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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations commit c6d2a4fb19b54c804029ae3d52eb9fb2619e4265
author imgteam
date Fri, 08 Mar 2024 11:00:41 +0000
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1 <tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with SciPy</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.12.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations>
10 <xrefs>
11 <xref type="biii">scipy</xref>
12 </xrefs>
13 <requirements>
14 <requirement type="package" version="1.12.0">scipy</requirement>
15 <requirement type="package" version="0.22.0">scikit-image</requirement>
16 </requirements>
17 <command><![CDATA[
18
19 ## Inputs
20
21 python '$__tool_directory__/morphological_operations.py' '$image'
22 --operation $operation
23 --selem-shape $selem_shape
24 --selem-size $selem_size
25
26 ## Outputs
27
28 ./result.tiff
29
30 ]]>
31 </command>
32 <inputs>
33 <param name="image" type="data" format="png,tiff" label="Input image" />
34 <param label="Morphological operation" argument="--operation" type="select">
35 <option value="erosion" selected="True">Erosion</option>
36 <option value="dilation">Dilation</option>
37 <option value="opening">Opening</option>
38 <option value="closing">Closing</option>
39 <option value="fill_holes">Fill holes</option>
40 </param>
41 <param label="Structuring element" argument="--selem-shape" type="select">
42 <option value="disk" selected="True">Disk</option>
43 <option value="square">Square</option>
44 </param>
45 <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." />
46 </inputs>
47 <outputs>
48 <data format="tiff" name="result" from_work_dir="result.tiff" />
49 </outputs>
50 <tests>
51 <!-- Test binary operations (input images with two distinct values) -->
52 <test>
53 <param name="image" value="input1.tiff" />
54 <param name="operation" value="erosion" />
55 <param name="selem_shape" value="disk" />
56 <param name="selem_size" value="1" />
57 <output name="result" value="output1_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" />
58 </test>
59 <test>
60 <param name="image" value="input1.tiff" />
61 <param name="operation" value="dilation" />
62 <param name="selem_shape" value="disk" />
63 <param name="selem_size" value="2" />
64 <output name="result" value="output1_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" />
65 </test>
66 <test>
67 <param name="image" value="input1.tiff" />
68 <param name="operation" value="opening" />
69 <param name="selem_shape" value="square" />
70 <param name="selem_size" value="1" />
71 <output name="result" value="output1_opening.tiff" ftype="tiff" compare="sim_size" delta="10" />
72 </test>
73 <test>
74 <param name="image" value="input1.tiff" />
75 <param name="operation" value="closing" />
76 <param name="selem_shape" value="square" />
77 <param name="selem_size" value="2" />
78 <output name="result" value="output1_closing.tiff" ftype="tiff" compare="sim_size" delta="10" />
79 </test>
80 <!-- Test intensity-based operations (more than two distinct values) -->
81 <test>
82 <param name="image" value="input3.png" />
83 <param name="operation" value="erosion" />
84 <param name="selem_shape" value="disk" />
85 <param name="selem_size" value="1" />
86 <output name="result" value="output3_erosion.tiff" ftype="tiff" compare="sim_size" delta="10" />
87 </test>
88 <test>
89 <param name="image" value="input3.png" />
90 <param name="operation" value="dilation" />
91 <param name="selem_shape" value="disk" />
92 <param name="selem_size" value="2" />
93 <output name="result" value="output3_dilation.tiff" ftype="tiff" compare="sim_size" delta="10" />
94 </test>
95 <test>
96 <param name="image" value="input3.png" />
97 <param name="operation" value="opening" />
98 <param name="selem_shape" value="square" />
99 <param name="selem_size" value="1" />
100 <output name="result" value="output3_opening.tiff" ftype="tiff" compare="sim_size" delta="10" />
101 </test>
102 <test>
103 <param name="image" value="input3.png" />
104 <param name="operation" value="closing" />
105 <param name="selem_shape" value="square" />
106 <param name="selem_size" value="2" />
107 <output name="result" value="output3_closing.tiff" ftype="tiff" compare="sim_size" delta="10" />
108 </test>
109 <!-- Test multi-channel image (with two distinct values per channel) -->
110 <test>
111 <param name="image" value="input2.png" />
112 <param name="operation" value="fill_holes" />
113 <param name="selem_shape" value="disk" />
114 <param name="selem_size" value="1" />
115 <output name="result" value="output2_fill_holes.tiff" ftype="tiff" compare="sim_size" delta="10" />
116 </test>
117 </tests>
118 <help>
119 Applies a morphological operation to a 2-D image.
120 For multi-channel images, the operation is applied to each channel separately.
121
122 The following operations are supported:
123
124 - **Erosion:** Shrink bright areas.
125 - **Dilation:** Grow bright areas.
126 - **Opening:** Erosion followed by Dilation. Erases tiny bright spots.
127 - **Closing:** Dilation followed by Erosion. Erases tiny dark holes.
128 - **Fill holes:** Fills the holes (dark areas) in binary images.
129 </help>
130 <citations>
131 <citation type="doi">10.1038/s41592-019-0686-2</citation>
132 </citations>
133 </tool>