--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/background_removal.py	Mon Jul 15 20:55:08 2024 +0000
@@ -0,0 +1,59 @@
+import argparse
+import warnings
+
+import numpy as np
+import skimage.io
+from skimage.filters import difference_of_gaussians
+from skimage.io import imread
+from skimage.morphology import disk, white_tophat
+from skimage.restoration import rolling_ball
+
+
+def process_image(args):
+    image = imread(args.input_image)
+
+    if args.filter == "rolling_ball":
+        background_rolling = rolling_ball(image, radius=args.radius)
+        output_image = image - background_rolling
+
+    elif args.filter == "dog":
+        output_image = difference_of_gaussians(image, low_sigma=0, high_sigma=args.radius)
+
+    elif args.filter == "top_hat":
+        output_image = white_tophat(image, disk(args.radius))
+
+    with warnings.catch_warnings():
+        output_image = convert_image_to_format_of(output_image, image)
+        skimage.io.imsave(args.output, output_image, plugin="tifffile")
+
+
+def convert_image_to_format_of(image, format_image):
+    """
+    Convert the first image to the format of the second image.
+    """
+    if format_image.dtype == image.dtype:
+        return image
+    elif format_image.dtype == np.uint8:
+        return skimage.util.img_as_ubyte(image)
+    elif format_image.dtype == np.uint16:
+        return skimage.util.img_as_uint(image)
+    elif format_image.dtype == np.int16:
+        return skimage.util.img_as_int(image)
+    else:
+        raise ValueError(f'Unsupported image data type: {format_image.dtype}')
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Background removal script using skiimage")
+    parser.add_argument('input_image', help="Input image path")
+    parser.add_argument('filter', choices=['rolling_ball', 'dog', 'top_hat'],
+                        help="Background removal algorithm")
+    parser.add_argument('radius', type=float, help="Radius")
+    parser.add_argument('output', help="Output image path")
+
+    args = parser.parse_args()
+    process_image(args)
+
+
+if __name__ == '__main__':
+    main()