# HG changeset patch # User galaxyp # Date 1682415006 0 # Node ID b5e9cebb27e393a60960cd044aefaf73d2ca3fd6 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909 diff -r 000000000000 -r b5e9cebb27e3 qupath_roi_splitter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qupath_roi_splitter.py Tue Apr 25 09:30:06 2023 +0000 @@ -0,0 +1,83 @@ +import argparse + +import cv2 +import geojson +import numpy as np +import pandas as pd + + +def draw_poly(input_df, input_img, col=(0, 0, 0)): + s = np.array(input_df) + output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col) + return output_img + + +def split_qupath_roi(in_roi): + with open(in_roi) as file: + qupath_roi = geojson.load(file) + + # HE dimensions + dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]] + + tma_name = qupath_roi["name"] + cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]] + + # create numpy array with white background + img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8") + img.fill(255) + + for cell_type in cell_types: + for i, roi in enumerate(qupath_roi["features"]): + if roi["properties"]["classification"]["name"] == cell_type: + if len(roi["geometry"]["coordinates"]) == 1: + # Polygon w/o holes + img = draw_poly(roi["geometry"]["coordinates"][0], img) + else: + first_roi = True + for sub_roi in roi["geometry"]["coordinates"]: + # Polygon with holes + if not isinstance(sub_roi[0][0], list): + if first_roi: + img = draw_poly(sub_roi, img) + first_roi = False + else: + # holes in ROI + img = draw_poly(sub_roi, img, col=(255, 255, 255)) + else: + # MultiPolygon with holes + for sub_coord in sub_roi: + if first_roi: + img = draw_poly(sub_coord, img) + first_roi = False + else: + # holes in ROI + img = draw_poly(sub_coord, img, col=(255, 255, 255)) + + # get all black pixel + coords_arr = np.column_stack(np.where(img == (0, 0, 0))) + + # remove duplicated rows + coords_arr_xy = coords_arr[coords_arr[:, 2] == 0] + + # remove last column + coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1) + + # to pandas and rename columns to x and y + coords_df = pd.DataFrame(coords_arr_xy, columns=['x', 'y']) + + # drop duplicates + coords_df = coords_df.drop_duplicates( + subset=['x', 'y'], + keep='last').reset_index(drop=True) + + coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)") + parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)") + parser.add_argument('--version', action='version', version='%(prog)s 0.1.0') + args = parser.parse_args() + + if args.qupath_roi: + split_qupath_roi(args.qupath_roi) diff -r 000000000000 -r b5e9cebb27e3 qupath_roi_splitter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qupath_roi_splitter.xml Tue Apr 25 09:30:06 2023 +0000 @@ -0,0 +1,55 @@ + + Split ROI coordinates of QuPath TMA annotation by cell type (classification) + + geojson + numpy + opencv + pandas + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r b5e9cebb27e3 test-data/annotations_TMA_E-5.geojson --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_TMA_E-5.geojson Tue Apr 25 09:30:06 2023 +0000 @@ -0,0 +1,4930 @@ +{ "name": "E-5","featureNames":[ + "E-5 - Tumor", + "E-5 - Stroma" +],"dim": {"width": 23840, "height": 18064},"type": "FeatureCollection","features":[ + { + "type": "Feature", + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [21383.93, 14321.04], + [21379.03, 14324.49], + [21377.1, 14325], + [21371.26, 14323.64], + [21369.59, 14324.75], + [21365.28, 14331.43], + [21365, 14335.41], + [21366.68, 14339.02], + [21369.8, 14341.47], + [21373.79, 14345.9], + [21377.38, 14347.67], + [21381.34, 14347.83], + [21384.67, 14345.66], + [21386.21, 14339.93], + 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