Mercurial > repos > imgteam > 2d_feature_extraction

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit b8e0b656d417db6e2ad0f187fc3c5afff0c3acd7
author imgteam
date Tue, 06 Jan 2026 09:25:17 +0000
parents 8e3a52b74876
children
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a4bc9dfde846 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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1 <tool id="ip_2d_feature_extraction" name="Extract image features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with scikit-image</description>
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3 <macros>
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4 <import>creators.xml</import>
5
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5 <import>validators.xml</import>
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6 <token name="@TOOL_VERSION@">0.25.2</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
5
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8 <xml name="features">
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9 <param name="features" type="select" label="Available features" multiple="true" display="checkboxes"
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10 help="*) Features marked with an asterisk are only available for 2-D images (not for 3-D images).">
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11 <option value="label" selected="true">Label from the label map</option>
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12 <yield/>
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13 <option value="area">Area</option>
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14 <option value="area_convex">Convex area</option>
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15 <option value="area_filled">Filled area</option>
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16 <option value="axis_major_length">Major axis length</option>
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17 <option value="axis_minor_length">Minor axis length</option>
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18 <option value="bbox">Bounding box</option>
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19 <option value="centroid">Centroid</option>
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20 <option value="eccentricity">Eccentricity*</option>
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21 <option value="equivalent_diameter_area">Equivalent diameter</option>
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22 <option value="euler_number">Euler number</option>
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23 <option value="extent">Extent</option>
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24 <option value="inertia_tensor_eigvals">Inertia tensor eigenvalues</option>
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25 <option value="moments">Moments</option>
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26 <option value="moments_hu">Moments Hu*</option>
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27 <option value="orientation">Orientation*</option>
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28 <option value="perimeter">Perimeter</option>
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29 <option value="solidity">Solidity</option>
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30 </param>
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31 </xml>
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32 <xml name="zarr-isolated-feature-test" tokens="feature">
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33 <test>
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34 <param name="labels" value="input/input13.zarr"/>
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35 <conditional name="setup">
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36 <param name="mode" value="with-intensities"/>
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37 <param name="intensities" value="input/input1_uint8.tiff"/>
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38 <param name="features" value="@FEATURE@"/>
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39 </conditional>
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40 <output name="output" ftype="tabular" value="output/input13-@FEATURE@.tsv" compare="re_match"/>
5
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41 </test>
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42 </xml>
4
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43 </macros>
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44 <creator>
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45 <expand macro="creators/bmcv"/>
5
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46 <expand macro="creators/kostrykin"/>
4
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47 </creator>
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48 <edam_operations>
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49 <edam_operation>operation_3443</edam_operation>
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50 </edam_operations>
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51 <xrefs>
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52 <xref type="bio.tools">scikit-image</xref>
5
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53 <xref type="bio.tools">giatools</xref>
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54 <xref type="bio.tools">galaxy_image_analysis</xref>
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55 <xref type="biii">scikit-image</xref>
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56 </xrefs>
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57 <requirements>
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58 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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59 <requirement type="package" version="2.2.2">pandas</requirement>
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60 <requirement type="package" version="0.7.3">giatools</requirement>
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61 <requirement type="package" version="0.12.2">ome-zarr</requirement>
0
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62 </requirements>
5
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63 <required_files>
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64 <include type="literal" path="2d_feature_extraction.py"/>
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65 </required_files>
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66 <command detect_errors="aggressive"><![CDATA[
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67
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68 python '$__tool_directory__/2d_feature_extraction.py'
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69
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70 #if $labels.extension == "zarr"
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71 --labels '$labels.extra_files_path/$labels.metadata.store_root'
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72 #else
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73 --labels '$labels'
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74 #end if
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75
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76 #if $setup.mode == "with-intensities"
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77 #if $setup.intensities.extension == "zarr"
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78 --intensities '$setup.intensities.extra_files_path/$setup.intensities.metadata.store_root'
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79 #else
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80 --intensities '$setup.intensities'
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81 #end if
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82 #end if
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83
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84 --output '$output'
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85 --params '$params'
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86 --verbose
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87
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88 ]]></command>
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89 <configfiles>
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90 <configfile name="params"><![CDATA[
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91 {
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92 "features": [
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93 ${ ', '.join('"%s"' % t.strip() for t in str( $setup['features'] ).split(',')) }
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94 ]
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95 }
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96 ]]></configfile>
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97 </configfiles>
0
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98 <inputs>
5
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99 <param name="labels" type="data" format="tiff,zarr,png" label="Label map">
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100 <expand macro="validators/is_single_channel"/>
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101 <expand macro="validators/is_single_frame"/>
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102 </param>
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103 <conditional name="setup">
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104 <param label="Features to compute" name="mode" type="select">
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105 <option value="without-intensities" selected="true">Only use the label map for feature extraction (no intensity-based features)</option>
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106 <option value="with-intensities">Use the intensity image to compute additional features</option>
0
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107 </param>
5
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108 <when value="without-intensities">
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109 <expand macro="features"/>
0
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110 </when>
5
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111 <when value="with-intensities">
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112 <param name="intensities" type="data" format="tiff,zarr,png,jpg" label="Intensity image">
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113 <expand macro="validators/is_single_channel"/>
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114 <expand macro="validators/is_single_frame"/>
0
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115 </param>
5
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116 <expand macro="features">
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117 <option value="max_intensity">Maximum intensity</option>
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118 <option value="mean_intensity">Mean intensity</option>
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119 <option value="min_intensity">Minimum intensity</option>
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120 </expand>
0
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121 </when>
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122 </conditional>
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123 </inputs>
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124 <outputs>
4
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125 <data format="tabular" name="output"/>
0
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126 </outputs>
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127 <tests>
5
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128 <!-- Single-channel 2-D -->
0
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129 <test>
5
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130 <param name="labels" value="input/input12.png"/>
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131 <conditional name="setup">
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132 <param name="mode" value="without-intensities"/>
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133 <param name="features" value="label,area,area_convex,solidity"/>
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134 </conditional>
6
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135 <output name="output" ftype="tabular" value="output/input12.tsv" compare="re_match"/>
5
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136 </test>
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137 <test>
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138 <param name="labels" value="input/input11.tiff"/>
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139 <conditional name="setup">
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140 <param name="mode" value="with-intensities"/>
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141 <param name="intensities" value="input/input1_uint8.tiff"/>
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142 <param name="features" value="area,mean_intensity,perimeter"/>
4
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143 </conditional>
6
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144 <output name="output" ftype="tabular" value="output/input11.tsv" compare="re_match"/>
5
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145 </test>
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146 <!-- Single-channel 2-D Zarr (isolated features, verify that Dask arrays are converted to NumPy arrays whenever necessary) -->
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147 <expand macro="zarr-isolated-feature-test" feature="area"/>
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148 <expand macro="zarr-isolated-feature-test" feature="area_convex"/>
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149 <expand macro="zarr-isolated-feature-test" feature="area_filled"/>
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150 <expand macro="zarr-isolated-feature-test" feature="axis_major_length"/>
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151 <expand macro="zarr-isolated-feature-test" feature="axis_minor_length"/>
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152 <expand macro="zarr-isolated-feature-test" feature="bbox"/>
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153 <expand macro="zarr-isolated-feature-test" feature="centroid"/>
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154 <expand macro="zarr-isolated-feature-test" feature="eccentricity"/>
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155 <expand macro="zarr-isolated-feature-test" feature="equivalent_diameter_area"/>
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156 <expand macro="zarr-isolated-feature-test" feature="euler_number"/>
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157 <expand macro="zarr-isolated-feature-test" feature="extent"/>
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158 <expand macro="zarr-isolated-feature-test" feature="inertia_tensor_eigvals"/>
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159 <expand macro="zarr-isolated-feature-test" feature="moments"/>
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160 <expand macro="zarr-isolated-feature-test" feature="moments_hu"/>
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161 <expand macro="zarr-isolated-feature-test" feature="orientation"/>
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162 <expand macro="zarr-isolated-feature-test" feature="perimeter"/>
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163 <expand macro="zarr-isolated-feature-test" feature="solidity"/>
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164 <expand macro="zarr-isolated-feature-test" feature="max_intensity"/>
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165 <expand macro="zarr-isolated-feature-test" feature="mean_intensity"/>
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166 <expand macro="zarr-isolated-feature-test" feature="min_intensity"/>
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167 <!-- Single-channel 3-D, test all features are supported in 3-D -->
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168 <test>
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169 <param name="labels" value="input/input9.zarr"/>
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170 <conditional name="setup">
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171 <param name="mode" value="with-intensities"/>
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172 <param name="intensities" value="input/input8_zyx.zarr"/>
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173 <param name="features" value="area,area_convex,area_filled,axis_major_length,axis_minor_length,bbox,centroid,eccentricity,equivalent_diameter_area,euler_number,extent,inertia_tensor_eigvals,moments,moments_hu,orientation,perimeter,solidity,max_intensity,mean_intensity,min_intensity"/>
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174 </conditional>
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175 <output name="output" ftype="tabular" value="output/input9.tsv" compare="re_match"/>
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176 <assert_stdout>
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177 <has_line line='Skip feature that is not available for 3-D images: "eccentricity"'/>
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178 <has_line line='Skip feature that is not available for 3-D images: "moments_hu"'/>
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179 <has_line line='Skip feature that is not available for 3-D images: "orientation"'/>
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180 </assert_stdout>
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181 </test>
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182 <!-- Multi-channel (forbidden) -->
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183 <test expect_failure="true">
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184 <param name="labels" value="input/input12.png"/>
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185 <conditional name="setup">
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186 <param name="mode" value="with-intensities"/>
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187 <param name="intensities" value="input/input3_uint16.tiff"/>
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188 <param name="features" value="label"/>
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189 </conditional>
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190 <assert_stderr>
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191 <!-- Rejected by validator -->
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192 <has_n_lines n="0"/>
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193 </assert_stderr>
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194 <assert_stdout>
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195 <!-- Rejected by validator -->
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196 <has_n_lines n="0"/>
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197 </assert_stdout>
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198 </test>
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199 <test expect_failure="true">
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200 <param name="labels" value="input/input10.zarr"/>
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201 <conditional name="setup">
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202 <param name="mode" value="without-intensities"/>
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203 <param name="features" value="label"/>
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204 </conditional>
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205 <assert_stderr>
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206 <!-- Rejected by py-script -->
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207 <has_text text="This tool is not applicable to images with CYX axes."/>
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208 </assert_stderr>
0
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209 </test>
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210 </tests>
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211 <help>
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212
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213 **Computes features of a label map.**
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214
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215 The computed features are computed based solely on the properties of the objects in the label map, or, optionally, by also taking the intensities from a corresponding intensity image into account. Labels with value 0 are ignored.
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216
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217 Both images must be 2-D or 3-D single-channel images.
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218
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219 Supported Features
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220 ==================
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221
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222 **Area:** Area of the region i.e. number of pixels of the region scaled by pixel-area.
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223
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224 **Convex area:** Area of the convex hull image, which is the smallest convex polygon that encloses the region.
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225
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226 **Filled area:** Area of the region with all the holes filled in.
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227
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228 **Major axis length:** The length of the major axis of the ellipse that has the same normalized second central moments as the region.
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229
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230 **Minor axis length:** The length of the minor axis of the ellipse that has the same normalized second central moments as the region.
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231
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232 **Bounding box:** Bounding box `(min_row, min_col, max_row, max_col)`. Pixels belonging to the bounding box are in the half-open interval `[min_row; max_row)` and `[min_col; max_col)`.
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233
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234 **Centroid:** Centroid coordinates in separate columns ``centroid_x``, ``centroid_y``, and ``centroid_z`` when processing 3-D data.
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235
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236 **Eccentricity:** Eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. The value is in the interval [0, 1). When it is 0, the ellipse becomes a circle.
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238 **Equivalent diameter:** The diameter of a circle with the same area as the region.
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240 **Euler number:** Euler characteristic of the set of non-zero pixels. Computed as number of connected components subtracted by number of holes (input.ndim connectivity). In 3-D, number of connected components plus number of holes subtracted by number of tunnels.
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242 **Extent:** Ratio of pixels in the region to pixels in the total bounding box. Computed as `area / (rows * cols)`.
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244 **Inertia tensor eigenvalues:** The eigenvalues of the inertia tensor in decreasing order.
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246 **Moments:** Spatial moments up to 3rd order: `m_ij = sum{ array(row, col) * row^i * col^j }` where the sum is over the row, col coordinates of the region.
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248 **Moments Hu:** Hu moments (translation, scale and rotation invariant).
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250 **Orientation:** Angle between the vertical axis (rows) and the major axis of the ellipse that has the same second moments as the region, ranging from `-pi/2` to `pi/2` counter-clockwise.
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252 **Perimeter:** Perimeter of object which approximates the contour as a line through the centers of border pixels using a 4-connectivity. Generalizes to the surface of an object in 3-D, which uses a different approximation.
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254 **Solidity:** Ratio of pixels in the region to pixels of the convex hull image.
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256 </help>
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257 <citations>
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258 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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259 </citations>
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260 </tool>