Mercurial > repos > galaxyp > qupath_roi_splitter

annotate 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
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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1 import argparse
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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3 import cv2
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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4 import geojson
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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5 import numpy as np
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6 import pandas as pd
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8
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9 def draw_poly(input_df, input_img, col=(0, 0, 0), fill=False):
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10 s = np.array(input_df)
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11 if fill:
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12 output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
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13 else:
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14 output_img = cv2.polylines(input_img, np.int32([s]), True, color=col, thickness=1)
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15 return output_img
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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17
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18 def draw_roi(input_roi, input_img, fill):
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19 if len(input_roi["geometry"]["coordinates"]) == 1:
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20 # Polygon w/o holes
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21 input_img = draw_poly(input_roi["geometry"]["coordinates"][0], input_img, fill=fill)
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22 else:
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23 first_roi = True
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24 for sub_roi in input_roi["geometry"]["coordinates"]:
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25 # Polygon with holes
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26 if not isinstance(sub_roi[0][0], list):
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27 if first_roi:
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28 first_roi = False
3
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29 col = (0, 0, 0)
2
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30 else:
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31 # holes in ROI
3
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32 col = (255, 255, 255) if not fill else (0, 0, 0)
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33 input_img = draw_poly(sub_roi, input_img, col=col, fill=fill)
2
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34 else:
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35 # MultiPolygon with holes
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36 for sub_coord in sub_roi:
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37 if first_roi:
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38 first_roi = False
3
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39 col = (0, 0, 0)
2
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40 else:
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41 # holes in ROI
3
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42 col = (255, 255, 255) if not fill else (0, 0, 0)
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43 input_img = draw_poly(sub_coord, input_img, col=col, fill=fill)
2
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45 return input_img
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47
0
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48 def split_qupath_roi(in_roi):
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49 with open(in_roi) as file:
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50 qupath_roi = geojson.load(file)
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51
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52 # HE dimensions
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53 dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]]
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55 tma_name = qupath_roi["name"]
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56 cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]]
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57
1
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58 for cell_type in cell_types:
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59 # create numpy array with white background
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60 img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8")
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61 img.fill(255)
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63 for i, roi in enumerate(qupath_roi["features"]):
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64 if not args.all:
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65 if "classification" not in roi["properties"]:
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66 continue
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67 if roi["properties"]["classification"]["name"] == cell_type:
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68 img = draw_roi(roi, img, args.fill)
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69 else:
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70 img = draw_roi(roi, img, args.fill)
0
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71
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72 # get all black pixel
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73 coords_arr = np.column_stack(np.where(img == (0, 0, 0)))
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75 # remove duplicated rows
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76 coords_arr_xy = coords_arr[coords_arr[:, 2] == 0]
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78 # remove last column
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79 coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1)
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81 # to pandas and rename columns to x and y
2
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82 coords_df = pd.DataFrame(coords_arr_xy, columns=['y', 'x'])
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83
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84 # reorder columns
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85 coords_df = coords_df[['x', 'y']]
0
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87 # drop duplicates
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88 coords_df = coords_df.drop_duplicates(
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89 subset=['x', 'y'],
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90 keep='last').reset_index(drop=True)
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92 coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
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93
3
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94 # img save
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95 if args.img:
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96 cv2.imwrite("{}_{}.png".format(tma_name, cell_type), img)
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97
0
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99 if __name__ == "__main__":
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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100 parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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101 parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
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102 parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs")
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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103 parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
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7bee859bbd11 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 7391296e0c7c8d48b42a129d154b50b29fd41737
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104 parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
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24ccdcfbabac planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 00029e8a3ee400f69a6dbe9e556ec9c27c6979cb
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105 parser.add_argument("--img", action="store_true", required=False, help="Generates image of ROIs")
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106 args = parser.parse_args()
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107
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108 if args.qupath_roi:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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109 split_qupath_roi(args.qupath_roi)