fix bug where cheese3d feature extraction crashes if pose3d is not there

Author: darsnack

packages/cheese3d/cheese3d/backends/dlc.py

@@ -250,5 +250,4 @@ def train(self, gpu, iterate_dataset: bool = True):
         dlc.train_network(config=self.config_path,
                           gputouse=gpu)
         dlc.evaluate_network(config=self.config_path,
-                             gputouse=gpu,
-                             per_keypoint_evaluation=True)
+                             gputouse=gpu)

packages/cheese3d/cheese3d/project.py

@@ -607,9 +607,13 @@ def triangulate(self, session: Optional[str] = None):
         if len(exclude_kps) > 0:
             rprint("[bold red]Keypoint configuration does not match default Cheese3D keypoints. "
                    "Some Cheese3D features may not be computed![/bold red]")
+        rprint("Generating Cheese3d features ...")
         for session_dir in sessions_to_process:
             if session_dir.is_dir():
                 landmarks = read_3d_data(session_dir)
+                if landmarks is None:
+                    rprint(f"[bold red]No landmarks found for {session_dir.name}, skipping![/bold red]")
+                    continue
                 c3d_features = compute_anatomical_measurements(landmarks, exclude_kps)
                 # write features to csv
                 c3d_features_df = pd.DataFrame({

packages/cheese3d/cheese3d/utils.py

@@ -185,6 +185,8 @@ def read_3d_data(data_dir: str | Path, extra_cols = None):
     to arrays of shape `(time,)`.
     """
     files = glob(str(Path(data_dir) / "pose-3d" / "*.csv"))
+    if len(files) == 0:
+        return None
     data = pd.read_csv(files[0])
     cols = data.head() # name of all the columns
     landmark_names = np.unique([s.split('_')[0]