Mercurial > repos > galaxyp > qupath_roi_splitter

comparison qupath_roi_splitter.py @ 3:24ccdcfbabac draft

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planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 00029e8a3ee400f69a6dbe9e556ec9c27c6979cb
author galaxyp
date Thu, 25 Apr 2024 15:13:22 +0000
parents 7bee859bbd11
children 9f136ebf73ac
comparison
equal deleted inserted replaced
2:7bee859bbd11 3:24ccdcfbabac
23 first_roi = True 23 first_roi = True
24 for sub_roi in input_roi["geometry"]["coordinates"]: 24 for sub_roi in input_roi["geometry"]["coordinates"]:
25 # Polygon with holes 25 # Polygon with holes
26 if not isinstance(sub_roi[0][0], list): 26 if not isinstance(sub_roi[0][0], list):
27 if first_roi: 27 if first_roi:
28 input_img = draw_poly(sub_roi, input_img, fill=fill)
29 first_roi = False 28 first_roi = False
29 col = (0, 0, 0)
30 else: 30 else:
31 # holes in ROI 31 # holes in ROI
32 input_img = draw_poly(sub_roi, input_img, col=(255, 255, 255), fill=fill) 32 col = (255, 255, 255) if not fill else (0, 0, 0)
33 input_img = draw_poly(sub_roi, input_img, col=col, fill=fill)
33 else: 34 else:
34 # MultiPolygon with holes 35 # MultiPolygon with holes
35 for sub_coord in sub_roi: 36 for sub_coord in sub_roi:
36 if first_roi: 37 if first_roi:
37 input_img = draw_poly(sub_coord, input_img, fill=fill)
38 first_roi = False 38 first_roi = False
39 col = (0, 0, 0)
39 else: 40 else:
40 # holes in ROI 41 # holes in ROI
41 input_img = draw_poly(sub_coord, input_img, col=(255, 255, 255), fill=fill) 42 col = (255, 255, 255) if not fill else (0, 0, 0)
43 input_img = draw_poly(sub_coord, input_img, col=col, fill=fill)
42 44
43 return input_img 45 return input_img
44 46
45 47
46 def split_qupath_roi(in_roi): 48 def split_qupath_roi(in_roi):
87 subset=['x', 'y'], 89 subset=['x', 'y'],
88 keep='last').reset_index(drop=True) 90 keep='last').reset_index(drop=True)
89 91
90 coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False) 92 coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
91 93
94 # img save
95 if args.img:
96 cv2.imwrite("{}_{}.png".format(tma_name, cell_type), img)
97
92 98
93 if __name__ == "__main__": 99 if __name__ == "__main__":
94 parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)") 100 parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
95 parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)") 101 parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
96 parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs") 102 parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs")
97 parser.add_argument('--version', action='version', version='%(prog)s 0.1.0') 103 parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
98 parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs") 104 parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
105 parser.add_argument("--img", action="store_true", required=False, help="Generates image of ROIs")
99 args = parser.parse_args() 106 args = parser.parse_args()
100 107
101 if args.qupath_roi: 108 if args.qupath_roi:
102 split_qupath_roi(args.qupath_roi) 109 split_qupath_roi(args.qupath_roi)