Mercurial > repos > imgteam > coordinates_of_roi
changeset 0:0d30ffea8874 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:33:43 -0500 |
| parents | |
| children | ee045a6bbdef |
| files | coordinates_of_roi.py coordinates_of_roi.xml test-data/table.tsv test-data/table2.tsv test-data/test.png |
| diffstat | 5 files changed, 104 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coordinates_of_roi.py Sat Feb 09 14:33:43 2019 -0500 @@ -0,0 +1,40 @@ +import argparse +import pandas as pd +import skimage.io +import skimage.color +import warnings + +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) + x = [] + y = [] + for i in range(data.shape[0]): + for j in range(data.shape[1]): + if white_obj == False: + if data[i,j] <= threshold: + x.append(j + offset[0]) + y.append(i + offset[1]) + elif data[i,j] >= threshold: + x.append(j + offset[0]) + y.append(i + 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('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])
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coordinates_of_roi.xml Sat Feb 09 14:33:43 2019 -0500 @@ -0,0 +1,50 @@ +<tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.3"> + <description></description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/coordinates_of_roi.py' + '$im' + '$pixel_table' + $offset_x $offset_y + $white_obj + --threshold $threshold + ]]> + </command> + <inputs> + <param name="im" type="data" format="png" label="Source file" /> + <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" /> + </outputs> + <tests> + <test> + <param name="im" value="test.png"/> + <param name="white_obj" value="true"/> + <output name="pixel_table" value="table.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="table2.tsv" ftype="tabular"/> + </test> + </tests> + <help> + **What it does** + + This tool creates a table containing the pixelcoordinates of the Region of Interest (ROI). + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table.tsv Sat Feb 09 14:33:43 2019 -0500 @@ -0,0 +1,7 @@ +x y +4 5 +5 5 +6 5 +7 5 +8 5 +9 5