Mercurial > repos > imgteam > 2d_histogram_equalization
changeset 2:3f3783846dc0 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author | imgteam |
---|---|
date | Thu, 04 Apr 2024 15:23:34 +0000 |
parents | 77f7159d775a |
children | b1c2c210813c |
files | creators.xml histogram_equalization.xml tests.xml |
diffstat | 3 files changed, 138 insertions(+), 8 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:23:34 2024 +0000 @@ -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>
--- a/histogram_equalization.xml Mon Nov 13 22:10:25 2023 +0000 +++ b/histogram_equalization.xml Thu Apr 04 15:23:34 2024 +0000 @@ -1,13 +1,23 @@ -<tool id="ip_histogram_equalization" name="Perform histogram equalization" version="0.0.1-2"> - <description>with scikit-image</description> +<tool id="ip_histogram_equalization" name="Perform histogram equalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>with scikit-image</description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">0.14.2</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <creator> + <expand macro="creators/bmcv" /> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> <xrefs> - <xref type="bio.tools">galaxy_image_analysis</xref> + <xref type="bio.tools">scikit-image</xref> + <xref type="biii">scikit-image</xref> </xrefs> <requirements> - <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement> <requirement type="package" version="1.15.4">numpy</requirement> <requirement type="package" version="5.3.0">pillow</requirement> <requirement type="package" version="0.15.1">tifffile</requirement> @@ -18,8 +28,8 @@ ]]> </command> <inputs> - <param name="input" type="data" format="tiff" label="Source file" /> - <param name="h_type" type="select" label="Histogram Equalization Algorithm"> + <param name="input" type="data" format="tiff" label="Input image" /> + <param name="h_type" type="select" label="Histogram equalization algorithm"> <option value="default">Stretching</option> <option value="clahe" selected="True">CLAHE</option> </param> @@ -30,12 +40,14 @@ <tests> <test> <param name="input" value="sample.tif"/> - <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> <param name="h_type" value="default"/> + <expand macro="tests/intensity_image_diff" name="output" value="out.tif" ftype="tiff"/> </test> </tests> <help> - Applies histogram equalization to an image. + + **Applies histogram equalization to an image.** + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:23:34 2024 +0000 @@ -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>