add script in preprocessing which can convert jpg to tiff pyramid large image type

preprocessing/cut_tumor_regions.py

@@ -68,6 +68,10 @@ def get_bbox(points):
             x, y, width, height = bbox
             tumour_img = wsi_img[y: y + height, x: x + width]
 
+            # pass wrong shape of tumour_img
+            if np.any(np.array(tumour_img.shape) == 0):
+                continue
+
             # fill irrelevant areas with solid colors
             if args.not_filled_other_regions:
                 mask_array = np.zeros((height, width), dtype=np.uint8)

preprocessing/cvt_jpg2tiff.py

@@ -0,0 +1,29 @@
+import os
+import glob
+import sys
+import pyvips
+
+def cvt_jpg2tiff(src_dir, dst_dir):
+    if not os.path.exists(dst_dir):
+        os.makedirs(dst_dir)
+
+    src_files = glob.glob(os.path.join(src_dir, '*.jpg'))
+    for src_file in src_files:
+        dst_file = os.path.join(dst_dir, os.path.basename(src_file).replace('.jpg', '.tiff'))
+
+        # convert jpg to tiff
+        filename = os.path.splitext(os.path.basename(src_file))[0]
+        print(filename)
+        im = pyvips.Image.new_from_file(src_file)
+        im.write_to_file(dst_file, pyramid=True, tile=True, bigtiff=True, compression="none")
+    print('Done.')
+
+if __name__ == '__main__':
+    args = sys.argv
+    if len(args) != 3:
+        print('Usage: python cvt_jpg2tiff.py src_dir dst_dir')
+        sys.exit(0)
+    src_dir = args[1]
+    dst_dir = args[2]
+    cvt_jpg2tiff(src_dir, dst_dir)
+