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comparison morphological_operations.xml @ 1:ad795d260ba8 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:44 +0000
parents f10112b317a1
children 4e25befab102
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0:f10112b317a1 1:ad795d260ba8
1 <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 1 <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with SciPy</description> 2 <description>with SciPy</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">1.12.0</token> 6 <token name="@TOOL_VERSION@">1.12.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 </creator>
7 <edam_operations> 12 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 14 </edam_operations>
10 <xrefs> 15 <xrefs>
11 <xref type="biii">scipy</xref> 16 <xref type="biii">scipy</xref>
12 </xrefs> 17 </xrefs>
13 <requirements> 18 <requirements>
14 <requirement type="package" version="1.12.0">scipy</requirement> 19 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
15 <requirement type="package" version="0.22.0">scikit-image</requirement> 20 <requirement type="package" version="0.22.0">scikit-image</requirement>
16 </requirements> 21 </requirements>
17 <command><![CDATA[ 22 <command><![CDATA[
18 23
19 ## Inputs 24 ## Inputs
52 <test> 57 <test>
53 <param name="image" value="input1.tiff" /> 58 <param name="image" value="input1.tiff" />
54 <param name="operation" value="erosion" /> 59 <param name="operation" value="erosion" />
55 <param name="selem_shape" value="disk" /> 60 <param name="selem_shape" value="disk" />
56 <param name="selem_size" value="1" /> 61 <param name="selem_size" value="1" />
57 <output name="result" value="output1_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> 62 <expand macro="tests/binary_image_diff" name="result" value="output1_erosion.tiff" ftype="tiff"/>
58 </test> 63 </test>
59 <test> 64 <test>
60 <param name="image" value="input1.tiff" /> 65 <param name="image" value="input1.tiff" />
61 <param name="operation" value="dilation" /> 66 <param name="operation" value="dilation" />
62 <param name="selem_shape" value="disk" /> 67 <param name="selem_shape" value="disk" />
63 <param name="selem_size" value="2" /> 68 <param name="selem_size" value="2" />
64 <output name="result" value="output1_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> 69 <expand macro="tests/binary_image_diff" name="result" value="output1_dilation.tiff" ftype="tiff"/>
65 </test> 70 </test>
66 <test> 71 <test>
67 <param name="image" value="input1.tiff" /> 72 <param name="image" value="input1.tiff" />
68 <param name="operation" value="opening" /> 73 <param name="operation" value="opening" />
69 <param name="selem_shape" value="square" /> 74 <param name="selem_shape" value="square" />
70 <param name="selem_size" value="1" /> 75 <param name="selem_size" value="1" />
71 <output name="result" value="output1_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> 76 <expand macro="tests/binary_image_diff" name="result" value="output1_opening.tiff" ftype="tiff"/>
72 </test> 77 </test>
73 <test> 78 <test>
74 <param name="image" value="input1.tiff" /> 79 <param name="image" value="input1.tiff" />
75 <param name="operation" value="closing" /> 80 <param name="operation" value="closing" />
76 <param name="selem_shape" value="square" /> 81 <param name="selem_shape" value="square" />
77 <param name="selem_size" value="2" /> 82 <param name="selem_size" value="2" />
78 <output name="result" value="output1_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> 83 <expand macro="tests/binary_image_diff" name="result" value="output1_closing.tiff" ftype="tiff"/>
79 </test> 84 </test>
80 <!-- Test intensity-based operations (more than two distinct values) --> 85 <!-- Test intensity-based operations (more than two distinct values) -->
81 <test> 86 <test>
82 <param name="image" value="input3.png" /> 87 <param name="image" value="input3.png" />
83 <param name="operation" value="erosion" /> 88 <param name="operation" value="erosion" />
84 <param name="selem_shape" value="disk" /> 89 <param name="selem_shape" value="disk" />
85 <param name="selem_size" value="1" /> 90 <param name="selem_size" value="1" />
86 <output name="result" value="output3_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" /> 91 <expand macro="tests/intensity_image_diff" name="result" value="output3_erosion.tiff" ftype="tiff"/>
87 </test> 92 </test>
88 <test> 93 <test>
89 <param name="image" value="input3.png" /> 94 <param name="image" value="input3.png" />
90 <param name="operation" value="dilation" /> 95 <param name="operation" value="dilation" />
91 <param name="selem_shape" value="disk" /> 96 <param name="selem_shape" value="disk" />
92 <param name="selem_size" value="2" /> 97 <param name="selem_size" value="2" />
93 <output name="result" value="output3_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" /> 98 <expand macro="tests/intensity_image_diff" name="result" value="output3_dilation.tiff" ftype="tiff"/>
94 </test> 99 </test>
95 <test> 100 <test>
96 <param name="image" value="input3.png" /> 101 <param name="image" value="input3.png" />
97 <param name="operation" value="opening" /> 102 <param name="operation" value="opening" />
98 <param name="selem_shape" value="square" /> 103 <param name="selem_shape" value="square" />
99 <param name="selem_size" value="1" /> 104 <param name="selem_size" value="1" />
100 <output name="result" value="output3_opening.tiff" ftype="tiff" compare="sim_size" delta="10" /> 105 <expand macro="tests/intensity_image_diff" name="result" value="output3_opening.tiff" ftype="tiff"/>
101 </test> 106 </test>
102 <test> 107 <test>
103 <param name="image" value="input3.png" /> 108 <param name="image" value="input3.png" />
104 <param name="operation" value="closing" /> 109 <param name="operation" value="closing" />
105 <param name="selem_shape" value="square" /> 110 <param name="selem_shape" value="square" />
106 <param name="selem_size" value="2" /> 111 <param name="selem_size" value="2" />
107 <output name="result" value="output3_closing.tiff" ftype="tiff" compare="sim_size" delta="10" /> 112 <expand macro="tests/intensity_image_diff" name="result" value="output3_closing.tiff" ftype="tiff"/>
108 </test> 113 </test>
109 <!-- Test multi-channel image (with two distinct values per channel) --> 114 <!-- Test multi-channel image (with two distinct values per channel) -->
110 <test> 115 <test>
111 <param name="image" value="input2.png" /> 116 <param name="image" value="input2.png" />
112 <param name="operation" value="fill_holes" /> 117 <param name="operation" value="fill_holes" />
113 <param name="selem_shape" value="disk" /> 118 <param name="selem_shape" value="disk" />
114 <param name="selem_size" value="1" /> 119 <param name="selem_size" value="1" />
115 <output name="result" value="output2_fill_holes.tiff" ftype="tiff" compare="sim_size" delta="10" /> 120 <expand macro="tests/intensity_image_diff" name="result" value="output2_fill_holes.tiff" ftype="tiff"/>
116 </test> 121 </test>
117 </tests> 122 </tests>
118 <help> 123 <help>
119 Applies a morphological operation to a 2-D image. 124
125 **Applies a morphological operation to a 2-D image.**
126
120 For multi-channel images, the operation is applied to each channel separately. 127 For multi-channel images, the operation is applied to each channel separately.
121 128
122 The following operations are supported: 129 The following operations are supported:
123 130
124 - **Erosion:** Shrink bright areas. 131 - **Erosion:** Shrink bright areas.
125 - **Dilation:** Grow bright areas. 132 - **Dilation:** Grow bright areas.
126 - **Opening:** Erosion followed by Dilation. Erases tiny bright spots. 133 - **Opening:** Erosion followed by Dilation. Erases tiny bright spots.
127 - **Closing:** Dilation followed by Erosion. Erases tiny dark holes. 134 - **Closing:** Dilation followed by Erosion. Erases tiny dark holes.
128 - **Fill holes:** Fills the holes (dark areas) in binary images. 135 - **Fill holes:** Fills the holes (dark areas) in binary images.
136
129 </help> 137 </help>
130 <citations> 138 <citations>
131 <citation type="doi">10.1038/s41592-019-0686-2</citation> 139 <citation type="doi">10.1038/s41592-019-0686-2</citation>
132 </citations> 140 </citations>
133 </tool> 141 </tool>