Mercurial > repos > imgteam > binaryimage2points
changeset 1:f38f42d55813 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:10:37 +0000 |
| parents | cb1eaebdb4c4 |
| children | |
| files | binaryimage2points.py binaryimage2points.xml |
| diffstat | 2 files changed, 35 insertions(+), 32 deletions(-) [+] |
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--- a/binaryimage2points.py Sat Feb 09 14:31:13 2019 -0500 +++ b/binaryimage2points.py Mon Nov 13 22:10:37 2023 +0000 @@ -1,53 +1,49 @@ import argparse -import sys +import warnings + +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 -import warnings - def binaryimage2points(input_file): # ignore warnings that arise when importing a package that was compiled against an older version of numpy than installed; https://github.com/numpy/numpy/pull/432 - warnings.filterwarnings("ignore") + warnings.filterwarnings("ignore") + + img_in = skimage.io.imread(input_file, plugin='tifffile') - img_in = skimage.io.imread(input_file, plugin='tifffile') - - #make label image + # make label image label = skimage.measure.label(img_in) - - #amount of regions + + # amount of regions amount_label = np.max(label) - + # 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(label==i) + for i in range(1, amount_label + 1): + # get coordinates of region + coord = np.where(label == 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__": parser = argparse.ArgumentParser() parser.add_argument('input_file', help='input file') parser.add_argument('out_file', help='out file (TSV)') - - args = parser.parse_args() - input_file = args.input_file - out_file = args.out_file - - #TOOL + + args = parser.parse_args() + input_file = args.input_file + out_file = args.out_file + + # TOOL out_dataFrame = binaryimage2points(input_file) - - #Print to csv file + + # Print to csv file out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")
--- a/binaryimage2points.xml Sat Feb 09 14:31:13 2019 -0500 +++ b/binaryimage2points.xml Mon Nov 13 22:10:37 2023 +0000 @@ -1,9 +1,16 @@ -<tool id="ip_binaryimage_to_points" name="Binary To Points" version="0.1"> - <description>Converts Binary Image to Points</description> +<tool id="ip_binaryimage_to_points" name="Convert binary image to points (center of masses)" version="0.1-2"> + <description></description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> <requirements> <requirement type="package" version="1.15.4">numpy</requirement><!--https://github.com/numpy/numpy/pull/432 --> - <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="0.14.2">scikit-image</requirement> <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> <command> <![CDATA[