From 5d73568fa24939cd9ea6ddbc8ef52ac92d76a4b6 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 17 Jun 2024 16:58:10 +0200
Subject: [PATCH 1/9] add custom behavior interface

---
 src/howe_lab_to_nwb/vu2024/__init__.py        |   1 -
 .../vu2024/interfaces/__init__.py             |   1 +
 .../interfaces/vu2024_behaviorinterface.py    | 225 ++++++++++++++++++
 .../vu2024/vu2024behaviorinterface.py         |  27 ---
 4 files changed, 226 insertions(+), 28 deletions(-)
 create mode 100644 src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
 delete mode 100644 src/howe_lab_to_nwb/vu2024/vu2024behaviorinterface.py

diff --git a/src/howe_lab_to_nwb/vu2024/__init__.py b/src/howe_lab_to_nwb/vu2024/__init__.py
index 7d9d095..127bd84 100644
--- a/src/howe_lab_to_nwb/vu2024/__init__.py
+++ b/src/howe_lab_to_nwb/vu2024/__init__.py
@@ -1,2 +1 @@
-from .vu2024behaviorinterface import Vu2024BehaviorInterface
 from .vu2024nwbconverter import Vu2024NWBConverter
diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/__init__.py b/src/howe_lab_to_nwb/vu2024/interfaces/__init__.py
index 3c99cfa..c917ba5 100644
--- a/src/howe_lab_to_nwb/vu2024/interfaces/__init__.py
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/__init__.py
@@ -1,2 +1,3 @@
 from .vu2024_fiberphotometryinterface import Vu2024FiberPhotometryInterface
 from .cxdimaginginterface import CxdImagingInterface
+from .vu2024_behaviorinterface import Vu2024BehaviorInterface
diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
new file mode 100644
index 0000000..b614d08
--- /dev/null
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
@@ -0,0 +1,225 @@
+from typing import Optional
+
+import numpy as np
+import pandas as pd
+from neuroconv import BaseTemporalAlignmentInterface
+from neuroconv.tools import get_module
+from neuroconv.utils import FilePathType
+from pymatreader import read_mat
+from pynwb import NWBFile
+from pynwb.behavior import SpatialSeries, CompassDirection, BehavioralTimeSeries
+from pynwb.epoch import TimeIntervals
+
+
+class Vu2024BehaviorInterface(BaseTemporalAlignmentInterface):
+    """
+    Interface for reading the processed behavior data from .mat files from the Howe Lab.
+    """
+
+    display_name = "Vu2024Behavior"
+    associated_suffixes = (".mat",)
+    info = "Interface for behavior data (.mat) from the Howe Lab."
+
+    def __init__(
+        self,
+        file_path: FilePathType,
+        verbose: bool = True,
+    ):
+        """
+        DataInterface for reading the processed behavior data from .mat files from the Howe Lab.
+
+        Parameters
+        ----------
+        file_path : FilePathType
+            Path to the .mat file that contains the fiber photometry data.
+        verbose : bool, default: True
+            controls verbosity.
+        """
+
+        super().__init__(file_path=file_path, verbose=verbose)
+        self._timestamps = None
+
+    def get_original_timestamps(self) -> np.ndarray:
+        filename = self.source_data["file_path"]
+        behavior_data = read_mat(filename=filename)
+        if "timestamp" not in behavior_data:
+            raise ValueError(f"Expected 'timestamp' is not in '{filename}'.")
+        timestamps = behavior_data["timestamp"]
+
+        return timestamps
+
+    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 get_metadata(self):
+        metadata = super().get_metadata()
+
+        metadata["Behavior"] = dict(
+            CompassDirection=dict(
+                SpatialSeries=dict(
+                    name="SpatialSeries",
+                    description="The yaw (rotational) velocity measured in degrees/s.",
+                    reference_frame="unknown",
+                    unit="degrees/s",
+                ),
+            ),
+            BehavioralTimeSeries=dict(
+                SpatialSeries=dict(
+                    name="SpatialSeries",
+                    description="Velocity for the roll and pitch (x, y) measured in m/s.",
+                    reference_frame="unknown",
+                    unit="m/s",
+                ),
+            ),
+            TimeIntervals=dict(
+                name="TimeIntervals",
+                description="The onset times of the events (licking, tone, light or reward delivery).",
+            ),
+        )
+
+        return metadata
+
+    def add_velocity_signals(self, nwbfile: NWBFile, metadata: dict, stub_test: Optional[bool] = False) -> None:
+        """
+        Add the velocity signals (yaw (z) velocity and the roll and pitch (x, y)) to the NWBFile.
+        The yaw velocity is measured in degrees/s and the roll and pitch velocities are measured in m/s.
+
+        Parameters
+        ----------
+        nwbfile : NWBFile
+            The NWBFile to which the velocity signals will be added.
+        metadata : dict
+            Metadata for the velocity signals.
+        stub_test : bool, optional
+            Whether to run a stub test, by default False.
+        """
+
+        end_frame = 6000 if stub_test else None
+
+        behavior_metadata = metadata["Behavior"]
+        spatial_series_metadata = behavior_metadata["CompassDirection"]["SpatialSeries"]
+
+        behavior_data = read_mat(filename=self.source_data["file_path"])
+        timestamps = self.get_timestamps(stub_test=stub_test)
+
+        compass_direction = CompassDirection(name="CompassDirection")
+
+        compass_direction.create_spatial_series(
+            **spatial_series_metadata,
+            data=behavior_data["ballYaw"][:end_frame],
+            timestamps=timestamps,
+        )
+
+        behavior = get_module(
+            nwbfile,
+            name="behavior",
+            description="Contains the velocity signals from two optical mouse sensors (Logitech G203 mice with hard plastic shells removed).",
+        )
+        behavior.add(compass_direction)
+
+        behavioral_time_series_metadata = behavior_metadata["BehavioralTimeSeries"]["SpatialSeries"]
+        behavioral_time_series = BehavioralTimeSeries(name="BehavioralTimeSeries")
+
+        data = np.column_stack((behavior_data["ballRoll"], behavior_data["ballPitch"]))
+        spatial_series = SpatialSeries(
+            **behavioral_time_series_metadata,
+            data=data[:end_frame],
+            timestamps=timestamps,
+        )
+        behavioral_time_series.add_timeseries(spatial_series)
+        behavior.add(behavioral_time_series)
+
+    def _get_start_end_times(self, binary_event_data: np.ndarray):
+
+        timestamps = self.get_timestamps()
+        ones_indices = np.where(binary_event_data == 1)[0]
+        if not len(ones_indices):
+            return [], []
+
+        # Calculate the differences between consecutive indices
+        diff = np.diff(ones_indices)
+
+        # Find where the difference is not 1
+        ends = np.where(diff != 1)[0]
+
+        # The start of an interval is one index after the end of the previous interval
+        starts = ends + 1
+
+        # Handle the case for the first interval
+        starts = np.insert(starts, 0, 0)
+
+        # Handle the case for the last interval
+        ends = np.append(ends, len(ones_indices) - 1)
+
+        # Return the start and end times of the intervals
+        start_times = timestamps[ones_indices[starts]]
+        end_times = timestamps[ones_indices[ends]]
+
+        return start_times, end_times
+
+    def add_binary_signals(self, nwbfile: NWBFile, metadata: dict):
+        behavior_data = read_mat(filename=self.source_data["file_path"])
+
+        events_metadata = metadata["Behavior"]["TimeIntervals"]
+
+        event_name_mapping = dict(
+            lick="Lick",
+            reward="Reward",
+            stimulus_led="Light",
+            stimulus_sound="Tone",
+        )
+
+        event_dfs = []
+        for event_name in ["lick", "reward", "stimulus_led", "stimulus_sound"]:
+            start_times, end_times = self._get_start_end_times(binary_event_data=behavior_data[event_name])
+            if not len(start_times):
+                continue
+
+            event_dfs.append(
+                pd.DataFrame(
+                    {
+                        "start_time": start_times,
+                        "stop_time": end_times,
+                        "event_type": event_name_mapping[event_name],
+                    }
+                )
+            )
+
+        if not len(event_dfs):
+            return
+
+        events = TimeIntervals(**events_metadata)
+        events.add_column(
+            name="event_type",
+            description="The type of event (licking, light, tone or reward delivery).",
+        )
+
+        event_df = pd.concat(event_dfs)
+        event_df = event_df.sort_values(by="start_time")
+        event_df = event_df.reset_index(drop=True)
+        for row_ind, row in event_df.iterrows():
+            events.add_interval(
+                start_time=row["start_time"],
+                stop_time=row["stop_time"],
+                event_type=row["event_type"],
+                id=row_ind,
+            )
+
+        behavior = get_module(nwbfile, name="behavior")
+        behavior.add(events)
+
+    def add_to_nwbfile(
+        self,
+        nwbfile: NWBFile,
+        metadata: dict,
+        stub_test: Optional[bool] = False,
+    ) -> None:
+
+        self.add_velocity_signals(nwbfile=nwbfile, metadata=metadata, stub_test=stub_test)
+        self.add_binary_signals(nwbfile=nwbfile, metadata=metadata)
diff --git a/src/howe_lab_to_nwb/vu2024/vu2024behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/vu2024behaviorinterface.py
deleted file mode 100644
index 9daa990..0000000
--- a/src/howe_lab_to_nwb/vu2024/vu2024behaviorinterface.py
+++ /dev/null
@@ -1,27 +0,0 @@
-"""Primary class for converting experiment-specific behavior."""
-
-from pynwb.file import NWBFile
-
-from neuroconv.basedatainterface import BaseDataInterface
-from neuroconv.utils import DeepDict
-
-
-class Vu2024BehaviorInterface(BaseDataInterface):
-    """Behavior interface for vu2024 conversion"""
-
-    keywords = ["behavior"]
-
-    def __init__(self):
-        # This should load the data lazily and prepare variables you need
-        pass
-
-    def get_metadata(self) -> DeepDict:
-        # Automatically retrieve as much metadata as possible from the source files available
-        metadata = super().get_metadata()
-
-        return metadata
-
-    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
-        # All the custom code to add the data the nwbfile
-
-        raise NotImplementedError()

From d21bb9d8742ce6abd29e53615ffd48d8d4979379 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 17 Jun 2024 16:58:33 +0200
Subject: [PATCH 2/9] add to converter

---
 src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py b/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
index aebda95..392278a 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
+++ b/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
@@ -4,7 +4,11 @@
 from neuroconv.datainterfaces import TiffImagingInterface
 from neuroconv.utils import DeepDict
 
-from howe_lab_to_nwb.vu2024.interfaces import Vu2024FiberPhotometryInterface, CxdImagingInterface
+from howe_lab_to_nwb.vu2024.interfaces import (
+    CxdImagingInterface,
+    Vu2024FiberPhotometryInterface,
+    Vu2024BehaviorInterface,
+)
 
 
 class Vu2024NWBConverter(NWBConverter):
@@ -14,6 +18,7 @@ class Vu2024NWBConverter(NWBConverter):
         Imaging=CxdImagingInterface,
         ProcessedImaging=TiffImagingInterface,
         FiberPhotometry=Vu2024FiberPhotometryInterface,
+        Behavior=Vu2024BehaviorInterface,
     )
 
     def get_metadata_schema(self) -> dict:

From 207024fd93222dc83e321db445abfa872ab2ca37 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 17 Jun 2024 16:58:46 +0200
Subject: [PATCH 3/9] modify convert session script

---
 .../vu2024/vu2024_convert_single_wavelength_session.py     | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
index 02af27b..e62b8e2 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
+++ b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
@@ -20,6 +20,7 @@ def single_wavelength_session_to_nwb(
     indicator: str,
     ttl_file_path: Union[str, Path],
     motion_corrected_imaging_file_path: Union[str, Path],
+    behavior_file_path: Union[str, Path],
     nwbfile_path: Union[str, Path],
     sampling_frequency: float = None,
     stub_test: bool = False,
@@ -87,6 +88,10 @@ def single_wavelength_session_to_nwb(
         dict(FiberPhotometry=dict(stub_test=stub_test, fiber_locations_metadata=fiber_locations_metadata))
     )
 
+    # Add behavior
+    source_data.update(dict(Behavior=dict(file_path=str(behavior_file_path))))
+    conversion_options.update(dict(Behavior=dict(stub_test=stub_test)))
+
     converter = Vu2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -128,6 +133,7 @@ def single_wavelength_session_to_nwb(
     ttl_file_path = Path("/Volumes/t7-ssd/Howe/DL18/211110/GridDL-18_2021.11.10_16.12.31.mat")
     fiber_locations_file_path = Path("/Volumes/t7-ssd/Howe/DL18/DL18_fiber_locations.xlsx")
     motion_corrected_imaging_file_path = Path("/Volumes/t7-ssd/Howe/DL18/211110/Data00217_crop_MC.tif")
+    behavior_file_path = Path("/Volumes/t7-ssd/Howe/DL18/211110/GridDL-18_2021.11.10_16.12.31_ttlIn1_movie1.mat")
 
     # The sampling frequency of the raw imaging data must be provided when it cannot be extracted from the .cxd file
     sampling_frequency = None
@@ -146,6 +152,7 @@ def single_wavelength_session_to_nwb(
         excitation_wavelength_in_nm=excitation_wavelength_in_nm,
         indicator=indicator,
         motion_corrected_imaging_file_path=motion_corrected_imaging_file_path,
+        behavior_file_path=behavior_file_path,
         nwbfile_path=nwbfile_path,
         sampling_frequency=sampling_frequency,
         stub_test=stub_test,

From 074e8011908818db821a1f94c93139726142929e Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Tue, 18 Jun 2024 12:25:56 +0200
Subject: [PATCH 4/9] add velocity as timeseries

---
 .../interfaces/vu2024_behaviorinterface.py    | 26 +++++++------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
index b614d08..7ae0c0c 100644
--- a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
@@ -6,8 +6,8 @@
 from neuroconv.tools import get_module
 from neuroconv.utils import FilePathType
 from pymatreader import read_mat
-from pynwb import NWBFile
-from pynwb.behavior import SpatialSeries, CompassDirection, BehavioralTimeSeries
+from pynwb import NWBFile, TimeSeries
+from pynwb.behavior import CompassDirection
 from pynwb.epoch import TimeIntervals
 
 
@@ -69,13 +69,10 @@ def get_metadata(self):
                     unit="degrees/s",
                 ),
             ),
-            BehavioralTimeSeries=dict(
-                SpatialSeries=dict(
-                    name="SpatialSeries",
-                    description="Velocity for the roll and pitch (x, y) measured in m/s.",
-                    reference_frame="unknown",
-                    unit="m/s",
-                ),
+            TimeSeries=dict(
+                name="Velocity",
+                description="Velocity for the roll and pitch (x, y) measured in m/s.",
+                unit="m/s",
             ),
             TimeIntervals=dict(
                 name="TimeIntervals",
@@ -123,17 +120,14 @@ def add_velocity_signals(self, nwbfile: NWBFile, metadata: dict, stub_test: Opti
         )
         behavior.add(compass_direction)
 
-        behavioral_time_series_metadata = behavior_metadata["BehavioralTimeSeries"]["SpatialSeries"]
-        behavioral_time_series = BehavioralTimeSeries(name="BehavioralTimeSeries")
-
+        velocity_metadata = behavior_metadata["TimeSeries"]
         data = np.column_stack((behavior_data["ballRoll"], behavior_data["ballPitch"]))
-        spatial_series = SpatialSeries(
-            **behavioral_time_series_metadata,
+        velocity_xy = TimeSeries(
+            **velocity_metadata,
             data=data[:end_frame],
             timestamps=timestamps,
         )
-        behavioral_time_series.add_timeseries(spatial_series)
-        behavior.add(behavioral_time_series)
+        behavior.add(velocity_xy)
 
     def _get_start_end_times(self, binary_event_data: np.ndarray):
 

From 1f6c7d1de9b6e0979549f529bd6be669b0d148b5 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Tue, 18 Jun 2024 15:44:14 +0200
Subject: [PATCH 5/9] define metadata schema for behavior interface

---
 .../interfaces/vu2024_behaviorinterface.py    | 44 ++++++++++++++++++-
 1 file changed, 43 insertions(+), 1 deletion(-)

diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
index 7ae0c0c..47ee636 100644
--- a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
@@ -4,7 +4,7 @@
 import pandas as pd
 from neuroconv import BaseTemporalAlignmentInterface
 from neuroconv.tools import get_module
-from neuroconv.utils import FilePathType
+from neuroconv.utils import FilePathType, get_base_schema
 from pymatreader import read_mat
 from pynwb import NWBFile, TimeSeries
 from pynwb.behavior import CompassDirection
@@ -57,6 +57,48 @@ def get_timestamps(self, stub_test: bool = False) -> np.ndarray:
     def set_aligned_timestamps(self, aligned_timestamps: np.ndarray) -> None:
         self._timestamps = np.array(aligned_timestamps)
 
+    def get_metadata_schema(self) -> dict:
+        metadata_schema = super().get_metadata_schema()
+        metadata_schema["properties"]["Behavior"] = get_base_schema(tag="Behavior")
+        metadata_schema["properties"]["Behavior"].update(
+            required=["CompassDirection", "TimeSeries", "TimeIntervals"],
+            properties=dict(
+                CompassDirection=dict(
+                    type="object",
+                    required=["SpatialSeries"],
+                    properties=dict(
+                        SpatialSeries=dict(
+                            type="object",
+                            required=["name", "description", "unit"],
+                            properties=dict(
+                                name=dict(type="string"),
+                                description=dict(type="string"),
+                                unit=dict(type="string"),
+                            ),
+                        ),
+                    ),
+                ),
+                TimeSeries=dict(
+                    type="object",
+                    required=["name", "description", "unit"],
+                    properties=dict(
+                        name=dict(type="string"),
+                        description=dict(type="string"),
+                        unit=dict(type="string"),
+                    ),
+                ),
+                TimeIntervals=dict(
+                    type="object",
+                    required=["name", "description"],
+                    properties=dict(
+                        name=dict(type="string"),
+                        description=dict(type="string"),
+                    ),
+                ),
+            ),
+        )
+        return metadata_schema
+
     def get_metadata(self):
         metadata = super().get_metadata()
 

From acd2a4e3953d301106db312e9aadea60a44d30e0 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Tue, 18 Jun 2024 15:46:01 +0200
Subject: [PATCH 6/9] add behavioral camera recording

---
 .../vu2024_convert_single_wavelength_session.py   |  9 +++++++++
 .../vu2024/vu2024_requirements.txt                |  1 +
 src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py  | 15 ++++++++++++++-
 3 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
index e62b8e2..fc8123f 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
+++ b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
@@ -22,6 +22,7 @@ def single_wavelength_session_to_nwb(
     motion_corrected_imaging_file_path: Union[str, Path],
     behavior_file_path: Union[str, Path],
     nwbfile_path: Union[str, Path],
+    behavior_avi_file_path: Union[str, Path] = None,
     sampling_frequency: float = None,
     stub_test: bool = False,
 ):
@@ -92,6 +93,11 @@ def single_wavelength_session_to_nwb(
     source_data.update(dict(Behavior=dict(file_path=str(behavior_file_path))))
     conversion_options.update(dict(Behavior=dict(stub_test=stub_test)))
 
+    # Add behavior camera recording
+    if behavior_avi_file_path is not None:
+        source_data.update(dict(Video=dict(file_paths=[str(behavior_avi_file_path)])))
+        conversion_options.update(dict(Video=dict(stub_test=stub_test)))
+
     converter = Vu2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -134,6 +140,8 @@ def single_wavelength_session_to_nwb(
     fiber_locations_file_path = Path("/Volumes/t7-ssd/Howe/DL18/DL18_fiber_locations.xlsx")
     motion_corrected_imaging_file_path = Path("/Volumes/t7-ssd/Howe/DL18/211110/Data00217_crop_MC.tif")
     behavior_file_path = Path("/Volumes/t7-ssd/Howe/DL18/211110/GridDL-18_2021.11.10_16.12.31_ttlIn1_movie1.mat")
+    # optional
+    behavior_camera_recording = Path("/Volumes/t7-ssd/Howe/DL18/211110/DL18-lick-11102021161113-0000.avi")
 
     # The sampling frequency of the raw imaging data must be provided when it cannot be extracted from the .cxd file
     sampling_frequency = None
@@ -153,6 +161,7 @@ def single_wavelength_session_to_nwb(
         indicator=indicator,
         motion_corrected_imaging_file_path=motion_corrected_imaging_file_path,
         behavior_file_path=behavior_file_path,
+        behavior_avi_file_path=behavior_camera_recording,
         nwbfile_path=nwbfile_path,
         sampling_frequency=sampling_frequency,
         stub_test=stub_test,
diff --git a/src/howe_lab_to_nwb/vu2024/vu2024_requirements.txt b/src/howe_lab_to_nwb/vu2024/vu2024_requirements.txt
index e375cd5..1e8a883 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024_requirements.txt
+++ b/src/howe_lab_to_nwb/vu2024/vu2024_requirements.txt
@@ -2,3 +2,4 @@ pymatreader==0.0.32
 ndx-fiber-photometry@git+https://github.com/catalystneuro/ndx-fiber-photometry.git@main
 openpyxl==3.1.2
 aicsimageio>=4.14.0
+neuroconv[video]
diff --git a/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py b/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
index 392278a..6c60823 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
+++ b/src/howe_lab_to_nwb/vu2024/vu2024nwbconverter.py
@@ -1,8 +1,10 @@
 """Primary NWBConverter class for this dataset."""
 
 from neuroconv import NWBConverter
-from neuroconv.datainterfaces import TiffImagingInterface
+from neuroconv.datainterfaces import TiffImagingInterface, VideoInterface
+from neuroconv.tools.signal_processing import get_rising_frames_from_ttl
 from neuroconv.utils import DeepDict
+from pymatreader import read_mat
 
 from howe_lab_to_nwb.vu2024.interfaces import (
     CxdImagingInterface,
@@ -19,6 +21,7 @@ class Vu2024NWBConverter(NWBConverter):
         ProcessedImaging=TiffImagingInterface,
         FiberPhotometry=Vu2024FiberPhotometryInterface,
         Behavior=Vu2024BehaviorInterface,
+        Video=VideoInterface,
     )
 
     def get_metadata_schema(self) -> dict:
@@ -49,3 +52,13 @@ def temporally_align_data_interfaces(self):
         # The timestamps from the fiber photometry data is from the TTL signals
         fiber_photometry_timestamps = fiber_photometry.get_timestamps()
         imaging.set_aligned_timestamps(aligned_timestamps=fiber_photometry_timestamps)
+
+        if "Video" in self.data_interface_objects:
+            video = self.data_interface_objects["Video"]
+            video_timestamps = video.get_timestamps()
+            ttl_file_path = fiber_photometry.source_data["ttl_file_path"]
+            ttl_data = read_mat(filename=ttl_file_path)
+            first_ttl_frame = get_rising_frames_from_ttl(trace=ttl_data["ttlIn3"])[0]
+            video.set_aligned_segment_starting_times(
+                aligned_segment_starting_times=[video_timestamps[0][first_ttl_frame]]
+            )

From f373860871732138f17adbfb53dcaf626cd7f9c7 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Tue, 18 Jun 2024 15:48:23 +0200
Subject: [PATCH 7/9] fill docstring

---
 .../vu2024_convert_single_wavelength_session.py  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
index fc8123f..1efe7fb 100644
--- a/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
+++ b/src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
@@ -31,15 +31,31 @@ def single_wavelength_session_to_nwb(
 
     Parameters
     ----------
+    raw_imaging_file_path : Union[str, Path]
+        The path to the .cxd file containing the raw imaging data.
     raw_fiber_photometry_file_path : Union[str, Path]
         The path to the .mat file containing the raw fiber photometry data.
     fiber_locations_file_path : Union[str, Path]
         The path to the .xlsx file containing the fiber locations.
+    excitation_wavelength_in_nm : int
+        The excitation wavelength in nm.
+    indicator : str
+        The name of the indicator used for the fiber photometry recording.
     ttl_file_path : Union[str, Path]
         The path to the .mat file containing the TTL signals.
+    motion_corrected_imaging_file_path : Union[str, Path]
+        The path to the .tif file containing the motion corrected imaging data.
+    behavior_file_path : Union[str, Path]
+        The path to the .mat file containing the processed behavior data.
+    nwbfile_path : Union[str, Path]
+        The path to the NWB file to be created.
+    behavior_avi_file_path : Union[str, Path], optional
+        The path to the .avi file containing the behavior camera recording. optional
     sampling_frequency : float, optional
         The sampling frequency of the data. If None, the sampling frequency will be read from the .cxd file.
         If missing from the file, the sampling frequency must be provided.
+    stub_test : bool, optional
+        Whether to run a stub test, by default False.
     """
 
     raw_fiber_photometry_file_path = Path(raw_fiber_photometry_file_path)

From dcfa7aa24e94a486a9c2c63159e43e8d9d57e2cf Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Fri, 28 Jun 2024 13:47:08 +0200
Subject: [PATCH 8/9] add all velocities as timeseries

---
 .../interfaces/vu2024_behaviorinterface.py    | 111 +++++++++---------
 1 file changed, 57 insertions(+), 54 deletions(-)

diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
index 47ee636..be93859 100644
--- a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
@@ -4,10 +4,9 @@
 import pandas as pd
 from neuroconv import BaseTemporalAlignmentInterface
 from neuroconv.tools import get_module
-from neuroconv.utils import FilePathType, get_base_schema
+from neuroconv.utils import FilePathType, get_base_schema, get_schema_from_hdmf_class
 from pymatreader import read_mat
 from pynwb import NWBFile, TimeSeries
-from pynwb.behavior import CompassDirection
 from pynwb.epoch import TimeIntervals
 
 
@@ -60,32 +59,14 @@ def set_aligned_timestamps(self, aligned_timestamps: np.ndarray) -> None:
     def get_metadata_schema(self) -> dict:
         metadata_schema = super().get_metadata_schema()
         metadata_schema["properties"]["Behavior"] = get_base_schema(tag="Behavior")
+        time_series_schema = get_schema_from_hdmf_class(TimeSeries)
         metadata_schema["properties"]["Behavior"].update(
-            required=["CompassDirection", "TimeSeries", "TimeIntervals"],
+            required=["TimeSeries", "TimeIntervals"],
             properties=dict(
-                CompassDirection=dict(
-                    type="object",
-                    required=["SpatialSeries"],
-                    properties=dict(
-                        SpatialSeries=dict(
-                            type="object",
-                            required=["name", "description", "unit"],
-                            properties=dict(
-                                name=dict(type="string"),
-                                description=dict(type="string"),
-                                unit=dict(type="string"),
-                            ),
-                        ),
-                    ),
-                ),
                 TimeSeries=dict(
-                    type="object",
-                    required=["name", "description", "unit"],
-                    properties=dict(
-                        name=dict(type="string"),
-                        description=dict(type="string"),
-                        unit=dict(type="string"),
-                    ),
+                    type="array",
+                    minItems=1,
+                    items=time_series_schema,
                 ),
                 TimeIntervals=dict(
                     type="object",
@@ -103,19 +84,18 @@ def get_metadata(self):
         metadata = super().get_metadata()
 
         metadata["Behavior"] = dict(
-            CompassDirection=dict(
-                SpatialSeries=dict(
-                    name="SpatialSeries",
-                    description="The yaw (rotational) velocity measured in degrees/s.",
-                    reference_frame="unknown",
-                    unit="degrees/s",
+            TimeSeries=[
+                dict(
+                    name="AngularVelocity",
+                    description="The angular velocity from yaw (rotational) velocity converted to radians/s.",
+                    unit="radians/s",
                 ),
-            ),
-            TimeSeries=dict(
-                name="Velocity",
-                description="Velocity for the roll and pitch (x, y) measured in m/s.",
-                unit="m/s",
-            ),
+                dict(
+                    name="Velocity",
+                    description="Velocity for the roll and pitch (x, y) measured in m/s.",
+                    unit="m/s",
+                ),
+            ],
             TimeIntervals=dict(
                 name="TimeIntervals",
                 description="The onset times of the events (licking, tone, light or reward delivery).",
@@ -124,10 +104,17 @@ def get_metadata(self):
 
         return metadata
 
-    def add_velocity_signals(self, nwbfile: NWBFile, metadata: dict, stub_test: Optional[bool] = False) -> None:
+    def add_velocity_signals(
+        self,
+        nwbfile: NWBFile,
+        metadata: dict,
+        ball_diameter_in_meters: float = None,
+        stub_test: Optional[bool] = False,
+    ) -> None:
         """
         Add the velocity signals (yaw (z) velocity and the roll and pitch (x, y)) to the NWBFile.
-        The yaw velocity is measured in degrees/s and the roll and pitch velocities are measured in m/s.
+        The yaw velocity is converted to radians/s using the calculation provided from the Howe Lab.
+        The roll and pitch velocities are in m/s.
 
         Parameters
         ----------
@@ -135,6 +122,10 @@ def add_velocity_signals(self, nwbfile: NWBFile, metadata: dict, stub_test: Opti
             The NWBFile to which the velocity signals will be added.
         metadata : dict
             Metadata for the velocity signals.
+        ball_diameter_in_meters : float, optional
+            The diameter of the ball in meters, optional.
+            Used to convert the yaw velocity from m/s to radians/s, when not specified default value is 0.2032.
+            Reference: https://zenodo.org/records/10272874 from ball2xy.m
         stub_test : bool, optional
             Whether to run a stub test, by default False.
         """
@@ -142,32 +133,38 @@ def add_velocity_signals(self, nwbfile: NWBFile, metadata: dict, stub_test: Opti
         end_frame = 6000 if stub_test else None
 
         behavior_metadata = metadata["Behavior"]
-        spatial_series_metadata = behavior_metadata["CompassDirection"]["SpatialSeries"]
+        time_series_metadata = behavior_metadata["TimeSeries"]
 
         behavior_data = read_mat(filename=self.source_data["file_path"])
         timestamps = self.get_timestamps(stub_test=stub_test)
 
-        compass_direction = CompassDirection(name="CompassDirection")
-
-        compass_direction.create_spatial_series(
-            **spatial_series_metadata,
-            data=behavior_data["ballYaw"][:end_frame],
-            timestamps=timestamps,
-        )
-
         behavior = get_module(
             nwbfile,
             name="behavior",
             description="Contains the velocity signals from two optical mouse sensors (Logitech G203 mice with hard plastic shells removed).",
         )
-        behavior.add(compass_direction)
 
-        velocity_metadata = behavior_metadata["TimeSeries"]
-        data = np.column_stack((behavior_data["ballRoll"], behavior_data["ballPitch"]))
+        # ballYaw is in m/s convert to radians/s using their code
+        # https://zenodo.org/records/10272874 ball2xy.m
+        angular_velocity_metadata = time_series_metadata[0]
+        yaw_in_meters = behavior_data["ballYaw"][:end_frame]
+        ball_diameter_in_meters = ball_diameter_in_meters or 0.2032
+        yaw_in_radians = yaw_in_meters / (np.pi * ball_diameter_in_meters) * 2 * np.pi
+
+        velocity_z = TimeSeries(
+            **angular_velocity_metadata,
+            data=yaw_in_radians,
+            timestamps=timestamps,
+        )
+        behavior.add(velocity_z)
+
+        velocity_metadata = time_series_metadata[1]
+        velocity_in_meters = np.column_stack((behavior_data["ballRoll"], behavior_data["ballPitch"]))
+        velocity_in_meters = velocity_in_meters[:end_frame]
         velocity_xy = TimeSeries(
             **velocity_metadata,
-            data=data[:end_frame],
-            timestamps=timestamps,
+            data=velocity_in_meters,
+            timestamps=velocity_z,
         )
         behavior.add(velocity_xy)
 
@@ -255,7 +252,13 @@ def add_to_nwbfile(
         nwbfile: NWBFile,
         metadata: dict,
         stub_test: Optional[bool] = False,
+        ball_diameter_in_meters: Optional[float] = None,
     ) -> None:
 
-        self.add_velocity_signals(nwbfile=nwbfile, metadata=metadata, stub_test=stub_test)
+        self.add_velocity_signals(
+            nwbfile=nwbfile,
+            metadata=metadata,
+            stub_test=stub_test,
+            ball_diameter_in_meters=ball_diameter_in_meters,
+        )
         self.add_binary_signals(nwbfile=nwbfile, metadata=metadata)

From 7cc648ee63d57421bb7c5e99facf93d8ea88e576 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Fri, 28 Jun 2024 13:51:59 +0200
Subject: [PATCH 9/9] update docstring

---
 .../vu2024/interfaces/vu2024_behaviorinterface.py              | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
index be93859..dbb14a1 100644
--- a/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
+++ b/src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py
@@ -30,7 +30,8 @@ def __init__(
         Parameters
         ----------
         file_path : FilePathType
-            Path to the .mat file that contains the fiber photometry data.
+            Path to the .mat file that contains the "binned" behavior data.
+            ("*ttlIn1_movie1.mat" files)
         verbose : bool, default: True
             controls verbosity.
         """