Mercurial > repos > thomaswollmann > labelimage2points
changeset 0:732d95b2b030 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
| author | thomaswollmann |
|---|---|
| date | Wed, 12 Dec 2018 04:38:34 -0500 |
| parents | |
| children | |
| files | labelimage2points.py labelimage2points.xml test-data/label.tif test-data/points.csv |
| diffstat | 4 files changed, 77 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/labelimage2points.py Wed Dec 12 04:38:34 2018 -0500 @@ -0,0 +1,48 @@ +import argparse +import sys +import pandas as pd +import skimage.io +from skimage.measure import label +from skimage.data import checkerboard +import numpy as np + + + +def labelimage2points(input_file): + img_in = skimage.io.imread(input_file) + + #amount of regions + amount_label = np.max(img_in) + + # iterate over all regions in order to calc center of mass + center_mass = [] + for i in range(1,amount_label+1): + #get coordinates of region + coord = np.where(img_in==i) + # be carefull with x,y coordinates + center_mass.append([np.mean(coord[1]),np.mean(coord[0])]) + + #make data frame of detections + out_dataFrame = pd.DataFrame(center_mass) + + + #return + return(out_dataFrame) + + + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('input_file', help='input file') + parser.add_argument('out_file', help='out file (CSV)') + + args = parser.parse_args() + input_file = args.input_file + out_file = args.out_file + + #TOOL + out_dataFrame = labelimage2points(input_file) + + #Print to csv file + out_dataFrame.to_csv(out_file,index=False,header=False)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/labelimage2points.xml Wed Dec 12 04:38:34 2018 -0500 @@ -0,0 +1,28 @@ +<tool id="labelimage2points" name="Label 2 Points" version="0.1"> + <description>Converts label image to points.</description> + <requirements> + <requirement type="package" version="0.12.3" >scikit-image</requirement> + <requirement type="package" version="0.21.0" >pandas</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/labelimage2points.py' '$input' '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff,png,jpg,bmp" label="Label image file"/> + </inputs> + <outputs> + <data format="csv" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="label.tif" /> + <output name="output" value="points.csv" ftype="csv" /> + </test> + </tests> + <help>Calculates the center of mass for all differently colored regions in the image.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>