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annotate ParseInput.py @ 1:aba3655fdef0 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
author watsocam
date Fri, 11 Mar 2022 23:35:52 +0000
parents 928db0f952e3
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1 #Functions for parsing command line arguments for ome ilastik prep
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2 import argparse
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5 def ParseInputDataExtract():
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6 """Function for parsing command line arguments for input to single-cell
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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7 data extraction"""
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9 #if __name__ == '__main__':
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument('--masks',nargs='+', required=True)
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12 parser.add_argument('--image', required=True)
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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13 parser.add_argument('--channel_names', required=True)
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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14 parser.add_argument('--output', required=True)
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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15 parser.add_argument(
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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16 '--mask_props', nargs = "+",
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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17 help="""
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18 Space separated list of additional metrics to be calculated for every mask.
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19 This is for metrics that depend only on the cell mask. If the metric depends
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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20 on signal intensity, use --intensity-props instead.
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21 See list at https://scikit-image.org/docs/dev/api/skimage.measure.html#regionprops
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22 """
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23 )
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24 parser.add_argument(
aba3655fdef0 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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25 '--intensity_props', nargs = "+",
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26 help="""
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27 Space separated list of additional metrics to be calculated for every marker separately.
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28 By default only mean intensity is calculated.
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29 If the metric doesn't depend on signal intensity, use --mask-props instead.
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30 See list at https://scikit-image.org/docs/dev/api/skimage.measure.html#regionprops
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31 Additionally available is gini_index, which calculates a single number
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32 between 0 and 1, representing how unequal the signal is distributed in each region.
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33 See https://en.wikipedia.org/wiki/Gini_coefficient
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34 """
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35 )
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36 #parser.add_argument('--suffix')
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37 args = parser.parse_args()
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38 #Create a dictionary object to pass to the next function
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39 dict = {'masks': args.masks, 'image': args.image,\
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40 'channel_names': args.channel_names,'output':args.output,
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41 'intensity_props': set(args.intensity_props if args.intensity_props is not None else []).union(["intensity_mean"]),
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42 'mask_props': args.mask_props,
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43 }
0
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44 #Print the dictionary object
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45 print(dict)
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46 #Return the dictionary
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47 return dict