annotate auto_threshold.xml @ 4:7d80eb2411fb draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651
author imgteam
date Sat, 07 Jun 2025 18:38:16 +0000
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4
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1 <tool id="ip_threshold" name="Threshold image" 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>
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5 <import>tests.xml</import>
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6 <token name="@TOOL_VERSION@">0.25.0</token>
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7 <token name="@VERSION_SUFFIX@">0</token>
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8 <xml name="inputs/offset">
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9 <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
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10 </xml>
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11 </macros>
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12 <creator>
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13 <expand macro="creators/bmcv"/>
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14 </creator>
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15 <edam_operations>
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16 <edam_operation>operation_3443</edam_operation>
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17 </edam_operations>
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18 <xrefs>
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19 <xref type="bio.tools">scikit-image</xref>
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20 <xref type="biii">scikit-image</xref>
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21 </xrefs>
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22 <requirements>
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23 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
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24 <requirement type="package" version="0.4.1">giatools</requirement>
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25 </requirements>
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26 <command detect_errors="aggressive">
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27 <![CDATA[
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28
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29 python '$__tool_directory__/auto_threshold.py'
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30
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31 '$input'
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32 ./out.tiff
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33
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34 '$th_method.method_id'
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35 '$th_method.block_size'
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36 '$th_method.offset'
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37 '$th_method.threshold1'
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38 $invert_output
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39
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40 #if str($th_method.threshold2) != '':
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41 --threshold2 '$th_method.threshold2'
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42 #end if
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43
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44 ]]>
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45 </command>
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46 <inputs>
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47 <param name="input" type="data" format="tiff,png" label="Input image" />
4
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48 <conditional name="th_method">
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49 <param name="method_id" type="select" label="Thresholding method">
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50 <option value="manual">Manual</option>
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51 <option value="otsu" selected="True">Globally adaptive / Otsu</option>
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52 <option value="li">Globally adaptive / Li's Minimum Cross Entropy</option>
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53 <option value="isodata">Globally adaptive / Isodata</option>
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54 <option value="yen">Globally adaptive / Yen</option>
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55 <option value="loc_gaussian">Locally adaptive / Gaussian</option>
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56 <option value="loc_median">Locally adaptive / Median</option>
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57 <option value="loc_mean">Locally adaptive / Mean</option>
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58 </param>
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59 <when value="manual">
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60 <param name="threshold1" type="float" value="0" label="Threshold value" />
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61 <param name="threshold2" type="float" value="" optional="true" label="Second threshold value for hysteresis thresholding" />
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62 <param name="block_size" type="hidden" value="0" />
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63 <param name="offset" type="hidden" value="0" />
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64 </when>
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65 <when value="otsu">
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66 <param name="threshold1" type="hidden" value="0" />
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67 <param name="threshold2" type="hidden" value="" />
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68 <param name="block_size" type="hidden" value="0" />
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69 <expand macro="inputs/offset" />
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70 </when>
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71 <when value="li">
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72 <param name="threshold1" type="hidden" value="0" />
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73 <param name="threshold2" type="hidden" value="" />
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74 <param name="block_size" type="hidden" value="0" />
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75 <expand macro="inputs/offset" />
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76 </when>
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77 <when value="isodata">
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78 <param name="threshold1" type="hidden" value="0" />
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79 <param name="threshold2" type="hidden" value="" />
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80 <param name="block_size" type="hidden" value="0" />
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81 <expand macro="inputs/offset" />
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82 </when>
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83 <when value="yen">
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84 <param name="threshold1" type="hidden" value="0" />
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85 <param name="threshold2" type="hidden" value="" />
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86 <param name="block_size" type="hidden" value="0" />
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87 <expand macro="inputs/offset" />
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88 </when>
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89 <when value="loc_gaussian">
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90 <param name="threshold1" type="hidden" value="0" />
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91 <param name="threshold2" type="hidden" value="" />
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92 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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93 <expand macro="inputs/offset" />
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94 </when>
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95 <when value="loc_median">
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96 <param name="threshold1" type="hidden" value="0" />
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97 <param name="threshold2" type="hidden" value="" />
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98 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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99 <expand macro="inputs/offset" />
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100 </when>
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101 <when value="loc_mean">
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102 <param name="threshold1" type="hidden" value="0" />
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103 <param name="threshold2" type="hidden" value="" />
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104 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
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105 <expand macro="inputs/offset" />
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106 </when>
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107 </conditional>
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108 <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
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109 </inputs>
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110 <outputs>
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111 <data format="tiff" name="output" from_work_dir="out.tiff" />
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112 </outputs>
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113 <tests>
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114 <!-- Tests for single-channel images (TIFF) -->
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115 <test>
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116 <param name="input" value="sample.tiff"/>
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117 <conditional name="th_method">
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118 <param name="method_id" value="loc_gaussian"/>
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119 <param name="block_size" value="51"/>
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120 </conditional>
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121 <expand macro="tests/binary_image_diff" name="output" value="out1.tiff" ftype="tiff"/>
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122 </test>
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123 <test>
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124 <param name="input" value="sample.tiff"/>
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125 <conditional name="th_method">
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126 <param name="method_id" value="loc_gaussian"/>
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127 <param name="block_size" value="51"/>
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128 <param name="offset" value="1"/>
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129 </conditional>
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130 <expand macro="tests/binary_image_diff" name="output" value="out2.tiff" ftype="tiff"/>
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131 </test>
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132 <test>
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133 <param name="input" value="sample.tiff"/>
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134 <conditional name="th_method">
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135 <param name="method_id" value="otsu"/>
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136 </conditional>
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137 <expand macro="tests/binary_image_diff" name="output" value="out3.tiff" ftype="tiff"/>
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138 </test>
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139 <test>
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140 <param name="input" value="sample.tiff"/>
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141 <param name="invert_output" value="True"/>
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142 <conditional name="th_method">
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143 <param name="method_id" value="manual"/>
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144 <param name="threshold1" value="64"/>
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145 </conditional>
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146 <expand macro="tests/binary_image_diff" name="output" value="out4.tiff" ftype="tiff"/>
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147 </test>
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148 <test>
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149 <param name="input" value="sample.tiff"/>
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150 <conditional name="th_method">
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151 <param name="method_id" value="manual"/>
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152 <param name="threshold1" value="180"/>
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153 <param name="threshold2" value="240"/>
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154 </conditional>
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155 <expand macro="tests/binary_image_diff" name="output" value="sample_manual_180_240.tiff" ftype="tiff"/>
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156 </test>
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157 <!-- Tests for multi-channel images (PNG) -->
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158 <test>
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159 <param name="input" value="rgb.png"/>
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160 <conditional name="th_method">
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161 <param name="method_id" value="otsu"/>
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162 </conditional>
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163 <expand macro="tests/binary_image_diff" name="output" value="rgb_otsu.tiff" ftype="tiff"/>
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164 </test>
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165 <!-- Tests for irregular files -->
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166 <test>
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167 <param name="input" value="sample2.tiff"/>
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168 <conditional name="th_method">
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169 <param name="method_id" value="otsu"/>
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170 </conditional>
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171 <expand macro="tests/binary_image_diff" name="output" value="out5.tiff" ftype="tiff"/>
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172 </test>
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173 </tests>
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174 <help>
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175
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176 **Applies a standard thresholding algorithm to a 2-D single-channel image. Yields a binary image.**
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177
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178 The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used).
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179 The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold,
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180 and black (pixel value 0) to image regions below or equal to the determined threshold.
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181
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182 The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set.
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183
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184 </help>
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185 <citations>
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186 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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187 </citations>
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188 </tool>