Interface each processing method with pydantic models

Aharoni-Lab · Dec 10, 2024 · 3bbab4d · 3bbab4d
1 parent fa9a036
commit 3bbab4d
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Showing 4 changed files with 85 additions and 81 deletions.
diff --git a/miniscope_io/data/config/process/denoise_example.yml b/miniscope_io/data/config/process/denoise_example.yml
@@ -1,11 +1,11 @@
 interactive_display:
   enable: True
   start_frame: 40
-  end_frame: 90
+  end_frame: 140
 noise_patch:
   enable: True
   method: "mean_error"
-  threshold: 30
+  threshold: 10
   buffer_size: 5032
   buffer_split: 10
   diff_multiply: 1
@@ -14,7 +14,7 @@ noise_patch:
   output_diff: True
 frequency_masking:
   enable: True
-  spatial_LPF_cutoff_radius: 15
+  spatial_LPF_cutoff_radius: 20
   vertical_BEF_cutoff: 2
   horizontal_BEF_cutoff: 0
   display_mask: False

diff --git a/miniscope_io/io.py b/miniscope_io/io.py
@@ -6,7 +6,7 @@
 import contextlib
 import csv
 from pathlib import Path
-from typing import Any, BinaryIO, Iterator, List, Literal, Optional, Union, overload
+from typing import Any, BinaryIO, Iterator, List, Literal, Optional, Tuple, Union, overload
 
 import cv2
 import numpy as np
@@ -92,19 +92,22 @@ def __init__(self, video_path: str):
 
         self.logger.info(f"Opened video at {video_path}")
 
-    def read_frames(self) -> Iterator[np.ndarray]:
+    def read_frames(self) -> Iterator[Tuple[int, np.ndarray]]:
         """
-        Read frames from the video file.
+        Read frames from the video file along with their index.
 
         Yields:
-        np.ndarray: The next frame in the video.
+        Tuple[int, np.ndarray]: The index and the next frame in the video.
         """
         while self.cap.isOpened():
             ret, frame = self.cap.read()
-            self.logger.debug(f"Reading frame {self.cap.get(cv2.CAP_PROP_POS_FRAMES)}")
+            index = int(self.cap.get(cv2.CAP_PROP_POS_FRAMES))
+            self.logger.debug(f"Reading frame {index}")
+
             if not ret:
                 break
-            yield frame
+
+            yield index, frame
 
     def release(self) -> None:
         """

diff --git a/miniscope_io/plots/video.py b/miniscope_io/plots/video.py
@@ -21,6 +21,7 @@
 
 logger = init_logger("videoplot")
 
+
 class VideoPlotter:
     """
     Class to display video streams and static images.
@@ -32,7 +33,7 @@ def show_video_with_controls(
         start_frame: int,
         end_frame: int,
         fps: int = 20,
-        ) -> None:
+    ) -> None:
         """
         Plot multiple video streams or static images side-by-side.
         Can play/pause and navigate frames.
@@ -64,7 +65,7 @@ def show_video_with_controls(
         titles = [video.name for video in videos]
 
         num_streams = len(video_frames)
-        
+
         logger.info(f"Displaying {num_streams} video streams.")
         if end_frame > start_frame:
             logger.info(f"Displaying frames {start_frame} to {end_frame}.")
@@ -73,7 +74,7 @@ def show_video_with_controls(
                 if len(video_frames[stream_index]) > 1:
                     video_frames[stream_index] = video_frames[stream_index][start_frame:end_frame]
                     logger.info(f"Trimmed stream length: {len(video_frames[stream_index])}")
-                
+
         num_frames = max(len(stream) for stream in video_frames)
         logger.info(f"Max stream length: {num_frames}")