added opto

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_optogeneticinterface.py

@@ -0,0 +1,88 @@
+"""Primary class for converting optogenetic stimulation."""
+from pynwb.file import NWBFile
+from pydantic import FilePath
+import numpy as np
+from pymatreader import read_mat
+from pynwb.device import Device
+from pynwb.ogen import OptogeneticSeries, OptogeneticStimulusSite
+
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.tools.optogenetics import create_optogenetic_stimulation_timeseries
+from neuroconv.utils import DeepDict, get_base_schema
+from neuroconv.tools import nwb_helpers
+
+
+class Schneider2024OptogeneticInterface(BaseDataInterface):
+    """Optogenetic interface for schneider_2024 conversion"""
+
+    keywords = ["optogenetics"]
+
+    def __init__(self, file_path: FilePath):
+        super().__init__(file_path=file_path)
+
+    def get_metadata(self) -> DeepDict:
+        metadata = super().get_metadata()
+
+        return metadata
+
+    def get_metadata_schema(self) -> dict:
+        metadata_schema = super().get_metadata_schema()
+        return metadata_schema
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        # Read Data
+        file_path = self.source_data["file_path"]
+        file = read_mat(file_path)
+        onset_times = file["events"]["push"]["opto_time"]
+        is_opto_trial = np.logical_not(np.isnan(onset_times))
+        onset_times = onset_times[is_opto_trial]
+        offset_times = file["events"]["push"]["opto_time_end"]
+        offset_times = offset_times[is_opto_trial]
+        assert np.all(
+            np.logical_not(np.isnan(offset_times))
+        ), "Some of the offset times are nan when onset times are not nan."
+        frequency = 1  # TODO: Get opto stim frequency from schneider lab
+        power = 0.1  # TODO: confirm power with schneider lab
+        pulse_width = 0.1  # TODO: confirm pulse width with schneider lab
+
+        timestamps, data = [0], [0]
+        for onset_time, offset_time in zip(onset_times, offset_times):
+            duration = offset_time - onset_time
+            num_pulses = int(duration * frequency)
+            inter_pulse_interval = 1 / frequency
+            for i in range(num_pulses):
+                pulse_onset_time = onset_time + i * inter_pulse_interval
+                timestamps.append(pulse_onset_time)
+                data.append(power)
+                pulse_offset_time = pulse_onset_time + pulse_width
+                timestamps.append(pulse_offset_time)
+                data.append(0)
+        timestamps, data = np.array(timestamps, dtype=np.float64), np.array(data, dtype=np.float64)
+
+        # Add Data to NWBFile
+        # Add Device
+        device = Device(**metadata["Optogenetics"]["Device"])
+        nwbfile.add_device(device)
+
+        # Add OptogeneticStimulusSite
+        site_metadata = metadata["Optogenetics"]["OptogeneticStimulusSite"]
+        location = f"Injection location: {site_metadata['injection_location']} \n Stimulation location: {site_metadata['stimulation_location']}"
+        ogen_site = OptogeneticStimulusSite(
+            name=site_metadata["name"],
+            device=device,
+            description=site_metadata["description"],
+            excitation_lambda=site_metadata["excitation_lambda"],
+            location=location,
+        )
+        nwbfile.add_ogen_site(ogen_site)
+
+        # Add OptogeneticSeries
+        series_metadata = metadata["Optogenetics"]["OptogeneticSeries"]
+        optogenetic_series = OptogeneticSeries(
+            name=series_metadata["name"],
+            site=ogen_site,
+            description=series_metadata["description"],
+            data=data,
+            timestamps=timestamps,
+        )
+        nwbfile.add_stimulus(optogenetic_series)