Mercurial > repos > imgteam > coordinates_of_roi
changeset 3:02a686fc1654 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
| author | imgteam |
|---|---|
| date | Mon, 25 Mar 2019 11:15:39 -0400 |
| parents | 24d9bd16c953 |
| children | 00175f4a2bbb |
| files | coordinates_of_roi.py coordinates_of_roi.xml |
| diffstat | 2 files changed, 2 insertions(+), 14 deletions(-) [+] |
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--- a/coordinates_of_roi.py Wed Mar 20 09:18:06 2019 -0400 +++ b/coordinates_of_roi.py Mon Mar 25 11:15:39 2019 -0400 @@ -14,7 +14,7 @@ img_width = data.shape[1] for j in range(img_width): for i in range(img_height): - if white_obj == False: + if white_obj == False: if data[i,j] <= threshold: x.append(i + offset[0]) y.append(j + offset[1]) @@ -31,12 +31,10 @@ 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('offset_x', type=int, help='offset in x direction (width)', default=0) - parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0) 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, [args.offset_x, args.offset_y]) + get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold)
--- a/coordinates_of_roi.xml Wed Mar 20 09:18:06 2019 -0400 +++ b/coordinates_of_roi.xml Mon Mar 25 11:15:39 2019 -0400 @@ -9,7 +9,6 @@ python '$__tool_directory__/coordinates_of_roi.py' '$im' '$pixel_table' - $offset_x $offset_y $white_obj --threshold $threshold ]]> @@ -19,8 +18,6 @@ <param name="white_obj" type="boolean" truevalue="--white_obj" falsevalue="" checked="false" label="Set to Yes if object is white and background black, otherwise set to No" /> <param name="threshold" type="float" value="0.5" label="Threshold value" /> - <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" /> - <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" /> </inputs> <outputs> <data format="tabular" name="pixel_table" /> @@ -31,13 +28,6 @@ <param name="white_obj" value="true"/> <output name="pixel_table" value="newtable.tsv" ftype="tabular"/> </test> - <test> - <param name="im" value="test.png"/> - <param name="white_obj" value="true"/> - <param name="offset_x" value="1"/> - <param name="offset_y" value="2"/> - <output name="pixel_table" value="newtable2.tsv" ftype="tabular"/> - </test> </tests> <help> **What it does**