| Previous changeset 3:9bb446db4a1e (2023-11-13) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 00199464fa2aa1928a49e2379edf199c3db91533 |
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modified:
binary2label.xml |
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added:
2d_split_binaryimage_by_watershed.py test-data/in.tif test-data/out.tif |
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| diff -r 9bb446db4a1e -r 984358e43242 2d_split_binaryimage_by_watershed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_split_binaryimage_by_watershed.py Tue Nov 14 08:27:27 2023 +0000 |
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| @@ -0,0 +1,28 @@ +import argparse +import sys + +import skimage.io +import skimage.util +from scipy import ndimage as ndi +from skimage.feature import peak_local_max +from skimage.morphology import watershed + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Split binaryimage by watershed') + parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') + parser.add_argument('min_distance', type=int, default=100, help='Minimum distance to next object') + args = parser.parse_args() + + img_in = skimage.io.imread(args.input_file.name) + distance = ndi.distance_transform_edt(img_in) + local_maxi = peak_local_max(distance, + indices=False, + min_distance=args.min_distance, + labels=img_in) + markers = ndi.label(local_maxi)[0] + res = watershed(-distance, markers, mask=img_in) + + res = skimage.util.img_as_uint(res) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |
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| diff -r 9bb446db4a1e -r 984358e43242 binary2label.xml --- a/binary2label.xml Mon Nov 13 22:10:33 2023 +0000 +++ b/binary2label.xml Tue Nov 14 08:27:27 2023 +0000 |
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| @@ -1,5 +1,9 @@ -<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="0.4-2"> +<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description></description> + <macros> + <token name="@TOOL_VERSION@">0.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -7,16 +11,34 @@ <xref type="bio.tools">galaxy_image_analysis</xref> </xrefs> <requirements> - <requirement type="package" version="0.12.3">scikit-image</requirement> + <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="0.15.1">tifffile</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="5.3.0">pillow</requirement> + <requirement type="package" version="1.2.1">scipy</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ - python '$__tool_directory__/binary2label.py' '$input' '$output' + #if str($mode.mode_selector) == 'cca': + python '$__tool_directory__/binary2label.py' '$input' '$output' + #elif str($mode.mode_selector) == 'watershed': + python '$__tool_directory__/2d_split_binaryimage_by_watershed.py' '$input' '$output' $min_distance + #end if ]]> </command> <inputs> - <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/> + <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary image"/> + <conditional name="mode"> + <param name="mode_selector" type="select" label="Mode"> + <option value="cca">Connected component analysis</option> + <option value="watershed">Watershed transform</option> + </param> + <when value="cca"> + </when> + <when value="watershed"> + <param name="min_distance" type="integer" min="0" value="5" label="Minimum distance between two objects" /> + </when> + </conditional> </inputs> <outputs> <data format="tiff" name="output"/> @@ -24,13 +46,24 @@ <tests> <test> <param name="input" value="galaxyIcon_noText.tif" /> + <conditional name="mode"> + <param name="mode_selector" value="cca" /> + </conditional> <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/> </test> + <test> + <param name="input" value="in.tif"/> + <conditional name="mode"> + <param name="mode_selector" value="watershed" /> + <param name="min_distance" value="10" /> + </conditional> + <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + </test> </tests> <help> - **What it does** + This tool assigns each object a unique label. - This tool assigns every object an own grey value. + Individual objects are determined using connected component analysis, or distance transform and watershed. </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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| diff -r 9bb446db4a1e -r 984358e43242 test-data/in.tif |
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| Binary file test-data/in.tif has changed |
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| diff -r 9bb446db4a1e -r 984358e43242 test-data/out.tif |
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| Binary file test-data/out.tif has changed |