From a01ab404da4359bbc9225c3e3d3cf55856ae1013 Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:10:57 +0100
Subject: [PATCH 01/10] resolve miniscope negative timestamps

---
 .../interfaces/miniscope_imaging_interface.py |  5 ----
 .../zaki_2024/zaki_2024_nwbconverter.py       | 29 +++++++++++++++++++
 2 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
index 9c514ff..688b04f 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
@@ -370,11 +370,6 @@ def get_original_timestamps(self) -> np.ndarray:
         timestamps_file_path = self.miniscope_folder / "timeStamps.csv"
         assert timestamps_file_path.exists(), f"Miniscope timestamps file not found in {self.miniscope_folder}"
         timestamps_seconds = get_miniscope_timestamps(file_path=timestamps_file_path)
-        # Shift when the first timestamp is negative
-        # TODO: Figure why, I copied from Miniscope. Need to shift also session_start_time
-        if timestamps_seconds[0] < 0.0:
-            timestamps_seconds += abs(timestamps_seconds[0])
-
         return timestamps_seconds
 
     def add_to_nwbfile(
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index 90c5712..06d4f60 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -1,7 +1,10 @@
 """Primary NWBConverter class for this dataset."""
 
+from datetime import timedelta
+
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import VideoInterface
+from neuroconv.utils.dict import DeepDict
 
 from interfaces import (
     MinianSegmentationInterface,
@@ -31,3 +34,29 @@ class Zaki2024NWBConverter(NWBConverter):
         ShockStimuli=Zaki2024ShockStimuliInterface,
         CellRegistration=Zaki2024CellRegistrationInterface,
     )
+
+    def get_metadata(self) -> DeepDict:
+        metadata = super().get_metadata()
+
+        if "MiniscopeImaging" in self.data_interface_objects:
+            imaging_interface = self.data_interface_objects["MiniscopeImaging"]
+            imaging_timestamps = imaging_interface.get_original_timestamps()
+            # If the first timestamp in the imaging data is negative, adjust the session start time
+            # to ensure all timestamps are positive. This is done by shifting the session start time
+            # backward by the absolute value of the negative timestamp.
+            if imaging_timestamps[0] < 0.0:
+                time_shift = timedelta(seconds=abs(imaging_timestamps[0]))
+                session_start_time = imaging_interface.get_metadata()["NWBFile"]["session_start_time"]
+                metadata["NWBFile"].update(session_start_time=session_start_time - time_shift)
+        return metadata
+
+    def temporally_align_data_interfaces(self):
+        if "MiniscopeImaging" in self.data_interface_objects:
+            imaging_interface = self.data_interface_objects["MiniscopeImaging"]
+            imaging_timestamps = imaging_interface.get_original_timestamps()
+            # Align the starting times of all data interfaces when the imaging data's first timestamp is negative.
+            # This is done by calculating a time shift based on the absolute value of the first negative timestamp.
+            # The time shift is applied to all relevant data interfaces to ensure temporal alignment.
+            if imaging_timestamps[0] < 0.0:
+                time_shift = abs(imaging_timestamps[0])
+                imaging_interface.set_aligned_timestamps(imaging_timestamps + time_shift)
\ No newline at end of file

From 9bdca3cb8009741ae90e12e053a62f15274df7c3 Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:12:28 +0100
Subject: [PATCH 02/10] align minian interface

---
 .../zaki_2024/interfaces/minian_interface.py  | 26 +++++++++++++++++--
 .../zaki_2024/zaki_2024_nwbconverter.py       | 12 ++++++++-
 2 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
index 8f64290..ad0dd52 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
@@ -154,7 +154,7 @@ def get_accepted_list(self) -> list:
         accepted_list: list
             List of accepted ROI ids.
         """
-        return list(range(self.get_num_rois()))
+        return self.get_roi_ids()
 
     def get_rejected_list(self) -> list:
         """Get a list of rejected ROI ids.
@@ -312,6 +312,28 @@ def get_dtype(self) -> DtypeType:
     def get_channel_names(self) -> list[str]:
         return ["OpticalChannel"]
 
+    def get_original_timestamps(self, stub_test: bool = False) -> list[np.ndarray]:
+        """
+        Retrieve the original unaltered timestamps for the data in this interface.
+
+        This function should retrieve the data on-demand by re-initializing the IO.
+
+        Returns
+        -------
+        timestamps : numpy.ndarray
+            The timestamps for the data stream.
+        stub_test : bool, default: False
+            This method scans through each video; a process which can take some time to complete.
+
+            To limit that scan to a small number of frames, set `stub_test=True`.
+        """
+        max_frames = 100 if stub_test else None
+        with self._video_capture(file_path=str(self.file_path)) as video:
+            # fps = video.get_video_fps()  # There is some debate about whether the OpenCV timestamp
+            # method is simply returning range(length) / fps 100% of the time for any given format
+            timestamps = video.get_video_timestamps(max_frames=max_frames)
+        return timestamps
+
     def get_video(
         self, start_frame: Optional[int] = None, end_frame: Optional[int] = None, channel: int = 0
     ) -> np.ndarray:
@@ -440,7 +462,7 @@ def add_to_nwbfile(
             xy_translation=xy_translation,
         )
 
-        ophys = get_module(nwbfile, "ophys")
+        ophys = get_module(nwbfile, name="ophys", description="Data processed with MiniAn software")
         if "MotionCorrection" not in ophys.data_interfaces:
             motion_correction = MotionCorrection(name="MotionCorrection")
             ophys.add(motion_correction)
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index 06d4f60..e1afc7b 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -59,4 +59,14 @@ def temporally_align_data_interfaces(self):
             # The time shift is applied to all relevant data interfaces to ensure temporal alignment.
             if imaging_timestamps[0] < 0.0:
                 time_shift = abs(imaging_timestamps[0])
-                imaging_interface.set_aligned_timestamps(imaging_timestamps + time_shift)
\ No newline at end of file
+                imaging_interface.set_aligned_timestamps(imaging_timestamps + time_shift)
+
+                if "MinianSegmentation" in self.data_interface_objects:
+                    segmentation_interface = self.data_interface_objects["MinianSegmentation"]
+                    segmentation_timestamps = segmentation_interface.get_original_timestamps()
+                    segmentation_interface.set_aligned_timestamps(segmentation_timestamps + time_shift)
+
+                # if "MinianMotionCorrection" in self.data_interface_objects:
+                #     motion_correction_interface = self.data_interface_objects["MinianMotionCorrection"]
+                #     motion_correction_timestamps = motion_correction_interface.get_original_timestamps()
+                #     motion_correction_interface.set_aligned_timestamps(segmentation_timestamps + time_shift)

From e9ef0ccf561fb46d1efc5c2897299659bb8ceb4b Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:12:58 +0100
Subject: [PATCH 03/10] align sleep intervals

---
 ...aki_2024_sleep_classification_interface.py | 53 +++++++++++--------
 .../zaki_2024/zaki_2024_nwbconverter.py       |  9 ++++
 2 files changed, 40 insertions(+), 22 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_sleep_classification_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_sleep_classification_interface.py
index 942a9b3..3cd5773 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_sleep_classification_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_sleep_classification_interface.py
@@ -1,12 +1,13 @@
 """Primary class for converting experiment-specific behavior."""
 
-from pynwb.file import NWBFile
+import pandas as pd
+from pydantic import FilePath
+from typing import Optional, List
 
+from pynwb.file import NWBFile
+from pynwb.epoch import TimeIntervals
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.utils import DeepDict
-from pydantic import FilePath
-from typing import Optional
-from pynwb.epoch import TimeIntervals
 
 
 class Zaki2024SleepClassificationInterface(BaseDataInterface):
@@ -14,12 +15,14 @@ class Zaki2024SleepClassificationInterface(BaseDataInterface):
 
     keywords = ["behavior", "sleep stages"]
 
-    def __init__(self, file_path: FilePath, video_sampling_frequency: float, verbose: bool = False):
+    def __init__(self, file_path: FilePath, sampling_frequency: float, verbose: bool = False):
         # This should load the data lazily and prepare variables you need
 
         self.file_path = file_path
         self.verbose = verbose
-        self.video_sampling_frequency = video_sampling_frequency
+        self.sampling_frequency = sampling_frequency
+        self._start_times = None
+        self._stop_times = None
 
     def get_metadata(self) -> DeepDict:
         # Automatically retrieve as much metadata as possible from the source files available
@@ -27,33 +30,40 @@ def get_metadata(self) -> DeepDict:
 
         return metadata
 
-    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
-
-        import pandas as pd
-
+    def get_sleep_states_times(self):
         sleep_behavior_df = pd.read_csv(self.file_path)
 
         import numpy as np
 
         # Note this will have the first row as None
-        shifted_sleep_state = sleep_behavior_df['SleepState'].shift()
-        start_indices = np.where(sleep_behavior_df['SleepState'] != shifted_sleep_state)[0]
+        shifted_sleep_state = sleep_behavior_df["SleepState"].shift()
+        start_indices = np.where(sleep_behavior_df["SleepState"] != shifted_sleep_state)[0]
         stop_indices = [i - 1 for i in start_indices[1:]]
         stop_indices.append(len(sleep_behavior_df) - 1)
         stop_indices = np.array(stop_indices)
 
-        start_frames = sleep_behavior_df['Frame'][start_indices].values
-        start_times = start_frames / self.video_sampling_frequency
-        stop_frames = sleep_behavior_df['Frame'][stop_indices].values
-        stop_times = stop_frames / self.video_sampling_frequency
-        sleep_state = sleep_behavior_df['SleepState'][start_indices].values
+        start_frames = sleep_behavior_df["Frame"][start_indices].values
+        start_times = self._start_times if self._start_times is not None else start_frames / self.sampling_frequency
+        stop_frames = sleep_behavior_df["Frame"][stop_indices].values
+        stop_times = self._stop_times if self._stop_times is not None else stop_frames / self.sampling_frequency
 
+        sleep_state = sleep_behavior_df["SleepState"][start_indices].values
+
+        return start_times, stop_times, sleep_state
+
+    def set_aligned_interval_times(self, start_times: List[float], stop_times: List[float]) -> None:
+        self._start_times = start_times
+        self._stop_times = stop_times
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
+
+        start_times, stop_times, sleep_state = self.get_sleep_states_times()
 
         description = (
             "Sleep states classified with custom algorithm using the data "
             "from the HD-X02 sensor (EEG, EMG, temperature, etc.)."
-        )        
-        
+        )
+
         sleep_intervals = TimeIntervals(name="SleepIntervals", description=description)
         column_description = """
             Sleep State Classification, it can be one of the following: 
@@ -63,7 +73,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
             - 'wake': State of full consciousness when the animal is alert, responsive to the environment, and capable of voluntary movement
         """
         sleep_intervals.add_column(name="sleep_state", description=column_description)
-        
+
         for start_time, stop_time, state in zip(start_times, stop_times, sleep_state):
             sleep_intervals.add_interval(start_time=start_time, stop_time=stop_time, sleep_state=state)
 
@@ -71,6 +81,5 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
             sleep_module = nwbfile.create_processing_module(name="sleep", description="Sleep data")
         else:
             sleep_module = nwbfile.processing["sleep"]
-        
-        sleep_module.add(sleep_intervals)
 
+        sleep_module.add(sleep_intervals)
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index e1afc7b..cfa980d 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -70,3 +70,12 @@ def temporally_align_data_interfaces(self):
                 #     motion_correction_interface = self.data_interface_objects["MinianMotionCorrection"]
                 #     motion_correction_timestamps = motion_correction_interface.get_original_timestamps()
                 #     motion_correction_interface.set_aligned_timestamps(segmentation_timestamps + time_shift)
+
+                if "SleepClassification" in self.data_interface_objects:
+                    sleep_classification_interface = self.data_interface_objects["SleepClassification"]
+                    start_times, stop_times, sleep_states = sleep_classification_interface.get_sleep_states_times()
+                    start_times += time_shift
+                    stop_times += time_shift
+                    sleep_classification_interface.set_aligned_interval_times(
+                        start_times=start_times, stop_times=stop_times
+                    )
\ No newline at end of file

From 4ccd3be7dab7c7132b4b8470544b465b1d56d5f4 Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:13:17 +0100
Subject: [PATCH 04/10] align edf singal

---
 .../interfaces/zaki_2024_edf_interface.py       | 17 +++++++++++------
 .../zaki_2024/zaki_2024_nwbconverter.py         |  5 ++++-
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_edf_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_edf_interface.py
index c123cfe..d5ccbd5 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_edf_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_edf_interface.py
@@ -5,7 +5,6 @@
 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
@@ -19,9 +18,13 @@ def __init__(
         verbose: bool = False,
     ):
         self.file_path = Path(file_path)
+        self._starting_time = None
         self.verbose = verbose
         super().__init__(file_path=file_path)
 
+    def set_aligned_starting_time(self, aligned_starting_time: float):
+        self._starting_time = aligned_starting_time
+
     def add_to_nwbfile(
         self,
         nwbfile: NWBFile,
@@ -49,8 +52,6 @@ def add_to_nwbfile(
         stop_datetime_timestamp : datetime, optional
             The ending timestamp for slicing the data. If specified, data will be included
             only up to this time. Default is None, which includes data until the end.
-        **conversion_options
-            Additional options for data conversion (not currently used directly in this function).
 
         Returns
         -------
@@ -73,8 +74,6 @@ def add_to_nwbfile(
                 "description": "EMG signal recorder with HD-X02 wireless telemetry probe",
                 "unit": "volts",
             },
-            # TODO: Figure out if the units of activity are correct, the raw format marks Volts
-            # TODO: My own reading of the header indicates that the physical units is counts
             "Activity": {
                 "name": "ActivitySignal",
                 "description": "Activity signal recorder with HD-X02 wireless telemetry probe. It refers to the motion of the probe relative to the receiver and it can be used as a proxy for locomotion.",
@@ -107,6 +106,8 @@ def add_to_nwbfile(
         else:
             data = data[:, start_idx:end_idx]
 
+        starting_time = self._starting_time if self._starting_time is not None else starting_time
+
         for channel_index, channel_name in enumerate(channels_dict.keys()):
             time_series_kwargs = channels_dict[channel_name].copy()
             time_series_kwargs.update(
@@ -132,8 +133,12 @@ def __init__(
     ):
         self.file_paths = file_paths
         self.verbose = verbose
+        self._starting_time = 0.0
         super().__init__(file_paths=file_paths)
 
+    def set_aligned_starting_time(self, aligned_starting_time: float):
+        self._starting_time = aligned_starting_time
+
     def add_to_nwbfile(
         self,
         nwbfile: NWBFile,
@@ -205,7 +210,7 @@ def add_to_nwbfile(
         for channel_index, channel_name in enumerate(channels_dict.keys()):
             time_series_kwargs = channels_dict[channel_name].copy()
             time_series_kwargs.update(
-                data=concatenated_data[channel_index], starting_time=0.0, rate=edf_reader.info["sfreq"]
+                data=concatenated_data[channel_index], starting_time=self._starting_time, rate=edf_reader.info["sfreq"]
             )
             time_series = TimeSeries(**time_series_kwargs)
             nwbfile.add_acquisition(time_series)
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index cfa980d..741ab86 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -78,4 +78,7 @@ def temporally_align_data_interfaces(self):
                     stop_times += time_shift
                     sleep_classification_interface.set_aligned_interval_times(
                         start_times=start_times, stop_times=stop_times
-                    )
\ No newline at end of file
+                    )
+                if "EDFSignals" in self.data_interface_objects:
+                    edf_signals_interface = self.data_interface_objects["EDFSignals"]
+                    edf_signals_interface.set_aligned_starting_time(time_shift)

From b5a6116cc6071f4077dd95838eb8157a563b6cfa Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:13:39 +0100
Subject: [PATCH 05/10] align eztrack and video

---
 .../zaki_2024/interfaces/eztrack_interface.py | 58 +++++++++++++------
 .../zaki_2024/zaki_2024_nwbconverter.py       | 17 ++++++
 2 files changed, 57 insertions(+), 18 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/eztrack_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/eztrack_interface.py
index 3787eb5..5001fbd 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/eztrack_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/eztrack_interface.py
@@ -1,6 +1,8 @@
 """Primary class for converting experiment-specific behavior."""
 
 import numpy as np
+import pandas as pd
+
 from pynwb import TimeSeries
 from pynwb.epoch import TimeIntervals
 from pynwb.file import NWBFile
@@ -8,7 +10,7 @@
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.utils import DeepDict
 from pydantic import FilePath
-from typing import Optional
+from typing import Optional, List
 
 
 class EzTrackFreezingBehaviorInterface(BaseDataInterface):
@@ -22,6 +24,9 @@ def __init__(self, file_path: FilePath, video_sampling_frequency: float, verbose
         self.file_path = file_path
         self.verbose = verbose
         self.video_sampling_frequency = video_sampling_frequency
+        self._start_times = None
+        self._stop_times = None
+        self._starting_time = None
 
     def get_metadata(self) -> DeepDict:
         # Automatically retrieve as much metadata as possible from the source files available
@@ -29,22 +34,52 @@ def get_metadata(self) -> DeepDict:
 
         return metadata
 
-    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
+    def get_interval_times(self):
+        # Extract start and stop times of the freezing events
+        # From the discussion wih the author, the freezing events are the frames where the freezing behavior is 100
+        freezing_behavior_df = pd.read_csv(self.file_path)
+        freezing_values = freezing_behavior_df["Freezing"].values
+        changes_in_freezing = np.diff(freezing_values)
+        freezing_start = np.where(changes_in_freezing == 100)[0] + 1
+        freezing_stop = np.where(changes_in_freezing == -100)[0] + 1
 
-        import pandas as pd
+        start_frames = freezing_behavior_df["Frame"].values[freezing_start]
+        stop_frames = freezing_behavior_df["Frame"].values[freezing_stop]
+
+        start_times = (
+            self._start_times if self._start_times is not None else start_frames / self.video_sampling_frequency
+        )
+        stop_times = self._stop_times if self._stop_times is not None else stop_frames / self.video_sampling_frequency
+        return start_times, stop_times
 
+    def get_starting_time(self) -> float:
         freezing_behavior_df = pd.read_csv(self.file_path)
+        return freezing_behavior_df["Frame"].values[0] / self.video_sampling_frequency
+
+    def set_aligned_interval_times(self, start_times: List[float], stop_times: List[float]) -> None:
+        self._start_times = start_times
+        self._stop_times = stop_times
+
+    def set_aligned_starting_time(self, aligned_start_time) -> None:
+        self._starting_time = aligned_start_time
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None, stub_test: bool = False):
+
+        freezing_behavior_df = pd.read_csv(self.file_path)
+
+        start_times, stop_times = self.get_interval_times()
 
         # Extract motion data
         motion_data = freezing_behavior_df["Motion"].values
+        starting_time = self._starting_time if self._starting_time is not None else self.get_starting_time()
 
         motion_series = TimeSeries(
             name="MotionSeries",
             description="ezTrack measures the motion of the animal by assessing the number of pixels of the behavioral "
             "video whose grayscale change exceeds a particular threshold from one frame to the next.",
-            data=motion_data,
+            data=motion_data[:100] if stub_test else motion_data,
             unit="n.a",
-            starting_time=freezing_behavior_df["Frame"][0] / self.video_sampling_frequency,
+            starting_time=starting_time,
             rate=self.video_sampling_frequency,
         )
 
@@ -54,19 +89,6 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: Optional[dict] = None):
         freeze_threshold = freezing_behavior_df["FreezeThresh"].unique()[0]
         min_freeze_duration = freezing_behavior_df["MinFreezeDuration"].unique()[0]
 
-        # Extract start and stop times of the freezing events
-        # From the discussion wih the author, the freezing events are the frames where the freezing behavior is 100
-        freezing_values = freezing_behavior_df["Freezing"].values
-        changes_in_freezing = np.diff(freezing_values)
-        freezing_start = np.where(changes_in_freezing == 100)[0] + 1
-        freezing_stop = np.where(changes_in_freezing == -100)[0] + 1
-
-        start_frames = freezing_behavior_df["Frame"].values[freezing_start]
-        stop_frames = freezing_behavior_df["Frame"].values[freezing_stop]
-
-        start_times = start_frames / self.video_sampling_frequency
-        stop_times = stop_frames / self.video_sampling_frequency
-
         description = f"""
             Freezing behavior intervals generated using EzTrack software for file {file}. 
             Parameters used include a motion cutoff of {motion_cutoff}, freeze threshold of {freeze_threshold}, 
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index 741ab86..a7412ce 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -82,3 +82,20 @@ def temporally_align_data_interfaces(self):
                 if "EDFSignals" in self.data_interface_objects:
                     edf_signals_interface = self.data_interface_objects["EDFSignals"]
                     edf_signals_interface.set_aligned_starting_time(time_shift)
+
+                if "FreezingBehavior" in self.data_interface_objects:
+                    freezing_behavior_interface = self.data_interface_objects["FreezingBehavior"]
+                    start_times, stop_times = freezing_behavior_interface.get_interval_times()
+                    start_times += time_shift
+                    stop_times += time_shift
+                    freezing_behavior_interface.set_aligned_interval_times(
+                        start_times=start_times, stop_times=stop_times
+                    )
+                    starting_time = freezing_behavior_interface.get_starting_time()
+                    freezing_behavior_interface.set_aligned_starting_time(starting_time + time_shift)
+
+                if "Video" in self.data_interface_objects:
+                    video_interface = self.data_interface_objects["Video"]
+                    video_timestamps = video_interface.get_original_timestamps()
+                    aligned_video_timestamps = video_timestamps + time_shift
+                    video_interface.set_aligned_timestamps(aligned_video_timestamps)

From ecca8a6cb7b1797610352c292e7ae228e0c4b8d7 Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 15:15:53 +0100
Subject: [PATCH 06/10] add session start time timezone

---
 .../zaki_2024/zaki_2024_convert_session.py    | 33 ++++++++++---------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
index 35b1965..4201505 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
@@ -1,7 +1,7 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
 
 import time
-
+import pytz
 from pathlib import Path
 from typing import Union
 from datetime import datetime, timedelta
@@ -62,16 +62,16 @@ def session_to_nwb(
         source_data.update(dict(MinianSegmentation=dict(folder_path=minian_folder_path)))
         conversion_options.update(dict(MinianSegmentation=dict(stub_test=stub_test)))
 
-        motion_corrected_video = minian_folder_path / "minian_mc.mp4"
-        if motion_corrected_video.is_file():
-            source_data.update(
-                dict(
-                    MinianMotionCorrection=dict(folder_path=minian_folder_path, video_file_path=motion_corrected_video)
-                )
-            )
-            conversion_options.update(dict(MinianMotionCorrection=dict(stub_test=stub_test)))
-        elif verbose and not motion_corrected_video.is_file():
-            print(f"No motion corrected data found at {motion_corrected_video}")
+        # motion_corrected_video = minian_folder_path / "minian_mc.mp4"
+        # if motion_corrected_video.is_file():
+        #     source_data.update(
+        #         dict(
+        #             MinianMotionCorrection=dict(folder_path=minian_folder_path, video_file_path=motion_corrected_video)
+        #         )
+        #     )
+        #     conversion_options.update(dict(MinianMotionCorrection=dict(stub_test=stub_test)))
+        # elif verbose and not motion_corrected_video.is_file():
+        #     print(f"No motion corrected data found at {motion_corrected_video}")
 
     # Add Behavioral Video
     if video_file_path:
@@ -133,7 +133,7 @@ def session_to_nwb(
         sleep_classification_file_path = Path(sleep_classification_file_path)
         assert sleep_classification_file_path.is_file(), f"{sleep_classification_file_path} does not exist"
         source_data.update(
-            dict(SleepClassification=dict(file_path=sleep_classification_file_path, video_sampling_frequency=30.0))
+            dict(SleepClassification=dict(file_path=sleep_classification_file_path, sampling_frequency=15.0))
         )
 
     # Add Shock Stimuli times for FC sessions
@@ -154,6 +154,9 @@ def session_to_nwb(
         session_start_time = datetime.strptime(datetime_str, "%Y_%m_%d %H_%M_%S")
         metadata["NWBFile"]["session_start_time"] = session_start_time
 
+    eastern = pytz.timezone("US/Eastern")
+    metadata["NWBFile"]["session_start_time"] = eastern.localize(metadata["NWBFile"]["session_start_time"])
+
     # Update default metadata with the editable in the corresponding yaml file
     editable_metadata_path = Path(__file__).parent / "zaki_2024_metadata.yaml"
     editable_metadata = load_dict_from_file(editable_metadata_path)
@@ -180,10 +183,10 @@ def session_to_nwb(
 
 if __name__ == "__main__":
 
-    subject_id = "Ca_EEG3-4"
-    session_type = "OfflineDay2Session1"
+    subject_id = "Ca_EEG2-1"
+    session_type = "NeutralExposure"  #
     session_id = subject_id + "_" + session_type
-    stub_test = False
+    stub_test = True
     verbose = True
     yaml_file_path = Path(__file__).parent / "utils/conversion_parameters.yaml"
     conversion_parameter_dict = load_dict_from_file(yaml_file_path)

From f981d9cf6ed10eea466bebaf61c059b42461eaec Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 16:09:55 +0100
Subject: [PATCH 07/10] minor fixes

---
 src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py   | 4 ----
 .../zaki_2024/zaki_2024_convert_all_sessions.py               | 4 ++--
 src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py     | 2 +-
 src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py        | 1 -
 4 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
index ad0dd52..4dbf01b 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/minian_interface.py
@@ -166,10 +166,6 @@ def get_rejected_list(self) -> list:
         """
         return list()
 
-    def get_roi_ids(self) -> list:
-        dataset = self._read_zarr_group("/A.zarr")
-        return list(dataset["unit_id"])
-
     def get_traces_dict(self) -> dict:
         """Get traces as a dictionary with key as the name of the ROiResponseSeries.
 
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_all_sessions.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_all_sessions.py
index 79ce922..c66d7fc 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_all_sessions.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_all_sessions.py
@@ -122,8 +122,8 @@ def get_session_to_nwb_kwargs_per_session(
     data_dir_path = Path("D:/")
     output_dir_path = Path("D:/cai_lab_conversion_nwb/")
     max_workers = 1
-    verbose = True
-    stub_test = True
+    verbose = False
+    stub_test = False
     dataset_to_nwb(
         data_dir_path=data_dir_path,
         output_dir_path=output_dir_path,
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
index 4201505..f274e63 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
@@ -186,7 +186,7 @@ def session_to_nwb(
     subject_id = "Ca_EEG2-1"
     session_type = "NeutralExposure"  #
     session_id = subject_id + "_" + session_type
-    stub_test = True
+    stub_test = False
     verbose = True
     yaml_file_path = Path(__file__).parent / "utils/conversion_parameters.yaml"
     conversion_parameter_dict = load_dict_from_file(yaml_file_path)
diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index a7412ce..abbcd14 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -60,7 +60,6 @@ def temporally_align_data_interfaces(self):
             if imaging_timestamps[0] < 0.0:
                 time_shift = abs(imaging_timestamps[0])
                 imaging_interface.set_aligned_timestamps(imaging_timestamps + time_shift)
-
                 if "MinianSegmentation" in self.data_interface_objects:
                     segmentation_interface = self.data_interface_objects["MinianSegmentation"]
                     segmentation_timestamps = segmentation_interface.get_original_timestamps()

From 07eb22d832c820f2de0b2588e0d4797e7de9532b Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 17:03:04 +0100
Subject: [PATCH 08/10] minor fixes

---
 .../zaki_2024/zaki_2024_convert_session.py            | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
index f274e63..88dea30 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
@@ -31,8 +31,9 @@ def session_to_nwb(
     sleep_classification_file_path: Union[str, Path] = None,
     shock_stimulus: dict = None,
 ):
-    print(f"Converting session {session_id}")
+
     if verbose:
+        print(f"Converting session {session_id}")
         start = time.time()
 
     output_dir_path = Path(output_dir_path)
@@ -87,9 +88,9 @@ def session_to_nwb(
         source_data.update(
             dict(FreezingBehavior=dict(file_path=freezing_output_file_path, video_sampling_frequency=30.0))
         )
+        conversion_options.update(dict(FreezingBehavior=dict(stub_test=stub_test)))
 
     # Add EEG, EMG, Temperature and Activity signals
-
     if edf_file_path:
         edf_file_path = Path(edf_file_path)
         assert edf_file_path.is_file(), f"{edf_file_path} does not exist"
@@ -144,7 +145,7 @@ def session_to_nwb(
             ShockStimuli=shock_stimulus,
         )
 
-    converter = Zaki2024NWBConverter(source_data=source_data)
+    converter = Zaki2024NWBConverter(source_data=source_data, verbose=verbose)
 
     # Add datetime to conversion
     metadata = converter.get_metadata()
@@ -184,9 +185,9 @@ def session_to_nwb(
 if __name__ == "__main__":
 
     subject_id = "Ca_EEG2-1"
-    session_type = "NeutralExposure"  #
+    session_type = "FC"  #
     session_id = subject_id + "_" + session_type
-    stub_test = False
+    stub_test = True
     verbose = True
     yaml_file_path = Path(__file__).parent / "utils/conversion_parameters.yaml"
     conversion_parameter_dict = load_dict_from_file(yaml_file_path)

From f1d52f075968f7518ca568b7c64b22ca4d6b360a Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sat, 7 Dec 2024 17:03:25 +0100
Subject: [PATCH 09/10] bug fix

---
 .../zaki_2024/interfaces/miniscope_imaging_interface.py         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py b/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
index 688b04f..0a1dfac 100644
--- a/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
+++ b/src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py
@@ -386,7 +386,7 @@ def add_to_nwbfile(
 
         from neuroconv.tools.roiextractors import add_photon_series_to_nwbfile
 
-        miniscope_timestamps = self.get_original_timestamps()
+        miniscope_timestamps = self.get_timestamps()
         imaging_extractor = self.imaging_extractor
 
         if stub_test:

From a32d893d4ef1bd63d15c38b8b6fcafb398c21c4f Mon Sep 17 00:00:00 2001
From: alessandratrapani <alessandramaria.trapani@gmail.com>
Date: Sun, 8 Dec 2024 10:54:52 +0100
Subject: [PATCH 10/10] minor fix

---
 src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
index abbcd14..c0ba848 100644
--- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
+++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py
@@ -68,7 +68,7 @@ def temporally_align_data_interfaces(self):
                 # if "MinianMotionCorrection" in self.data_interface_objects:
                 #     motion_correction_interface = self.data_interface_objects["MinianMotionCorrection"]
                 #     motion_correction_timestamps = motion_correction_interface.get_original_timestamps()
-                #     motion_correction_interface.set_aligned_timestamps(segmentation_timestamps + time_shift)
+                #     motion_correction_interface.set_aligned_timestamps(motion_correction_timestamps + time_shift)
 
                 if "SleepClassification" in self.data_interface_objects:
                     sleep_classification_interface = self.data_interface_objects["SleepClassification"]