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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit c045f067a57e8308308cf6329060c7ccd3fc372f |
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modified:
projective_transformation.xml 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 |
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added:
creators.xml tests.xml |
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| diff -r f5744f0e5a81 -r 2f504e075496 creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:26:07 2024 +0000 |
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| @@ -0,0 +1,23 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + +</macros> |
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| diff -r f5744f0e5a81 -r 2f504e075496 projective_transformation.xml --- a/projective_transformation.xml Mon Nov 13 22:12:05 2023 +0000 +++ b/projective_transformation.xml Thu Apr 04 15:26:07 2024 +0000 |
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| @@ -1,5 +1,14 @@ -<tool id="ip_projective_transformation" name="Performs projective transformation with/without labels" version="0.1.2-2" profile="20.05"> +<tool id="ip_projective_transformation" name="Perform projective transformation of an image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description></description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@VERSION_SUFFIX@">3</token> + </macros> + <creator> + <expand macro="creators/bmcv"/> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -7,11 +16,11 @@ <xref type="bio.tools">galaxy_image_analysis</xref> </xrefs> <requirements> - <requirement type="package" version="0.18.1">scikit-image</requirement> + <requirement type="package" version="0.18.3">scikit-image</requirement> <requirement type="package" version="1.2.4">pandas</requirement> - <requirement type="package" version="1.20.2">numpy</requirement> - <requirement type="package" version="1.6.2">scipy</requirement> - <requirement type="package" version="2020.10.1">tifffile</requirement> + <requirement type="package" version="1.24.4">numpy</requirement> + <requirement type="package" version="1.10.1">scipy</requirement> + <requirement type="package" version="2021.7.2">tifffile</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ @@ -25,9 +34,9 @@ ]]> </command> <inputs> - <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" /> + <param name="moving" type="data" format="tiff,png" label="Moving image" help="The image to be transformed." /> + <param name="fixed" type="data" format="tiff,png" label="Fixed image" help="The reference image." /> + <param name="tmat" type="data" format="tabular" label="Transformation matrix" help="Homogeneous transformation matrix (3⨉3)." /> </inputs> <outputs> <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" /> @@ -37,27 +46,28 @@ <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" /> + <expand macro="tests/intensity_image_diff" name="warped" value="moving_warped.png" ftype="png"/> </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" /> + <expand macro="tests/intensity_image_diff" name="warped" value="moving_rgb_warped.png" ftype="png"/> </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" /> + <expand macro="tests/intensity_image_diff" name="warped" value="multi_m_warped.tif" ftype="tiff"/> </test> </tests> <help> -**What it does** + **Performs projective transformation.** - This tool performs a projective transformation of the moving 2D image so that it fits the fixed 2D image. - Multi-channel and RGB images are supported. + This tool performs a projective transformation of 2-D image into the coordinate system of another 2-D image. + Multi-channel images are supported (e.g., RGB). + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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| diff -r f5744f0e5a81 -r 2f504e075496 tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:26:07 2024 +0000 |
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| @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros> |
