Mercurial > repos > imgteam > binaryimage2points
changeset 0:cb1eaebdb4c4 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:31:13 -0500 |
| parents | |
| children | f38f42d55813 |
| files | binaryimage2points.py binaryimage2points.xml test-data/galaxyIcon_noText.tif test-data/points.tsv |
| diffstat | 4 files changed, 86 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/binaryimage2points.py Sat Feb 09 14:31:13 2019 -0500 @@ -0,0 +1,53 @@ +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 +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") + + img_in = skimage.io.imread(input_file, plugin='tifffile') + + #make label image + label = skimage.measure.label(img_in) + + #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) + # 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 (TSV)') + + args = parser.parse_args() + input_file = args.input_file + out_file = args.out_file + + #TOOL + out_dataFrame = binaryimage2points(input_file) + + #Print to csv file + out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/binaryimage2points.xml Sat Feb 09 14:31:13 2019 -0500 @@ -0,0 +1,32 @@ +<tool id="ip_binaryimage_to_points" name="Binary To Points" version="0.1"> + <description>Converts Binary Image to Points</description> + <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="0.23.4">pandas</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/binaryimage2points.py' '$input' '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Binary Image File"/> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif" /> + <output name="output" value="points.tsv" ftype="tabular" /> + </test> + </tests> + <help> + **What it does** + + This tool converts an image to points.</help> + <citations> + <citation type="doi">10.7717/peerj.453</citation> + </citations> +</tool>