handle multi edf file

src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_edf_interface.py

@@ -1,8 +1,12 @@
 from typing import Union
 from pathlib import Path
-from neuroconv.basedatainterface import BaseDataInterface
+
 from pynwb import NWBFile, TimeSeries
 from pynwb.device import Device
+
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.utils import DeepDict
+
 from mne.io import read_raw_edf
 from datetime import datetime, timedelta
 import numpy as np
@@ -179,18 +183,23 @@ def add_to_nwbfile(
                 "unit": "n.a.",
             },
         }
-        concatenated_data = []
+        concatenated_data = None
         concatenated_times = []
 
         # Loop over each EDF file and concatenate data and timestamps
         for file_path in self.file_paths:
             edf_reader = read_raw_edf(input_fname=file_path, verbose=self.verbose)
             data, times = edf_reader.get_data(picks=list(channels_dict.keys()), return_times=True)
+            data = data.astype(np.float32)
             # Slice the data and timestamps within the time range
             if stub_test:
                 concatenated_data = data[:, :stub_frames]
                 break
-            concatenated_data.append(data.astype("float32"))
+            # Concatenate along the time axis
+            if concatenated_data is None:
+                concatenated_data = data
+            else:
+                concatenated_data = np.concatenate((concatenated_data, data), axis=1)
             concatenated_times.extend(times)
 
         for channel_index, channel_name in enumerate(channels_dict.keys()):

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_week_session.py

@@ -1,7 +1,7 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
 
 import time
-
+from natsort import natsorted
 from pathlib import Path
 from typing import Union
 from datetime import datetime, timedelta
@@ -11,20 +11,15 @@
 
 from zaki_2024_nwbconverter import Zaki2024NWBConverter
 
-# TODO:
-# 1. aggiungere sessions start time da edf.info["meas_date"]
-# 2. creare un interfaccia per multi edf files
-
 
 def session_to_nwb(
     data_dir_path: Union[str, Path],
     output_dir_path: Union[str, Path],
     subject_id: str,
     stub_test: bool = False,
     verbose: bool = True,
-    include_eeg_emg_signals: bool = True,
 ):
-    print(f"Converting session {session_id}")
+    print(f"Converting week-long session")
     if verbose:
         start = time.time()
 
@@ -40,34 +35,30 @@ def session_to_nwb(
     conversion_options = dict()
 
     # Add EEG, EMG, Temperature and Activity signals
-    datetime_obj = datetime.strptime(date_str, "%Y_%m_%d")
-    reformatted_date_str = datetime_obj.strftime("_%m%d%y")
-    edf_file_path = data_dir_path / "Ca_EEG_EDF" / (subject_id + "_EDF") / (subject_id + reformatted_date_str + ".edf")
-
-    if edf_file_path.is_file() and include_eeg_emg_signals:
-
+    edf_folder_path = data_dir_path / "Ca_EEG_EDF" / (subject_id + "_EDF")
+    edf_file_paths = natsorted(edf_folder_path.glob("*.edf"))
+    if len(edf_file_paths) > 0:
         source_data.update(
             dict(
-                EDFSignals=dict(
-                    file_path=edf_file_path,
+                MultiEDFSignals=dict(
+                    file_paths=edf_file_paths,
                 )
             )
         )
-        conversion_options.update(dict(EDFSignals=dict(stub_test=stub_test)))
-    elif verbose and not include_eeg_emg_signals:
-        print(f"The EEG, EMG, Temperature and Activity signals will not be included for session {session_id}")
-    elif verbose and not edf_file_path.is_file():
-        print(f"No .edf file found at {edf_file_path}")
+        conversion_options.update(dict(MultiEDFSignals=dict(stub_test=stub_test)))
+    else:
+        print(f"No .edf file found in {edf_folder_path}")
 
     converter = Zaki2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
     metadata = converter.get_metadata()
-    # if session_start_time has been already set from other interfaces do not override
-    if not metadata["NWBFile"]["session_start_time"]:
-        datetime_str = date_str + " " + time_str
-        session_start_time = datetime.strptime(datetime_str, "%Y_%m_%d %H_%M_%S")
-        metadata["NWBFile"]["session_start_time"] = session_start_time
+
+    from mne.io import read_raw_edf
+
+    edf_reader = read_raw_edf(input_fname=edf_file_paths[0], verbose=verbose)
+    session_start_time = edf_reader.info["meas_date"]
+    metadata["NWBFile"]["session_start_time"] = session_start_time
 
     # Update default metadata with the editable in the corresponding yaml file
     editable_metadata_path = Path(__file__).parent / "zaki_2024_metadata.yaml"
@@ -96,22 +87,12 @@ def session_to_nwb(
 
     # Parameters for conversion
     data_dir_path = Path("D:/")
-    subject_id = "Ca_EEG3-4"
-    task = "OfflineDay1Session1"
-    session_id = subject_id + "_" + task
     output_dir_path = Path("D:/cai_lab_conversion_nwb/")
+    subject_id = "Ca_EEG3-4"
     stub_test = False
-    session_times_file_path = data_dir_path / "Ca_EEG_Experiment" / subject_id / (subject_id + "_SessionTimes.csv")
-    df = pd.read_csv(session_times_file_path)
-    session_row = df[df["Session"] == task].iloc[0]
-    date_str = session_row["Date"]
-    time_str = session_row["Time"]
     session_to_nwb(
         data_dir_path=data_dir_path,
         output_dir_path=output_dir_path,
         stub_test=stub_test,
         subject_id=subject_id,
-        session_id=session_id,
-        date_str=date_str,
-        time_str=time_str,
     )