Quickfix: Run add_optogenetic_epochs

CHANGELOG.md

@@ -0,0 +1,10 @@
+# Change Log
+
+## [0.1.10] (Unreleased)
+
+### Release Notes
+
+### Optogenetics
+
+- fix hfpy write error when different number of spatial node regions between epochs #135
+- Run `add_optogenetic_epochs` in the create nwb function #135

src/trodes_to_nwb/convert.py

@@ -17,7 +17,7 @@
 from trodes_to_nwb.convert_dios import add_dios
 from trodes_to_nwb.convert_ephys import RecFileDataChunkIterator, add_raw_ephys
 from trodes_to_nwb.convert_intervals import add_epochs, add_sample_count
-from trodes_to_nwb.convert_optogenetics import add_optogenetics
+from trodes_to_nwb.convert_optogenetics import add_optogenetic_epochs, add_optogenetics
 from trodes_to_nwb.convert_position import add_associated_video_files, add_position
 from trodes_to_nwb.convert_rec_header import (
     add_header_device,
@@ -109,6 +109,7 @@ def create_nwbs(
     output_dir: str = "/stelmo/nwb/raw",
     video_directory: str = "",
     convert_video: bool = False,
+    fs_gui_dir: str = "",
     n_workers: int = 1,
     query_expression: str | None = None,
     disable_ptp: bool = False,
@@ -131,6 +132,8 @@ def create_nwbs(
         Directory containing the video files, by default "".
     convert_video : bool, optional
         Whether to convert the video files, by default False.
+    fs_gui_dir : str, optional
+        Optional alternative directory to find optogenetic files, by default "".
     n_workers : int, optional
         Number of workers to use for parallel processing, by default 1.
     query_expression : str, optional
@@ -170,6 +173,8 @@ def pass_func(args):
                     output_dir,
                     video_directory,
                     convert_video,
+                    fs_gui_dir,
+                    disable_ptp,
                     behavior_only=behavior_only,
                 )
                 return True
@@ -198,6 +203,7 @@ def pass_func(args):
                 output_dir,
                 video_directory,
                 convert_video,
+                fs_gui_dir,
                 disable_ptp,
                 behavior_only=behavior_only,
             )
@@ -211,6 +217,7 @@ def _create_nwb(
     output_dir: str = "/stelmo/nwb/raw",
     video_directory: str = "",
     convert_video: bool = False,
+    fs_gui_dir: str = "",
     disable_ptp: bool = False,
     behavior_only: bool = False,
 ):
@@ -311,6 +318,7 @@ def _create_nwb(
         session_df=session_df,
         neo_io=rec_dci.neo_io,
     )
+    add_optogenetic_epochs(nwb_file, metadata, fs_gui_dir)
     logger.info("ADDING POSITION")
     # add position
     if disable_ptp:

src/trodes_to_nwb/convert_optogenetics.py

@@ -46,7 +46,7 @@ def add_optogenetics(nwbfile: NWBFile, metadata: dict, device_metadata: List[dic
         return
 
     # Add optogenetic experiment metadata
-
+    logger.info("Adding optogenetic experiment metadata")
     virus, virus_injection = make_virus_injecton(
         metadata.get("virus_injection"), device_metadata
     )
@@ -306,11 +306,12 @@ def add_optogenetic_epochs(
     file_dir : str, optional
         Directory appended to the file path given in the metadata. Default is empty string.
     """
-
+    logger = logging.getLogger("convert")
     opto_epochs_metadata = metadata.get("fs_gui_yamls", [])
     if len(opto_epochs_metadata) == 0:
-        print("No optogenetic epochs found in metadata.")
+        logger.info("No optogenetic epochs found in metadata.")
         return
+    logger.info(f"Adding {len(opto_epochs_metadata)} optogenetic epochs.")
 
     from ndx_franklab_novela import FrankLabOptogeneticEpochsTable
 
@@ -320,14 +321,47 @@ def add_optogenetic_epochs(
     )
 
     # loop through each fsgui script, which can apply to multiple epochs
+    rows = []
     for fs_gui_metadata in opto_epochs_metadata:
         new_rows = compile_opto_entries(
             fs_gui_metadata=fs_gui_metadata,
             nwbfile=nwbfile,
             file_dir=file_dir,
         )
-        for row in new_rows:
-            opto_epochs_table.add_row(**row)
+        rows.extend(new_rows)
+
+    # ensure spatial geometry nodes have same shape in each row
+    max_shape = [0, 0, 0]
+    for row in rows:
+        nodes = row.get("spatial_filter_region_node_coordinates_in_pixels", None)
+        if nodes is not None:
+            max_shape = [
+                max(max_shape[0], nodes.shape[0]),
+                max(max_shape[1], nodes.shape[1]),
+                max(max_shape[2], nodes.shape[2]),
+            ]
+    if max_shape != [0, 0, 0]:
+        for row in rows:
+            nodes = row.get("spatial_filter_region_node_coordinates_in_pixels", None)
+            if nodes is None:
+                row["spatial_filter_region_node_coordinates_in_pixels"] = (
+                    np.ones(max_shape) * np.nan
+                )
+            else:
+                nodes = np.pad(
+                    nodes,
+                    (
+                        (0, max_shape[0] - nodes.shape[0]),
+                        (0, max_shape[1] - nodes.shape[1]),
+                        (0, max_shape[2] - nodes.shape[2]),
+                    ),
+                    mode="constant",
+                    constant_values=np.nan,
+                )
+                row["spatial_filter_region_node_coordinates_in_pixels"] = nodes
+
+    for row in rows:
+        opto_epochs_table.add_row(**row)
 
     nwbfile.add_time_intervals(opto_epochs_table)
 

src/trodes_to_nwb/tests/test_convert.py

@@ -61,6 +61,7 @@ def test_convert_full():
         output_dir=str(data_path),
         n_workers=1,
         query_expression=f"animal == 'sample' and full_path != '{exclude_reconfig_yaml}'",
+        fs_gui_dir=data_path,
     )
 
     output_file_path = data_path / "sample20230622.nwb"
@@ -105,6 +106,7 @@ def do_nothing(nwbfile, metadata_dict):
         path=data_path,
         device_metadata_paths=device_metadata,
         output_dir=str(data_path),
+        fs_gui_dir=data_path,
         n_workers=1,
         query_expression=f"animal == 'sample' and full_path != '{exclude_reconfig_yaml}'",
     )

src/trodes_to_nwb/tests/test_convert_optogenetics.py

@@ -75,7 +75,7 @@ def test_add_optogenetic_epochs():
     np.allclose(opto_df.stop_time.values, np.array([1.68747481e09, 1.68747484e09]))
     assert opto_df.stimulation_on.values[0]
     assert opto_df.spatial_filter_region_node_coordinates_in_pixels.values[0].shape == (
-        1,
+        3,
         7,
         2,
     )