Mercurial > repos > imgteam > mergeneighboursinlabelimage
changeset 0:07ac39c0e949 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\mergeneighboursinlabelimage commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:38:38 -0500 |
| parents | |
| children | c6a6ab7c9940 |
| files | mergeneighboursinlabelimage.py mergeneighboursinlabelimage.xml test-data/galaxyIcon_noText.tif test-data/out.tiff |
| diffstat | 4 files changed, 82 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mergeneighboursinlabelimage.py Sat Feb 09 14:38:38 2019 -0500 @@ -0,0 +1,48 @@ +import argparse +import sys +import skimage.io +import skimage.util +from skimage.measure import regionprops +import scipy.spatial.distance +import numpy as np +import warnings + +def merge_n(img, dist=50): + props = regionprops(img) + found = False + for i in range(0, len(props)): + i_coords = props[i].coords + for q in range(0, len(props)): + if i==q: + continue + q_coords = props[q].coords + iq_dist = np.min(scipy.spatial.distance.cdist(i_coords, q_coords, 'euclidean')) + if iq_dist <= dist: + props[q].label = props[i].label + for a_point in range(0, q_coords.shape[0]): + img[q_coords[a_point, 0], q_coords[a_point, 1]] = props[i].label + found = True + if found: + merge_n(img, dist) + return img + +if __name__ == "__main__": + 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( + '-c', + dest='cluster_merge', + type=int, + required=False, + default=50, + help='Distance in pixel of clusters which are merged', + ) + args = parser.parse_args() + + label_image = skimage.io.imread(args.input_file.name) + label_image = merge_n(label_image, args.cluster_merge) + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + res = skimage.util.img_as_uint(label_image) + skimage.io.imsave(args.out_file.name, res, plugin="tifffile")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mergeneighboursinlabelimage.xml Sat Feb 09 14:38:38 2019 -0500 @@ -0,0 +1,34 @@ +<tool id="ip_merge_neighbours_in_label" name="Merge Neighbours in Label" version="0.2"> + <description>Merge Neighbours in Label Image</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/mergeneighboursinlabelimage.py' '$input' ./tmp.tiff -c $c + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff,png,jpg,bmp" label="Label Image File"/> + <param label="Distance in pixel of objects which are merged" name="c" type="integer" value="50"/> + </inputs> + <outputs> + <data format="tiff" name="output" from_work_dir="tmp.tiff"/> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif"/> + <param name="c" value="10"/> + <output name="output" file="out.tiff" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help> + **What it does** + + This tools merges nearby objects in a label image using the minimum pixel distance. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>