Mercurial > repos > imgteam > labelimage2points
diff labelimage2points.py @ 2:3b7460735223 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:11:16 +0000 |
| parents | 07525a7d9ea0 |
| children |
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--- a/labelimage2points.py Mon Jul 22 05:03:12 2019 -0400 +++ b/labelimage2points.py Mon Nov 13 22:11:16 2023 +0000 @@ -1,33 +1,29 @@ import argparse -import sys + +import numpy as np 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 + 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) + 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])]) + center_mass.append([np.mean(coord[1]), np.mean(coord[0])]) - #make data frame of detections + # make data frame of detections out_dataFrame = pd.DataFrame(center_mass) - - #return - return(out_dataFrame) + # return + return out_dataFrame if __name__ == "__main__": @@ -35,12 +31,12 @@ 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 + args = parser.parse_args() + input_file = args.input_file + out_file = args.out_file - #TOOL + # TOOL out_dataFrame = labelimage2points(input_file) - #Print to csv file + # Print to csv file out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")