Handle non-ptp datasets

src/spikegadgets_to_nwb/convert.py

@@ -13,9 +13,11 @@
 from spikegadgets_to_nwb.convert_position import (
     add_position,
     add_associated_video_files,
+    find_camera_dio_channel,
 )
 from spikegadgets_to_nwb.convert_rec_header import (
     add_header_device,
+    detect_ptp_from_header,
     make_hw_channel_map,
     make_ref_electrode_map,
     read_header,
@@ -249,24 +251,32 @@ def _create_nwb(
     add_analog_data(nwb_file, rec_filepaths, timestamps=rec_dci_timestamps)
     logger.info("ADDING SAMPLE COUNTS")
     add_sample_count(nwb_file, rec_dci)
-    logger.info("ADDING POSITION")
-    ### add position ###
-    add_position(
-        nwb_file,
-        metadata,
-        session_df,
-        rec_header,
-    )
-
-    # add epochs
     logger.info("ADDING EPOCHS")
     add_epochs(
         nwbfile=nwb_file,
-        file_info=session_df,
-        date=session[0],
-        animal=session[1],
+        session_df=session_df,
         neo_io=rec_dci.neo_io,
     )
+    logger.info("ADDING POSITION")
+    ### add position ###
+    ptp_enabled = detect_ptp_from_header(rec_header)
+    if ptp_enabled:
+        add_position(
+            nwb_file,
+            metadata,
+            session_df,
+        )
+    else:
+        add_position(
+            nwb_file,
+            metadata,
+            session_df,
+            ptp_enabled=ptp_enabled,
+            rec_dci_timestamps=rec_dci_timestamps,
+            sample_count=nwb_file.processing["sample_count"]
+            .data_interfaces["sample_count"]
+            .data,
+        )
 
     # write file
     logger.info(f"WRITING: {output_dir}/{session[1]}{session[0]}.nwb")

src/spikegadgets_to_nwb/convert_intervals.py

@@ -14,9 +14,7 @@
 
 def add_epochs(
     nwbfile: NWBFile,
-    file_info: pd.DataFrame,
-    date: int,
-    animal: str,
+    session_df: pd.DataFrame,
     neo_io: List[SpikeGadgetsRawIO],
 ):
     """add epochs to nwbfile
@@ -35,11 +33,13 @@ def add_epochs(
         neo_io iterators for each rec file. Contains time information
     """
     logger = logging.getLogger("convert")
-    session_info = file_info[(file_info.date == date) & (file_info.animal == animal)]
-    for epoch in set(session_info.epoch):
-        rec_file_list = session_info[
-            (session_info.epoch == epoch) & (session_info.file_extension == ".rec")
+    for epoch in set(session_df.epoch):
+        rec_file_list = session_df[
+            (session_df.epoch == epoch) & (session_df.file_extension == ".rec")
         ]
+        if len(rec_file_list) == 0:
+            logger.info(f"no rec files for epoch {epoch}, No epoch interval created")
+            continue
         start_time = None
         end_time = None
         logger.info(list(rec_file_list.full_path))
@@ -58,7 +58,7 @@ def add_epochs(
                     )
                 else:
                     file_end_time = np.max(
-                        io._get_systime_from_trodes_timestamps(n_time - 1, n_time)
+                        io.get_systime_from_trodes_timestamps(n_time - 1, n_time)
                     )
                 if end_time is None or file_end_time > end_time:
                     end_time = float(file_end_time)