Align the starting_time of the processed fiber photometry data

src/dombeck_lab_to_nwb/azcorra2023/azcorra2023nwbconverter.py

@@ -29,3 +29,11 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata, conversion_options: Optiona
 
         backend_configuration = get_default_backend_configuration(nwbfile=nwbfile, backend="hdf5")
         configure_backend(nwbfile=nwbfile, backend_configuration=backend_configuration)
+
+    def temporally_align_data_interfaces(self):
+        """
+        Align the starting time of processed fiber photometry data after cropping.
+        """
+        processed_interface = self.data_interface_objects["ProcessedFiberPhotometry"]
+        aligned_starting_time = processed_interface.get_starting_time()
+        processed_interface.set_aligned_starting_time(aligned_starting_time=aligned_starting_time)

src/dombeck_lab_to_nwb/azcorra2023/interfaces/azcorra2023_fiberphotometryinterface.py

@@ -1,15 +1,16 @@
 from pathlib import Path
 from typing import Optional
 
-from neuroconv.basedatainterface import BaseDataInterface
+import numpy as np
+from neuroconv import BaseTemporalAlignmentInterface
 from neuroconv.utils import FilePathType
 from pymatreader import read_mat
 from pynwb import NWBFile
 
 from dombeck_lab_to_nwb.azcorra2023.photometry_utils.add_fiber_photometry import add_fiber_photometry_series
 
 
-class Azcorra2023FiberPhotometryInterface(BaseDataInterface):
+class Azcorra2023FiberPhotometryInterface(BaseTemporalAlignmentInterface):
     """Data interface for Azcorra2023 fiber photometry data conversion."""
 
     display_name = "Azcorra2023BinnedPhotometry"
@@ -36,6 +37,8 @@ def __init__(
         self.verbose = verbose
         binned_photometry_data = read_mat(filename=str(self.file_path))
         self._photometry_data = binned_photometry_data["#subsystem#"]["MCOS"][2]
+        self._sampling_frequency = 100.0
+        self._timestamps = None
 
         depth_ids = binned_photometry_data["#subsystem#"]["MCOS"][5]
         depth_ids = [depth_ids] if isinstance(depth_ids, str) else depth_ids
@@ -48,6 +51,24 @@ def __init__(
 
         self.column_names = binned_photometry_data["#subsystem#"]["MCOS"][7]
 
+    def get_original_timestamps(self) -> np.ndarray:
+        binned_photometry_data = read_mat(filename=str(self.file_path))["#subsystem#"]["MCOS"][2]
+        channel_index = self.column_names.index("chMov")
+        data = binned_photometry_data[channel_index]
+        if len(self.depth_ids) > 1:
+            data = data[self.depth_index]
+        num_frames = len(data)
+        return np.arange(num_frames) / self._sampling_frequency
+
+    def get_timestamps(self, stub_test: bool = False) -> np.ndarray:
+        timestamps = self._timestamps if self._timestamps is not None else self.get_original_timestamps()
+        if stub_test:
+            return timestamps[:6000]
+        return timestamps
+
+    def set_aligned_timestamps(self, aligned_timestamps: np.ndarray) -> None:
+        self._timestamps = np.array(aligned_timestamps)
+
     def add_to_nwbfile(
         self,
         nwbfile: NWBFile,
@@ -87,11 +108,12 @@ def add_to_nwbfile(
             if len(self.depth_ids) > 1:
                 data = data[self.depth_index]
 
+            timestamps = self.get_timestamps(stub_test=stub_test)
             add_fiber_photometry_series(
                 nwbfile=nwbfile,
                 metadata=metadata,
                 data=data if not stub_test else data[:6000],
-                rate=100.0,
+                timestamps=timestamps,
                 fiber_photometry_series_name=series_name,
                 table_region_ind=series_ind,
                 parent_container="acquisition",

src/dombeck_lab_to_nwb/azcorra2023/interfaces/azcorra2023_processedfiberphotometryinterface.py

@@ -43,6 +43,20 @@ def __init__(
         self._processed_photometry_data = processed_photometry_data["data"]
         self._timestamps = None
         self._sampling_frequency = 100.0
+        crop_point = processed_photometry_data["cropStart"]
+        # If the crop point is a list, it means that the end of the recording was cropped as well
+        self._crop_start = crop_point[0] if isinstance(crop_point, np.ndarray) else crop_point
+
+    def get_starting_time(self) -> float:
+        """
+        Return the starting time of the processed photometry data.
+        If the start of the picoscope recording had artefacts, the corrupted segment was cut off manually and the cropping point
+        was saved as "cropStart". We are using this value to align the starting time of the processed data with the
+        picoscope data.
+        """
+        if self._crop_start == 1:
+            return 0.0
+        return self._crop_start / self._sampling_frequency
 
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
@@ -76,12 +90,7 @@ def get_metadata(self) -> dict:
 
     def get_original_timestamps(self) -> np.ndarray:
         processed_photometry_data = read_mat(filename=str(self.file_path))["data6"]["data"]
-        traces = (
-            processed_photometry_data["chGreen"]
-            if "chGreen" in processed_photometry_data
-            else processed_photometry_data["chRed"]
-        )
-        num_frames = len(traces)
+        num_frames = len(processed_photometry_data["chMov"])
         return np.arange(num_frames) / self._sampling_frequency
 
     def get_timestamps(self, stub_test: bool = False) -> np.ndarray:
@@ -105,9 +114,13 @@ def add_continuous_behavior(self, nwbfile: NWBFile, metadata: dict):
         ), f"Velocity data not found in {self.source_data['file_path']}."
         velocity = self._processed_photometry_data["chMov"]
         velocity_metadata = behavior_metadata["Velocity"]
+
+        timestamps = self.get_timestamps()
+
         velocity_ts = TimeSeries(
             data=velocity,
             rate=self._sampling_frequency,
+            starting_time=timestamps[0],
             **velocity_metadata,
         )
 
@@ -119,6 +132,7 @@ def add_continuous_behavior(self, nwbfile: NWBFile, metadata: dict):
         acceleration_ts = TimeSeries(
             data=acceleration,
             rate=self._sampling_frequency,
+            starting_time=timestamps[0],
             **acceleration_metadata,
         )
 
@@ -155,6 +169,8 @@ def add_delta_f_over_f_traces(
         """
         ophys_module = get_module(nwbfile=nwbfile, name="ophys", description=f"Processed fiber photometry data.")
 
+        timestamps = self.get_timestamps(stub_test=stub_test)
+
         for series_ind, (channel_name, series_name) in enumerate(
             channel_name_to_photometry_series_name_mapping.items()
         ):
@@ -181,6 +197,7 @@ def add_delta_f_over_f_traces(
                     data=data_to_add,
                     unit="n.a.",
                     rate=self._sampling_frequency,
+                    starting_time=timestamps[0],
                     fiber_photometry_table_region=fiber_photometry_table_region,
                 )
 
@@ -196,8 +213,7 @@ def add_delta_f_over_f_traces(
                     nwbfile=nwbfile,
                     metadata=metadata,
                     data=data_to_add,
-                    rate=self._sampling_frequency,
-                    unit="n.a.",
+                    timestamps=timestamps,
                     fiber_photometry_series_name=series_name,
                     table_region_ind=series_ind,
                     parent_container="processing/ophys",

src/dombeck_lab_to_nwb/azcorra2023/photometry_utils/add_fiber_photometry.py

@@ -3,6 +3,7 @@
 
 import numpy as np
 from neuroconv.tools import get_module
+from neuroconv.utils import calculate_regular_series_rate
 from pynwb import NWBFile
 from ndx_fiber_photometry import (
     FiberPhotometryTable,
@@ -40,10 +41,9 @@ def add_fiber_photometry_series(
     nwbfile: NWBFile,
     metadata: dict,
     data: np.ndarray,
-    rate: float,
+    timestamps: np.ndarray,
     fiber_photometry_series_name: str,
     table_region_ind: int = 0,
-    unit: str = "F",
     parent_container: Literal["acquisition", "processing/ophys"] = "acquisition",
 ):
     fiber_photometry_metadata = metadata["Ophys"]["FiberPhotometry"]
@@ -207,13 +207,20 @@ def add_fiber_photometry_series(
         region=[table_region_ind], description="source fibers"
     )
 
+    timing_kwargs = dict()
+    rate = calculate_regular_series_rate(series=timestamps)
+    if rate is not None:
+        timing_kwargs.update(rate=rate, starting_time=timestamps[0])
+    else:
+        timing_kwargs.update(timestamps=timestamps)
+
     fiber_photometry_response_series = FiberPhotometryResponseSeries(
         name=trace_metadata["name"],
         description=trace_metadata["description"],
         data=data,
-        unit=unit,
-        rate=rate,
+        unit="n.a.",
         fiber_photometry_table_region=fiber_photometry_table_region,
+        **timing_kwargs,
     )
 
     if parent_container == "acquisition":