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annotate labelimage2points.py @ 2:3b7460735223 draft default tip

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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
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
3 import numpy as np
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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4 import pandas as pd
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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5 import skimage.io
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 def labelimage2points(input_file):
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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9 img_in = skimage.io.imread(input_file)
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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11 # amount of regions
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 amount_label = np.max(img_in)
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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14 # iterate over all regions in order to calc center of mass
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 center_mass = []
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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16 for i in range(1, amount_label + 1):
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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17 # get coordinates of region
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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18 coord = np.where(img_in == i)
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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19 # be carefull with x,y coordinates
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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20 center_mass.append([np.mean(coord[1]), np.mean(coord[0])])
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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22 # make data frame of detections
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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23 out_dataFrame = pd.DataFrame(center_mass)
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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25 # return
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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26 return out_dataFrame
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 if __name__ == "__main__":
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 parser = argparse.ArgumentParser()
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 parser.add_argument('input_file', help='input file')
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 parser.add_argument('out_file', help='out file (CSV)')
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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34 args = parser.parse_args()
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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35 input_file = args.input_file
3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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36 out_file = args.out_file
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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38 # TOOL
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 out_dataFrame = labelimage2points(input_file)
39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3b7460735223 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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41 # Print to csv file
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39e6d6a84257 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/labelimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")