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comparison image_math.xml @ 1:f8b7770cbca5 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:35 +0000
parents 33b2ca53a566
children 48fa3ac55df2
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0:33b2ca53a566 1:f8b7770cbca5
1 <tool id="image_math" name="Process images using arithmetic expressions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 1 <tool id="image_math" name="Process images using arithmetic expressions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with NumPy</description> 2 <description>with NumPy</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">1.26.4</token> 6 <token name="@TOOL_VERSION@">1.26.4</token>
5 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">1</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 <requirements> 15 <requirements>
11 <requirement type="package" version="1.26.4">numpy</requirement> 16 <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
12 <requirement type="package" version="0.22.0">scikit-image</requirement> 17 <requirement type="package" version="0.22.0">scikit-image</requirement>
13 </requirements> 18 </requirements>
14 <command><![CDATA[ 19 <command><![CDATA[
15 20
16 ## Inputs 21 ## Inputs
47 <param name="expression" value="input1 * 2" /> 52 <param name="expression" value="input1 * 2" />
48 <repeat name="inputs"> 53 <repeat name="inputs">
49 <param name="image" value="input1.tiff" /> 54 <param name="image" value="input1.tiff" />
50 <param name="name" value="input1" /> 55 <param name="name" value="input1" />
51 </repeat> 56 </repeat>
52 <output name="result" value="input1_times_2.tiff" ftype="tiff" compare="sim_size" delta="0" /> 57 <expand macro="tests/intensity_image_diff" name="result" value="input1_times_2.tiff" ftype="tiff"/>
53 </test> 58 </test>
54 <!-- Unary negation operator --> 59 <!-- Unary negation operator -->
55 <test> 60 <test>
56 <param name="expression" value="-input1" /> 61 <param name="expression" value="-input1" />
57 <repeat name="inputs"> 62 <repeat name="inputs">
58 <param name="image" value="input1.tiff" /> 63 <param name="image" value="input1.tiff" />
59 <param name="name" value="input1" /> 64 <param name="name" value="input1" />
60 </repeat> 65 </repeat>
61 <output name="result" value="minus_input1.tiff" ftype="tiff" compare="sim_size" delta="0" /> 66 <expand macro="tests/intensity_image_diff" name="result" value="minus_input1.tiff" ftype="tiff"/>
62 </test> 67 </test>
63 <!-- Binary addition, neutral element, addition with scalar --> 68 <!-- Binary addition, neutral element, addition with scalar -->
64 <test> 69 <test>
65 <param name="expression" value="input1 + input2 + 1" /> 70 <param name="expression" value="input1 + input2 + 1" />
66 <repeat name="inputs"> 71 <repeat name="inputs">
69 </repeat> 74 </repeat>
70 <repeat name="inputs"> 75 <repeat name="inputs">
71 <param name="image" value="minus_input1.tiff" /> 76 <param name="image" value="minus_input1.tiff" />
72 <param name="name" value="input2" /> 77 <param name="name" value="input2" />
73 </repeat> 78 </repeat>
74 <output name="result" value="ones.tiff" ftype="tiff" compare="sim_size" delta="0" /> 79 <expand macro="tests/intensity_image_diff" name="result" value="ones.tiff" ftype="tiff"/>
75 </test> 80 </test>
76 <!-- Parentheses --> 81 <!-- Parentheses -->
77 <test> 82 <test>
78 <param name="expression" value="(input1 + input2) / 2" /> 83 <param name="expression" value="(input1 + input2) / 2" />
79 <repeat name="inputs"> 84 <repeat name="inputs">
82 </repeat> 87 </repeat>
83 <repeat name="inputs"> 88 <repeat name="inputs">
84 <param name="image" value="ones.tiff" /> 89 <param name="image" value="ones.tiff" />
85 <param name="name" value="input2" /> 90 <param name="name" value="input2" />
86 </repeat> 91 </repeat>
87 <output name="result" value="half_of_input1_plus_one.tiff" ftype="tiff" compare="sim_size" delta="0" /> 92 <expand macro="tests/intensity_image_diff" name="result" value="half_of_input1_plus_one.tiff" ftype="tiff"/>
88 </test> 93 </test>
89 <!-- Abs --> 94 <!-- Abs -->
90 <test> 95 <test>
91 <param name="expression" value="abs(input)" /> 96 <param name="expression" value="abs(input)" />
92 <repeat name="inputs"> 97 <repeat name="inputs">
93 <param name="image" value="input1.tiff" /> 98 <param name="image" value="input1.tiff" />
94 <param name="name" value="input" /> 99 <param name="name" value="input" />
95 </repeat> 100 </repeat>
96 <output name="result" value="input1_abs.tiff" ftype="tiff" compare="sim_size" delta="0" /> 101 <expand macro="tests/intensity_image_diff" name="result" value="input1_abs.tiff" ftype="tiff"/>
97 </test> 102 </test>
98 </tests> 103 </tests>
99 <help> 104 <help>
100 105
101 This tool processes images according to pixel-wise arithmetic expressions. 106 **Processes images according to pixel-wise arithmetic expressions.**
102 107
103 The supported pixel-wise expressions are: 108 The supported pixel-wise expressions are:
104 109
105 - Addition, subtraction, multiplication, and division (``+``, ``-``, ``*``, ``/``) 110 - Addition, subtraction, multiplication, and division (``+``, ``-``, ``*``, ``/``)
106 - Integer division (e.g., ``input // 2``) 111 - Integer division (e.g., ``input // 2``)