From 247fe6d1573f546178df5121f5adae226fab8444 Mon Sep 17 00:00:00 2001
From: lauraporta <29216006+lauraporta@users.noreply.github.com>
Date: Thu, 19 Oct 2023 12:57:02 +0100
Subject: [PATCH] Add script to add masks on top

---
 derotation/scripts/apply_mask.py | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 derotation/scripts/apply_mask.py

diff --git a/derotation/scripts/apply_mask.py b/derotation/scripts/apply_mask.py
new file mode 100644
index 0000000..34a4973
--- /dev/null
+++ b/derotation/scripts/apply_mask.py
@@ -0,0 +1,30 @@
+from pathlib import Path
+
+import numpy as np
+from tifffile import imread, imsave
+
+
+def apply_mask(path_of_video):
+    img_stack = imread(path_of_video)
+    img_height = img_stack.shape[1]
+    xx, yy = np.mgrid[:img_height, :img_height]
+    circle = (xx - img_height / 2) ** 2 + (yy - img_height / 2) ** 2
+    mask = circle < (img_height / 2) ** 2
+    img_min = np.nanmin(img_stack)
+    masked_img_array = []
+    for img in img_stack:
+        masked_img_array.append(np.where(mask, img, img_min))
+    masked_img_array = np.array(masked_img_array)
+    return masked_img_array
+
+
+if "__main__" == __name__:
+    # path_of_video = Path(sys.argv[1])
+    path_of_video = Path(
+        "/Users/lauraporta/local_data/rotation/230802_CAA_1120182/imaging/translation2_00001_ce.tif"
+    )
+    masked_video = apply_mask(path_of_video)
+    saving_path = path_of_video.parent / f"masked_raw_{path_of_video.name}"
+    imsave(saving_path, masked_video)
+
+    print(f"Masked video saved at {saving_path}")