netCDF4

EthoML · Nov 21, 2024 · f5daf2c · f5daf2c
1 parent 678aad5
commit f5daf2c
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Showing 5 changed files with 44 additions and 27 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -15,4 +15,5 @@ imageio==2.34.1
 imageio-ffmpeg==0.5.1
 pynwb==2.8.1
 tables>=3.10.0
-movement==0.0.20
+movement==0.0.20
+netCDF4>=1.7.2
diff --git a/src/vame/analysis/generative_functions.py b/src/vame/analysis/generative_functions.py
@@ -281,7 +281,10 @@ def generative_model(
 
             if mode == "sampling":
                 latent_vector = np.load(
-                    os.path.join(path_to_file, "latent_vector_" + session + ".npy")
+                    os.path.join(
+                        path_to_file,
+                        "latent_vector_" + session + ".npy",
+                    )
                 )
                 return random_generative_samples(
                     cfg,
@@ -291,7 +294,10 @@ def generative_model(
 
             if mode == "reconstruction":
                 latent_vector = np.load(
-                    os.path.join(path_to_file, "latent_vector_" + session + ".npy")
+                    os.path.join(
+                        path_to_file,
+                        "latent_vector_" + session + ".npy",
+                    )
                 )
                 return random_reconstruction_samples(
                     cfg,
@@ -305,7 +311,10 @@ def generative_model(
                         f"Algorithm {segmentation_algorithm} not supported for cluster center visualization."
                     )
                 cluster_center = np.load(
-                    os.path.join(path_to_file, "cluster_center_" + session + ".npy")
+                    os.path.join(
+                        path_to_file,
+                        "cluster_center_" + session + ".npy",
+                    )
                 )
                 return visualize_cluster_center(
                     cfg,
@@ -315,7 +324,10 @@ def generative_model(
 
             if mode == "motifs":
                 latent_vector = np.load(
-                    os.path.join(path_to_file, "latent_vector_" + session + ".npy")
+                    os.path.join(
+                        path_to_file,
+                        "latent_vector_" + session + ".npy",
+                    )
                 )
                 labels = np.load(
                     os.path.join(
@@ -330,11 +342,11 @@ def generative_model(
                     )
                 )
                 return random_generative_samples_motif(
-                    cfg,
-                    model,
-                    latent_vector,
-                    labels,
-                    n_clusters,
+                    cfg=cfg,
+                    model=model,
+                    latent_vector=latent_vector,
+                    labels=labels,
+                    n_clusters=n_clusters,
                 )
     except Exception as e:
         logger.exception(str(e))

diff --git a/src/vame/io/load_poses.py b/src/vame/io/load_poses.py
@@ -50,4 +50,4 @@ def load_vame_dataset(ds_path: Path | str) -> xr.Dataset:
     Returns:
     --------
     """
-    return xr.open_dataset(ds_path)
+    return xr.open_dataset(ds_path, engine="netcdf4")
diff --git a/src/vame/util/align_egocentrical.py b/src/vame/util/align_egocentrical.py
@@ -81,12 +81,14 @@ def align_mouse(
         i = interpol_first_rows_nans(i)
 
     if use_video:
-        video_path = str(os.path.join(
-            project_path,
-            "data",
-            "raw",
-            session + video_format,
-        ))
+        video_path = str(
+            os.path.join(
+                project_path,
+                "data",
+                "raw",
+                session + video_format,
+            )
+        )
         capture = cv.VideoCapture(video_path)
         if not capture.isOpened():
             raise Exception(f"Unable to open video file: {video_path}")
@@ -304,12 +306,14 @@ def alignment(
 
     if use_video:
         # compute background
-        video_path = str(os.path.join(
-            project_path,
-            "data",
-            "raw",
-            session + video_format,
-        ))
+        video_path = str(
+            os.path.join(
+                project_path,
+                "data",
+                "raw",
+                session + video_format,
+            )
+        )
         bg = background(
             project_path=project_path,
             session=session,

diff --git a/tests/test_analysis.py b/tests/test_analysis.py
@@ -339,16 +339,16 @@ def test_gif_frames_files_exists(setup_project_and_evaluate_model, label):
         vame.segment_session(setup_project_and_evaluate_model["config_path"])
 
     def mock_background(
-        path_to_file=None,
-        filename=None,
+        project_path=None,
+        session=None,
         video_path=None,
         num_frames=None,
         save_background=True,
     ):
         num_frames = 100
         return background(
-            project_path=path_to_file,
-            session=filename,
+            project_path=project_path,
+            session=session,
             video_path=video_path,
             num_frames=num_frames,
             save_background=save_background,