From 4b68a77751b604c2e3ca489dae72925a426120f1 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Thu, 9 Mar 2023 16:36:01 +0100
Subject: [PATCH 01/20] rename

---
 .../{another_conversion => fiber_photometry}/__init__.py          | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename src/tye_lab_to_nwb/{another_conversion => fiber_photometry}/__init__.py (100%)

diff --git a/src/tye_lab_to_nwb/another_conversion/__init__.py b/src/tye_lab_to_nwb/fiber_photometry/__init__.py
similarity index 100%
rename from src/tye_lab_to_nwb/another_conversion/__init__.py
rename to src/tye_lab_to_nwb/fiber_photometry/__init__.py

From 1407c389c8ffdef8d8ff9909494f89a0aff7144a Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Thu, 9 Mar 2023 16:37:06 +0100
Subject: [PATCH 02/20] add ndx-photometry

---
 src/tye_lab_to_nwb/fiber_photometry/requirements.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/requirements.txt

diff --git a/src/tye_lab_to_nwb/fiber_photometry/requirements.txt b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
new file mode 100644
index 0000000..faa38d8
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
@@ -0,0 +1 @@
+ndx-photometry>=0.1.0

From dcd77ab3464e8960248a41cbf912e0ae68f60508 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Thu, 9 Mar 2023 17:58:18 +0100
Subject: [PATCH 03/20] add metadata

---
 .../metadata/fiber_photometry_metadata.yaml   | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml

diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
new file mode 100644
index 0000000..e62e808
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
@@ -0,0 +1,28 @@
+ExcitationSourcesTable:
+  - name: LED415
+    peak_wavelength: 415.0 # in nanometers
+    source_type: LED
+  - name: LED470
+    peak_wavelength: 470.0 # in nanometers
+    source_type: LED
+  - name: LED560
+    peak_wavelength: 560.0 # in nanometers
+    source_type: LED
+PhotodetectorsTable:
+    description: The metadata for the photodetector.
+    type: CMOS camera
+FluorophoresTable:
+    description: The neurotensin-fluorescent sensor was injected into the BLA. The coordinates are in unit meters relative to Bregma (AP, ML, DV).
+    label: neurotensin-fluorescent sensor (green)
+    location: BLA
+    coordinates:
+      - -0.0016 # AP (in meters)
+      - 0.0035 # ML (in meters)
+      - -0.005 # DV (in meters relative to Bregma)
+FibersTable:
+    description: The metadata for the optical fiber.
+    location: BLA
+    notes: The optical fiber was implanted above the BLA.
+RoiResponseSeries:
+    description: The photometry intensity values measured in arbitrary units.
+    unit: a.u.

From 901318f65bcad1b12b59488d1817caf8b33832b2 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Thu, 9 Mar 2023 17:58:55 +0100
Subject: [PATCH 04/20] create utility function for adding photometry to nwb

---
 .../fiber_photometry/tools/photometry.py      | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
new file mode 100644
index 0000000..8a45909
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -0,0 +1,72 @@
+from typing import Optional
+
+import pandas as pd
+from hdmf.common import DynamicTableRegion
+from ndx_photometry import FibersTable, FiberPhotometry, ExcitationSourcesTable, PhotodetectorsTable, FluorophoresTable
+from pynwb import NWBFile
+from pynwb.ophys import RoiResponseSeries
+
+
+def add_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadata: Optional[dict]):
+    # Create the ExcitationSourcesTable that holds metadata for the LED sources
+    excitation_sources_table = ExcitationSourcesTable(description="The metadata for the excitation sources.")
+    for source_metadata in metadata["ExcitationSourcesTable"]:
+        excitation_sources_table.add_row(
+            peak_wavelength=source_metadata["peak_wavelength"],
+            source_type=source_metadata["source_type"],
+        )
+
+    # Create the PhotodetectorsTable that holds metadata for the photodetector.
+    photodetectors_table = PhotodetectorsTable(description=metadata["PhotodetectorsTable"]["description"])
+    photodetectors_table.add_row(type=metadata["PhotodetectorsTable"]["type"])
+
+    # Create the FluorophoresTable that holds metadata for the fluorophores.
+    fluorophores_table = FluorophoresTable(description=metadata["FluorophoresTable"]["description"])
+
+    fluorophores_table.add_row(
+        label=metadata["FluorophoresTable"]["label"],
+        location=metadata["FluorophoresTable"]["location"],
+        coordinates=metadata["FluorophoresTable"]["coordinates"],
+    )
+
+    # Create the FibersTable that holds metadata for fibers
+    fibers_table = FibersTable(description=metadata["FibersTable"]["description"])
+    fiber_photometry = FiberPhotometry(
+        fibers=fibers_table,
+        excitation_sources=excitation_sources_table,
+        photodetectors=photodetectors_table,
+        fluorophores=fluorophores_table,
+    )
+
+    # Add the metadata tables to the metadata section
+    nwbfile.add_lab_meta_data(fiber_photometry)
+
+    # Add row for each fiber defined in metadata
+    fibers_table.add_fiber(
+        excitation_source=0,
+        photodetector=0,
+        fluorophores=[0],
+        location=metadata["FibersTable"]["location"],
+        notes=metadata["FibersTable"]["notes"],
+        # from article, confirm?
+    )
+
+    # Create reference for fibers
+    rois = DynamicTableRegion(
+        name="rois",
+        data=[0],
+        description="source fibers",
+        table=fibers_table,
+    )
+    # Create the RoiResponseSeries that holds the intensity values
+    roi_response_series_name = "RoiResponseSeries"
+    roi_response_series = RoiResponseSeries(
+        name=roi_response_series_name,
+        description=metadata[roi_response_series_name]["description"],
+        data=photometry_dataframe["Region1R"].values,
+        unit=metadata[roi_response_series_name]["unit"],
+        timestamps=photometry_dataframe["Timestamp"].values,
+        rois=rois,
+    )
+
+    nwbfile.add_acquisition(roi_response_series)

From 3a2d8967f2d2abab25db57a2dd43e1b84f7a5938 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Thu, 9 Mar 2023 17:59:14 +0100
Subject: [PATCH 05/20] create interface

---
 .../fiber_photometry/__init__.py              |   1 +
 .../fiber_photometry/convert_session.py       |  42 +++++++
 .../fiberphotometrydatainterface.py           | 105 ++++++++++++++++++
 3 files changed, 148 insertions(+)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/convert_session.py
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py

diff --git a/src/tye_lab_to_nwb/fiber_photometry/__init__.py b/src/tye_lab_to_nwb/fiber_photometry/__init__.py
index e69de29..2e4ff6f 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/__init__.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/__init__.py
@@ -0,0 +1 @@
+from .fiberphotometrydatainterface import FiberPhotometryInterface
diff --git a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
new file mode 100644
index 0000000..0abdff1
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
@@ -0,0 +1,42 @@
+from datetime import datetime
+from pathlib import Path
+from zoneinfo import ZoneInfo
+
+from neuroconv.utils import FilePathType
+
+from tye_lab_to_nwb.fiber_photometry import FiberPhotometryInterface
+
+
+def session_to_nwb(
+    file_path: FilePathType,
+    output_dir_path: FilePathType,
+    stub_test: bool = False,
+):
+    output_dir_path = Path(output_dir_path)
+    if stub_test:
+        output_dir_path = output_dir_path / "nwb_stub"
+    output_dir_path.mkdir(parents=True, exist_ok=True)
+
+    interface = FiberPhotometryInterface(file_path=str(file_path))
+    metadata = interface.get_metadata()
+
+    nwbfile_path = output_dir_path / "fiber_photometry.nwb"
+
+    # Add datetime to conversion
+    date = datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))  # TO-DO: Get this from author
+    metadata["NWBFile"]["session_start_time"] = date
+
+    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, stub_test=stub_test)
+
+
+if __name__ == "__main__":
+    # Parameters for conversion
+    photometry_file_path = Path("/Volumes/t7-ssd/Hao_NWB/recording/Photometry_data0.csv")
+    output_dir_path = Path("/Volumes/t7-ssd/Hao_NWB/nwbfiles")
+    stub_test = False
+
+    session_to_nwb(
+        file_path=photometry_file_path,
+        output_dir_path=output_dir_path,
+        stub_test=stub_test,
+    )
diff --git a/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
new file mode 100644
index 0000000..9f517f8
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
@@ -0,0 +1,105 @@
+"""Primary class for converting fiber photometry data."""
+from pathlib import Path
+from typing import Optional
+
+import numpy as np
+import pandas as pd
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.tools.nwb_helpers import make_or_load_nwbfile
+from neuroconv.utils import FilePathType, load_dict_from_file, OptionalFilePathType
+from pynwb import NWBFile
+
+from tye_lab_to_nwb.fiber_photometry.tools.photometry import add_photometry
+
+
+class FiberPhotometryInterface(BaseDataInterface):
+    """Primary interface for converting fiber photometry data in custom CSV format."""
+
+    def __init__(
+        self,
+        file_path: FilePathType,
+        verbose: bool = True,
+    ):
+        """
+        Interface for writing fiber photometry data from CSV to NWB.
+
+        Parameters
+        ----------
+        file_path : FilePathType
+            path to the CSV file that contains the intensity values.
+        verbose: bool, default: True
+            controls verbosity.
+        """
+        self.verbose = verbose
+        super().__init__(file_path=file_path)
+
+    def get_metadata(self) -> dict:
+        metadata = super().get_metadata()
+
+        photometry_metadata = load_dict_from_file(
+            file_path=Path(__file__).parent / "metadata" / "fiber_photometry_metadata.yaml"
+        )
+        metadata.update(photometry_metadata)
+
+        return metadata
+
+    def _load_source_data(self) -> pd.DataFrame:
+        return pd.read_csv(self.source_data["file_path"], header=0)
+
+    def get_original_timestamps(self) -> 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.
+        """
+        raise NotImplementedError(
+            "Unable to retrieve the original unaltered timestamps for this interface! "
+            "Define the `get_original_timestamps` method for this interface."
+        )
+
+    def get_timestamps(self) -> np.ndarray:
+        """
+        Retrieve the timestamps for the data in this interface.
+
+        Returns
+        -------
+        timestamps: numpy.ndarray
+            The timestamps for the data stream.
+        """
+        raise NotImplementedError(
+            "Unable to retrieve timestamps for this interface! Define the `get_timestamps` method for this interface."
+        )
+
+    def align_timestamps(self, aligned_timestamps: np.ndarray):
+        """
+        Replace all timestamps for this interface with those aligned to the common session start time.
+
+        Must be in units seconds relative to the common 'session_start_time'.
+
+        Parameters
+        ----------
+        aligned_timestamps : numpy.ndarray
+            The synchronized timestamps for data in this interface.
+        """
+        raise NotImplementedError(
+            "The protocol for synchronizing the timestamps of this interface has not been specified!"
+        )
+
+    def run_conversion(
+        self,
+        nwbfile_path: OptionalFilePathType = None,
+        nwbfile: Optional[NWBFile] = None,
+        metadata: Optional[dict] = None,
+        stub_test: bool = False,
+        overwrite: bool = False,
+    ):
+        with make_or_load_nwbfile(
+            nwbfile_path=nwbfile_path, nwbfile=nwbfile, metadata=metadata, overwrite=overwrite, verbose=self.verbose
+        ) as nwbfile_out:
+            photometry_data = self._load_source_data()
+            add_photometry(photometry_dataframe=photometry_data, nwbfile=nwbfile_out, metadata=metadata)

From 03dfd94895fc28f4b3df0b220208787e0a88a629 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 13 Mar 2023 14:56:50 +0100
Subject: [PATCH 06/20] add events

---
 .../fiberphotometrydatainterface.py              |  6 +++++-
 .../metadata/fiber_photometry_metadata.yaml      | 16 ++++++++++++++++
 .../fiber_photometry/requirements.txt            |  1 +
 .../fiber_photometry/tools/photometry.py         | 16 ++++++++++++++++
 4 files changed, 38 insertions(+), 1 deletion(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
index 9f517f8..e5c58a2 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
@@ -9,7 +9,10 @@
 from neuroconv.utils import FilePathType, load_dict_from_file, OptionalFilePathType
 from pynwb import NWBFile
 
-from tye_lab_to_nwb.fiber_photometry.tools.photometry import add_photometry
+from tye_lab_to_nwb.fiber_photometry.tools import (
+    add_photometry,
+    add_events_from_photometry,
+)
 
 
 class FiberPhotometryInterface(BaseDataInterface):
@@ -102,4 +105,5 @@ def run_conversion(
             nwbfile_path=nwbfile_path, nwbfile=nwbfile, metadata=metadata, overwrite=overwrite, verbose=self.verbose
         ) as nwbfile_out:
             photometry_data = self._load_source_data()
+            add_events_from_photometry(photometry_dataframe=photometry_data, nwbfile=nwbfile_out, metadata=metadata)
             add_photometry(photometry_dataframe=photometry_data, nwbfile=nwbfile_out, metadata=metadata)
diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
index e62e808..947f64a 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
@@ -26,3 +26,19 @@ FibersTable:
 RoiResponseSeries:
     description: The photometry intensity values measured in arbitrary units.
     unit: a.u.
+Events:
+    name: LabeledEvents
+    description: The LED events during photometry.
+    labels:
+      17: LED415
+      18: LED470
+      20: LED560
+      273: Stimulus presentation while LED415
+      274: Stimulus presentation while LED470
+      276: Stimulus presentation while LED560
+      529: Lick while LED415
+      530: Lick while LED470
+      532: Lick while LED560
+      785: TODO while LED415 # missing description
+      786: TODO while LED470 # missing description
+      788: TODO while LED560 # missing description
diff --git a/src/tye_lab_to_nwb/fiber_photometry/requirements.txt b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
index faa38d8..b19ad26 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
+++ b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
@@ -1 +1,2 @@
 ndx-photometry>=0.1.0
+ndx-events>=0.2.0
diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
index 8a45909..ba81586 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -2,6 +2,7 @@
 
 import pandas as pd
 from hdmf.common import DynamicTableRegion
+from ndx_events import LabeledEvents, AnnotatedEventsTable
 from ndx_photometry import FibersTable, FiberPhotometry, ExcitationSourcesTable, PhotodetectorsTable, FluorophoresTable
 from pynwb import NWBFile
 from pynwb.ophys import RoiResponseSeries
@@ -70,3 +71,18 @@ def add_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadat
     )
 
     nwbfile.add_acquisition(roi_response_series)
+
+
+def add_events_from_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadata: Optional[dict]):
+    annotated_events = AnnotatedEventsTable(
+        name=metadata["Events"]["name"],
+        description=metadata["Events"]["description"],
+    )
+    for event_num, event_label in metadata["Events"]["labels"].items():
+        annotated_events.add_event_type(
+            label=event_label,
+            event_description=f"The times when the {event_label} was on.",
+            event_times=photometry_dataframe.loc[photometry_dataframe["Flags"] == event_num, "Timestamp"].values,
+        )
+
+    nwbfile.add_acquisition(annotated_events)

From 9b61f60b17159a688467f183c8f6c3acfc4d41e1 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 13 Mar 2023 14:59:57 +0100
Subject: [PATCH 07/20] remove unused import

---
 src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
index ba81586..3333599 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -2,7 +2,7 @@
 
 import pandas as pd
 from hdmf.common import DynamicTableRegion
-from ndx_events import LabeledEvents, AnnotatedEventsTable
+from ndx_events import AnnotatedEventsTable
 from ndx_photometry import FibersTable, FiberPhotometry, ExcitationSourcesTable, PhotodetectorsTable, FluorophoresTable
 from pynwb import NWBFile
 from pynwb.ophys import RoiResponseSeries

From 20e9620e911c4f84cad176ed63b997bf1bd9a8f3 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 13 Mar 2023 15:02:30 +0100
Subject: [PATCH 08/20] remove unused stub_test

---
 src/tye_lab_to_nwb/fiber_photometry/convert_session.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
index 0abdff1..4775ef9 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
@@ -10,11 +10,8 @@
 def session_to_nwb(
     file_path: FilePathType,
     output_dir_path: FilePathType,
-    stub_test: bool = False,
 ):
     output_dir_path = Path(output_dir_path)
-    if stub_test:
-        output_dir_path = output_dir_path / "nwb_stub"
     output_dir_path.mkdir(parents=True, exist_ok=True)
 
     interface = FiberPhotometryInterface(file_path=str(file_path))
@@ -26,17 +23,15 @@ def session_to_nwb(
     date = datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))  # TO-DO: Get this from author
     metadata["NWBFile"]["session_start_time"] = date
 
-    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, stub_test=stub_test)
+    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
 
 
 if __name__ == "__main__":
     # Parameters for conversion
     photometry_file_path = Path("/Volumes/t7-ssd/Hao_NWB/recording/Photometry_data0.csv")
     output_dir_path = Path("/Volumes/t7-ssd/Hao_NWB/nwbfiles")
-    stub_test = False
 
     session_to_nwb(
         file_path=photometry_file_path,
         output_dir_path=output_dir_path,
-        stub_test=stub_test,
     )

From 5ebcc8d35c47f02f7b0379e21b7e0eab20cc611a Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 13 Mar 2023 15:18:03 +0100
Subject: [PATCH 09/20] remove unused stub_test

---
 src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
index 3333599..8b58bc4 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -49,7 +49,6 @@ def add_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadat
         fluorophores=[0],
         location=metadata["FibersTable"]["location"],
         notes=metadata["FibersTable"]["notes"],
-        # from article, confirm?
     )
 
     # Create reference for fibers

From 8136b936e7f83f020236d81862f78b3884e2a4a7 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 13 Mar 2023 15:50:43 +0100
Subject: [PATCH 10/20] add init

---
 src/tye_lab_to_nwb/fiber_photometry/tools/__init__.py | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/tools/__init__.py

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/__init__.py b/src/tye_lab_to_nwb/fiber_photometry/tools/__init__.py
new file mode 100644
index 0000000..dcdd050
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/__init__.py
@@ -0,0 +1 @@
+from .photometry import add_photometry, add_events_from_photometry

From c33f5d712976df16ec0c8c146e000df4639a2f45 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 20 Mar 2023 10:32:03 +0100
Subject: [PATCH 11/20] edit metadata

---
 .../metadata/fiber_photometry_metadata.yaml          | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
index 947f64a..c85921f 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
@@ -33,12 +33,12 @@ Events:
       17: LED415
       18: LED470
       20: LED560
-      273: Stimulus presentation while LED415
-      274: Stimulus presentation while LED470
-      276: Stimulus presentation while LED560
+      273: Cued stimulus while LED415
+      274: Cued stimulus while LED470
+      276: Cued stimulus while LED560
       529: Lick while LED415
       530: Lick while LED470
       532: Lick while LED560
-      785: TODO while LED415 # missing description
-      786: TODO while LED470 # missing description
-      788: TODO while LED560 # missing description
+      785: Both cued stimulus and lick while LED415
+      786: Both cued stimulus and lick while LED470
+      788: Both cued stimulus and lick while LED560

From 8261763ae353ca899e619874fb8e70a0e560f114 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 20 Mar 2023 10:48:18 +0100
Subject: [PATCH 12/20] fill timestamps methods

---
 .../fiberphotometrydatainterface.py           | 29 ++++++++-----------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
index e5c58a2..a681b38 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/fiberphotometrydatainterface.py
@@ -35,6 +35,7 @@ def __init__(
         """
         self.verbose = verbose
         super().__init__(file_path=file_path)
+        self.photometry_dataframe = self._read_file()
 
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
@@ -46,10 +47,10 @@ def get_metadata(self) -> dict:
 
         return metadata
 
-    def _load_source_data(self) -> pd.DataFrame:
+    def _read_file(self) -> pd.DataFrame:
         return pd.read_csv(self.source_data["file_path"], header=0)
 
-    def get_original_timestamps(self) -> np.ndarray:
+    def get_original_timestamps(self, column: str = "Timestamp") -> np.ndarray:
         """
         Retrieve the original unaltered timestamps for the data in this interface.
 
@@ -60,12 +61,9 @@ def get_original_timestamps(self) -> np.ndarray:
         timestamps: numpy.ndarray
             The timestamps for the data stream.
         """
-        raise NotImplementedError(
-            "Unable to retrieve the original unaltered timestamps for this interface! "
-            "Define the `get_original_timestamps` method for this interface."
-        )
+        return self._read_file()[column].values
 
-    def get_timestamps(self) -> np.ndarray:
+    def get_timestamps(self, column: str = "Timestamp") -> np.ndarray:
         """
         Retrieve the timestamps for the data in this interface.
 
@@ -74,11 +72,9 @@ def get_timestamps(self) -> np.ndarray:
         timestamps: numpy.ndarray
             The timestamps for the data stream.
         """
-        raise NotImplementedError(
-            "Unable to retrieve timestamps for this interface! Define the `get_timestamps` method for this interface."
-        )
+        return self.photometry_dataframe[column].values
 
-    def align_timestamps(self, aligned_timestamps: np.ndarray):
+    def align_timestamps(self, aligned_timestamps: np.ndarray, column: str = "Timestamp"):
         """
         Replace all timestamps for this interface with those aligned to the common session start time.
 
@@ -89,9 +85,7 @@ def align_timestamps(self, aligned_timestamps: np.ndarray):
         aligned_timestamps : numpy.ndarray
             The synchronized timestamps for data in this interface.
         """
-        raise NotImplementedError(
-            "The protocol for synchronizing the timestamps of this interface has not been specified!"
-        )
+        self.photometry_dataframe[column] = aligned_timestamps
 
     def run_conversion(
         self,
@@ -104,6 +98,7 @@ def run_conversion(
         with make_or_load_nwbfile(
             nwbfile_path=nwbfile_path, nwbfile=nwbfile, metadata=metadata, overwrite=overwrite, verbose=self.verbose
         ) as nwbfile_out:
-            photometry_data = self._load_source_data()
-            add_events_from_photometry(photometry_dataframe=photometry_data, nwbfile=nwbfile_out, metadata=metadata)
-            add_photometry(photometry_dataframe=photometry_data, nwbfile=nwbfile_out, metadata=metadata)
+            add_events_from_photometry(
+                photometry_dataframe=self.photometry_dataframe, nwbfile=nwbfile_out, metadata=metadata
+            )
+            add_photometry(photometry_dataframe=self.photometry_dataframe, nwbfile=nwbfile_out, metadata=metadata)

From ccbea14c5eeb35ad441db20cd885641cebcc3174 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Mon, 20 Mar 2023 10:48:28 +0100
Subject: [PATCH 13/20] edit metadata

---
 .../metadata/fiber_photometry_metadata.yaml                 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
index c85921f..3c4abe2 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
@@ -39,6 +39,6 @@ Events:
       529: Lick while LED415
       530: Lick while LED470
       532: Lick while LED560
-      785: Both cued stimulus and lick while LED415
-      786: Both cued stimulus and lick while LED470
-      788: Both cued stimulus and lick while LED560
+      785: Cued stimulus and lick while LED415
+      786: Cued stimulus and lick while LED470
+      788: Cued stimulus and lick while LED560

From 49c2c1f172266d26f8d634d52ca79106f083785a Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 11:45:46 +0100
Subject: [PATCH 14/20] exclude LED560 events

---
 .../metadata/fiber_photometry_metadata.yaml           | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
index 3c4abe2..8fe4455 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/fiber_photometry_metadata.yaml
@@ -5,9 +5,6 @@ ExcitationSourcesTable:
   - name: LED470
     peak_wavelength: 470.0 # in nanometers
     source_type: LED
-  - name: LED560
-    peak_wavelength: 560.0 # in nanometers
-    source_type: LED
 PhotodetectorsTable:
     description: The metadata for the photodetector.
     type: CMOS camera
@@ -24,7 +21,9 @@ FibersTable:
     location: BLA
     notes: The optical fiber was implanted above the BLA.
 RoiResponseSeries:
-    description: The photometry intensity values measured in arbitrary units.
+  - region: Region0G
+    name: RoiResponseSeriesRegion0G
+    description: The photometry intensity values measured in arbitrary units and recorded from BLA.
     unit: a.u.
 Events:
     name: LabeledEvents
@@ -32,13 +31,9 @@ Events:
     labels:
       17: LED415
       18: LED470
-      20: LED560
       273: Cued stimulus while LED415
       274: Cued stimulus while LED470
-      276: Cued stimulus while LED560
       529: Lick while LED415
       530: Lick while LED470
-      532: Lick while LED560
       785: Cued stimulus and lick while LED415
       786: Cued stimulus and lick while LED470
-      788: Cued stimulus and lick while LED560

From 066aa1a43257303ac9f8521abad45840edab2c3d Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 11:47:00 +0100
Subject: [PATCH 15/20] adjust RoiResponseSeries metadata

---
 .../fiber_photometry/tools/photometry.py      | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
index 8b58bc4..a3f3963 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -59,17 +59,19 @@ def add_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadat
         table=fibers_table,
     )
     # Create the RoiResponseSeries that holds the intensity values
-    roi_response_series_name = "RoiResponseSeries"
-    roi_response_series = RoiResponseSeries(
-        name=roi_response_series_name,
-        description=metadata[roi_response_series_name]["description"],
-        data=photometry_dataframe["Region1R"].values,
-        unit=metadata[roi_response_series_name]["unit"],
-        timestamps=photometry_dataframe["Timestamp"].values,
-        rois=rois,
-    )
+    for photometry_metadata in metadata["RoiResponseSeries"]:
+        column = photometry_metadata["region"]
+        roi_response_series_name = photometry_metadata["name"]
+        roi_response_series = RoiResponseSeries(
+            name=roi_response_series_name,
+            description=photometry_metadata["description"],
+            data=photometry_dataframe[column].values,
+            unit=photometry_metadata["unit"],
+            timestamps=photometry_dataframe["Timestamp"].values,
+            rois=rois,
+        )
 
-    nwbfile.add_acquisition(roi_response_series)
+        nwbfile.add_acquisition(roi_response_series)
 
 
 def add_events_from_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadata: Optional[dict]):

From e9749eee0a36a379f7f7648a9f57d14245633045 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 12:08:08 +0100
Subject: [PATCH 16/20] add general metadata

---
 .../fiber_photometry/convert_session.py            | 14 ++++++++++----
 .../metadata/general_metadata.yaml                 |  9 +++++++++
 2 files changed, 19 insertions(+), 4 deletions(-)
 create mode 100644 src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml

diff --git a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
index 4775ef9..448c5ac 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 from zoneinfo import ZoneInfo
 
-from neuroconv.utils import FilePathType
+from neuroconv.utils import FilePathType, load_dict_from_file, dict_deep_update
 
 from tye_lab_to_nwb.fiber_photometry import FiberPhotometryInterface
 
@@ -17,11 +17,17 @@ def session_to_nwb(
     interface = FiberPhotometryInterface(file_path=str(file_path))
     metadata = interface.get_metadata()
 
-    nwbfile_path = output_dir_path / "fiber_photometry.nwb"
+    # Update default metadata with the editable in the corresponding yaml file
+    editable_metadata_path = Path(__file__).parent / "metadata" / "general_metadata.yaml"
+    editable_metadata = load_dict_from_file(editable_metadata_path)
+    metadata = dict_deep_update(metadata, editable_metadata)
+
+    nwbfile_path = output_dir_path / f"{photometry_file_path.stem}.nwb"
 
     # Add datetime to conversion
-    date = datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))  # TO-DO: Get this from author
-    metadata["NWBFile"]["session_start_time"] = date
+    if "session_start_time" not in metadata["NWBFile"]:
+        date = datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))  # TO-DO: Get this from author
+        metadata["NWBFile"].update(session_start_time=date)
 
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
 
diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml
new file mode 100644
index 0000000..fbedba5
--- /dev/null
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml
@@ -0,0 +1,9 @@
+NWBFile:
+  session_description: Contains photometry intensity values obtained from a single fiber implanted in BLA.
+  institution: Salk Institute for Biological Studies
+  lab: Tye
+  experimenter:
+    - Li, Hao
+  related_publications: https://doi.org/10.1038/s41586-022-04964-y
+Subject:
+  species: Mus musculus

From 51a65298002de107e07d0e651919865d6b866253 Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 12:11:19 +0100
Subject: [PATCH 17/20] add compression

---
 src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
index a3f3963..d07fe2c 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/tools/photometry.py
@@ -1,6 +1,7 @@
 from typing import Optional
 
 import pandas as pd
+from hdmf.backends.hdf5 import H5DataIO
 from hdmf.common import DynamicTableRegion
 from ndx_events import AnnotatedEventsTable
 from ndx_photometry import FibersTable, FiberPhotometry, ExcitationSourcesTable, PhotodetectorsTable, FluorophoresTable
@@ -65,9 +66,9 @@ def add_photometry(photometry_dataframe: pd.DataFrame, nwbfile: NWBFile, metadat
         roi_response_series = RoiResponseSeries(
             name=roi_response_series_name,
             description=photometry_metadata["description"],
-            data=photometry_dataframe[column].values,
+            data=H5DataIO(photometry_dataframe[column].values, compression=True),
             unit=photometry_metadata["unit"],
-            timestamps=photometry_dataframe["Timestamp"].values,
+            timestamps=H5DataIO(photometry_dataframe["Timestamp"].values, compression=True),
             rois=rois,
         )
 

From bfce1f3130801403dc7e36dd2964874f750b9bea Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 12:39:52 +0100
Subject: [PATCH 18/20] update metadata

---
 .../fiber_photometry/convert_session.py       | 24 ++++++++++++++-----
 .../metadata/general_metadata.yaml            |  3 +++
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
index 448c5ac..1622af7 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
@@ -1,5 +1,6 @@
 from datetime import datetime
 from pathlib import Path
+from uuid import uuid4
 from zoneinfo import ZoneInfo
 
 from neuroconv.utils import FilePathType, load_dict_from_file, dict_deep_update
@@ -11,10 +12,9 @@ def session_to_nwb(
     file_path: FilePathType,
     output_dir_path: FilePathType,
 ):
-    output_dir_path = Path(output_dir_path)
-    output_dir_path.mkdir(parents=True, exist_ok=True)
-
+    # Initalize interface with photometry source data
     interface = FiberPhotometryInterface(file_path=str(file_path))
+    # Update metadata from interface
     metadata = interface.get_metadata()
 
     # Update default metadata with the editable in the corresponding yaml file
@@ -22,12 +22,22 @@ def session_to_nwb(
     editable_metadata = load_dict_from_file(editable_metadata_path)
     metadata = dict_deep_update(metadata, editable_metadata)
 
-    nwbfile_path = output_dir_path / f"{photometry_file_path.stem}.nwb"
-
     # Add datetime to conversion
     if "session_start_time" not in metadata["NWBFile"]:
         date = datetime(year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern"))  # TO-DO: Get this from author
         metadata["NWBFile"].update(session_start_time=date)
+    # Generate subject identifier if missing from metadata
+    subject_id = "1"
+    if "subject_id" not in metadata["Subject"]:
+        metadata["Subject"].update(subject_id=subject_id)
+    session_id = str(uuid4())
+    if "session_id" not in metadata["NWBFile"]:
+        metadata["NWBFile"].update(session_id=session_id)
+
+    output_dir_path = Path(output_dir_path) / f"sub-{metadata['Subject']['subject_id']}"
+    output_dir_path.mkdir(parents=True, exist_ok=True)
+    nwbfile_name = f"sub-{subject_id}_ses-{session_id}.nwb"
+    nwbfile_path = output_dir_path / nwbfile_name
 
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
 
@@ -35,7 +45,9 @@ def session_to_nwb(
 if __name__ == "__main__":
     # Parameters for conversion
     photometry_file_path = Path("/Volumes/t7-ssd/Hao_NWB/recording/Photometry_data0.csv")
-    output_dir_path = Path("/Volumes/t7-ssd/Hao_NWB/nwbfiles")
+    output_dir_path = Path(
+        "/Users/weian/Library/Mobile Documents/com~apple~CloudDocs/catalystneuro/tye-lab-to-nwb/204134"
+    )
 
     session_to_nwb(
         file_path=photometry_file_path,
diff --git a/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml b/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml
index fbedba5..1738da6 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml
+++ b/src/tye_lab_to_nwb/fiber_photometry/metadata/general_metadata.yaml
@@ -7,3 +7,6 @@ NWBFile:
   related_publications: https://doi.org/10.1038/s41586-022-04964-y
 Subject:
   species: Mus musculus
+  age: P8W/P20W # male and female mice between the ages of 8-20 weeks were used for all experiments
+  sex: U # "M" is for male, "F" is for female (for this session it is unknown)
+  #strain: C57BL/6J # the strain of the mouse for this session

From b14cefd2c40950c64538b597e7f717908878dbba Mon Sep 17 00:00:00 2001
From: weiglszonja <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 12:55:04 +0100
Subject: [PATCH 19/20] rollback output_dir_path

---
 src/tye_lab_to_nwb/fiber_photometry/convert_session.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
index 1622af7..48c23b9 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
+++ b/src/tye_lab_to_nwb/fiber_photometry/convert_session.py
@@ -45,9 +45,7 @@ def session_to_nwb(
 if __name__ == "__main__":
     # Parameters for conversion
     photometry_file_path = Path("/Volumes/t7-ssd/Hao_NWB/recording/Photometry_data0.csv")
-    output_dir_path = Path(
-        "/Users/weian/Library/Mobile Documents/com~apple~CloudDocs/catalystneuro/tye-lab-to-nwb/204134"
-    )
+    output_dir_path = Path("/Volumes/t7-ssd/Hao_NWB/nwbfiles")
 
     session_to_nwb(
         file_path=photometry_file_path,

From 0b2250c26c3212597377d06b9138687dbc657cce Mon Sep 17 00:00:00 2001
From: Szonja Weigl <wszonja@gmail.com>
Date: Wed, 22 Mar 2023 15:56:39 +0100
Subject: [PATCH 20/20] Update
 src/tye_lab_to_nwb/fiber_photometry/requirements.txt

---
 src/tye_lab_to_nwb/fiber_photometry/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tye_lab_to_nwb/fiber_photometry/requirements.txt b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
index b19ad26..ede7304 100644
--- a/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
+++ b/src/tye_lab_to_nwb/fiber_photometry/requirements.txt
@@ -1,2 +1,2 @@
-ndx-photometry>=0.1.0
+git+https://github.com/catalystneuro/ndx-photometry
 ndx-events>=0.2.0