Mercurial > repos > thomaswollmann > points2labelimage
changeset 0:14525b8c8d67 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 356f2556bd629e5473d6711ec71372ea17d3e28f
| author | thomaswollmann |
|---|---|
| date | Wed, 12 Dec 2018 05:12:06 -0500 |
| parents | |
| children | |
| files | points2label.py points2label.xml test-data/galaxyIcon_noText.tif test-data/out.tif test-data/points.csv |
| diffstat | 5 files changed, 84 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/points2label.py Wed Dec 12 05:12:06 2018 -0500 @@ -0,0 +1,44 @@ +import argparse +import sys +import numpy as np +import skimage.io +import pandas as pd +import warnings + +def points2label(labels, shape, output_file=None, has_header=False, is_TSV=False): + labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32) + + if is_TSV: + if has_header: + df = pd.read_csv(labels, sep='\t', skiprows=1, header=None) + else: + df = pd.read_csv(labels, sep='\t', header=None) + else: + if has_header: + df = pd.read_csv(labels, skiprows=1, header=None) + else: + df = pd.read_csv(labels, header=None) + + for i in range(0, len(df)): + a_row = df.iloc[i] + labelimg[a_row[0], a_row[1]] = i+1 + + if output_file is not None: + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + skimage.io.imsave(output_file, labelimg, plugin='tifffile') + else: + return labelimg + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file') + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file') + parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file') + parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header') + parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=False, help='label file is TSV') + args = parser.parse_args() + + original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape + + points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/points2label.xml Wed Dec 12 05:12:06 2018 -0500 @@ -0,0 +1,33 @@ +<tool id="points2labelimage" name="Points 2 Label" version="0.2"> + <description>Points to Label Image</description> + <requirements> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="0.14.0">scikit-image</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header $is_tsv + ]]> + </command> + <inputs> + <param name="input" type="data" format="csv" label="Point CSV file"/> + <param name="org_file" type="data" format="tiff" label="Original label image file"/> + <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> + <param name="is_tsv" optional="true" type="boolean" checked="false" truevalue="--is_tsv True" falsevalue="" help="tab separated input file"/> + </inputs> + <outputs> + <data name="output" format="tiff"/> + </outputs> + <tests> + <test> + <param name="input" value="points.csv"/> + <param name="org_file" value="galaxyIcon_noText.tif"/> + <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/><!--to allow a change in e.g. date--> + </test> + </tests> + <help> This tool converts points to a label image. </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>