Mercurial > repos > galaxyp > qupath_roi_splitter

annotate qupath_roi_splitter.py @ 1:064b53fd3131 draft

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planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
author galaxyp
date Wed, 14 Jun 2023 16:37:01 +0000
parents b5e9cebb27e3
children 7bee859bbd11
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
1 import argparse
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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3 import cv2
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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4 import geojson
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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5 import numpy as np
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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6 import pandas as pd
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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9 def draw_poly(input_df, input_img, col=(0, 0, 0)):
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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10 s = np.array(input_df)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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11 output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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12 return output_img
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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15 def split_qupath_roi(in_roi):
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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16 with open(in_roi) as file:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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17 qupath_roi = geojson.load(file)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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19 # HE dimensions
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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20 dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]]
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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22 tma_name = qupath_roi["name"]
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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23 cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]]
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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24
1
064b53fd3131 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
galaxyp
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25 for cell_type in cell_types:
064b53fd3131 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
galaxyp
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26 # create numpy array with white background
064b53fd3131 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
galaxyp
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27 img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8")
064b53fd3131 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
galaxyp
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28 img.fill(255)
0
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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29
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galaxyp
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30 for i, roi in enumerate(qupath_roi["features"]):
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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31 if roi["properties"]["classification"]["name"] == cell_type:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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32 if len(roi["geometry"]["coordinates"]) == 1:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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33 # Polygon w/o holes
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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34 img = draw_poly(roi["geometry"]["coordinates"][0], img)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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35 else:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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36 first_roi = True
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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37 for sub_roi in roi["geometry"]["coordinates"]:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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38 # Polygon with holes
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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39 if not isinstance(sub_roi[0][0], list):
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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40 if first_roi:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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41 img = draw_poly(sub_roi, img)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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42 first_roi = False
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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43 else:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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44 # holes in ROI
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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45 img = draw_poly(sub_roi, img, col=(255, 255, 255))
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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46 else:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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47 # MultiPolygon with holes
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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48 for sub_coord in sub_roi:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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49 if first_roi:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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50 img = draw_poly(sub_coord, img)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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51 first_roi = False
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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52 else:
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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53 # holes in ROI
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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54 img = draw_poly(sub_coord, img, col=(255, 255, 255))
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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55
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56 # get all black pixel
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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57 coords_arr = np.column_stack(np.where(img == (0, 0, 0)))
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58
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59 # remove duplicated rows
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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60 coords_arr_xy = coords_arr[coords_arr[:, 2] == 0]
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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61
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62 # remove last column
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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63 coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1)
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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64
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65 # to pandas and rename columns to x and y
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galaxyp
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66 coords_df = pd.DataFrame(coords_arr_xy, columns=['x', 'y'])
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67
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68 # drop duplicates
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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69 coords_df = coords_df.drop_duplicates(
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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70 subset=['x', 'y'],
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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71 keep='last').reset_index(drop=True)
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72
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73 coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
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74
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75
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76 if __name__ == "__main__":
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galaxyp
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77 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
galaxyp
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78 parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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79 parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
b5e9cebb27e3 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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80 args = parser.parse_args()
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81
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82 if args.qupath_roi:
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83 split_qupath_roi(args.qupath_roi)