open video file only at init

dreem/datasets/microscopy_dataset.py

@@ -62,7 +62,7 @@ def __init__(
             seed,
         )
 
-        self.videos = videos
+        self.vid_files = videos
         self.tracks = tracks
         self.chunk = chunk
         self.clip_length = clip_length
@@ -92,13 +92,19 @@ def __init__(
             parser(self.tracks[video_idx]) for video_idx in range(len(self.tracks))
         ]
 
+        self.videos = []
+        for vid_file in self.vid_files:
+            if not isinstance(vid_file, list):
+                self.videos.append(data_utils.LazyTiffStack(vid_file))
+            else:
+                self.videos.append([Image.open(frame_file) for frame_file in vid_file])
         self.frame_idx = [
             (
                 torch.arange(Image.open(video).n_frames)
                 if isinstance(video, str)
                 else torch.arange(len(video))
             )
-            for video in self.videos
+            for video in self.vid_files
         ]
 
         # Method in BaseDataset. Creates label_idx and chunked_frame_idx to be
@@ -128,17 +134,14 @@ def get_instances(self, label_idx: list[int], frame_idx: list[int]) -> list[Fram
 
         video = self.videos[label_idx]
 
-        if not isinstance(video, list):
-            video = data_utils.LazyTiffStack(self.videos[label_idx])
-
         frames = []
         for frame_id in frame_idx:
             instances, gt_track_ids, centroids = [], [], []
 
             img = (
                 video.get_section(frame_id)
                 if not isinstance(video, list)
-                else np.array(Image.open(video[frame_id]))
+                else np.array(video[frame_id])
             )
 
             lf = labels[labels["FRAME"].astype(int) == frame_id.item()]
@@ -202,3 +205,12 @@ def get_instances(self, label_idx: list[int], frame_idx: list[int]) -> list[Fram
             )
 
         return frames
+
+    def __del__(self):
+        """Handle file closing before deletion."""
+        for vid_reader in self.videos:
+            if not isinstance(vid_reader, list):
+                vid_reader.close()
+            else:
+                for frame_reader in vid_reader:
+                    frame_reader.close()

dreem/datasets/sleap_dataset.py

@@ -106,7 +106,7 @@ def __init__(
         # if self.seed is not None:
         #     np.random.seed(self.seed)
         self.labels = [sio.load_slp(slp_file) for slp_file in self.slp_files]
-
+        self.videos = [imageio.get_reader(vid_file) for vid_file in self.vid_files]
         # do we need this? would need to update with sleap-io
 
         # for label in self.labels:
@@ -140,7 +140,7 @@ def get_instances(self, label_idx: list[int], frame_idx: list[int]) -> list[Fram
 
         video_name = self.video_files[label_idx]
 
-        vid_reader = imageio.get_reader(video_name, "ffmpeg")
+        vid_reader = self.videos[label_idx]
 
         img = vid_reader.get_data(0)
 
@@ -370,3 +370,8 @@ def get_instances(self, label_idx: list[int], frame_idx: list[int]) -> list[Fram
             frames.append(frame)
 
         return frames
+
+    def __del__(self):
+        """Handle file closing before garbage collection."""
+        for reader in self.videos:
+            reader.close()