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annotate morphological_operations.xml @ 2:4e25befab102 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c86a1b93cb7732f7331a981d13465653cc1a2790
author imgteam
date Wed, 24 Apr 2024 08:12:39 +0000
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1 <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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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>
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6 <token name="@TOOL_VERSION@">1.12.0</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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8 </macros>
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9 <creator>
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10 <expand macro="creators/bmcv"/>
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11 </creator>
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12 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
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14 </edam_operations>
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15 <xrefs>
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16 <xref type="biii">scipy</xref>
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17 </xrefs>
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18 <requirements>
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19 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
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20 <requirement type="package" version="0.22.0">scikit-image</requirement>
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21 <requirement type="package" version="0.1">giatools</requirement>
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22 </requirements>
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23 <command><![CDATA[
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25 ## Inputs
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27 python '$__tool_directory__/morphological_operations.py' '$image'
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28 --operation $operation
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29 --selem-shape $selem_shape
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30 --selem-size $selem_size
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32 ## Outputs
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34 ./result.tiff
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35
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36 ]]>
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37 </command>
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38 <inputs>
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39 <param name="image" type="data" format="png,tiff" label="Input image" />
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40 <param label="Morphological operation" argument="--operation" type="select">
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41 <option value="erosion" selected="True">Erosion</option>
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42 <option value="dilation">Dilation</option>
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43 <option value="opening">Opening</option>
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44 <option value="closing">Closing</option>
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45 <option value="fill_holes">Fill holes</option>
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46 </param>
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47 <param label="Structuring element" argument="--selem-shape" type="select">
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48 <option value="disk" selected="True">Disk</option>
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49 <option value="square">Square</option>
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50 </param>
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51 <param label="Structuring element size" argument="--selem-size" type="integer" min="1" max="256" value="1" help="The radius of the disk, or the width of the square, in pixels." />
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52 </inputs>
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53 <outputs>
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54 <data format="tiff" name="result" from_work_dir="result.tiff" />
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55 </outputs>
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56 <tests>
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57 <!-- Test binary operations (input images with two distinct values) -->
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58 <test>
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59 <param name="image" value="input1.tiff" />
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60 <param name="operation" value="erosion" />
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61 <param name="selem_shape" value="disk" />
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62 <param name="selem_size" value="1" />
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63 <expand macro="tests/binary_image_diff" name="result" value="output1_erosion.tiff" ftype="tiff"/>
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64 </test>
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65 <test>
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66 <param name="image" value="input1.tiff" />
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67 <param name="operation" value="dilation" />
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68 <param name="selem_shape" value="disk" />
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69 <param name="selem_size" value="2" />
1
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70 <expand macro="tests/binary_image_diff" name="result" value="output1_dilation.tiff" ftype="tiff"/>
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71 </test>
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72 <test>
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73 <param name="image" value="input1.tiff" />
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74 <param name="operation" value="opening" />
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75 <param name="selem_shape" value="square" />
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76 <param name="selem_size" value="1" />
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77 <expand macro="tests/binary_image_diff" name="result" value="output1_opening.tiff" ftype="tiff"/>
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78 </test>
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79 <test>
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80 <param name="image" value="input1.tiff" />
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81 <param name="operation" value="closing" />
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82 <param name="selem_shape" value="square" />
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83 <param name="selem_size" value="2" />
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84 <expand macro="tests/binary_image_diff" name="result" value="output1_closing.tiff" ftype="tiff"/>
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85 </test>
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86 <!-- Test intensity-based operations (more than two distinct values) -->
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87 <test>
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88 <param name="image" value="input3.png" />
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89 <param name="operation" value="erosion" />
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90 <param name="selem_shape" value="disk" />
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91 <param name="selem_size" value="1" />
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92 <expand macro="tests/intensity_image_diff" name="result" value="output3_erosion.tiff" ftype="tiff"/>
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93 </test>
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94 <test>
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95 <param name="image" value="input3.png" />
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96 <param name="operation" value="dilation" />
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97 <param name="selem_shape" value="disk" />
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98 <param name="selem_size" value="2" />
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99 <expand macro="tests/intensity_image_diff" name="result" value="output3_dilation.tiff" ftype="tiff"/>
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100 </test>
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101 <test>
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102 <param name="image" value="input3.png" />
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103 <param name="operation" value="opening" />
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104 <param name="selem_shape" value="square" />
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105 <param name="selem_size" value="1" />
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106 <expand macro="tests/intensity_image_diff" name="result" value="output3_opening.tiff" ftype="tiff"/>
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107 </test>
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108 <test>
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109 <param name="image" value="input3.png" />
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110 <param name="operation" value="closing" />
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111 <param name="selem_shape" value="square" />
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112 <param name="selem_size" value="2" />
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113 <expand macro="tests/intensity_image_diff" name="result" value="output3_closing.tiff" ftype="tiff"/>
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114 </test>
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115 <!-- Test multi-channel image (with two distinct values per channel) -->
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116 <test>
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117 <param name="image" value="input2.png" />
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118 <param name="operation" value="fill_holes" />
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119 <param name="selem_shape" value="disk" />
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120 <param name="selem_size" value="1" />
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121 <expand macro="tests/intensity_image_diff" name="result" value="output2_fill_holes.tiff" ftype="tiff"/>
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122 </test>
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123 </tests>
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124 <help>
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125
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126 **Applies a morphological operation to a 2-D image.**
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127
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128 For multi-channel images, the operation is applied to each channel separately.
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129
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130 The following operations are supported:
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131
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132 - **Erosion:** Shrink bright areas.
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133 - **Dilation:** Grow bright areas.
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134 - **Opening:** Erosion followed by Dilation. Erases tiny bright spots.
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135 - **Closing:** Dilation followed by Erosion. Erases tiny dark holes.
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136 - **Fill holes:** Fills the holes (dark areas) in binary images.
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137
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138 </help>
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139 <citations>
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140 <citation type="doi">10.1038/s41592-019-0686-2</citation>
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141 </citations>
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142 </tool>