| Previous changeset 4:37662cbf44b8 (2023-11-17) Next changeset 6:2495f8b2aefd (2024-04-24) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c045f067a57e8308308cf6329060c7ccd3fc372f |
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modified:
overlay_images.xml test-data/test4.png |
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added:
creators.xml test-data/sample1_uint8_rgb.png test-data/test5.png tests.xml |
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| diff -r 37662cbf44b8 -r 002f7bad3e82 creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:25:58 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 37662cbf44b8 -r 002f7bad3e82 overlay_images.xml --- a/overlay_images.xml Fri Nov 17 23:34:57 2023 +0000 +++ b/overlay_images.xml Thu Apr 04 15:25:58 2024 +0000 |
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| @@ -1,9 +1,15 @@ <tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description></description> <macros> + <import>creators.xml</import> + <import>tests.xml</import> <token name="@TOOL_VERSION@">0.0.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> + <creator> + <expand macro="creators/bmcv"/> + <expand macro="creators/thawn"/> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -38,10 +44,10 @@ </command> <inputs> <conditional name="method_option"> - <param name="method" type="select" label="How to visualize the overlay?"> + <param name="method" type="select" label="Type of the overlay"> <option value="coloc_vis" selected="True">Colocalization</option> - <option value="blending">Blending</option> - <option value="seg_contour">Segmentation mask over image</option> + <option value="blending">Linear blending</option> + <option value="seg_contour">Segmentation contours over image</option> </param> <when value="coloc_vis"> <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" /> @@ -53,7 +59,7 @@ <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/> </when> <when value="seg_contour"> - <param name="im1" type="data" format="tiff,png" label="Image" /> + <param name="im1" type="data" format="tiff,png" label="Intensity image" /> <param name="im2" type="data" format="tiff,png" label="Label image" /> <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" /> <param name="color" type="color" value="#ff0000" label="Contour color"/> @@ -75,14 +81,14 @@ <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="coloc_vis"/> - <output name="out_tiff" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/> </test> <test expect_num_outputs="1"> <param name="im1" value="mask1.tif"/> <param name="im2" value="mask1r.tif"/> <param name="method" value="blending"/> <param name="alpha" value="0.3"/> - <output name="out_tiff" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/> </test> <test expect_num_outputs="1"> <param name="im1" value="sample1_uint8.tif"/> @@ -91,15 +97,15 @@ <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> <param name="show_label" value="--show_label"/> - <output name="out_png" value="test3.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/> </test> - <test expect_num_outputs="1"><!-- segemtation overlay, 8bit test --> + <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test --> <param name="im1" value="sample1_uint8.tif"/> <param name="im2" value="mask2.tif"/> <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> - <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/> </test> <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test --> <param name="im1" value="sample1_uint16.tif"/> @@ -107,14 +113,26 @@ <param name="method" value="seg_contour"/> <param name="thickness" value="2"/> <param name="color" value="#ff0000"/> - <output name="out_png" value="test4.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/> + </test> + <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test --> + <param name="im1" value="sample1_uint8_rgb.png"/> + <param name="im2" value="mask2.tif"/> + <param name="method" value="seg_contour"/> + <param name="thickness" value="2"/> + <param name="color" value="#ff0000"/> + <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/> </test> </tests> - <help> - <![CDATA[ - This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image. - ]]> - </help> + <help><![CDATA[ + + **Overlays two images for visualization.** + + This tool overlays two image to visualize *linear image blending*, *colocalization*, or *segmentation contours* + over an intensity image. For *image blending* and *colocalization*, the input images must be single-channel 2-D + images. For *segmentation contours*, the intensity must be a 2-D single-channel or 2-D RGB image. + + ]]></help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> </citations> |
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| diff -r 37662cbf44b8 -r 002f7bad3e82 test-data/sample1_uint8_rgb.png |
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| diff -r 37662cbf44b8 -r 002f7bad3e82 test-data/test4.png |
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| diff -r 37662cbf44b8 -r 002f7bad3e82 test-data/test5.png |
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| diff -r 37662cbf44b8 -r 002f7bad3e82 tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:25:58 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> |
