.search.params.min_sigma
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238 max_sigma: $search_options.search.params.max_sigma
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239 sigma_ratio: $search_options.search.params.sigma_ratio
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240 threshold: $search_options.search.params.threshold
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241 overlap: $search_options.search.params.overlap
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242 #elif $search_options.search.params.method == 'blob_log'
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243 blob_log:
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244 min_sigma: $search_options.search.params.min_sigma
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245 max_sigma: $search_options.search.params.max_sigma
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246 num_sigma: $search_options.search.params.num_sigma
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247 threshold: $search_options.search.params.threshold
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248 overlap: $search_options.search.params.overlap
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249 #end if
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250 # this is the on-map threshold using in the scoring
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251 # defaults to 1
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252 #end if
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253 threshold: $on_map_threshold
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254
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255 omega:
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256 tolerance: $omega.omega_tolerance # in degrees, defaults to 2x ome step
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257
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258 eta:
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259 tolerance: $eta.eta_tolerance # in degrees, defaults to 2x ome step
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260 mask: $eta.eta_mask # degrees, mask angles close to ome rotation axis, defaults to 5
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261
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262 clustering:
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263 # algorithm choices are
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264 # sph-dbscan
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265 # ort-dbscn
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266 # dbscan <default>
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267 # fclusterdata; this is a fallback and won't work for large problems
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268 algorithm: $clustering.clustering_algorithm
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269 radius: $clustering.clustering_radius
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270 completeness: $clustering.clustering_completeness
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271
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272 ]]></token>
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273
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274 <xml name="fit_grains_config">
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275 <expand macro="common_config" token_multiple_inputs="true"/>
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276 <param name="ome_map" type="data" format="hexrd.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
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277 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/>
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278 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
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279 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
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280 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
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281 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
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282 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
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283 <repeat name="tolerance_lists" title="Tolerance values" min="1">
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284 <param name="tth" type="float" value="" min="0" label="tth"/>
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285 <param name="eta" type="float" value="" min="0" label="eta"/>
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286 <param name="omega" type="float" value="" min="0" label="omega"/>
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287 </repeat>
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288 <param name="refit" type="text" value="1" label="refit">
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289 <validator type="regex" message="">^\d(,\d)*$</validator>
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290 </param>
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291 <param name="tth_max" type="float" value="14.25" label="tth_max"/>
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292 </section>
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293 </xml>
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294
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295 <token name="@FIT_GRAINS_YML@"><![CDATA[@COMMON_YML@
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296 find_orientations:
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297 orientation_maps:
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298 # A file name must be specified. If it doesn't exist, one will be created
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299 file: $ln_name($ome_map,'npz')
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300
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301 fit_grains:
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302 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
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303
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304 # estimate: null
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305
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306 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
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307
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308 threshold: $threshold
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309
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310 #set $tth = []
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311 #set $eta = []
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312 #set $omega = []
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313 #set refit = '[' + str($tolerance.refit) + ']'
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314 #for $tol in $tolerance.tolerance_lists
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315 $tth.append(float($tol.tth))
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316 $eta.append(float($tol.eta))
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317 $omega.append(float($tol.omega))
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318 #end for
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319 tolerance:
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320 tth: $tth # tolerance lists must be identical length
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321 eta: $eta
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322 omega: $omega
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323
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324 refit: $refit
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325 tth_max: $tolerance.tth_max # true, false, or a non-negative value, defaults to true
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326 ]]></token>
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327
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328 </macros>