Mercurial > repos > imgteam > coordinates_of_roi
changeset 4:00175f4a2bbb draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:10:52 +0000 |
| parents | 02a686fc1654 |
| children | |
| files | coordinates_of_roi.py coordinates_of_roi.xml |
| diffstat | 2 files changed, 31 insertions(+), 24 deletions(-) [+] |
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--- a/coordinates_of_roi.py Mon Mar 25 11:15:39 2019 -0400 +++ b/coordinates_of_roi.py Mon Nov 13 22:10:52 2023 +0000 @@ -1,10 +1,11 @@ import argparse + import pandas as pd -import skimage.io import skimage.color -import warnings +import skimage.io -def get_pixel_values(im, pixel_table, white_obj, threshold, offset=[0,0]): + +def get_pixel_values(im, pixel_table, white_obj, threshold, offset=[0, 0]): data = skimage.io.imread(im) if len(data.shape) == 3 and data.shape[-1] > 1: data = skimage.color.rgb2grey(data) @@ -14,27 +15,26 @@ img_width = data.shape[1] for j in range(img_width): for i in range(img_height): - if white_obj == False: - if data[i,j] <= threshold: + if not white_obj: + if data[i, j] <= threshold: x.append(i + offset[0]) y.append(j + offset[1]) - elif data[i,j] >= threshold: - x.append(i + offset[0]) - y.append(j + offset[1]) - + elif data[i, j] >= threshold: + x.append(i + offset[0]) + y.append(j + offset[1]) + df = pd.DataFrame() df['x'] = x df['y'] = y - df.to_csv(pixel_table, sep="\t", index = False) - -if __name__=="__main__": - parser = argparse.ArgumentParser(description = "Create a csv table with Coordinates of the ROI") - parser.add_argument("im", help = "Paste path to out.png (output created by transformation)") - parser.add_argument("pixel_table", help = "Paste path to file in which list with all pixles > threshold should be saved") - parser.add_argument("--white_obj", dest = "white_obj", default=False, help = "If set objects in image are white otherwise black", action = "store_true") - parser.add_argument("--threshold", dest = "threshold", default = 0.5, help = "Enter desired threshold value", type = float) - - args = parser.parse_args() - # with warnings.catch_warnings(): - # warnings.simplefilter("ignore") - get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold) + df.to_csv(pixel_table, sep="\t", index=False) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Create a csv table with Coordinates of the ROI") + parser.add_argument("im", help="Paste path to out.png (output created by transformation)") + parser.add_argument("pixel_table", help="Paste path to file in which list with all pixles > threshold should be saved") + parser.add_argument("--white_obj", dest="white_obj", default=False, help="If set objects in image are white otherwise black", action="store_true") + parser.add_argument("--threshold", dest="threshold", default=0.5, help="Enter desired threshold value", type=float) + + args = parser.parse_args() + get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold)
--- a/coordinates_of_roi.xml Mon Mar 25 11:15:39 2019 -0400 +++ b/coordinates_of_roi.xml Mon Nov 13 22:10:52 2023 +0000 @@ -1,14 +1,21 @@ -<tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.4"> +<tool id="ip_coordinates_of_roi" name="Convert binary image to points (point coordinates)" version="0.0.4-2"> <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="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 detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/coordinates_of_roi.py' '$im' - '$pixel_table' + '$pixel_table' $white_obj --threshold $threshold ]]>