MedPC data conversion

MedPC output files contain information about operant behavior such as nose pokes and rewards. Install NeuroConv with the additional dependencies necessary for writing medpc behavioral data.

pip install neuroconv[medpc]

Convert MedPC output data to NWB using MedPCInterface.

from datetime import datetime
from zoneinfo import ZoneInfo
from neuroconv.datainterfaces import MedPCInterface

# For this data interface we need to pass the output file from MedPC
file_path = f"{BEHAVIOR_DATA_PATH}/medpc/example_medpc_file_06_06_2024.txt"
# Change the folder_path to the appropriate location in your system
session_conditions = {"Start Date": "04/18/19", "Start Time": "10:41:42"}
start_variable = "Start Date",
metadata_medpc_name_to_info_dict = dict(
    "Start Date": {"name": "start_date", "is_array": False},
    "Start Time": {"name": "start_time", "is_array": False},
    "Subject": {"name": "subject", "is_array": False},
    "Box": {"name": "box", "is_array": False},
    "MSN": {"name": "MSN", "is_array": False},
)
interface = MedPCInterface(
    file_path=file_path,
    session_conditions=session_conditions,
    start_variable=start_variable,
    metadata_medpc_name_to_info_dict=metadata_medpc_name_to_info_dict
)

# Extract what metadata we can from the source file
metadata = interface.get_metadata()
# We add the time zone information, which is required by NWB
session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=ZoneInfo("US/Pacific"))
metadata["NWBFile"].update(session_start_time=session_start_time)
metadata["MedPC"]["medpc_name_to_info_dict"] = {
        "A": {"name": "left_nose_poke_times", "is_array": True},
        "B": {"name": "left_reward_times", "is_array": True},
        "C": {"name": "right_nose_poke_times", "is_array": True},
        "D": {"name": "right_reward_times", "is_array": True},
        "E": {"name": "duration_of_port_entry", "is_array": True},
        "G": {"name": "port_entry_times", "is_array": True},
        "H": {"name": "footshock_times", "is_array": True},
}
metadata["MedPC"]["Events"] = [
    {
        "name": "left_nose_poke_times",
        "description": "Left nose poke times.",
    },
    {
        "name": "left_reward_times",
        "description": "Left reward times.",
    },
    {
        "name": "right_nose_poke_times",
        "description": "Right nose poke times.",
    },
    {
        "name": "right_reward_times",
        "description": "Right reward times.",
    },
    {
        "name": "footshock_times",
        "description": "Footshock times.",
    },
]
metadata["MedPC"]["IntervalSeries"] = [
    {
        "name": "reward_port_intervals",
        "description": "Interval of time spent in reward port (1 is entry, -1 is exit).",
        "onset_name": "port_entry_times",
        "duration_name": "duration_of_port_entry",
    },
]

# Choose a path for saving the nwb file and run the conversion
nwbfile_path = f"{path_to_save_nwbfile}"  # This should be something like: "./saved_file.nwb"
interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)