--- /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)