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comparison projective_transformation.xml @ 3:be9a815e2240 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
author imgteam
date Thu, 20 Jan 2022 17:14:55 +0000
parents 1ffdb07020ee
children 37b079c98c38
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2:1ffdb07020ee 3:be9a815e2240
1 <tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.0" profile="20.05"> 1 <tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.1" profile="20.05">
2 <description>2D Projective Transformation</description> 2 <description>of 2D images</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.18.1">scikit-image</requirement> 4 <requirement type="package" version="0.18.1">scikit-image</requirement>
5 <requirement type="package" version="1.2.4">pandas</requirement> 5 <requirement type="package" version="1.2.4">pandas</requirement>
6 <requirement type="package" version="1.20.2">numpy</requirement> 6 <requirement type="package" version="1.20.2">numpy</requirement>
7 <requirement type="package" version="1.6.2">scipy</requirement> 7 <requirement type="package" version="1.6.2">scipy</requirement>
8 <requirement type="package" version="2020.10.1">tifffile</requirement> 8 <requirement type="package" version="2020.10.1">tifffile</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="aggressive"> 10 <command detect_errors="aggressive">
11 <![CDATA[ 11 <![CDATA[
12 python '$__tool_directory__/projective_transformation.py' 12 ln -s '$moving' ./in.${moving.ext} &&
13 '$fixed_image' 13 python '$__tool_directory__/projective_transformation.py'
14 '$moving_image' 14 '$fixed'
15 '$warp_matrix' 15 ./in.${moving.ext}
16 ./out 16 '$tmat'
17 ./out.${moving.ext}
18 && mv ./out.${moving.ext} ./result_image
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <param name="moving_image" type="data" format="tiff,png,jpg" label="Moving image (to be transformed)" /> 22 <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" />
21 <param name="fixed_image" type="data" format="tiff,png,jpg" label="Fixed image (the reference)" /> 23 <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" />
22 <param name="warp_matrix" type="data" format="tabular" label="Transformation matrix" /> 24 <param name="tmat" type="data" format="tabular" label="Transformation matrix" />
23 </inputs> 25 </inputs>
24 <outputs> 26 <outputs>
25 <data format_source="moving_image" name="warped_image" from_work_dir="out" /> 27 <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
26 </outputs> 28 </outputs>
27 <tests> 29 <tests>
28 <test> 30 <test>
29 <param name="fixed_image" value="sample1.png"/> 31 <param name="fixed" value="fixed.png"/>
30 <param name="moving_image" value="sample2.png"/> 32 <param name="moving" value="moving.png"/>
31 <param name="warp_matrix" value="warp_matrix.tsv"/> 33 <param name="tmat" value="tmat.tsv"/>
32 <output name="warped_image" value="yam.png" ftype="png" compare="sim_size"/> 34 <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
35 </test>
36 <test>
37 <param name="fixed" value="fixed_rgb.png"/>
38 <param name="moving" value="moving_rgb.png"/>
39 <param name="tmat" value="tmat.tsv"/>
40 <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
41 </test>
42 <test>
43 <param name="fixed" value="multi_f.tif"/>
44 <param name="moving" value="multi_m.tif"/>
45 <param name="tmat" value="tmat.tsv"/>
46 <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" />
33 </test> 47 </test>
34 </tests> 48 </tests>
35 <help> 49 <help>
36 **What it does** 50
51 **What it does**
37 52
38 This tool performs a projective transformation of the moving image so that it fits the fixed image. 53 This tool performs a projective transformation of the moving image so that it fits the fixed image.
39 Multi-channel and RGB images are supported. 54 Multi-channel and RGB images are supported.
40 </help> 55 </help>
41 <citations> 56 <citations>