Merge branch 'master' of https://github.com/LorenFrankLab/spyglass

src/spyglass/common/common_position.py

@@ -23,7 +23,7 @@
     plot_track_graph,
 )
 
-from ..settings import raw_dir
+from ..settings import raw_dir, video_dir
 from ..utils.dj_helper_fn import fetch_nwb
 from .common_behav import RawPosition, VideoFile
 from .common_interval import IntervalList  # noqa F401
@@ -248,51 +248,6 @@ def _fix_kwargs(
             max_plausible_speed,
         )
 
-    @staticmethod
-    def _fix_col_names(spatial_df):
-        """Renames columns in spatial dataframe according to previous norm
-
-        Accepts unnamed first led, 1 or 0 indexed.
-        Prompts user for confirmation of renaming unexpected columns.
-        For backwards compatibility, renames to "xloc", "yloc", "xloc2", "yloc2"
-        """
-
-        DEFAULT_COLS = ["xloc", "yloc", "xloc2", "yloc2"]
-        ONE_IDX_COLS = ["xloc1", "yloc1", "xloc2", "yloc2"]
-        ZERO_IDX_COLS = ["xloc0", "yloc0", "xloc1", "yloc1"]
-
-        input_cols = list(spatial_df.columns)
-
-        has_default = all([c in input_cols for c in DEFAULT_COLS])
-        has_0_idx = all([c in input_cols for c in ZERO_IDX_COLS])
-        has_1_idx = all([c in input_cols for c in ONE_IDX_COLS])
-
-        # if unexpected columns, ask user to confirm
-        if len(input_cols) != 4 or not (has_default or has_0_idx or has_1_idx):
-            choice = dj.utils.user_choice(
-                "Unexpected columns in raw position. Assume "
-                + f"{DEFAULT_COLS[:4]}?\n{spatial_df}\n"
-            )
-            if choice.lower() not in ["yes", "y"]:
-                raise ValueError(
-                    f"Unexpected columns in raw position: {input_cols}"
-                )
-            spatial_df.columns = DEFAULT_COLS + input_cols[4:]
-
-        # Ensure data order, only 4 col
-        spatial_df = (
-            spatial_df[DEFAULT_COLS]
-            if has_default
-            else spatial_df[ZERO_IDX_COLS]
-            if has_0_idx
-            else spatial_df[ONE_IDX_COLS]
-        )
-
-        # rename to default
-        spatial_df.columns = DEFAULT_COLS
-
-        return spatial_df
-
     @staticmethod
     def _upsample(
         front_LED,
@@ -378,7 +333,7 @@ def calculate_position_info(
             **kwargs,
         )
 
-        spatial_df = self._fix_col_names(spatial_df)
+        spatial_df = _fix_col_names(spatial_df)
         # Get spatial series properties
         time = np.asarray(spatial_df.index)  # seconds
         position = np.asarray(spatial_df.iloc[:, :4])  # meters
@@ -898,17 +853,26 @@ def make(self, key):
             VideoFile()
             & {"nwb_file_name": key["nwb_file_name"], "epoch": epoch}
         ).fetch1()
-        io = pynwb.NWBHDF5IO(raw_dir() + video_info["nwb_file_name"], "r")
+        io = pynwb.NWBHDF5IO(raw_dir + "/" + video_info["nwb_file_name"], "r")
         nwb_file = io.read()
         nwb_video = nwb_file.objects[video_info["video_file_object_id"]]
-        video_filename = nwb_video.external_file.value[0]
+        video_filename = nwb_video.external_file[0]
 
         nwb_base_filename = key["nwb_file_name"].replace(".nwb", "")
         output_video_filename = (
             f"{nwb_base_filename}_{epoch:02d}_"
             f'{key["position_info_param_name"]}.mp4'
         )
 
+        # ensure standardized column names
+        raw_position_df = _fix_col_names(raw_position_df)
+        # if IntervalPositionInfo supersampled position, downsample to video
+        if position_info_df.shape[0] > raw_position_df.shape[0]:
+            ind = np.digitize(
+                raw_position_df.index, position_info_df.index, right=True
+            )
+            position_info_df = position_info_df.iloc[ind]
+
         centroids = {
             "red": np.asarray(raw_position_df[["xloc", "yloc"]]),
             "green": np.asarray(raw_position_df[["xloc2", "yloc2"]]),
@@ -925,7 +889,7 @@ def make(self, key):
 
         print("Making video...")
         self.make_video(
-            video_filename,
+            f"{video_dir}/{video_filename}",
             centroids,
             head_position_mean,
             head_orientation_mean,
@@ -1082,3 +1046,48 @@ def make_video(
         video.release()
         out.release()
         cv2.destroyAllWindows()
+
+
+def _fix_col_names(spatial_df):
+    """Renames columns in spatial dataframe according to previous norm
+
+    Accepts unnamed first led, 1 or 0 indexed.
+    Prompts user for confirmation of renaming unexpected columns.
+    For backwards compatibility, renames to "xloc", "yloc", "xloc2", "yloc2"
+    """
+
+    DEFAULT_COLS = ["xloc", "yloc", "xloc2", "yloc2"]
+    ONE_IDX_COLS = ["xloc1", "yloc1", "xloc2", "yloc2"]
+    ZERO_IDX_COLS = ["xloc0", "yloc0", "xloc1", "yloc1"]
+
+    input_cols = list(spatial_df.columns)
+
+    has_default = all([c in input_cols for c in DEFAULT_COLS])
+    has_0_idx = all([c in input_cols for c in ZERO_IDX_COLS])
+    has_1_idx = all([c in input_cols for c in ONE_IDX_COLS])
+
+    if has_default:
+        # move the 4 position columns to front, continue
+        spatial_df = spatial_df[DEFAULT_COLS]
+    elif has_0_idx:
+        # move the 4 position columns to front, rename to default, continue
+        spatial_df = spatial_df[ZERO_IDX_COLS]
+        spatial_df.columns = DEFAULT_COLS
+    elif has_1_idx:
+        # move the 4 position columns to front, rename to default, continue
+        spatial_df = spatial_df[ONE_IDX_COLS]
+        spatial_df.columns = DEFAULT_COLS
+    else:
+        if len(input_cols) != 4 or not has_default:
+            choice = dj.utils.user_choice(
+                "Unexpected columns in raw position. Assume "
+                + f"{DEFAULT_COLS[:4]}?\n{spatial_df}\n"
+            )
+            if choice.lower() not in ["yes", "y"]:
+                raise ValueError(
+                    f"Unexpected columns in raw position: {input_cols}"
+                )
+        # rename first 4 columns, keep rest. Rest dropped below
+        spatial_df.columns = DEFAULT_COLS + input_cols[4:]
+
+    return spatial_df

src/spyglass/settings.py

@@ -438,4 +438,5 @@ def debug_mode(self) -> bool:
 analysis_dir = sg_config.analysis_dir
 sorting_dir = sg_config.sorting_dir
 waveform_dir = sg_config.waveform_dir
+video_dir = sg_config.video_dir
 debug_mode = sg_config.debug_mode