Mercurial > repos > imgteam > 2d_simple_filter

annotate filter.xml @ 2:b2d9c92bc431 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
author imgteam
date Fri, 12 Dec 2025 21:18:04 +0000
parents e2542d0ac64f
children 53c55776a974
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2
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
imgteam
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1 <tool id="ip_filter_standard" name="Apply 2-D image filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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2 <description>with scipy</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>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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6 <token name="@TOOL_VERSION@">1.16.3</token>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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7 <token name="@VERSION_SUFFIX@">0</token>
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8 <xml name="select_axis">
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9 <param name="axis" type="select" label="Direction">
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10 <option value="1" selected="true">Horizontal</option>
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11 <option value="0">Vertical</option>
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12 </param>
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13 </xml>
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14 </macros>
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15 <creator>
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16 <expand macro="creators/bmcv"/>
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17 <expand macro="creators/kostrykin"/>
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18 </creator>
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19 <edam_operations>
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20 <edam_operation>operation_3443</edam_operation>
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21 </edam_operations>
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22 <xrefs>
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23 <xref type="bio.tools">galaxy_image_analysis</xref>
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24 <xref type="biii">scipy</xref>
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25 </xrefs>
0
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26 <requirements>
2
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27 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
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28 <requirement type="package" version="2.3.5">numpy</requirement>
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29 <requirement type="package" version="0.25.2">scikit-image</requirement>
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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30 <requirement type="package" version="2025.10.16">tifffile</requirement>
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31 <requirement type="package" version="0.5.2">giatools</requirement>
0
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32 </requirements>
2
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33 <command detect_errors="aggressive"><![CDATA[
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34
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35 python '$__tool_directory__/filter.py'
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36
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37 '$input'
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38 '$output'
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39 '$params'
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40
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41 ]]></command>
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42 <configfiles>
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43 <configfile name="params"><![CDATA[
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44 {
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45
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46 ## =====================================================================
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47 #if $filter.filter_type == "gaussian"
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48 "sigma": $filter.sigma,
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49 "order": $filter.derivative.order,
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50
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51 #if $filter.derivative.order != "0"
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52 "axis": $filter.derivative.axis,
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53 #end if
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54
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55 ## =====================================================================
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56 #elif $filter.filter_type == "uniform"
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57 "size": $filter.size,
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58
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59 ## =====================================================================
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60 #elif $filter.filter_type == "median"
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61 "radius": $filter.radius,
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62
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63 ## =====================================================================
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64 #elif $filter.filter_type == "prewitt" or $filter.filter_type == "sobel"
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65 "axis": $filter.axis,
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66
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67 ## =====================================================================
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68 #end if
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69
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70 "filter_type": "$filter.filter_type"
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71
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72 }
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73 ]]></configfile>
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74 </configfiles>
0
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75 <inputs>
2
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76 <param name="input" type="data" format="tiff,png" label="Input image"/>
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77 <conditional name="filter">
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78 <param name="filter_type" type="select" label="Filter type">
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79 <option value="gaussian" selected="True">Gaussian</option>
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80 <option value="uniform">Box filter (uniform filter)</option>
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81 <option value="median">Median</option>
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82 <option value="prewitt">Prewitt</option>
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83 <option value="sobel">Sobel</option>
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84 </param>
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85 <when value="gaussian">
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86 <param name="sigma" type="float" value="3" min="0.1" label="Sigma"
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87 help="The half width of the Gaussian bell (in pixels)."/>
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88 <conditional name="derivative">
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89 <param name="order" type="select" label="Use a derivative?">
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90 <option value="0">No derivative (mean filter)</option>
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91 <option value="1">1st-order derivative</option>
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92 <option value="2">2nd-order derivative</option>
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93 </param>
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94 <when value="0">
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95 </when>
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96 <when value="1">
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97 <expand macro="select_axis"/>
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98 </when>
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99 <when value="2">
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100 <expand macro="select_axis"/>
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101 </when>
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102 </conditional>
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103 </when>
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104 <when value="uniform">
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105 <param name="size" type="integer" min="2" value="3" label="Size"
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106 help="Edge length of the neighborhood (square, in pixels)."/>
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107 </when>
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108 <when value="median">
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109 <param name="radius" type="integer" min="2" value="3" label="Radius"
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110 help="Radius of the neighborhood (circle, in pixels)." />
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111 </when>
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112 <when value="prewitt">
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113 <expand macro="select_axis"/>
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114 </when>
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115 <when value="sobel">
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116 <expand macro="select_axis"/>
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117 </when>
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118 </conditional>
0
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119 </inputs>
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120 <outputs>
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121 <data format="tiff" name="output" />
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122 </outputs>
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123 <tests>
2
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124 <!-- Tests with uint8 TIFF input image -->
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125 <test>
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126 <param name="input" value="input1_uint8.tiff"/>
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127 <conditional name="filter">
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128 <param name="filter_type" value="gaussian"/>
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129 </conditional>
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130 <expand macro="tests/intensity_image_diff" name="output" value="input1_gaussian.tiff" ftype="tiff">
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131 <!--
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132
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133 The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67.
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134
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135 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
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136 values is preserved. The motiviation behind this is that the expectation images are usually checked
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137 visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
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138 the image is correct, thus it's good to double-check the range of values (hence the comparably large
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139 value for `eps`). This also concerns the median filter.
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140
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141 -->
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142 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
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143 </expand>
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144 </test>
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145 <test>
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146 <param name="input" value="input1_uint8.tiff"/>
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147 <conditional name="filter">
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148 <param name="filter_type" value="median"/>
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149 </conditional>
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150 <expand macro="tests/intensity_image_diff" name="output" value="input1_median.tiff" ftype="tiff">
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151 <!-- See note for Gaussian filter above. -->
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152 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
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153 </expand>
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154 </test>
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155 <test>
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156 <param name="input" value="input1_uint8.tiff"/>
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157 <conditional name="filter">
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158 <param name="filter_type" value="prewitt"/>
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159 <param name="axis" value="1"/>
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160 </conditional>
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161 <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_h.tiff" ftype="tiff"/>
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162 </test>
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163 <test>
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164 <param name="input" value="input1_uint8.tiff"/>
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165 <conditional name="filter">
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166 <param name="filter_type" value="prewitt"/>
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167 <param name="axis" value="0"/>
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168 </conditional>
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169 <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_v.tiff" ftype="tiff"/>
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170 </test>
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171 <test>
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172 <param name="input" value="input1_uint8.tiff"/>
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173 <conditional name="filter">
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174 <param name="filter_type" value="sobel"/>
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175 <param name="axis" value="1"/>
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176 </conditional>
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177 <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_h.tiff" ftype="tiff"/>
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178 </test>
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179 <test>
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180 <param name="input" value="input1_uint8.tiff"/>
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181 <conditional name="filter">
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182 <param name="filter_type" value="sobel"/>
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183 <param name="axis" value="0"/>
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184 </conditional>
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185 <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_v.tiff" ftype="tiff"/>
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186 </test>
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187 <!-- Tests with float TIFF input image -->
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188 <test>
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189 <param name="input" value="input2_float.tiff"/>
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190 <conditional name="filter">
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191 <param name="filter_type" value="gaussian"/>
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192 </conditional>
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193 <expand macro="tests/intensity_image_diff" name="output" value="input2_gaussian.tiff" ftype="tiff">
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194 <!-- See note for Gaussian filter above. -->
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195 <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/>
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196 </expand>
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197 </test>
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198 <test>
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199 <param name="input" value="input2_float.tiff"/>
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200 <conditional name="filter">
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201 <param name="filter_type" value="uniform"/>
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202 <param name="size" value="4"/>
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203 </conditional>
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204 <expand macro="tests/intensity_image_diff" name="output" value="input2_uniform.tiff" ftype="tiff">
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205 <!-- See note for Gaussian filter above. -->
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206 <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/>
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207 </expand>
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208 </test>
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209 <!-- Tests with multi-channel image (RGB) -->
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210 <test>
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211 <param name="input" value="scikit-image/retina.png"/>
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212 <conditional name="filter">
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213 <param name="filter_type" value="gaussian"/>
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214 <param name="sigma" value="5"/>
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215 <conditional name="derivative">
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216 <param name="order" value="0"/>
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217 </conditional>
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218 </conditional>
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219 <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order0.tiff" ftype="tiff"/>
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220 </test>
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221 <test>
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222 <param name="input" value="scikit-image/retina.png"/>
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223 <conditional name="filter">
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224 <param name="filter_type" value="gaussian"/>
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225 <param name="sigma" value="3"/>
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226 <conditional name="derivative">
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227 <param name="order" value="2"/>
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228 <param name="axis" value="0"/>
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229 </conditional>
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230 </conditional>
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231 <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order2_axis0.tiff" ftype="tiff"/>
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232 </test>
0
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233 </tests>
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234 <help>
2
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235
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236 **Applies a standard, general-purpose 2-D filter to an image.**
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237
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238 Support for different image types:
0
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239
2
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240 - For 3-D images, the filter is applied to all z-slices of the image.
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241 - For multi-channel images, the filter is applied to all channels of the image.
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242 - For time-series images, the filter is also applied for all time steps.
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243
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244 Mean filters like the Gaussian filter, the box filter, or the median filter preserve both the brightness of the image, and
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245 the range of values. This does not hold for the derivative variants of the Gaussian filter, which may produce negative values.
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246
0
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247 </help>
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248 <citations>
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249 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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250 </citations>
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251 </tool>