Mercurial > repos > imgteam > projective_transformation
changeset 3:be9a815e2240 draft
"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 |
| files | projective_transformation.py projective_transformation.xml test-data/fixed.png test-data/fixed_rgb.png test-data/moving.png test-data/moving_rgb.png test-data/moving_rgb_warped.png test-data/moving_warped.png test-data/multi_f.tif test-data/multi_m.tif test-data/multi_m_warped.tif test-data/sample1.png test-data/sample2.png test-data/tmat.tsv test-data/warp_matrix.tsv test-data/yam.png |
| diffstat | 16 files changed, 37 insertions(+), 24 deletions(-) [+] |
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--- a/projective_transformation.py Fri Jan 14 03:07:08 2022 +0000 +++ b/projective_transformation.py Thu Jan 20 17:14:55 2022 +0000 @@ -7,7 +7,6 @@ """ import argparse -import imghdr import warnings import numpy as np @@ -50,7 +49,6 @@ def transform(moving_fn, fixed_fn, warp_mat, output_fn): moving = skimage.io.imread(moving_fn) - extension = imghdr.what(moving_fn) nDims = len(moving.shape) assert nDims in [2, 3, 4, 5, 6], 'this tool only supports up to 6 dimensions' @@ -96,9 +94,9 @@ with warnings.catch_warnings(): warnings.simplefilter("ignore") if isMulCh: - tifffile.imwrite(output_fn + '.tif', warped_moving, imagej=True, metadata={'mode': 'composite'}) + tifffile.imwrite(output_fn, warped_moving, imagej=True, metadata={'mode': 'composite'}) else: - skimage.io.imsave(output_fn + '.' + extension, warped_moving) + skimage.io.imsave(output_fn, warped_moving) if __name__ == "__main__":
--- a/projective_transformation.xml Fri Jan 14 03:07:08 2022 +0000 +++ b/projective_transformation.xml Thu Jan 20 17:14:55 2022 +0000 @@ -1,5 +1,5 @@ -<tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.0" profile="20.05"> - <description>2D Projective Transformation</description> +<tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.1" profile="20.05"> + <description>of 2D images</description> <requirements> <requirement type="package" version="0.18.1">scikit-image</requirement> <requirement type="package" version="1.2.4">pandas</requirement> @@ -9,31 +9,46 @@ </requirements> <command detect_errors="aggressive"> <![CDATA[ - python '$__tool_directory__/projective_transformation.py' - '$fixed_image' - '$moving_image' - '$warp_matrix' - ./out + ln -s '$moving' ./in.${moving.ext} && + python '$__tool_directory__/projective_transformation.py' + '$fixed' + ./in.${moving.ext} + '$tmat' + ./out.${moving.ext} + && mv ./out.${moving.ext} ./result_image ]]> </command> <inputs> - <param name="moving_image" type="data" format="tiff,png,jpg" label="Moving image (to be transformed)" /> - <param name="fixed_image" type="data" format="tiff,png,jpg" label="Fixed image (the reference)" /> - <param name="warp_matrix" type="data" format="tabular" label="Transformation matrix" /> + <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" /> + <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" /> + <param name="tmat" type="data" format="tabular" label="Transformation matrix" /> </inputs> <outputs> - <data format_source="moving_image" name="warped_image" from_work_dir="out" /> + <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" /> </outputs> <tests> - <test> - <param name="fixed_image" value="sample1.png"/> - <param name="moving_image" value="sample2.png"/> - <param name="warp_matrix" value="warp_matrix.tsv"/> - <output name="warped_image" value="yam.png" ftype="png" compare="sim_size"/> + <test> + <param name="fixed" value="fixed.png"/> + <param name="moving" value="moving.png"/> + <param name="tmat" value="tmat.tsv"/> + <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" /> + </test> + <test> + <param name="fixed" value="fixed_rgb.png"/> + <param name="moving" value="moving_rgb.png"/> + <param name="tmat" value="tmat.tsv"/> + <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" /> + </test> + <test> + <param name="fixed" value="multi_f.tif"/> + <param name="moving" value="multi_m.tif"/> + <param name="tmat" value="tmat.tsv"/> + <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" /> </test> </tests> <help> - **What it does** + +**What it does** This tool performs a projective transformation of the moving image so that it fits the fixed image. Multi-channel and RGB images are supported.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmat.tsv Thu Jan 20 17:14:55 2022 +0000 @@ -0,0 +1,3 @@ +0.9406756518941536 -0.2954926628589712 45.11224440565029 +0.3009254584199789 0.949530052611427 -32.079361599470666 +0.0 0.0 1.0