From b756643ef4ede2f09e319776abbd1a9f6a5fee7a Mon Sep 17 00:00:00 2001
From: lauraporta <29216006+lauraporta@users.noreply.github.com>
Date: Wed, 27 Mar 2024 16:44:32 +0000
Subject: [PATCH] Add script to make mean image

---
 examples/make_mean_image_every_10deg.py | 46 +++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 examples/make_mean_image_every_10deg.py

diff --git a/examples/make_mean_image_every_10deg.py b/examples/make_mean_image_every_10deg.py
new file mode 100644
index 0000000..abe2f74
--- /dev/null
+++ b/examples/make_mean_image_every_10deg.py
@@ -0,0 +1,46 @@
+import sys
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import tifffile as tiff
+
+
+def make_mean_image_every_10deg(dataset_path):
+    full_video = tiff.imread(
+        f"{dataset_path}/derotated_image_stack_full_and_incremental.tif"
+    )
+    full_csv = pd.read_csv(
+        f"{dataset_path}/derotated_image_stack_full_and_incremental.csv",
+        delimiter=",",
+    )
+
+    mean_images = []
+    #  images around 5, 10, 15, 20, etc. degrees
+    tollerace_deg = 1
+    for angle in range(0, 360, 10):
+        images = full_video[
+            np.where(
+                np.abs(full_csv["rotation_angle"] - angle) < tollerace_deg
+            )
+        ]
+        mean_image = np.mean(images, axis=0)
+        mean_images.append(mean_image)
+
+    mean_images = np.array(mean_images)
+
+    path_for_mean_images = Path(dataset_path) / "mean_images"
+    Path(path_for_mean_images).mkdir(exist_ok=True)
+    for i, mean_image in enumerate(mean_images):
+        angle = i * 10
+        plt.imsave(
+            f"{path_for_mean_images}/mean_image_{angle}.png",
+            mean_image,
+            cmap="gray",
+        )
+
+
+if __name__ == "__main__":
+    dataset_path = sys.argv[1]
+    make_mean_image_every_10deg(dataset_path)