Mercurial > repos > imgteam > binary2labelimage
changeset 3:a041e4e9d449 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
| author | imgteam |
|---|---|
| date | Mon, 12 May 2025 08:15:32 +0000 |
| parents | 938e2358eb80 |
| children | |
| files | 2d_split_binaryimage_by_watershed.py binary2label.py binary2label.xml creators.xml test-data/galaxyIcon_noText.tif test-data/galaxyIcon_noText.tiff test-data/in.tiff test-data/label.tif test-data/label.tiff test-data/out.tiff test-data/uint8_z12_x11_y10-output.tiff test-data/uint8_z12_x11_y10.tiff |
| diffstat | 12 files changed, 146 insertions(+), 25 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2d_split_binaryimage_by_watershed.py Mon May 12 08:15:32 2025 +0000 @@ -0,0 +1,33 @@ +import argparse +import sys + +import numpy as np +import skimage.io +import skimage.util +from scipy import ndimage as ndi +from skimage.feature import peak_local_max +from skimage.segmentation 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_max_indices = peak_local_max( + distance, + min_distance=args.min_distance, + labels=img_in, + ) + local_max_mask = np.zeros(img_in.shape, dtype=bool) + local_max_mask[tuple(local_max_indices.T)] = True + markers = ndi.label(local_max_mask)[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")
--- a/binary2label.py Wed Dec 18 09:56:41 2019 +0000 +++ b/binary2label.py Mon May 12 08:15:32 2025 +0000 @@ -1,20 +1,27 @@ import argparse -import sys -import skimage.io -from skimage.measure import label -import numpy as np -import warnings -from PIL import Image -import skimage.util +import giatools +import scipy.ndimage as ndi +import tifffile + + +# Parse CLI parameters parser = argparse.ArgumentParser() -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('input', type=str, help='input file') +parser.add_argument('output', type=str, help='output file (TIFF)') args = parser.parse_args() - -img_in = skimage.io.imread(args.input_file.name) > 0 -res = label(img_in) -res = skimage.util.img_as_uint(res) + +# Read the input image with the original axes +img = giatools.Image.read(args.input) +img = img.normalize_axes_like( + img.original_axes, +) -res = Image.fromarray(res) -res.save(args.out_file.name, "tiff") +# Make sure the image is truly binary +img_arr_bin = (img.data > 0) + +# Perform the labeling +img.data = ndi.label(img_arr_bin)[0] + +# Write the result image (same axes as input image) +tifffile.imwrite(args.output, img.data, metadata=dict(axes=img.axes))
--- a/binary2label.xml Wed Dec 18 09:56:41 2019 +0000 +++ b/binary2label.xml Mon May 12 08:15:32 2025 +0000 @@ -1,30 +1,83 @@ -<tool id="ip_binary_to_labelimage" name="Binary 2 Label" version="0.4"> - <description>Converts Binary to Label Image</description> +<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description></description> + <macros> + <import>creators.xml</import> + <token name="@TOOL_VERSION@">0.6</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> + </xrefs> <requirements> - <requirement type="package" version="0.12.3">scikit-image</requirement> - <requirement type="package" version="0.15.1">tifffile</requirement> + <requirement type="package" version="0.4.0">giatools</requirement> + <requirement type="package" version="1.12.0">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" selected="true">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"/> </outputs> <tests> <test> - <param name="input" value="galaxyIcon_noText.tif" /> - <output name="output" value="label.tif" ftype="tiff" compare="sim_size"/> + <param name="input" value="galaxyIcon_noText.tiff" /> + <conditional name="mode"> + <param name="mode_selector" value="cca" /> + </conditional> + <output name="output" value="label.tiff" ftype="tiff" compare="image_diff"/> + </test> + <test> + <param name="input" value="in.tiff"/> + <conditional name="mode"> + <param name="mode_selector" value="watershed" /> + <param name="min_distance" value="10" /> + </conditional> + <output name="output" value="out.tiff" ftype="tiff" compare="image_diff"/> + </test> + <test> + <param name="input" value="uint8_z12_x11_y10.tiff"/> + <conditional name="mode"> + <param name="mode_selector" value="cca" /> + </conditional> + <output name="output" value="uint8_z12_x11_y10-output.tiff" ftype="tiff" compare="image_diff"> + <assert_contents> + <has_image_width width="11"/> + <has_image_height height="10"/> + <has_image_depth depth="12"/> + </assert_contents> + </output> </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Mon May 12 08:15:32 2025 +0000 @@ -0,0 +1,28 @@ +<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/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <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>