Add intensity masking script

Author: constantinpape

scripts/intensity_masking.py

@@ -0,0 +1,50 @@
+import argparse
+
+import imageio.v3 as imageio
+import numpy as np
+from scipy.ndimage import binary_dilation, binary_closing, distance_transform_edt
+
+
+def intensity_masking(image_path, seg_path, out_path, modulation_strength=10, dilation=2, view=False):
+    seg = imageio.imread(seg_path)
+    mask = binary_dilation(seg != 0, iterations=2)
+    mask = binary_closing(mask, iterations=4)
+
+    image = imageio.imread(image_path)
+    lo, hi = np.percentile(image, 2), np.percentile(image, 98)
+    print(lo, hi)
+    image_modulated = np.clip(image, lo, hi).astype("float32")
+    image_modulated -= lo
+    image_modulated /= image_modulated.max()
+
+    modulation_mask = distance_transform_edt(~mask)
+    modulation_mask /= modulation_mask.max()
+    modulation_mask = 1 - modulation_mask
+    modulation_mask[mask] = 1
+    modulation_mask = np.pow(modulation_mask, 3)
+    modulation_mask *= modulation_strength
+    image_modulated *= modulation_mask
+
+    if view:
+        import napari
+        v = napari.Viewer()
+        v.add_image(modulation_mask)
+        v.add_image(image, visible=False)
+        v.add_image(image_modulated)
+        v.add_labels(mask, visible=False)
+        napari.run()
+        return
+    imageio.imwrite(out_path, image_modulated, compression="zlib")
+
+
+# image_path = "M_LR_000227_R/scale3/PV.tif"
+# seg_path = "M_LR_000227_R/scale3/SGN_v2.tif"
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("image_path")
+    parser.add_argument("seg_path")
+    parser.add_argument("out_path")
+    parser.add_argument("--view", "-v", action="store_true")
+    parser.add_argument("--dilation", type=int, default=2)
+    args = parser.parse_args()
+    intensity_masking(args.image_path, args.seg_path, args.out_path, view=args.view, dilation=args.dilation)