Correctly handle missing poses (#11)

talmolab · Jun 15, 2023 · d2aae82 · d2aae82
1 parent da79d10
commit d2aae82
Show file tree

Hide file tree

Showing 3 changed files with 25 additions and 9 deletions.
diff --git a/biogtr/datasets/data_utils.py b/biogtr/datasets/data_utils.py
@@ -458,9 +458,15 @@ def view_training_batch(
     for i in range(num_frames):
         for j, data in enumerate(instances[i]["crops"]):
             try:
-                ax = axes[j] if num_frames == 1 else axes[i, j]
+                ax = (
+                    axes[j]
+                    if num_frames == 1
+                    else (axes[i] if num_crops == 1 else axes[i, j])
+                )
+
                 ax.imshow(data.T)
                 ax.axis("off")
+
             except Exception as e:
                 print(e)
                 pass

diff --git a/biogtr/datasets/sleap_dataset.py b/biogtr/datasets/sleap_dataset.py
@@ -135,12 +135,15 @@ def __getitem__(self, idx) -> list[dict]:
         anchors = [
             video.skeletons[0].node_names.index(anchor_name)
             for anchor_name in self.anchor_names[label_idx]
-        ]  # get the nodes from the skeleton
+        ]
 
         video_name = self.video_files[label_idx]
 
         vid_reader = imageio.get_reader(video_name, "ffmpeg")
 
+        img = vid_reader.get_data(0)
+        crop_shape = (img.shape[-1], *(self.crop_size + 2 * self.padding,) * 2)
+
         instances = []
 
         for i in frame_idx:
@@ -179,10 +182,13 @@ def __getitem__(self, idx) -> list[dict]:
                     if isinstance(transform, A.CoarseDropout):
                         transform.fill_value = random.randint(0, 255)
 
-                augmented = self.augmentations(
-                    image=img,
-                    keypoints=np.vstack([list(s.values()) for s in shown_poses]),
-                )
+                if shown_poses:
+                    keypoints = np.vstack([list(s.values()) for s in shown_poses])
+
+                else:
+                    keypoints = []
+
+                augmented = self.augmentations(image=img, keypoints=keypoints)
 
                 img, aug_poses = augmented["image"], augmented["keypoints"]
 
@@ -217,15 +223,19 @@ def __getitem__(self, idx) -> list[dict]:
                 bboxes.append(bbox)
                 crops.append(crop)
 
+            stacked_crops = (
+                torch.stack(crops) if crops else torch.empty((0, *crop_shape))
+            )
+
             instances.append(
                 {
                     "video_id": torch.tensor([label_idx]),
                     "img_shape": torch.tensor([img.shape]),
                     "frame_id": torch.tensor([i]),
                     "num_detected": torch.tensor([len(bboxes)]),
                     "gt_track_ids": torch.tensor(gt_track_ids),
-                    "bboxes": torch.stack(bboxes),
-                    "crops": torch.stack(crops),
+                    "bboxes": torch.stack(bboxes) if bboxes else torch.empty((0, 4)),
+                    "crops": stacked_crops,
                     "features": torch.tensor([]),
                     "pred_track_ids": torch.tensor([-1 for _ in range(len(bboxes))]),
                     "asso_output": torch.tensor([]),

diff --git a/biogtr/inference/track.py b/biogtr/inference/track.py
@@ -64,7 +64,7 @@ def inference(
             save_dict["Frame"] = frame_ids
             save_dict["X"] = X
             save_dict["Y"] = Y
-            save_dict["Predicted Track ID"] = pred_track_ids
+            save_dict["Pred_track_id"] = pred_track_ids
             save_df = pd.DataFrame(save_dict)
             saved.append(save_df)