From de0016397bb1e3af8191875339b6ca8b2664d0c2 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Fri, 29 Sep 2023 09:50:43 -0700
Subject: [PATCH 01/16] Add ability to split memmap from large rec file between
 multiple iterators

---
 src/spikegadgets_to_nwb/convert_ephys.py      |  33 ++++-
 .../spike_gadgets_raw_io.py                   | 140 ++++++++++++++++++
 2 files changed, 172 insertions(+), 1 deletion(-)

diff --git a/src/spikegadgets_to_nwb/convert_ephys.py b/src/spikegadgets_to_nwb/convert_ephys.py
index 00d1e92..ebd8b29 100644
--- a/src/spikegadgets_to_nwb/convert_ephys.py
+++ b/src/spikegadgets_to_nwb/convert_ephys.py
@@ -10,12 +10,13 @@
 
 from spikegadgets_to_nwb import convert_rec_header
 
-from .spike_gadgets_raw_io import SpikeGadgetsRawIO
+from .spike_gadgets_raw_io import SpikeGadgetsRawIO, SpikeGadgetsRawIOPartial
 
 MICROVOLTS_PER_VOLT = 1e6
 VOLTS_PER_MICROVOLT = 1e-6
 MILLISECONDS_PER_SECOND = 1e3
 NANOSECONDS_PER_SECOND = 1e9
+MAXIMUM_ITERATOR_SIZE = int(30000 * 5)  # * 60 * 60  # 1 hour of data at 30 kHz
 
 
 class RecFileDataChunkIterator(GenericDataChunkIterator):
@@ -83,6 +84,36 @@ def __init__(
         else:
             self.nwb_hw_channel_order = nwb_hw_channel_order
 
+        """split excessively large iterators into smaller ones
+        """
+        iterator_size = [neo_io._raw_memmap.shape[0] for neo_io in self.neo_io]
+        iterator_size.reverse()
+        for i, size in enumerate(
+            iterator_size
+        ):  # iterate backwards so can insert new iterators
+            if size > MAXIMUM_ITERATOR_SIZE:
+                # split into smaller iterators
+                sub_iterators = []
+                j = 0
+                previous_multiplex_state = None
+                iterator_loc = len(iterator_size) - i - 1
+                while j < size:
+                    sub_iterators.append(
+                        SpikeGadgetsRawIOPartial(
+                            self.neo_io[iterator_loc],
+                            start_index=j,
+                            stop_index=j + MAXIMUM_ITERATOR_SIZE,
+                            previous_multiplex_state=previous_multiplex_state,
+                        )
+                    )
+                    if self.n_multiplexed_channel > 0:
+                        previous_multiplex_state = sub_iterators[
+                            -1
+                        ].get_analogsignal_multiplexed()[-1]
+                    j += MAXIMUM_ITERATOR_SIZE
+            self.neo_io.pop(iterator_loc)
+            self.neo_io[iterator_loc:iterator_loc] = sub_iterators
+
         # NOTE: this will read all the timestamps from the rec file, which can be slow
         if timestamps is not None:
             self.timestamps = timestamps
diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index 40bf435..2512dcd 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -692,3 +692,143 @@ def access_coordinates(self, index):
         # if list of indeces
         else:
             return self.mapped_index[index]
+
+
+class SpikeGadgetsRawIOPartial(SpikeGadgetsRawIO):
+    extensions = ["rec"]
+    rawmode = "one-file"
+
+    def __init__(
+        self,
+        full_io: SpikeGadgetsRawIO,
+        start_index: int,
+        stop_index: int,
+        previous_multiplex_state: np.ndarray = None,
+    ):
+        """Initialize a partial SpikeGadgetsRawIO object.
+
+        Parameters
+        ----------
+        full_io : SpikeGadgetsRawIO
+            The SpikeGadgetsRawIO for the complete rec file
+        start_index : int
+            Where this partial file starts in the complete file
+        stop_index : int
+            Where this partial file stops in the complete file
+        previous_multiplex_state : np.ndarray, optional
+            The last multiplex state in the previous partial file.
+            If None, will default to behavior of SpikeGadgetsRawIO.
+            Use None if first partial iterator for the rec file or if not accessing multiplex data.
+            By default None
+        """
+        # initialization from the base class
+        BaseRawIO.__init__(self)
+        self.filename = full_io.filename
+        self.selected_streams = full_io.selected_streams
+        self.interpolate_dropped_packets = full_io.interpolate_dropped_packets
+
+        # define some key information
+        self.interpolate_index = None
+        self.previous_multiplex_state = previous_multiplex_state
+
+        # copy conserved information from parsed_header from full_io
+        self.header = full_io.header
+        self.system_time_at_creation = full_io.system_time_at_creation
+        self.timestamp_at_creation = full_io.timestamp_at_creation
+        self._sampling_rate = full_io._sampling_rate
+        self.sysClock_byte = full_io.sysClock_byte
+        self._timestamp_byte = full_io._timestamp_byte
+        self._mask_channels_ids = full_io._mask_channels_ids
+        self._mask_channels_bytes = full_io._mask_channels_bytes
+        self._mask_channels_bits = full_io._mask_channels_bits
+        self.multiplexed_channel_xml = full_io.multiplexed_channel_xml
+        self._multiplexed_byte_start = full_io._multiplexed_byte_start
+        self._mask_streams = full_io._mask_streams
+        self.selected_streams = full_io.selected_streams
+        self._generate_minimal_annotations()
+
+        # crop key information to range of interest
+        header_size = None
+        with open(self.filename, mode="rb") as f:
+            while True:
+                line = f.readline()
+                if b"</Configuration>" in line:
+                    header_size = f.tell()
+                    break
+
+            if header_size is None:
+                ValueError(
+                    "SpikeGadgets: the xml header does not contain '</Configuration>'"
+                )
+
+        raw_memmap = np.memmap(self.filename, mode="r", offset=header_size, dtype="<u1")
+        packet_size = full_io._raw_memmap.shape[1]
+        num_packet = raw_memmap.size // packet_size
+        raw_memmap = raw_memmap[: num_packet * packet_size]
+        self._raw_memmap = raw_memmap.reshape(-1, packet_size)
+        self._raw_memmap = self._raw_memmap[start_index:stop_index]
+
+    @functools.lru_cache(maxsize=2)
+    def get_analogsignal_multiplexed(self, channel_names=None) -> np.ndarray:
+        """
+        Overide of the superclass to use the last state of the previous file segment
+        to define the first state of the current file segment.
+        """
+        print("compute multiplex cache", self.filename)
+        if channel_names is None:
+            # read all multiplexed channels
+            channel_names = list(self.multiplexed_channel_xml.keys())
+        else:
+            for ch_name in channel_names:
+                if ch_name not in self.multiplexed_channel_xml:
+                    raise ValueError(f"Channel name '{ch_name}' not found in file.")
+
+        # because of the encoding scheme, it is easiest to read all the data in sequence
+        # one packet at a time
+        num_packet = self._raw_memmap.shape[0]
+        analog_multiplexed_data = np.empty(
+            (num_packet, len(channel_names)), dtype=np.int16
+        )
+
+        # precompute the static data offsets
+        data_offsets = np.empty((len(channel_names), 3), dtype=int)
+        for j, ch_name in enumerate(channel_names):
+            ch_xml = self.multiplexed_channel_xml[ch_name]
+            data_offsets[j, 0] = int(
+                self._multiplexed_byte_start + int(ch_xml.attrib["startByte"])
+            )
+            data_offsets[j, 1] = int(ch_xml.attrib["interleavedDataIDByte"])
+            data_offsets[j, 2] = int(ch_xml.attrib["interleavedDataIDBit"])
+        interleaved_data_id_byte_values = self._raw_memmap[:, data_offsets[:, 1]]
+        interleaved_data_id_bit_values = (
+            interleaved_data_id_byte_values >> data_offsets[:, 2]
+        ) & 1
+        # calculate which packets encode for which channel
+        initialize_stream_mask = np.logical_or(
+            (np.arange(num_packet) == 0)[:, None], interleaved_data_id_bit_values == 1
+        )
+        # read the data into int16
+        data = (
+            self._raw_memmap[:, data_offsets[:, 0]]
+            + self._raw_memmap[:, data_offsets[:, 0] + 1] * 256
+        )
+        # initialize the first row
+        # if no previous state, assume first segment. Default to superclass behavior
+        analog_multiplexed_data[0] = data[0]
+        if not self.previous_multiplex_state is None:
+            # if previous state, use it to initialize elements of first row not updated in that packet
+            ind = np.where(initialize_stream_mask[0])[0]
+            analog_multiplexed_data[0][ind] = self.previous_multiplex_state[ind]
+        # for packets that do not have an update for a channel, use the previous value
+        for i in range(1, num_packet):
+            analog_multiplexed_data[i] = np.where(
+                initialize_stream_mask[i], data[i], analog_multiplexed_data[i - 1]
+            )
+        return analog_multiplexed_data
+
+    def get_digitalsignal(self, stream_id, channel_id):
+        dio_change_times, change_dir_trim = super().get_digitalsignal(
+            stream_id, channel_id
+        )
+        # clip the setting of the first state
+        return dio_change_times[1:], change_dir_trim[1:]

From cade841a82a6756666b66a8dace062907565f10d Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Fri, 29 Sep 2023 09:57:40 -0700
Subject: [PATCH 02/16] Update add epochs test to use rec_dci, which will split
 large rec files between iterators

---
 .../tests/test_convert_intervals.py                    | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index 1d763cf..ee5b1c9 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -30,12 +30,10 @@ def test_add_epochs():
         file_info = get_file_info(Path(path))
         rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
     # get all streams for all files
-    neo_io = [
-        SpikeGadgetsRawIO(filename=file)
-        for file in file_info[file_info.file_extension == ".rec"].full_path
-    ]
-    [neo_io.parse_header() for neo_io in neo_io]
-    add_epochs(nwbfile, file_info, 20230622, "sample", neo_io)
+    rec_dci = RecFileDataChunkIterator(
+        file_info[file_info.file_extension == ".rec"].full_path.to_list()
+    )
+    add_epochs(nwbfile, file_info, 20230622, "sample", rec_dci.neo_io)
     epochs_df = nwbfile.epochs.to_dataframe()
     # load old nwb versio
     io = NWBHDF5IO(rec_to_nwb_file, "r")

From 5a58a5aab64b28309ecef58a4229d5caa381414a Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Mon, 2 Oct 2023 13:42:36 -0700
Subject: [PATCH 03/16] Correct indentation

---
 src/spikegadgets_to_nwb/convert_ephys.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/spikegadgets_to_nwb/convert_ephys.py b/src/spikegadgets_to_nwb/convert_ephys.py
index ebd8b29..e2bc6ca 100644
--- a/src/spikegadgets_to_nwb/convert_ephys.py
+++ b/src/spikegadgets_to_nwb/convert_ephys.py
@@ -16,7 +16,7 @@
 VOLTS_PER_MICROVOLT = 1e-6
 MILLISECONDS_PER_SECOND = 1e3
 NANOSECONDS_PER_SECOND = 1e9
-MAXIMUM_ITERATOR_SIZE = int(30000 * 5)  # * 60 * 60  # 1 hour of data at 30 kHz
+MAXIMUM_ITERATOR_SIZE = int(30000 * 60 * 30)  # 30 min of data at 30 kHz
 
 
 class RecFileDataChunkIterator(GenericDataChunkIterator):
@@ -111,9 +111,9 @@ def __init__(
                             -1
                         ].get_analogsignal_multiplexed()[-1]
                     j += MAXIMUM_ITERATOR_SIZE
-            self.neo_io.pop(iterator_loc)
-            self.neo_io[iterator_loc:iterator_loc] = sub_iterators
-
+                self.neo_io.pop(iterator_loc)
+                self.neo_io[iterator_loc:iterator_loc] = sub_iterators
+        print("# iterators:", len(self.neo_io))
         # NOTE: this will read all the timestamps from the rec file, which can be slow
         if timestamps is not None:
             self.timestamps = timestamps

From e85c73f67ad83fe2029c4bb67943e70d57658bdb Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Mon, 2 Oct 2023 15:01:32 -0700
Subject: [PATCH 04/16] Restrict selection of rec files to sample dataset

---
 src/spikegadgets_to_nwb/tests/test_convert_intervals.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index ee5b1c9..31d0bb3 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -29,6 +29,8 @@ def test_add_epochs():
         # running locally
         file_info = get_file_info(Path(path))
         rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
+    file_info = file_info[file_info.animal == "sample"]
+    # assert file_info[file_info.file_extension == ".rec"].full_path.to_list() == []
     # get all streams for all files
     rec_dci = RecFileDataChunkIterator(
         file_info[file_info.file_extension == ".rec"].full_path.to_list()

From 1f7fd569be0114bc18c495f50fda257122f119c7 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 4 Oct 2023 13:43:01 -0700
Subject: [PATCH 05/16] Reduce concatenations in add_dio

---
 src/spikegadgets_to_nwb/convert_dios.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/spikegadgets_to_nwb/convert_dios.py b/src/spikegadgets_to_nwb/convert_dios.py
index e67c5d0..8161c53 100644
--- a/src/spikegadgets_to_nwb/convert_dios.py
+++ b/src/spikegadgets_to_nwb/convert_dios.py
@@ -72,15 +72,18 @@ def add_dios(nwbfile: NWBFile, recfile: list[str], metadata: dict) -> None:
 
     for channel_name in channel_name_map:
         # merge streams from multiple files
-        all_timestamps = np.array([], dtype=np.float64)
-        all_state_changes = np.array([], dtype=np.uint8)
+        all_timestamps = []
+        all_state_changes = []
         for io in neo_io:
             timestamps, state_changes = io.get_digitalsignal(
                 stream_name, prefix + channel_name
             )
-            all_timestamps = np.concatenate((all_timestamps, timestamps))
-            all_state_changes = np.concatenate((all_state_changes, state_changes))
-
+            all_timestamps.append(timestamps)
+            all_state_changes.append(state_changes)
+        all_timestamps = np.concatenate(all_timestamps)
+        all_state_changes = np.concatenate(all_state_changes)
+        assert isinstance(all_timestamps[0], np.float64)
+        assert isinstance(all_timestamps, np.ndarray)
         ts = TimeSeries(
             name=channel_name_map[channel_name],
             description=channel_name,

From 1549d4cb00031288401ccea013e673b5bf730b3c Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 4 Oct 2023 15:49:31 -0700
Subject: [PATCH 06/16] Add method to read multiplexed data without loading
 full series

---
 src/spikegadgets_to_nwb/convert_ephys.py      |  9 +-
 .../spike_gadgets_raw_io.py                   | 87 +++++++++++++++++++
 2 files changed, 95 insertions(+), 1 deletion(-)

diff --git a/src/spikegadgets_to_nwb/convert_ephys.py b/src/spikegadgets_to_nwb/convert_ephys.py
index b0fb33a..4104d6d 100644
--- a/src/spikegadgets_to_nwb/convert_ephys.py
+++ b/src/spikegadgets_to_nwb/convert_ephys.py
@@ -107,9 +107,16 @@ def __init__(
                         )
                     )
                     if self.n_multiplexed_channel > 0:
+                        partial_size = sub_iterators[-1]._raw_memmap.shape[0]
                         previous_multiplex_state = sub_iterators[
                             -1
-                        ].get_analogsignal_multiplexed()[-1]
+                        ].get_analogsignal_multiplexed_partial(
+                            i_start=partial_size - 10,
+                            i_stop=partial_size,
+                            padding=30000,
+                        )[
+                            -1
+                        ]
                     j += MAXIMUM_ITERATOR_SIZE
                 self.neo_io.pop(iterator_loc)
                 self.neo_io[iterator_loc:iterator_loc] = sub_iterators
diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index e9de235..bbf9d71 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -537,6 +537,93 @@ def get_analogsignal_multiplexed(self, channel_names=None) -> np.ndarray:
             )
         return analog_multiplexed_data
 
+    def get_analogsignal_multiplexed_partial(
+        self,
+        i_start: int,
+        i_stop: int,
+        channel_names: list = None,
+        padding: int = 30000,
+    ) -> np.ndarray:
+        """Alternative method to access part of the multiplexed data.
+        Not memory efficient for many calls because it reads a buffer chunk before the requested data.
+        Better than get_analogsignal_multiplexed when need one call to specific time region
+
+        Parameters
+        ----------
+        i_start : int
+            index start
+        i_stop : int
+            index stop
+        channel_names : list[str], optional
+            channels to get, by default None will get all multiplex channels
+        padding : int, optional
+            how many packets before the desired series to load to ensure every channel receives update before requested,
+            by default 30000
+
+        Returns
+        -------
+        np.ndarray
+            multiplex data
+
+        Raises
+        ------
+        ValueError
+            _description_
+        """
+        print("compute multiplex cache", self.filename)
+        if channel_names is None:
+            # read all multiplexed channels
+            channel_names = list(self.multiplexed_channel_xml.keys())
+        else:
+            for ch_name in channel_names:
+                if ch_name not in self.multiplexed_channel_xml:
+                    raise ValueError(f"Channel name '{ch_name}' not found in file.")
+        # determine which packets to get from data
+        padding = min(padding, i_start)
+        i_start = i_start - padding
+        if i_stop is None:
+            i_stop = self._raw_memmap.shape[0]
+
+        # Make object to hold data
+        num_packet = i_stop - i_start
+        analog_multiplexed_data = np.empty(
+            (num_packet, len(channel_names)), dtype=np.int16
+        )
+
+        # precompute the static data offsets
+        data_offsets = np.empty((len(channel_names), 3), dtype=int)
+        for j, ch_name in enumerate(channel_names):
+            ch_xml = self.multiplexed_channel_xml[ch_name]
+            data_offsets[j, 0] = int(
+                self._multiplexed_byte_start + int(ch_xml.attrib["startByte"])
+            )
+            data_offsets[j, 1] = int(ch_xml.attrib["interleavedDataIDByte"])
+            data_offsets[j, 2] = int(ch_xml.attrib["interleavedDataIDBit"])
+        interleaved_data_id_byte_values = self._raw_memmap[
+            i_start:i_stop, data_offsets[:, 1]
+        ]
+        interleaved_data_id_bit_values = (
+            interleaved_data_id_byte_values >> data_offsets[:, 2]
+        ) & 1
+        # calculate which packets encode for which channel
+        initialize_stream_mask = np.logical_or(
+            (np.arange(num_packet) == 0)[:, None], interleaved_data_id_bit_values == 1
+        )
+        # read the data into int16
+        data = (
+            self._raw_memmap[i_start:i_stop, data_offsets[:, 0]]
+            + self._raw_memmap[i_start:i_stop, data_offsets[:, 0] + 1] * 256
+        )
+        # initialize the first row
+        analog_multiplexed_data[0] = data[0]
+        # for packets that do not have an update for a channel, use the previous value
+        # this method assumes that every channel has an update within the buffer
+        for i in range(1, num_packet):
+            analog_multiplexed_data[i] = np.where(
+                initialize_stream_mask[i], data[i], analog_multiplexed_data[i - 1]
+            )
+        return analog_multiplexed_data[padding:]
+
     def get_digitalsignal(self, stream_id, channel_id):
         # stream_id = self.header["signal_streams"][stream_index]["id"]
 

From cb52f19631e2e1f7277e40d93396ae738c374018 Mon Sep 17 00:00:00 2001
From: Eric Denovellis <edeno@bu.edu>
Date: Fri, 27 Oct 2023 14:55:07 -0700
Subject: [PATCH 07/16] Revert "Merge branch 'main' into split_iterator"

This reverts commit dc56f90e7ac1e82e22280053abace1722b9c318a, reversing
changes made to 1549d4cb00031288401ccea013e673b5bf730b3c.
---
 .github/workflows/test_package_build.yml      |     9 +-
 environment.yml                               |     3 +-
 pyproject.toml                                |     3 +-
 src/spikegadgets_to_nwb/convert.py            |    75 +-
 src/spikegadgets_to_nwb/convert_analog.py     |     1 +
 src/spikegadgets_to_nwb/convert_dios.py       |    24 +-
 src/spikegadgets_to_nwb/convert_intervals.py  |    16 +-
 src/spikegadgets_to_nwb/convert_position.py   |   390 +-
 src/spikegadgets_to_nwb/convert_yaml.py       |    21 +-
 .../metadata_validation.py                    |    75 -
 src/spikegadgets_to_nwb/nwb_schema.json       | 35971 ----------------
 .../spike_gadgets_raw_io.py                   |    11 +-
 .../tests/integration-tests/__init__.py       |     0
 .../test_metadata_validation_it.py            |   190 -
 src/spikegadgets_to_nwb/tests/test_convert.py |    66 +-
 .../tests/test_convert_analog.py              |    21 +-
 .../tests/test_convert_dios.py                |    47 +-
 .../tests/test_convert_ephys.py               |   103 +-
 .../tests/test_convert_intervals.py           |    60 +-
 .../tests/test_convert_position.py            |    90 +-
 .../tests/test_convert_rec_header.py          |    48 +-
 .../tests/test_convert_yaml.py                |    90 +-
 .../test_data/20230622_sample_metadata.yml    |    13 +-
 .../tests/test_data/nonptp_metadata.yml       |  1225 -
 .../test_data/test_metadata_dict_samples.py   |   212 -
 .../tests/test_metadata_validation.py         |    25 -
 .../tests/test_spikegadgets_io.py             |    12 +-
 src/spikegadgets_to_nwb/tests/utils.py        |    23 -
 28 files changed, 473 insertions(+), 38351 deletions(-)
 delete mode 100644 src/spikegadgets_to_nwb/metadata_validation.py
 delete mode 100644 src/spikegadgets_to_nwb/nwb_schema.json
 delete mode 100644 src/spikegadgets_to_nwb/tests/integration-tests/__init__.py
 delete mode 100644 src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
 delete mode 100644 src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
 delete mode 100644 src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
 delete mode 100644 src/spikegadgets_to_nwb/tests/test_metadata_validation.py
 delete mode 100644 src/spikegadgets_to_nwb/tests/utils.py

diff --git a/.github/workflows/test_package_build.yml b/.github/workflows/test_package_build.yml
index 880a840..a49a53e 100644
--- a/.github/workflows/test_package_build.yml
+++ b/.github/workflows/test_package_build.yml
@@ -46,8 +46,6 @@ jobs:
     strategy:
       matrix:
         package: ['wheel', 'sdist', 'archive', 'editable']
-    env:
-      DOWNLOAD_DIR: ${{ github.workspace }}/test_data
     steps:
       - name: Download sdist and wheel artifacts
         if: matrix.package != 'archive'
@@ -68,7 +66,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: 3
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Update pip
@@ -92,14 +90,19 @@ jobs:
           UCSF_BOX_TOKEN: ${{ secrets.UCSF_BOX_TOKEN }}
           UCSF_BOX_USER: ${{ secrets.UCSF_BOX_USER }}
           WEBSITE: ftps://ftp.box.com/spikegadgets_to_nwb_test_data/
+          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: |
           wget --recursive --no-verbose --no-host-directories --no-directories --user $UCSF_BOX_USER --password $UCSF_BOX_TOKEN -P $DOWNLOAD_DIR $WEBSITE
           tree $DOWNLOAD_DIR
       - name: Run tests without coverage
         if: matrix.package != 'editable'
+        env:
+          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: pytest --doctest-modules -v --pyargs spikegadgets_to_nwb
       - name: Run tests with coverage
         if: matrix.package == 'editable'
+        env:
+          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: pytest --cov=src --cov-report=xml --doctest-modules -v --pyargs spikegadgets_to_nwb
       - name: Upload coverage reports to Codecov
         if: matrix.package == 'editable'
diff --git a/environment.yml b/environment.yml
index 95ccd1b..63dcffa 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,9 +15,8 @@ dependencies:
 - pytest-cov
 - pip
 - pyyaml
-- jsonschema
 - ffmpeg
 - pip:
     - ndx-franklab-novela
     - neo
-    - hdmf==3.8.1
+    - hdmf=3.8.1
diff --git a/pyproject.toml b/pyproject.toml
index 04f93e3..4d3b5b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,9 +10,8 @@ requires-python = ">=3.8"
 license = { file = "LICENSE" }
 authors = [
     { name = "Sam Bray", email = "sam.bray@ucsf.edu" },
-    { name = "Eric Denovellis", email = "eric.denovellis@ucsf.edu" },
     { name = "Ryan Ly", email = "rly@lbl.gov" },
-    { name = "Philip Adenekan", email = "phil.adenekan@ucsf.edu" },
+    { name = "Eric Denovellis", email = "eric.denovellis@ucsf.edu" },
     { name = "Loren Frank", email = "loren.frank@ucsf.edu" },
 ]
 classifiers = [
diff --git a/src/spikegadgets_to_nwb/convert.py b/src/spikegadgets_to_nwb/convert.py
index e2ec922..6318a61 100644
--- a/src/spikegadgets_to_nwb/convert.py
+++ b/src/spikegadgets_to_nwb/convert.py
@@ -10,13 +10,9 @@
 from spikegadgets_to_nwb.convert_dios import add_dios
 from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator, add_raw_ephys
 from spikegadgets_to_nwb.convert_intervals import add_epochs, add_sample_count
-from spikegadgets_to_nwb.convert_position import (
-    add_associated_video_files,
-    add_position,
-)
+from spikegadgets_to_nwb.convert_position import add_position
 from spikegadgets_to_nwb.convert_rec_header import (
     add_header_device,
-    detect_ptp_from_header,
     make_hw_channel_map,
     make_ref_electrode_map,
     read_header,
@@ -109,34 +105,7 @@ def create_nwbs(
     video_directory: str = "",
     convert_video: bool = False,
     n_workers: int = 1,
-    query_expression: str | None = None,
 ):
-    """
-    Convert SpikeGadgets data to NWB format.
-
-    Parameters
-    ----------
-    path : Path
-        Path to the SpikeGadgets data file.
-    header_reconfig_path : Path, optional
-        Path to the header reconfiguration file, by default None.
-    probe_metadata_paths : list[Path], optional
-        List of paths to the probe metadata files, by default None.
-    output_dir : str, optional
-        Output directory for the NWB files, by default "/home/stelmo/nwb/raw".
-    video_directory : str, optional
-        Directory containing the video files, by default "".
-    convert_video : bool, optional
-        Whether to convert the video files, by default False.
-    n_workers : int, optional
-        Number of workers to use for parallel processing, by default 1.
-    query_expression : str, optional
-        Pandas query expression to filter the data, by default None.
-        e.g. "animal == 'sample' and epoch == 1"
-        See https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html.
-
-    """
-
     if not isinstance(path, Path):
         path = Path(path)
 
@@ -146,9 +115,6 @@ def create_nwbs(
 
     file_info = get_file_info(path)
 
-    if query_expression is not None:
-        file_info = file_info.query(query_expression)
-
     if n_workers > 1:
 
         def pass_func(args):
@@ -259,9 +225,6 @@ def _create_nwb(
         nwb_file, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
     add_header_device(nwb_file, rec_header)
-    add_associated_video_files(
-        nwb_file, metadata, session_df, video_directory, convert_video
-    )
 
     logger.info("ADDING EPHYS DATA")
     ### add rec file data ###
@@ -280,32 +243,26 @@ def _create_nwb(
     add_analog_data(nwb_file, rec_filepaths, timestamps=rec_dci_timestamps)
     logger.info("ADDING SAMPLE COUNTS")
     add_sample_count(nwb_file, rec_dci)
+    logger.info("ADDING POSITION")
+    ### add position ###
+    add_position(
+        nwb_file,
+        metadata,
+        session_df,
+        rec_header,
+        video_directory=video_directory,
+        convert_video=convert_video,
+    )
+
+    # add epochs
     logger.info("ADDING EPOCHS")
     add_epochs(
         nwbfile=nwb_file,
-        session_df=session_df,
+        file_info=session_df,
+        date=session[0],
+        animal=session[1],
         neo_io=rec_dci.neo_io,
     )
-    logger.info("ADDING POSITION")
-    ### add position ###
-    ptp_enabled = detect_ptp_from_header(rec_header)
-    if ptp_enabled:
-        add_position(
-            nwb_file,
-            metadata,
-            session_df,
-        )
-    else:
-        add_position(
-            nwb_file,
-            metadata,
-            session_df,
-            ptp_enabled=ptp_enabled,
-            rec_dci_timestamps=rec_dci_timestamps,
-            sample_count=nwb_file.processing["sample_count"]
-            .data_interfaces["sample_count"]
-            .data,
-        )
 
     # write file
     logger.info(f"WRITING: {output_dir}/{session[1]}{session[0]}.nwb")
diff --git a/src/spikegadgets_to_nwb/convert_analog.py b/src/spikegadgets_to_nwb/convert_analog.py
index f0c2ad1..0bdfb3e 100644
--- a/src/spikegadgets_to_nwb/convert_analog.py
+++ b/src/spikegadgets_to_nwb/convert_analog.py
@@ -1,3 +1,4 @@
+from warnings import warn
 from xml.etree import ElementTree
 
 import numpy as np
diff --git a/src/spikegadgets_to_nwb/convert_dios.py b/src/spikegadgets_to_nwb/convert_dios.py
index b28341e..8161c53 100644
--- a/src/spikegadgets_to_nwb/convert_dios.py
+++ b/src/spikegadgets_to_nwb/convert_dios.py
@@ -70,24 +70,26 @@ def add_dios(nwbfile: NWBFile, recfile: list[str], metadata: dict) -> None:
             prefix = "ECU_"
             break
 
-    # compile data for all dio channels in all files
-    all_timestamps = [np.array([], dtype=np.float64) for i in channel_name_map]
-    all_state_changes = [np.array([], dtype=np.float64) for i in channel_name_map]
-    for io in neo_io:
-        for i, channel_name in enumerate(channel_name_map):
+    for channel_name in channel_name_map:
+        # merge streams from multiple files
+        all_timestamps = []
+        all_state_changes = []
+        for io in neo_io:
             timestamps, state_changes = io.get_digitalsignal(
                 stream_name, prefix + channel_name
             )
-            all_timestamps[i] = np.concatenate((all_timestamps[i], timestamps))
-            all_state_changes[i] = np.concatenate((all_state_changes[i], state_changes))
-    # Add each channel as a behavioral event time series
-    for i, channel_name in enumerate(channel_name_map):
+            all_timestamps.append(timestamps)
+            all_state_changes.append(state_changes)
+        all_timestamps = np.concatenate(all_timestamps)
+        all_state_changes = np.concatenate(all_state_changes)
+        assert isinstance(all_timestamps[0], np.float64)
+        assert isinstance(all_timestamps, np.ndarray)
         ts = TimeSeries(
             name=channel_name_map[channel_name],
             description=channel_name,
-            data=all_state_changes[i],
+            data=all_state_changes,
             unit="-1",  # TODO change to "N/A",
-            timestamps=all_timestamps[i],  # TODO adjust timestamps
+            timestamps=all_timestamps,  # TODO adjust timestamps
         )
         beh_events.add_timeseries(ts)
 
diff --git a/src/spikegadgets_to_nwb/convert_intervals.py b/src/spikegadgets_to_nwb/convert_intervals.py
index e76843a..709d76b 100644
--- a/src/spikegadgets_to_nwb/convert_intervals.py
+++ b/src/spikegadgets_to_nwb/convert_intervals.py
@@ -14,7 +14,9 @@
 
 def add_epochs(
     nwbfile: NWBFile,
-    session_df: pd.DataFrame,
+    file_info: pd.DataFrame,
+    date: int,
+    animal: str,
     neo_io: List[SpikeGadgetsRawIO],
 ):
     """add epochs to nwbfile
@@ -33,13 +35,11 @@ def add_epochs(
         neo_io iterators for each rec file. Contains time information
     """
     logger = logging.getLogger("convert")
-    for epoch in set(session_df.epoch):
-        rec_file_list = session_df[
-            (session_df.epoch == epoch) & (session_df.file_extension == ".rec")
+    session_info = file_info[(file_info.date == date) & (file_info.animal == animal)]
+    for epoch in set(session_info.epoch):
+        rec_file_list = session_info[
+            (session_info.epoch == epoch) & (session_info.file_extension == ".rec")
         ]
-        if len(rec_file_list) == 0:
-            logger.info(f"no rec files for epoch {epoch}, No epoch interval created")
-            continue
         start_time = None
         end_time = None
         logger.info(list(rec_file_list.full_path))
@@ -58,7 +58,7 @@ def add_epochs(
                     )
                 else:
                     file_end_time = np.max(
-                        io.get_systime_from_trodes_timestamps(n_time - 1, n_time)
+                        io._get_systime_from_trodes_timestamps(n_time - 1, n_time)
                     )
                 if end_time is None or file_end_time > end_time:
                     end_time = float(file_end_time)
diff --git a/src/spikegadgets_to_nwb/convert_position.py b/src/spikegadgets_to_nwb/convert_position.py
index eedbc58..a2ae0d8 100644
--- a/src/spikegadgets_to_nwb/convert_position.py
+++ b/src/spikegadgets_to_nwb/convert_position.py
@@ -3,6 +3,7 @@
 import re
 import subprocess
 from pathlib import Path
+from xml.etree import ElementTree
 
 import numpy as np
 import pandas as pd
@@ -12,6 +13,8 @@
 from scipy.ndimage import label
 from scipy.stats import linregress
 
+from spikegadgets_to_nwb.convert_rec_header import detect_ptp_from_header
+
 NANOSECONDS_PER_SECOND = 1e9
 
 
@@ -124,7 +127,7 @@ def get_framerate(timestamps: np.ndarray) -> float:
     Parameters
     ----------
     timestamps : np.ndarray
-        An array of timestamps for each frame in the video, units = nanoseconds.
+        An array of timestamps for each frame in the video.
 
     Returns
     -------
@@ -147,7 +150,7 @@ def find_acquisition_timing_pause(
     Parameters
     ----------
     timestamps : np.ndarray
-        An array of timestamps for each frame in the video. Expects units=nanoseconds.
+        An array of timestamps for each frame in the video.
     min_duration : float, optional
         The minimum duration of the pause in seconds, by default 0.4.
     max_duration : float, optional
@@ -158,7 +161,7 @@ def find_acquisition_timing_pause(
     Returns
     -------
     pause_mid_time : float
-        The midpoint time of the timing pause in nanoseconds.
+        The midpoint time of the timing pause.
 
     """
     timestamps = np.asarray(timestamps)
@@ -371,69 +374,20 @@ def correct_timestamps_for_camera_to_mcu_lag(
     corrected_camera_systime = (
         regression_result.intercept + frame_count * regression_result.slope
     )
-    # corrected_camera_systime /= NANOSECONDS_PER_SECOND
+    corrected_camera_systime /= NANOSECONDS_PER_SECOND
 
     return corrected_camera_systime
 
 
-def find_camera_dio_channel(nwb_file):
-    dio_camera_name = [
-        key
-        for key in nwb_file.processing["behavior"]
-        .data_interfaces["behavioral_events"]
-        .time_series
-        if "camera ticks" in key
-    ]
-    if len(dio_camera_name) > 1:
-        raise ValueError(
-            "Multiple camera dio channels found by name. Not implemented for multiple cameras without PTP yet."
-        )
-
-    if len(dio_camera_name) == 0:
-        raise ValueError(
-            "No camera dio channel found by name. Check metadata YAML. Name must contain 'camera ticks'"
-        )
-
-    return (
-        nwb_file.processing["behavior"]
-        .data_interfaces["behavioral_events"]
-        .time_series[dio_camera_name[0]]
-        .timestamps
-    )
-
-
-def get_video_timestamps(video_timestamps_filepath: Path) -> np.ndarray:
-    """
-    Get video timestamps.
-
-    Parameters
-    ----------
-    video_timestamps_filepath : Path
-        Path to the video timestamps file.
-
-    Returns
-    -------
-    np.ndarray
-        An array of video timestamps.
-    """
-    # Get video timestamps
-    video_timestamps = (
-        pd.DataFrame(read_trodes_datafile(video_timestamps_filepath)["data"])
-        .set_index("PosTimestamp")
-        .rename(columns={"frameCount": "HWframeCount"})
-    )
-    return (
-        np.asarray(video_timestamps.HWTimestamp, dtype=np.float64)
-        / NANOSECONDS_PER_SECOND
-    )
+def find_camera_dio_channel(dios):
+    raise NotImplementedError
 
 
 def get_position_timestamps(
     position_timestamps_filepath: Path,
     position_tracking_filepath=None | Path,
-    rec_dci_timestamps=None | np.ndarray,
-    dio_camera_timestamps=None | np.ndarray,
-    sample_count=None | np.ndarray,
+    mcu_neural_timestamps=None | np.ndarray,
+    dios=None,
     ptp_enabled: bool = True,
 ):
     logger = logging.getLogger("convert")
@@ -507,57 +461,57 @@ def get_position_timestamps(
             )[0][0]
             + 1
         )
+        original_video_timestamps = video_timestamps.copy()
         video_timestamps = video_timestamps.iloc[pause_mid_ind:]
         logger.info(
             "Camera frame rate estimated from MCU timestamps:"
             f" {1 / np.median(np.diff(video_timestamps.index)):0.1f} frames/s"
         )
-        return video_timestamps
+        return video_timestamps, original_video_timestamps
     else:
-        try:
-            pause_mid_time = (
-                find_acquisition_timing_pause(
-                    dio_camera_timestamps * NANOSECONDS_PER_SECOND
-                )
-                / NANOSECONDS_PER_SECOND
-            )
-            frame_rate_from_dio = get_framerate(
-                dio_camera_timestamps[dio_camera_timestamps > pause_mid_time]
-            )
-            logger.info(
-                "Camera frame rate estimated from DIO camera ticks:"
-                f" {frame_rate_from_dio:0.1f} frames/s"
-            )
-        except IndexError:
-            pause_mid_time = -1
+        dio_camera_ticks = find_camera_dio_channel(dios)
+        is_valid_tick = np.isin(dio_camera_ticks, mcu_neural_timestamps.index)
+        dio_systime = np.asarray(
+            mcu_neural_timestamps.loc[dio_camera_ticks[is_valid_tick]]
+        )
+        # The DIOs and camera frames are initially unaligned. There is a
+        # half second pause at the start to allow for alignment.
+        pause_mid_time = find_acquisition_timing_pause(dio_systime)
 
+        # Estimate the frame rate from the DIO camera ticks as a sanity check.
+        frame_rate_from_dio = get_framerate(dio_systime[dio_systime > pause_mid_time])
+        logger.info(
+            "Camera frame rate estimated from DIO camera ticks:"
+            f" {frame_rate_from_dio:0.1f} frames/s"
+        )
         frame_count = np.asarray(video_timestamps.HWframeCount)
 
-        is_valid_camera_time = np.isin(video_timestamps.index, sample_count)
-
-        camera_systime = rec_dci_timestamps[
-            np.digitize(video_timestamps.index[is_valid_camera_time], sample_count)
-        ]
+        camera_systime, is_valid_camera_time = estimate_camera_time_from_mcu_time(
+            video_timestamps, mcu_neural_timestamps
+        )
         (
-            dio_camera_timestamps,
+            dio_systime,
             frame_count,
             is_valid_camera_time,
             camera_systime,
         ) = remove_acquisition_timing_pause_non_ptp(
-            dio_camera_timestamps,
+            dio_systime,
             frame_count,
             camera_systime,
             is_valid_camera_time,
             pause_mid_time,
         )
+        original_video_timestamps = video_timestamps.copy()
         video_timestamps = video_timestamps.iloc[is_valid_camera_time]
+
         frame_rate_from_camera_systime = get_framerate(camera_systime)
         logger.info(
-            "Camera frame rate estimated from camera sys time:"
+            "Camera frame rate estimated from MCU timestamps:"
             f" {frame_rate_from_camera_systime:0.1f} frames/s"
         )
+
         camera_to_mcu_lag = estimate_camera_to_mcu_lag(
-            camera_systime, dio_camera_timestamps, len(non_repeat_timestamp_labels_id)
+            camera_systime, dio_systime, len(non_repeat_timestamp_labels_id)
         )
         corrected_camera_systime = []
         for id in non_repeat_timestamp_labels_id:
@@ -570,73 +524,22 @@ def get_position_timestamps(
                 )
             )
         corrected_camera_systime = np.concatenate(corrected_camera_systime)
-
-        video_timestamps = video_timestamps.set_index(
-            pd.Index(corrected_camera_systime, name="time")
-        )
-        return video_timestamps.groupby(
-            video_timestamps.index
-        ).first()  # TODO: Figure out why duplicate timesteps make it to this point and why this line is necessary
-
-
-def find_camera_dio_channel_per_epoch(
-    nwb_file: NWBFile, epoch_start: float, epoch_end: float
-):
-    """Find the camera dio channel for a given epoch.
-    Searches through dio channels with "camera ticks" in the name.
-    Selects first one with at least 100 ticks in the epoch.
-
-    Parameters
-    ----------
-    nwb_file : NWBFile
-        The NWBFile to find the dio channel in.
-    epoch_start : float
-        timestamp of the start of the epoch
-    epoch_end : float
-        timestamp of the end of the epoch
-
-    Returns
-    -------
-    dio_camera_timestamps : np.ndarray
-        The dio timestamps for the camera restricted to the epoch of interest
-
-    Raises
-    ------
-    ValueError
-        Error if dio's  are not added to the nwbfile
-    ValueError
-        Error if no camera dio channel is found
-    """
-    dio_camera_list = [
-        key
-        for key in nwb_file.processing["behavior"]["behavioral_events"].time_series
-        if "camera ticks" in key
-    ]
-    if not dio_camera_list:
-        raise ValueError(
-            "No camera dio channel found by name. Check metadata YAML. Name must contain 'camera ticks'"
+        video_timestamps.iloc[
+            is_valid_camera_time
+        ].index = corrected_camera_systime.index
+        return (
+            video_timestamps.set_index(pd.Index(corrected_camera_systime, name="time")),
+            original_video_timestamps,
         )
-    for camera in dio_camera_list:
-        dio_camera_timestamps = (
-            nwb_file.processing["behavior"]["behavioral_events"]
-            .time_series[camera]
-            .timestamps
-        )
-        epoch_ind = np.logical_and(
-            dio_camera_timestamps >= epoch_start, dio_camera_timestamps <= epoch_end
-        )
-        if np.sum(epoch_ind) > 100:
-            return dio_camera_timestamps[epoch_ind]
-    raise ValueError("No camera dio has sufficient ticks for this epoch")
 
 
 def add_position(
     nwb_file: NWBFile,
     metadata: dict,
     session_df: pd.DataFrame,
-    ptp_enabled: bool = True,
-    rec_dci_timestamps: np.ndarray | None = None,
-    sample_count: np.ndarray | None = None,
+    rec_header: ElementTree.ElementTree,
+    video_directory: str,
+    convert_video: bool = False,
 ):
     """
     Add position data to an NWBFile.
@@ -649,12 +552,12 @@ def add_position(
         Metadata about the experiment.
     session_df : pd.DataFrame
         A DataFrame containing information about the session.
-    ptp_enabled : bool, optional
-        Whether PTP was enabled, by default True.
-    rec_dci_timestamps : np.ndarray, optional
-        The recording timestamps, by default None. Only used if ptp not enabled.
-    sample_count : np.ndarray, optional
-        The trodes sample count, by default None. Only used if ptp not enabled.
+    rec_header : ElementTree.ElementTree
+        The recording header.
+    video_directory : str
+        The directory containing the video files.
+    convert_video : bool, optional
+        Whether to convert the video files to NWB format, by default False.
     """
     logger = logging.getLogger("convert")
 
@@ -685,21 +588,29 @@ def add_position(
     epoch_to_camera_ids = pd.concat(df).set_index("epoch").sort_index()
 
     position = Position(name="position")
+    ptp_enabled = detect_ptp_from_header(rec_header)
 
     # Make a processing module for behavior and add to the nwbfile
     if not "behavior" in nwb_file.processing:
         nwb_file.create_processing_module(
             name="behavior", description="Contains all behavior-related data"
         )
-    # get epoch data to seperate dio timestamps into epochs
-    if (not ptp_enabled) and (not len(nwb_file.epochs)):
-        raise ValueError(
-            "add_epochs() must be run before add_position() for non-ptp data"
-        )
-    if not ptp_enabled:
-        epoch_df = nwb_file.epochs.to_dataframe()
+
+    # make processing module for video files
+    nwb_file.create_processing_module(
+        name="video_files", description="Contains all associated video files data"
+    )
+    # make a behavioral Event object to hold videos
+    video = BehavioralEvents(name="video")
 
     for epoch in session_df.epoch.unique():
+        position_timestamps_filepath = session_df.loc[
+            np.logical_and(
+                session_df.epoch == epoch,
+                session_df.file_extension == ".cameraHWSync",
+            )
+        ].full_path.to_list()[0]
+
         try:
             position_tracking_filepath = session_df.loc[
                 np.logical_and(
@@ -707,21 +618,6 @@ def add_position(
                     session_df.file_extension == ".videoPositionTracking",
                 )
             ].full_path.to_list()[0]
-            # find the matching hw timestamps filepath
-            video_index = position_tracking_filepath.split(".")[-2]
-            video_hw_df = session_df.loc[
-                np.logical_and(
-                    session_df.epoch == epoch,
-                    session_df.file_extension == ".cameraHWSync",
-                )
-            ]
-            position_timestamps_filepath = video_hw_df[
-                [
-                    full_path.split(".")[-3] == video_index
-                    for full_path in video_hw_df.full_path
-                ]
-            ].full_path.to_list()[0]
-
         except IndexError:
             position_tracking_filepath = None
 
@@ -729,23 +625,10 @@ def add_position(
         logger.info(f"\tposition_timestamps_filepath: {position_timestamps_filepath}")
         logger.info(f"\tposition_tracking_filepath: {position_tracking_filepath}")
 
-        # restrict dio camera timestamps to the current epoch
-        if not ptp_enabled:
-            epoch_start = epoch_df[epoch_df.index == epoch - 1]["start_time"].iloc[0]
-            epoch_end = epoch_df[epoch_df.index == epoch - 1]["stop_time"].iloc[0]
-            dio_camera_timestamps_epoch = find_camera_dio_channel_per_epoch(
-                nwb_file=nwb_file, epoch_start=epoch_start, epoch_end=epoch_end
-            )
-        else:
-            dio_camera_timestamps_epoch = None
-
-        position_df = get_position_timestamps(
+        position_df, original_video_timestamps = get_position_timestamps(
             position_timestamps_filepath,
             position_tracking_filepath,
             ptp_enabled=ptp_enabled,
-            rec_dci_timestamps=rec_dci_timestamps,
-            dio_camera_timestamps=dio_camera_timestamps_epoch,
-            sample_count=sample_count,
         )
 
         # TODO: Doesn't handle multiple cameras currently
@@ -767,7 +650,14 @@ def add_position(
                         timestamps=np.asarray(position_df.index),
                     )
         else:
-            logging.warning(f"No position tracking data found for epoch {epoch}")
+            position.create_spatial_series(
+                name=f"series_{epoch}",
+                description=", ".join(["xloc", "yloc"]),
+                data=np.asarray([]),
+                conversion=meters_per_pixel,
+                reference_frame="Upper left corner of video frame",
+                timestamps=np.asarray(position_df.index),
+            )
 
         # add the video frame index as a new processing module
         if "position_frame_index" not in nwb_file.processing:
@@ -800,10 +690,41 @@ def add_position(
             )
         )
 
+        # add the video file data
+        # find the video metadata for this epoch
+        video_metadata = None
+        for vid_ in metadata["associated_video_files"]:
+            if vid_["task_epochs"][0] == epoch:
+                video_metadata = vid_
+                break
+        if video_metadata is None:
+            raise KeyError(f"Missing video metadata for epoch {epoch}")
+
+        if convert_video:
+            video_file_name = convert_h264_to_mp4(
+                os.path.join(video_directory, video_metadata["name"])
+            )
+        else:
+            video_file_name = os.path.join(video_directory, video_metadata["name"])
+
+        video.add_timeseries(
+            ImageSeries(
+                device=nwb_file.devices[
+                    "camera_device " + str(video_metadata["camera_id"])
+                ],
+                name=video_metadata["name"],
+                timestamps=np.asarray(position_df.index),
+                external_file=[video_file_name],
+                format="external",
+                starting_frame=[0],
+                description="video of animal behavior from epoch",
+            )
+        )
     nwb_file.processing["behavior"].add(position)
+    nwb_file.processing["video_files"].add(video)
 
 
-def convert_h264_to_mp4(file: str, video_directory: str) -> str:
+def convert_h264_to_mp4(file: str) -> str:
     """
     Converts h264 file to mp4 file using ffmpeg.
 
@@ -811,8 +732,6 @@ def convert_h264_to_mp4(file: str, video_directory: str) -> str:
     ----------
     file : str
         The path to the input h264 file.
-    video_directory : str
-        Where to save the output mp4 file.
 
     Returns
     -------
@@ -826,7 +745,6 @@ def convert_h264_to_mp4(file: str, video_directory: str) -> str:
 
     """
     new_file_name = file.replace(".h264", ".mp4")
-    new_file_name = video_directory + "/" + new_file_name.split("/")[-1]
     logger = logging.getLogger("convert")
     if os.path.exists(new_file_name):
         return new_file_name
@@ -842,95 +760,3 @@ def convert_h264_to_mp4(file: str, video_directory: str) -> str:
             f"Video conversion FAILED. {file} has NOT been converted to {new_file_name}"
         )
         raise e
-
-
-def copy_video_to_directory(file: str, video_directory: str) -> str:
-    """Copies video file to video directory without conversion"""
-    new_file_name = video_directory + "/" + file.split("/")[-1]
-    logger = logging.getLogger("convert")
-    if os.path.exists(new_file_name):
-        return new_file_name
-    try:
-        # Construct the ffmpeg command
-        subprocess.run(f"cp {file} {new_file_name}", shell=True)
-        logger.info(f"Video copy completed. {file} has been copied to {new_file_name}")
-        return new_file_name
-    except subprocess.CalledProcessError as e:
-        logger.error(
-            f"Video copy FAILED. {file} has NOT been copied to {new_file_name}"
-        )
-        raise e
-
-
-def add_associated_video_files(
-    nwb_file: NWBFile,
-    metadata: dict,
-    session_df: pd.DataFrame,
-    video_directory: str,
-    convert_video: bool = False,
-):
-    # make processing module for video files
-    nwb_file.create_processing_module(
-        name="video_files", description="Contains all associated video files data"
-    )
-    # make a behavioral Event object to hold videos
-    video = BehavioralEvents(name="video")
-    # add the video file data
-    for video_metadata in metadata["associated_video_files"]:
-        epoch = video_metadata["task_epochs"][0]
-        # get the video file path
-        video_path = None
-        for file in session_df[session_df.file_extension == ".h264"].full_path:
-            if video_metadata["name"].rsplit(".", 1)[0] in file:
-                video_path = file
-                break
-        if video_path is None:
-            raise FileNotFoundError(
-                f"Could not find video file {video_metadata['name']} in session_df"
-            )
-
-        # get timestamps for this video
-        # find the matching hw timestamps filepath
-        video_index = video_path.split(".")[-2]
-        video_hw_df = session_df.loc[
-            np.logical_and(
-                session_df.epoch == epoch,
-                session_df.file_extension == ".cameraHWSync",
-            )
-        ]
-        if not len(video_hw_df):
-            raise ValueError(
-                f"No cameraHWSync found for epoch {epoch}, video {video_index} in session_df"
-            )
-        video_timestamps_filepath = video_hw_df[
-            [
-                full_path.split(".")[-3] == video_index
-                for full_path in video_hw_df.full_path
-            ]
-        ].full_path.to_list()[0]
-        # get the timestamps
-        video_timestamps = get_video_timestamps(video_timestamps_filepath)
-
-        if convert_video:
-            video_file_name = convert_h264_to_mp4(video_path, video_directory)
-        else:
-            video_file_name = copy_video_to_directory(video_path, video_directory)
-
-        video.add_timeseries(
-            ImageSeries(
-                device=nwb_file.devices[
-                    "camera_device " + str(video_metadata["camera_id"])
-                ],
-                name=video_metadata["name"],
-                timestamps=video_timestamps,
-                external_file=[video_file_name.split("/")[-1]],
-                format="external",
-                starting_frame=[0],
-                description="video of animal behavior from epoch",
-            )
-        )
-    if video_metadata is None:
-        raise KeyError(f"Missing video metadata for epoch {epoch}")
-
-    nwb_file.processing["video_files"].add(video)
-    return
diff --git a/src/spikegadgets_to_nwb/convert_yaml.py b/src/spikegadgets_to_nwb/convert_yaml.py
index 6cd4d1e..c0bd4a0 100644
--- a/src/spikegadgets_to_nwb/convert_yaml.py
+++ b/src/spikegadgets_to_nwb/convert_yaml.py
@@ -20,9 +20,6 @@
 from pynwb.ecephys import ElectrodeGroup
 from pynwb.file import ProcessingModule, Subject
 
-import spikegadgets_to_nwb.metadata_validation
-from spikegadgets_to_nwb import __version__
-
 
 def load_metadata(
     metadata_path: str, probe_metadata_paths: list[str]
@@ -41,16 +38,8 @@ def load_metadata(
     tuple[dict, list[dict]]
         the yaml generator metadata and list of probe metadatas
     """
-    metadata = None
     with open(metadata_path, "r") as stream:
         metadata = yaml.safe_load(stream)
-    (
-        is_metadata_valid,
-        metadata_errors,
-    ) = spikegadgets_to_nwb.metadata_validation.validate(metadata)
-    if not is_metadata_valid:
-        logger = logging.getLogger("convert")
-        logger.exception("".join(metadata_errors))
     probe_metadata = []
     for path in probe_metadata_paths:
         with open(path, "r") as stream:
@@ -93,8 +82,6 @@ def initialize_nwb(metadata: dict, first_epoch_config: ElementTree) -> NWBFile:
         session_id=metadata["session_id"],
         # notes=self.link_to_notes, TODO
         experiment_description=metadata["experiment_description"],
-        source_script="spikegadgets_to_nwb " + __version__,
-        source_script_file_name="convert.py",
     )
     return nwbfile
 
@@ -405,13 +392,15 @@ def add_associated_files(nwbfile: NWBFile, metadata: dict) -> None:
         # read file content
         content = ""
         try:
-            with open(file["path"], "r") as open_file:
+            with open(file["path"] + file["name"], "r") as open_file:
                 content = open_file.read()
         except FileNotFoundError as err:
-            logger.info(f"ERROR: associated file {file['path']} does not exist")
+            logger.info(
+                f"ERROR: associated file {file['path']+file['name']} does not exist"
+            )
             logger.info(str(err))
         except IOError as err:
-            logger.info(f"ERROR: Cannot read file at {file['path']}")
+            logger.info(f"ERROR: Cannot read file at {file['path']+file['name']}")
             logger.info(str(err))
         # convert task epoch values into strings
         task_epochs = "".join([str(element) + ", " for element in file["task_epochs"]])
diff --git a/src/spikegadgets_to_nwb/metadata_validation.py b/src/spikegadgets_to_nwb/metadata_validation.py
deleted file mode 100644
index 8856e8e..0000000
--- a/src/spikegadgets_to_nwb/metadata_validation.py
+++ /dev/null
@@ -1,75 +0,0 @@
-import copy
-import datetime
-import os
-
-import jsonschema
-import yaml
-
-
-def _get_nwb_json_schema_path() -> str:
-    """Get the NWB JSON Schema file path
-
-    Returns
-    -------
-    str
-        NWB Schema file Path
-    """
-    current_path = os.path.dirname(os.path.abspath(__file__))
-    json_schema_file = "/./nwb_schema.json"
-    return f"{current_path}{os.path.normpath(json_schema_file)}"
-
-
-def _get_json_schema() -> str:
-    """Get JSON Schema
-
-    Returns
-    -------
-    str
-        JSON Schema content
-    """
-    json_schema = None
-    json_schema_path = _get_nwb_json_schema_path()
-    with open(json_schema_path, "r") as stream:
-        json_schema = yaml.safe_load(stream)
-    return json_schema
-
-
-def validate(metadata: dict) -> tuple:
-    """Validates metadata
-
-    Parameters
-    ----------
-    metadata : dict
-        metadata documenting the particulars of a session
-
-    Returns
-    -------
-    tuple
-        information of the validity of the metadata data and any errors
-    """
-    assert metadata is not None  # metadata cannot be null
-    assert isinstance(metadata, dict)  # cannot proceed if metadata is not a dictionary
-
-    # date_of_birth is set to a datetime by the YAML-to-dict converter.
-    # This code converts date_of_birth  to string
-    metadata_content = copy.deepcopy(metadata) or {}
-    if (
-        metadata_content["subject"]
-        and metadata_content["subject"]["date_of_birth"]
-        and type(metadata_content["subject"]["date_of_birth"]) is datetime.datetime
-    ):
-        metadata_content["subject"]["date_of_birth"] = (
-            metadata_content["subject"]["date_of_birth"].utcnow().isoformat()
-        )
-
-    schema = _get_json_schema()
-    validator = jsonschema.Draft202012Validator(schema)
-    metadata_validation_errors = validator.iter_errors(metadata_content)
-    errors = []
-
-    for metadata_validation_error in metadata_validation_errors:
-        errors.append(metadata_validation_error.message)
-
-    is_valid = len(errors) == 0
-
-    return is_valid, errors
diff --git a/src/spikegadgets_to_nwb/nwb_schema.json b/src/spikegadgets_to_nwb/nwb_schema.json
deleted file mode 100644
index f7f82f4..0000000
--- a/src/spikegadgets_to_nwb/nwb_schema.json
+++ /dev/null
@@ -1,35971 +0,0 @@
-{
-    "definitions": {},
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "https://lorenfranklab.github.io/rec_to_nwb_yaml_creator/v1.0.0",
-    "title": "Spikegadgets to NWB Validator",
-    "type": "object",
-    "description": "Spikegadgets to NWB Validator YAML schema version",
-    "required": [
-        "experimenter_name",
-        "lab",
-        "institution",
-        "data_acq_device",
-        "times_period_multiplier",
-        "raw_data_to_volts"
-    ],
-    "properties": {
-        "experimenter_name": {
-            "$id": "#root/experimenter_name",
-            "title": "experimenter_name",
-            "type": "array",
-            "default": [],
-            "examples": [
-                "Jennifer Guidera",
-                "Alison Comrie"
-            ],
-            "minItems": 1,
-            "uniqueItems": true,
-            "description": "Name of experimenter performing current session",
-            "items": {
-                "$id": "#root/experimenter_name/items",
-                "title": "items",
-                "type": "string",
-                "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-            }
-        },
-        "lab": {
-            "$id": "#root/lab",
-            "title": "lab",
-            "type": "string",
-            "default": "",
-            "examples": [
-                "Frank"
-            ],
-            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-            "description": "Laboratory where the experiment is conducted"
-        },
-        "institution": {
-            "$id": "#root/institution",
-            "title": "institution",
-            "type": "string",
-            "default": "University of California, San Francisco",
-            "examples": [
-                "Air Force Institute of Technology Graduate School of Engineering & Management",
-                "Albert Einstein College of Medicine",
-                "American University",
-                "Arizona State University Campus Immersion",
-                "Arizona State University Digital Immersion",
-                "Arkansas State University",
-                "Augusta University",
-                "Auburn University",
-                "Azusa Pacific University",
-                "Ball State University",
-                "Baylor College of Medicine",
-                "Baylor University",
-                "Binghamton University",
-                "Boise State University",
-                "Boston College",
-                "Boston University",
-                "Bowling Green State University",
-                "Brandeis University",
-                "Brigham Young University",
-                "Brown University",
-                "California Institute of Technology",
-                "California State University, East Bay",
-                "California State University, Fresno",
-                "California State University, Fullerton",
-                "California State University, Long Beach",
-                "California State University, San Bernardino",
-                "Carnegie Mellon University",
-                "Case Western Reserve University",
-                "Catholic University of America",
-                "Central Michigan University",
-                "Chapman University",
-                "Claremont Graduate University",
-                "Clark Atlanta University",
-                "Clark University",
-                "Clarkson University",
-                "Clemson University",
-                "Cleveland State University",
-                "College of William and Mary",
-                "Colorado School of Mines",
-                "Colorado State University",
-                "Columbia University",
-                "Cornell University",
-                "Creighton University",
-                "CUNY City College",
-                "Dartmouth College",
-                "DePaul University",
-                "Drexel University",
-                "Duke University",
-                "Duquesne University",
-                "East Carolina University",
-                "East Tennessee State University",
-                "Eastern Michigan University",
-                "Eastern Virginia Medical School",
-                "Emory University",
-                "Florida Agricultural and Mechanical University",
-                "Florida Atlantic University",
-                "Florida Institute of Technology",
-                "Florida International University",
-                "Florida State University",
-                "Fordham University",
-                "George Mason University",
-                "George Washington University",
-                "Georgetown University",
-                "Georgia Institute of Technology",
-                "Georgia Southern University",
-                "Georgia State University",
-                "Graduate Center, CUNY",
-                "Harvard University",
-                "Howard University",
-                "Icahn School of Medicine at Mount Sinai",
-                "Idaho State University",
-                "Illinois Institute of Technology",
-                "Illinois State University",
-                "Indiana University – Purdue University Indianapolis",
-                "Indiana University Bloomington",
-                "Indiana University of Pennsylvania",
-                "Iowa State University",
-                "Jackson State University",
-                "James Madison University",
-                "Johns Hopkins University",
-                "Kansas State University",
-                "Kennesaw State University",
-                "Kent State University",
-                "Lehigh University",
-                "Loma Linda University",
-                "Long Island University",
-                "Louisiana State University",
-                "Louisiana Tech University",
-                "Loyola Marymount University",
-                "Loyola University Chicago",
-                "Marquette University",
-                "Marshall University",
-                "Massachusetts Institute of Technology",
-                "Mayo Clinic College of Medicine and Science",
-                "Medical College of Wisconsin",
-                "Medical University of South Carolina",
-                "Mercer University",
-                "Miami University",
-                "Michigan State University",
-                "Michigan Technological University",
-                "Middle Tennessee State University",
-                "Mississippi State University",
-                "Missouri University of Science and Technology",
-                "Montana State University",
-                "Montclair State University",
-                "Morgan State University",
-                "New Jersey Institute of Technology",
-                "New Mexico State University",
-                "New York University",
-                "North Carolina A & T State University",
-                "North Carolina State University",
-                "North Dakota State University",
-                "Northeastern University",
-                "Northern Arizona University",
-                "Northern Illinois University",
-                "Northwestern University",
-                "Nova Southeastern University",
-                "Oakland University",
-                "Ohio State University",
-                "Ohio University",
-                "Oklahoma State University–Stillwater",
-                "Old Dominion University",
-                "Oregon Health & Science University",
-                "Oregon State University",
-                "Pennsylvania State University",
-                "Portland State University",
-                "Prairie View A&M University",
-                "Princeton University",
-                "Purdue University",
-                "Rensselaer Polytechnic Institute",
-                "Rice University",
-                "Rochester Institute of Technology",
-                "Rockefeller University",
-                "Rowan University",
-                "Rutgers University–Camden",
-                "Rutgers University–New Brunswick",
-                "Rutgers University–Newark",
-                "Saint Louis University",
-                "Sam Houston State University",
-                "San Diego State University",
-                "San Francisco State University",
-                "Seton Hall University",
-                "South Dakota State University",
-                "Southern Illinois University Carbondale",
-                "Southern Methodist University",
-                "Southern University",
-                "Stanford University",
-                "Stevens Institute of Technology",
-                "Stony Brook University",
-                "SUNY College of Environmental Science and Forestry",
-                "Syracuse University",
-                "Tarleton State University",
-                "Teachers College at Columbia University",
-                "Temple University",
-                "Tennessee State University",
-                "Tennessee Technological University",
-                "Texas A&M University",
-                "Texas A&M University–Corpus Christi",
-                "Texas A&M University–Kingsville",
-                "Texas Christian University",
-                "Texas Southern University",
-                "Texas State University",
-                "Texas Tech University",
-                "Texas Tech University Health Sciences Center",
-                "The New School",
-                "Thomas Jefferson University",
-                "Tufts University",
-                "Tulane University",
-                "Uniformed Services University of the Health Sciences",
-                "University at Albany, SUNY",
-                "University at Buffalo",
-                "University of Akron Main Campus",
-                "University of Alabama",
-                "University of Alabama at Birmingham",
-                "University of Alabama in Huntsville",
-                "University of Alaska Fairbanks",
-                "University of Arizona",
-                "University of Arkansas",
-                "University of Arkansas at Little Rock",
-                "University of Arkansas for Medical Sciences",
-                "University of California, Berkeley",
-                "University of California, Davis",
-                "University of California, Irvine",
-                "University of California, Los Angeles",
-                "University of California, Merced",
-                "University of California, Riverside",
-                "University of California, San Diego",
-                "University of California, San Francisco",
-                "University of California, Santa Barbara",
-                "University of California, Santa Cruz",
-                "University of Central Florida",
-                "University of Chicago",
-                "University of Cincinnati",
-                "University of Colorado Boulder",
-                "University of Colorado Colorado Springs",
-                "University of Colorado Denver",
-                "University of Connecticut",
-                "University of Dayton",
-                "University of Delaware",
-                "University of Denver",
-                "University of Florida",
-                "University of Georgia",
-                "University of Hawaii at Manoa",
-                "University of Houston",
-                "University of Idaho",
-                "University of Illinois Chicago",
-                "University of Illinois Urbana-Champaign",
-                "University of Iowa",
-                "University of Kansas",
-                "University of Kentucky",
-                "University of Louisiana at Lafayette",
-                "University of Louisville",
-                "University of Maine",
-                "University of Maryland, Baltimore",
-                "University of Maryland, Baltimore County",
-                "University of Maryland, College Park",
-                "University of Maryland, Eastern Shore",
-                "University of Massachusetts Amherst",
-                "University of Massachusetts Boston",
-                "University of Massachusetts Chan Medical School",
-                "University of Massachusetts Dartmouth",
-                "University of Massachusetts Lowell",
-                "University of Memphis",
-                "University of Miami",
-                "University of Michigan",
-                "University of Minnesota",
-                "University of Mississippi",
-                "University of Missouri",
-                "University of Missouri–Kansas City",
-                "University of Missouri–St. Louis",
-                "University of Montana",
-                "University of Nebraska at Omaha",
-                "University of Nebraska Medical Center",
-                "University of Nebraska–Lincoln",
-                "University of Nevada, Las Vegas",
-                "University of Nevada, Reno",
-                "University of New England",
-                "University of New Hampshire",
-                "University of New Mexico",
-                "University of New Orleans",
-                "University of North Carolina at Chapel Hill",
-                "University of North Carolina at Charlotte",
-                "University of North Carolina at Greensboro",
-                "University of North Carolina Wilmington",
-                "University of North Dakota",
-                "University of North Florida",
-                "University of North Texas",
-                "University of Notre Dame",
-                "University of Oklahoma",
-                "University of Oklahoma Health Sciences Center",
-                "University of Oregon",
-                "University of Pennsylvania",
-                "University of Pittsburgh",
-                "University of Puerto Rico at Río Piedras",
-                "University of Rhode Island",
-                "University of Rochester",
-                "University of San Diego",
-                "University of South Alabama",
-                "University of South Carolina",
-                "University of South Dakota",
-                "University of South Florida",
-                "University of Southern California",
-                "University of Southern Mississippi",
-                "University of Tennessee",
-                "University of Tennessee Health Science Center",
-                "University of Texas at Arlington",
-                "University of Texas at Austin",
-                "University of Texas at Dallas",
-                "University of Texas at El Paso",
-                "University of Texas at San Antonio",
-                "University of Texas Health Science Center at Houston",
-                "University of Texas Health Science Center at San Antonio",
-                "University of Texas Medical Branch",
-                "University of Texas Southwestern Medical Center",
-                "University of Toledo",
-                "University of Tulsa",
-                "University of Utah",
-                "University of Vermont",
-                "University of Virginia",
-                "University of Washington",
-                "University of Wisconsin–Madison",
-                "University of Wisconsin–Milwaukee",
-                "University of Wyoming",
-                "Utah State University",
-                "Vanderbilt University",
-                "Villanova University",
-                "Virginia Commonwealth University",
-                "Virginia Tech",
-                "Wake Forest University",
-                "Washington State University",
-                "Washington University in St. Louis",
-                "Wayne State University",
-                "Weill Cornell Medicine",
-                "West Chester University of Pennsylvania",
-                "West Virginia University",
-                "Western Michigan University",
-                "Wichita State University",
-                "Worcester Polytechnic Institute",
-                "Wright State University",
-                "Yale University"
-            ],
-            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-            "description": "Type to search for institution ..."
-        },
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-            "type": "string",
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-            ],
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-            ],
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-            "type": "array",
-            "default": [],
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-            ],
-            "minItems": 1,
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-            "description": "keywords",
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-                "sex",
-                "species",
-                "subject_id",
-                "weight",
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-            "properties": {
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-                    "title": "description",
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-                    "examples": [
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-                    ],
-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
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-                    "default": "",
-                    "examples": [
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-                    ],
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-                        "M",
-                        "F",
-                        "U",
-                        "O"
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-                    "examples": [
-                        "M",
-                        "F",
-                        "U",
-                        "O"
-                    ],
-                    "description": "Gender of animal model/patient"
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-                    "title": "species",
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-                    "default": "",
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-                    ],
-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                    "description": "Category of animal model/patient"
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-                    ],
-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                    "description": "Identification code/number of animal model/patient"
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-                    "title": "weight",
-                    "type": "number",
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-                },
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-                    "type": "string",
-                    "default": "",
-                    "pattern": "(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d\\.\\d+)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d)",
-                    "description": "date of birth of animal model/patient, in ISO 8061 format"
-                }
-            }
-        },
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-            "$id": "#root/data_acq_device",
-            "title": "data_acq_device",
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-                        "title": "name",
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-                        ],
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-                        "examples": [
-                            "MCU"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
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-                        "default": "",
-                        "description": "Amplifier device",
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-                        ],
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-                        "description": "adc circuit",
-                        "examples": [
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-                        ],
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-                    }
-                }
-            }
-        },
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-            "type": "array",
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-                    "path",
-                    "task_epochs"
-                ],
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-                        "title": "name",
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-                        "default": "",
-                        "description": "File name",
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-                        ],
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-                    },
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-                        "default": "",
-                        "description": "Purpose of file",
-                        "examples": [
-                            "stateScriptLog epoch r1"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "path": {
-                        "$id": "#root/associated_files/items/path",
-                        "title": "path",
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-                        "default": "",
-                        "description": "File location",
-                        "examples": [
-                            "/nimbus/jguidera/J16/raw/20210606/20210606_J16_02_r1.stateScriptLog"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "task_epochs": {
-                        "$id": "#root/associated_files/items/task_epochs",
-                        "title": "task_epochs",
-                        "type": "integer",
-                        "default": 0,
-                        "description": "task epoch"
-                    }
-                }
-            }
-        },
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-            "title": "units",
-            "type": "object",
-            "required": [
-                "analog",
-                "behavioral_events"
-            ],
-            "properties": {
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-                    "$id": "#root/units/analog",
-                    "title": "analog",
-                    "type": "string",
-                    "default": "",
-                    "description": "analog",
-                    "examples": [
-                        "unspecified"
-                    ],
-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                },
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-                    "$id": "#root/units/behavioral_events",
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-                    "type": "string",
-                    "default": "",
-                    "description": "behavioral_events",
-                    "examples": [
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-                    ],
-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                }
-            }
-        },
-        "times_period_multiplier": {
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-            "title": "times_period_multiplier",
-            "type": "number",
-            "examples": [
-                1.5
-            ],
-            "default": 0.0
-        },
-        "raw_data_to_volts": {
-            "$id": "#root/raw_data_to_volts",
-            "title": "raw_data_to_volts",
-            "type": "number",
-            "examples": [
-                1.95e-7
-            ],
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-            "title": "default_header_file_path",
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-            "default": "",
-            "examples": [
-                "default_header.xml"
-            ],
-            "pattern": "^(.|\\s)*\\S(.|\\s)*$"
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-            "title": "cameras",
-            "type": "array",
-            "default": [],
-            "items": {
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-                "title": "Items",
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-                    "meters_per_pixel",
-                    "manufacturer",
-                    "model",
-                    "lens",
-                    "camera_name"
-                ],
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-                        "title": "id",
-                        "type": "integer",
-                        "examples": [
-                            0
-                        ],
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-                    "meters_per_pixel": {
-                        "$id": "#root/cameras/items/meters_per_pixel",
-                        "title": "meters_per_pixel",
-                        "type": "number",
-                        "examples": [
-                            0.000842
-                        ],
-                        "default": 0.0,
-                        "description": "meter per pixel"
-                    },
-                    "manufacturer": {
-                        "$id": "#root/cameras/items/manufacturer",
-                        "title": "manufacturer",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "Manta"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Manufacturer"
-                    },
-                    "model": {
-                        "$id": "#root/cameras/items/model",
-                        "title": "model",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "unknown"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Model"
-                    },
-                    "lens": {
-                        "$id": "#root/cameras/items/lens",
-                        "title": "lens",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "unknown"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Len"
-                    },
-                    "camera_name": {
-                        "$id": "#root/cameras/items/camera_name",
-                        "title": "camera_name",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "HomeBox_camera"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Camera Name"
-                    }
-                }
-            }
-        },
-        "tasks": {
-            "$id": "#root/tasks",
-            "title": "tasks",
-            "type": "array",
-            "default": [],
-            "items": {
-                "$id": "#root/tasks/items",
-                "title": "items",
-                "type": "object",
-                "required": [
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-                    "task_environment",
-                    "camera_id",
-                    "task_epochs"
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-                        "title": "task_name",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "home"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Task name"
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-                    "task_description": {
-                        "$id": "#root/tasks/items/task_description",
-                        "title": "task_description",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "The animal rests in a box"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Task description"
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-                    "task_environment": {
-                        "$id": "#root/tasks/items/task_environment",
-                        "title": "task_environment",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "HomeBox"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "description": "Task environment"
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-                        "$id": "#root/tasks/items/camera_id",
-                        "title": "camera_id",
-                        "type": "array",
-                        "description": "Comma separated camera ids, from camera list",
-                        "examples": [],
-                        "default": [],
-                        "items": {
-                            "$id": "#root/tasks/items/camera_id/items",
-                            "title": "Items",
-                            "uniqueItems": true,
-                            "type": "integer",
-                            "examples": [
-                                0
-                            ],
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-                        }
-                    },
-                    "task_epochs": {
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-                        "title": "task_epochs",
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-                        "examples": [],
-                        "default": [],
-                        "items": {
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-                            "title": "Items",
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-                            ],
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-                        }
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-            "type": "array",
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-                "title": "Items",
-                "type": "object",
-                "required": [
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-                    "task_epochs"
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-                        "title": "name",
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-                        "description": "File name",
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-                        "title": "description",
-                        "type": "string",
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-                            "Din",
-                            "Dout",
-                            "Accel",
-                            "Gyro",
-                            "Mag"
-                        ],
-                        "description": "Behavioral Events",
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "name": {
-                        "$id": "#root/behavioral_events/items/name",
-                        "title": "name",
-                        "type": "string",
-                        "default": "Home box camera",
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-                            "Poke",
-                            "Light",
-                            "Pump",
-                            "Run Camera Ticks",
-                            "Sleep"
-                        ],
-                        "description": "Type of behavioral events",
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    }
-                }
-            }
-        },
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-            "title": "device",
-            "type": "object",
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-            "properties": {
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-                    "title": "name",
-                    "type": "array",
-                    "minItems": 1,
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-                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
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-            }
-        },
-        "electrode_groups": {
-            "$id": "#root/electrode_groups",
-            "title": "electrode_groups",
-            "type": "array",
-            "default": [],
-            "items": {
-                "$id": "#root/electrode_groups/items",
-                "title": "Items",
-                "type": "object",
-                "required": [
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-                    "device_type",
-                    "description",
-                    "targeted_location",
-                    "targeted_x",
-                    "targeted_y",
-                    "targeted_z",
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-                "properties": {
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-                        "title": "id",
-                        "type": "integer",
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-                        ],
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-                        "description": "electrode/probe identification code/number"
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-                    "location": {
-                        "$id": "#root/electrode_groups/items/location",
-                        "title": "location",
-                        "type": "string",
-                        "default": "Cornu ammonis 1 (CA1)",
-                        "description": "Exact location of electrode/probe",
-                        "examples": [
-                            "Brain (Brain)",
-                            "White matter (wmt)",
-                            "Olfactory white matter (olf)",
-                            "lateral olfactory tract (lot)",
-                            "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)",
-                            "Anterior commissure (ac)",
-                            "anterior commissure, anterior limb (aca)",
-                            "anterior commissure, posterior limb (acp)",
-                            "anterior commissure, intrabulbar part (aci)",
-                            "Hippocampal white matter (hiw)",
-                            "alveus of the hippocampus (alv)",
-                            "ventral hippocampal commissure (vhc)",
-                            "fornix (f)",
-                            "fimbria of the hippocampus (fi)",
-                            "Corticofugal pathways (cfp)",
-                            "corticofugal tract and corona radiata (ic-cp-lfp-py)",
-                            "pyramidal decussation (pyx)",
-                            "Medial lemniscus (ml)",
-                            "medial lemniscus, unspecified (ml-u)",
-                            "medial lemniscus decussation (mlx)",
-                            "Thalamic tracts (tht)",
-                            "External medullary lamina (eml)",
-                            "external medullary lamina, unspecified (eml-u)",
-                            "external medullary lamina, auditory radiation (eml-ar)",
-                            "internal medullary lamina (iml)",
-                            "intramedullary thalamic area (ima)",
-                            "superior cerebellar peduncle and prerubral field (scp-pr)",
-                            "pretectothalamic lamina (ptl)",
-                            "mammillotegmental tract (mtg)",
-                            "commissural stria terminalis (cst)",
-                            "fasciculus retroflexus (fr)",
-                            "stria medullaris thalami (sm)",
-                            "stria terminalis (st)",
-                            "habenular commissure (hbc)",
-                            "posterior commissure (pc)",
-                            "Facial nerve (7n)",
-                            "facial nerve, unspecified (7n-u)",
-                            "ascending fibers of the facial nerve (asc7)",
-                            "genu of the facial nerve (g7)",
-                            "Optic fiber system and supraoptic decussation (ofs)",
-                            "optic nerve (2n)",
-                            "optic tract and optic chiasm (opt-och)",
-                            "supraoptic decussation (sox)",
-                            "White matter of the tectum (tew)",
-                            "commissure of the superior colliculus (csc)",
-                            "brachium of the superior colliculus (bsc)",
-                            "inferior colliculus, commissure (cic)",
-                            "inferior colliculus, brachium (bic)",
-                            "Cerebellar and precerebellar white matter (cbt)",
-                            "inferior cerebellar peduncle (icp)",
-                            "middle cerebellar peduncle (mcp)",
-                            "transverse fibers of the pons (tfp)",
-                            "White matter of the brainstem (bsw)",
-                            "Lateral lemniscus (ll)",
-                            "lateral lemniscus, commissure (ll-c)",
-                            "lateral lemniscus, unspecified (ll-u)",
-                            "acoustic striae (as)",
-                            "trapezoid body (tz)",
-                            "spinal trigeminal tract (sp5t)",
-                            "Gray matter (GM)",
-                            "Telencephalon (Tel)",
-                            "Laminated pallium (LamP)",
-                            "Olfactory bulb (OB)",
-                            "Glomerular layer of the accessory olfactory bulb (GlA)",
-                            "Glomerular layer of the olfactory bulb (Gl)",
-                            "Olfactory bulb, unspecified (OB-u)",
-                            "Nucleus of the lateral olfactory tract (NLOT)",
-                            "Cerebral cortex (Cx)",
-                            "Hippocampal region (HR)",
-                            "Hippocampal formation (HF)",
-                            "Fasciola cinereum (FC)",
-                            "Subiculum (SUB)",
-                            "Cornu Ammonis (CA)",
-                            "Cornu ammonis 1 (CA1)",
-                            "Cornu ammonis 2 (CA2)",
-                            "Cornu ammonis 3 (CA3)",
-                            "Dentate gyrus (DG)",
-                            "Parahippocampal region (PHR)",
-                            "Postrhinal cortex (POR)",
-                            "Presubiculum (PrS)",
-                            "Parasubiculum (PaS)",
-                            "Perirhinal cortex (PER)",
-                            "Perirhinal area 35 (PER35)",
-                            "Perirhinal area 36 (PER36)",
-                            "Entorhinal cortex (EC)",
-                            "Medial entorhinal cortex (MEC)",
-                            "Lateral entorhinal cortex (LEC)",
-                            "Piriform cortex (PIR)",
-                            "Piriform cortex, layer 1 (PIR1)",
-                            "Piriform cortex, layer 2 (PIR2)",
-                            "Piriform cortex, layer 3 (PIR3)",
-                            "Cingulate region (CgR)",
-                            "Cingulate cortex (Cg)",
-                            "Cingulate area 1 (Cg1)",
-                            "Cingulate area 2 (Cg2)",
-                            "Retrosplenial cortex (RS)",
-                            "Retrosplenial dysgranular area (RSD)",
-                            "Retrosplenial granular area (RSG)",
-                            "Insular region (INS)",
-                            "Agranular insular cortex (AI)",
-                            "Agranular insular cortex, ventral area (AI-v)",
-                            "Agranular insular cortex dorsal area  (AI-d)",
-                            "Agranular insular cortex, posterior area  (AI-p)",
-                            "Dysgranular insular cortex (DI)",
-                            "Granular insular cortex (GI)",
-                            "Frontal region (Front)",
-                            "Frontal association cortex (FrA)",
-                            "Orbitofrontal cortex (Orb)",
-                            "Medial orbital area (MO)",
-                            "Ventral orbital area (VO)",
-                            "Ventrolateral orbital area (VLO)",
-                            "Lateral orbital area (LO)",
-                            "Dorsolateral orbital area (DLO)",
-                            "Mediofrontal cortex (MFC)",
-                            "Prelimbic area (PrL)",
-                            "Infralimbic area (IL)",
-                            "Motor cortex (M)",
-                            "Primary motor area (M1)",
-                            "Secondary motor area (M2)",
-                            "Frontal association area 3 (Fr3)",
-                            "Parietal region (Par)",
-                            "Somatosensory cortex (SS)",
-                            "Primary somatosensory area (S1)",
-                            "Primary somatosensory area, face representation (S1-f)",
-                            "Primary somatosensory area, barrel field (S1-bf)",
-                            "Primary somatosensory area, dysgranular zone (S1-dz)",
-                            "Primary somatosensory area, forelimb representation (S1-fl)",
-                            "Primary somatosensory area, hindlimb representation (S1-hl)",
-                            "Primary somatosensory area, trunk representation (S1-tr)",
-                            "Secondary somatosensory area (S2)",
-                            "Posterior parietal cortex (PPC)",
-                            "Parietal association cortex, medial area (mPPC)",
-                            "Parietal association cortex, lateral area (lPPC)",
-                            "Parietal association cortex, posterior area  (PtP)",
-                            "Occipital region (Oc)",
-                            "Visual cortex (Vis)",
-                            "Primary visual area (V1)",
-                            "Secondary visual area (V2)",
-                            "Secondary visual area, medial part (V2M)",
-                            "Secondary visual area, lateral part (V2L)",
-                            "Temporal region (Te)",
-                            "Temporal association cortex (TeA)",
-                            "Auditory cortex (Au)",
-                            "Primary auditory area (Au1)",
-                            "Secondary auditory area (Au2)",
-                            "Secondary auditory area, dorsal part (Au2-d)",
-                            "Secondary auditory area, ventral part (Au2-v)",
-                            "Non-laminated pallium (N-LamP)",
-                            "Claustrum (CLA)",
-                            "Endopiriform nucleus (Endo)",
-                            "Amygdaloid area, unspecified (Am-u)",
-                            " Subpallium (SubPAL)",
-                            "Striatum (Str)",
-                            "Caudate putamen (CPu)",
-                            "Nucleus accumbens (NAc)",
-                            "Nucleus accumbens, core (NAc-c)",
-                            "Nucleus accumbens, shell (NAc-sh)",
-                            "Ventral striatal region, unspecified (VSR-u)",
-                            "Pallidum (PAL)",
-                            "Globus pallidus external (GPe)",
-                            "Globus pallidus external, medial part (GPe-m)",
-                            "Globus pallidus external, lateral part (GPe-l)",
-                            "Entopeduncular nucleus (EP)",
-                            "Ventral pallidum (VP)",
-                            "Basal forebrain region  (BRF)",
-                            "Basal forebrain region, unspecified (BFR-u)",
-                            "Bed nucleus of the stria terminalis (BNST)",
-                            "Septal region (Sep)",
-                            "Subthalamic nucleus (STh)",
-                            "Diencephalon (Dien)",
-                            "Prethalamus (Thal-Pre)",
-                            "Reticular (pre)thalamic nucleus (RT)",
-                            "Reticular (pre)thalamic nucleus, unspecified (RT-u)",
-                            "Reticular (pre)thalamic nucleus, auditory segment (RT-a)",
-                            "Zona incerta (ZI)",
-                            "Zona incerta, dorsal part (ZI-d)",
-                            "Zona incerta, ventral part (ZI-v)",
-                            "Zona incerta, rostral part (ZI-r)",
-                            "Zona incerta, caudal part (ZI-c)",
-                            "Zona incerta, A13 dopamine cells (ZI-A13)",
-                            "Zona incerta, A11 dopamine cells (ZI-A11)",
-                            "Fields of Forel (FoF)",
-                            "Pregeniculate nucleus (PrG)",
-                            "Subgeniculate nucleus (SubG)",
-                            "Intergeniculate leaflet (IGL)",
-                            "Epithalamus (Thal-EPI)",
-                            "Lateral habenular nucleus (LHb)",
-                            "Medial habenular nucleus (MHb)",
-                            "Nucleus of the stria medullaris (SMn)",
-                            "Pineal gland (PG)",
-                            "Dorsal thalamus (Thal-D)",
-                            "Anterior nuclei of the dorsal thalamus (ANT)",
-                            "Anterodorsal thalamic nucleus (AD)",
-                            "Anteroventral thalamic nucleus (AV)",
-                            "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)",
-                            "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)",
-                            "Anteromedial thalamic nucleus (AM)",
-                            "Interanteromedial thalamic nucleus (IAM)",
-                            "Paraventricular thalamic nuclei (anterior and posterior) (PV)",
-                            "Intermediodorsal thalamic nucleus (IMD)",
-                            "Parataenial thalamic nucleus (PT)",
-                            "Subparafascicular nucleus (SPF)",
-                            "Posterior intralaminar nucleus (PIL)",
-                            "Ventral midline group of the dorsal thalamus (V-MID)",
-                            "Rhomboid thalamic nucleus (Rh)",
-                            "Reuniens thalamic nucleus (Re)",
-                            "Retroreuniens thalamic nucleus (RRe)",
-                            "Xiphoid thalamic nucleus (Xi)",
-                            "Mediodorsal nucleus of the dorsal thalamus (MD)",
-                            "Mediodorsal thalamic nucleus, lateral part (MD-l)",
-                            "Mediodorsal thalamic nucleus, central part (MD-c)",
-                            "Mediodorsal thalamic nucleus, medial part (MD-m)",
-                            "Ventral nuclei of the dorsal thalamus (VENT)",
-                            "Ventral anterior thalamic nucleus (VA)",
-                            "Ventromedial thalamic nucleus (VM)",
-                            "Ventrolateral thalamic nucleus (VL)",
-                            "Angular thalamic nucleus (Ang)",
-                            "Ventral posterior thalamic nucleus (VPN)",
-                            "Ventral posteromedial thalamic nucleus (VPM)",
-                            "Ventral posterolateral thalamic nucleus (VPL)",
-                            "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)",
-                            "Submedius thalamic nucleus (SMT)",
-                            "Intralaminar nuclei of the dorsal thalamus (ILM)",
-                            "Paracentral thalamic nucleus (PCN)",
-                            "Central medial thalamic nucleus (CM)",
-                            "Central lateral thalamic nucleus (CL)",
-                            "Parafascicular thalamic nucleus (PF)",
-                            "Ethmoid-Limitans nucleus (Eth)",
-                            "Posterior complex of the dorsal thalamus (PoC)",
-                            "Posterior thalamic nucleus (Po)",
-                            "Posterior thalamic nuclear group, triangular part (Po-t)",
-                            "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)",
-                            "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)",
-                            "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)",
-                            "Lateral posterior thalamic nucleus, lateral part (LP-l)",
-                            "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)",
-                            "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)",
-                            "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)",
-                            "Dorsal lateral geniculate nucleus (DLG)",
-                            "Medial geniculate complex of the dorsal thalamus (MG)",
-                            "Medial geniculate body, ventral division (MG-v)",
-                            "Medial geniculate body, dorsal division (MG-d)",
-                            "Medial geniculate body, marginal zone (MG-mz)",
-                            "Medial geniculate body, medial division (MG-m)",
-                            "Medial geniculate body, suprageniculate nucleus (MG-sg)",
-                            "Hypothalamus (HY)",
-                            "Hypothalamic region, unspecified (HTh-u)",
-                            "Pretectum (PreT)",
-                            "Pretectal region (PRT)",
-                            "Nucleus sagulum (Sag)",
-                            "Mesencephalon (Mes)",
-                            "Midbrain (MB)",
-                            "Tectum (Tc)",
-                            "Inferior colliculus (IC)",
-                            "Inferior colliculus, dorsal cortex (DCIC)",
-                            "Inferior colliculus, central nucleus (CNIC)",
-                            "Inferior colliculus, external cortex (ECIC)",
-                            "Superior colliculus (Su)",
-                            "Superficial gray layer of the superior colliculus (SuG)",
-                            "Deeper layers of the superior colliculus (SuD)",
-                            "Tegmentum (Tg)",
-                            "Substantia nigra (SN)",
-                            "Substantia nigra, reticular part (SN-r)",
-                            "Substantia nigra, compact part (SN-c)",
-                            "Substantia nigra, lateral part (SN-l)",
-                            "Ventral tegmental area (VTA)",
-                            "Peripeduncular nucleus (PP)",
-                            "Interpeduncular nucleus (IP)",
-                            "Periaqueductal gray (PAG)",
-                            "Brainstem, unspecified (BS-u)",
-                            "Rhombencephalon (Rho)",
-                            "Metencephalon (Met)",
-                            "Pontine nuclei (Pn)",
-                            "Cerebellum (Cb)",
-                            "Molecular cell layer of the cerebellum (Cb-m)",
-                            "Cerebellum, unspecified (Cb-u)",
-                            "Myelencephalon (Myel)",
-                            "Cochlear nucleus, ventral part (VCN)",
-                            "Ventral cochlear nucleus, anterior part (AVCN)",
-                            "Ventral cochlear nucleus, posterior part (PVCN)",
-                            "Ventral cochlear nucleus, cap area (Cap)",
-                            "Ventral cochlear nucleus, granule cell layer (GCL)",
-                            "Cochlear nucleus, dorsal part (DCN)",
-                            "Dorsal cochlear nucleus, molecular layer (DCNM)",
-                            "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)",
-                            "Dorsal cochlear nucleus, deep core (DCND)",
-                            "Spinal trigeminal nucleus (Sp5n)",
-                            "Periventricular gray (PVG)",
-                            "Superior olivary complex (SO)",
-                            "Nucleus of the trapezoid body (NTB)",
-                            "Superior paraolivary nucleus (SPN)",
-                            "Medial superior olive (MSO)",
-                            "Lateral superior olive (LSO)",
-                            "Superior periolivary region (SPR)",
-                            "Ventral periolivary nuclei (VPO)",
-                            "Nuclei of the lateral lemniscus (NLL)",
-                            "Lateral lemniscus, ventral nucleus (VLL)",
-                            "Lateral lemniscus, intermediate nucleus (ILL)",
-                            "Lateral lemniscus, dorsal nucleus (DLL)",
-                            "Inferior olive (IO)",
-                            "Ventricular system (V)",
-                            "ventricular system, unspecified (V-u)",
-                            "4th ventricle (4V)",
-                            "central canal (CC)",
-                            "spinal cord (SpC)",
-                            "Inner ear (IE)",
-                            "vestibular apparatus (VeA)",
-                            "cochlea (Co)",
-                            "cochlear nerve (8cn)",
-                            "vestibular nerve (8vn)",
-                            "spiral ganglion (SpG)"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "device_type": {
-                        "$id": "#root/electrode_groups/items/device_type",
-                        "title": "device_type",
-                        "type": "string",
-                        "default": "",
-                        "examples": [
-                            "",
-                            "tetrode_12.5",
-                            "A1x32-6mm-50-177-H32_21mm",
-                            "128c-4s8mm6cm-20um-40um-sl",
-                            "128c-4s6mm6cm-15um-26um-sl",
-                            "32c-2s8mm6cm-20um-40um-dl",
-                            "64c-4s6mm6cm-20um-40um-dl",
-                            "64c-3s6mm6cm-20um-40um-sl"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
-                        "enum": [
-                            "tetrode_12.5",
-                            "A1x32-6mm-50-177-H32_21mm",
-                            "128c-4s8mm6cm-20um-40um-sl",
-                            "128c-4s6mm6cm-15um-26um-sl",
-                            "32c-2s8mm6cm-20um-40um-dl",
-                            "64c-4s6mm6cm-20um-40um-dl",
-                            "64c-3s6mm6cm-20um-40um-sl"
-                        ]
-                    },
-                    "description": {
-                        "$id": "#root/electrode_groups/items/description",
-                        "title": "description",
-                        "type": "string",
-                        "default": "",
-                        "description": "electrode groups description",
-                        "examples": [
-                            "tetrode"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "targeted_location": {
-                        "$id": "#root/electrode_groups/items/targeted_location",
-                        "title": "targeted_location",
-                        "type": "string",
-                        "default": "Cornu ammonis 1 (CA1)",
-                        "description": "Planned location of electrode/probe",
-                        "examples": [
-                            "Brain (Brain)",
-                            "White matter (wmt)",
-                            "Olfactory white matter (olf)",
-                            "lateral olfactory tract (lot)",
-                            "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)",
-                            "Anterior commissure (ac)",
-                            "anterior commissure, anterior limb (aca)",
-                            "anterior commissure, posterior limb (acp)",
-                            "anterior commissure, intrabulbar part (aci)",
-                            "Hippocampal white matter (hiw)",
-                            "alveus of the hippocampus (alv)",
-                            "ventral hippocampal commissure (vhc)",
-                            "fornix (f)",
-                            "fimbria of the hippocampus (fi)",
-                            "Corticofugal pathways (cfp)",
-                            "corticofugal tract and corona radiata (ic-cp-lfp-py)",
-                            "pyramidal decussation (pyx)",
-                            "Medial lemniscus (ml)",
-                            "medial lemniscus, unspecified (ml-u)",
-                            "medial lemniscus decussation (mlx)",
-                            "Thalamic tracts (tht)",
-                            "External medullary lamina (eml)",
-                            "external medullary lamina, unspecified (eml-u)",
-                            "external medullary lamina, auditory radiation (eml-ar)",
-                            "internal medullary lamina (iml)",
-                            "intramedullary thalamic area (ima)",
-                            "superior cerebellar peduncle and prerubral field (scp-pr)",
-                            "pretectothalamic lamina (ptl)",
-                            "mammillotegmental tract (mtg)",
-                            "commissural stria terminalis (cst)",
-                            "fasciculus retroflexus (fr)",
-                            "stria medullaris thalami (sm)",
-                            "stria terminalis (st)",
-                            "habenular commissure (hbc)",
-                            "posterior commissure (pc)",
-                            "Facial nerve (7n)",
-                            "facial nerve, unspecified (7n-u)",
-                            "ascending fibers of the facial nerve (asc7)",
-                            "genu of the facial nerve (g7)",
-                            "Optic fiber system and supraoptic decussation (ofs)",
-                            "optic nerve (2n)",
-                            "optic tract and optic chiasm (opt-och)",
-                            "supraoptic decussation (sox)",
-                            "White matter of the tectum (tew)",
-                            "commissure of the superior colliculus (csc)",
-                            "brachium of the superior colliculus (bsc)",
-                            "inferior colliculus, commissure (cic)",
-                            "inferior colliculus, brachium (bic)",
-                            "Cerebellar and precerebellar white matter (cbt)",
-                            "inferior cerebellar peduncle (icp)",
-                            "middle cerebellar peduncle (mcp)",
-                            "transverse fibers of the pons (tfp)",
-                            "White matter of the brainstem (bsw)",
-                            "Lateral lemniscus (ll)",
-                            "lateral lemniscus, commissure (ll-c)",
-                            "lateral lemniscus, unspecified (ll-u)",
-                            "acoustic striae (as)",
-                            "trapezoid body (tz)",
-                            "spinal trigeminal tract (sp5t)",
-                            "Gray matter (GM)",
-                            "Telencephalon (Tel)",
-                            "Laminated pallium (LamP)",
-                            "Olfactory bulb (OB)",
-                            "Glomerular layer of the accessory olfactory bulb (GlA)",
-                            "Glomerular layer of the olfactory bulb (Gl)",
-                            "Olfactory bulb, unspecified (OB-u)",
-                            "Nucleus of the lateral olfactory tract (NLOT)",
-                            "Cerebral cortex (Cx)",
-                            "Hippocampal region (HR)",
-                            "Hippocampal formation (HF)",
-                            "Fasciola cinereum (FC)",
-                            "Subiculum (SUB)",
-                            "Cornu Ammonis (CA)",
-                            "Cornu ammonis 1 (CA1)",
-                            "Cornu ammonis 2 (CA2)",
-                            "Cornu ammonis 3 (CA3)",
-                            "Dentate gyrus (DG)",
-                            "Parahippocampal region (PHR)",
-                            "Postrhinal cortex (POR)",
-                            "Presubiculum (PrS)",
-                            "Parasubiculum (PaS)",
-                            "Perirhinal cortex (PER)",
-                            "Perirhinal area 35 (PER35)",
-                            "Perirhinal area 36 (PER36)",
-                            "Entorhinal cortex (EC)",
-                            "Medial entorhinal cortex (MEC)",
-                            "Lateral entorhinal cortex (LEC)",
-                            "Piriform cortex (PIR)",
-                            "Piriform cortex, layer 1 (PIR1)",
-                            "Piriform cortex, layer 2 (PIR2)",
-                            "Piriform cortex, layer 3 (PIR3)",
-                            "Cingulate region (CgR)",
-                            "Cingulate cortex (Cg)",
-                            "Cingulate area 1 (Cg1)",
-                            "Cingulate area 2 (Cg2)",
-                            "Retrosplenial cortex (RS)",
-                            "Retrosplenial dysgranular area (RSD)",
-                            "Retrosplenial granular area (RSG)",
-                            "Insular region (INS)",
-                            "Agranular insular cortex (AI)",
-                            "Agranular insular cortex, ventral area (AI-v)",
-                            "Agranular insular cortex dorsal area  (AI-d)",
-                            "Agranular insular cortex, posterior area  (AI-p)",
-                            "Dysgranular insular cortex (DI)",
-                            "Granular insular cortex (GI)",
-                            "Frontal region (Front)",
-                            "Frontal association cortex (FrA)",
-                            "Orbitofrontal cortex (Orb)",
-                            "Medial orbital area (MO)",
-                            "Ventral orbital area (VO)",
-                            "Ventrolateral orbital area (VLO)",
-                            "Lateral orbital area (LO)",
-                            "Dorsolateral orbital area (DLO)",
-                            "Mediofrontal cortex (MFC)",
-                            "Prelimbic area (PrL)",
-                            "Infralimbic area (IL)",
-                            "Motor cortex (M)",
-                            "Primary motor area (M1)",
-                            "Secondary motor area (M2)",
-                            "Frontal association area 3 (Fr3)",
-                            "Parietal region (Par)",
-                            "Somatosensory cortex (SS)",
-                            "Primary somatosensory area (S1)",
-                            "Primary somatosensory area, face representation (S1-f)",
-                            "Primary somatosensory area, barrel field (S1-bf)",
-                            "Primary somatosensory area, dysgranular zone (S1-dz)",
-                            "Primary somatosensory area, forelimb representation (S1-fl)",
-                            "Primary somatosensory area, hindlimb representation (S1-hl)",
-                            "Primary somatosensory area, trunk representation (S1-tr)",
-                            "Secondary somatosensory area (S2)",
-                            "Posterior parietal cortex (PPC)",
-                            "Parietal association cortex, medial area (mPPC)",
-                            "Parietal association cortex, lateral area (lPPC)",
-                            "Parietal association cortex, posterior area  (PtP)",
-                            "Occipital region (Oc)",
-                            "Visual cortex (Vis)",
-                            "Primary visual area (V1)",
-                            "Secondary visual area (V2)",
-                            "Secondary visual area, medial part (V2M)",
-                            "Secondary visual area, lateral part (V2L)",
-                            "Temporal region (Te)",
-                            "Temporal association cortex (TeA)",
-                            "Auditory cortex (Au)",
-                            "Primary auditory area (Au1)",
-                            "Secondary auditory area (Au2)",
-                            "Secondary auditory area, dorsal part (Au2-d)",
-                            "Secondary auditory area, ventral part (Au2-v)",
-                            "Non-laminated pallium (N-LamP)",
-                            "Claustrum (CLA)",
-                            "Endopiriform nucleus (Endo)",
-                            "Amygdaloid area, unspecified (Am-u)",
-                            " Subpallium (SubPAL)",
-                            "Striatum (Str)",
-                            "Caudate putamen (CPu)",
-                            "Nucleus accumbens (NAc)",
-                            "Nucleus accumbens, core (NAc-c)",
-                            "Nucleus accumbens, shell (NAc-sh)",
-                            "Ventral striatal region, unspecified (VSR-u)",
-                            "Pallidum (PAL)",
-                            "Globus pallidus external (GPe)",
-                            "Globus pallidus external, medial part (GPe-m)",
-                            "Globus pallidus external, lateral part (GPe-l)",
-                            "Entopeduncular nucleus (EP)",
-                            "Ventral pallidum (VP)",
-                            "Basal forebrain region  (BRF)",
-                            "Basal forebrain region, unspecified (BFR-u)",
-                            "Bed nucleus of the stria terminalis (BNST)",
-                            "Septal region (Sep)",
-                            "Subthalamic nucleus (STh)",
-                            "Diencephalon (Dien)",
-                            "Prethalamus (Thal-Pre)",
-                            "Reticular (pre)thalamic nucleus (RT)",
-                            "Reticular (pre)thalamic nucleus, unspecified (RT-u)",
-                            "Reticular (pre)thalamic nucleus, auditory segment (RT-a)",
-                            "Zona incerta (ZI)",
-                            "Zona incerta, dorsal part (ZI-d)",
-                            "Zona incerta, ventral part (ZI-v)",
-                            "Zona incerta, rostral part (ZI-r)",
-                            "Zona incerta, caudal part (ZI-c)",
-                            "Zona incerta, A13 dopamine cells (ZI-A13)",
-                            "Zona incerta, A11 dopamine cells (ZI-A11)",
-                            "Fields of Forel (FoF)",
-                            "Pregeniculate nucleus (PrG)",
-                            "Subgeniculate nucleus (SubG)",
-                            "Intergeniculate leaflet (IGL)",
-                            "Epithalamus (Thal-EPI)",
-                            "Lateral habenular nucleus (LHb)",
-                            "Medial habenular nucleus (MHb)",
-                            "Nucleus of the stria medullaris (SMn)",
-                            "Pineal gland (PG)",
-                            "Dorsal thalamus (Thal-D)",
-                            "Anterior nuclei of the dorsal thalamus (ANT)",
-                            "Anterodorsal thalamic nucleus (AD)",
-                            "Anteroventral thalamic nucleus (AV)",
-                            "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)",
-                            "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)",
-                            "Anteromedial thalamic nucleus (AM)",
-                            "Interanteromedial thalamic nucleus (IAM)",
-                            "Paraventricular thalamic nuclei (anterior and posterior) (PV)",
-                            "Intermediodorsal thalamic nucleus (IMD)",
-                            "Parataenial thalamic nucleus (PT)",
-                            "Subparafascicular nucleus (SPF)",
-                            "Posterior intralaminar nucleus (PIL)",
-                            "Ventral midline group of the dorsal thalamus (V-MID)",
-                            "Rhomboid thalamic nucleus (Rh)",
-                            "Reuniens thalamic nucleus (Re)",
-                            "Retroreuniens thalamic nucleus (RRe)",
-                            "Xiphoid thalamic nucleus (Xi)",
-                            "Mediodorsal nucleus of the dorsal thalamus (MD)",
-                            "Mediodorsal thalamic nucleus, lateral part (MD-l)",
-                            "Mediodorsal thalamic nucleus, central part (MD-c)",
-                            "Mediodorsal thalamic nucleus, medial part (MD-m)",
-                            "Ventral nuclei of the dorsal thalamus (VENT)",
-                            "Ventral anterior thalamic nucleus (VA)",
-                            "Ventromedial thalamic nucleus (VM)",
-                            "Ventrolateral thalamic nucleus (VL)",
-                            "Angular thalamic nucleus (Ang)",
-                            "Ventral posterior thalamic nucleus (VPN)",
-                            "Ventral posteromedial thalamic nucleus (VPM)",
-                            "Ventral posterolateral thalamic nucleus (VPL)",
-                            "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)",
-                            "Submedius thalamic nucleus (SMT)",
-                            "Intralaminar nuclei of the dorsal thalamus (ILM)",
-                            "Paracentral thalamic nucleus (PCN)",
-                            "Central medial thalamic nucleus (CM)",
-                            "Central lateral thalamic nucleus (CL)",
-                            "Parafascicular thalamic nucleus (PF)",
-                            "Ethmoid-Limitans nucleus (Eth)",
-                            "Posterior complex of the dorsal thalamus (PoC)",
-                            "Posterior thalamic nucleus (Po)",
-                            "Posterior thalamic nuclear group, triangular part (Po-t)",
-                            "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)",
-                            "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)",
-                            "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)",
-                            "Lateral posterior thalamic nucleus, lateral part (LP-l)",
-                            "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)",
-                            "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)",
-                            "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)",
-                            "Dorsal lateral geniculate nucleus (DLG)",
-                            "Medial geniculate complex of the dorsal thalamus (MG)",
-                            "Medial geniculate body, ventral division (MG-v)",
-                            "Medial geniculate body, dorsal division (MG-d)",
-                            "Medial geniculate body, marginal zone (MG-mz)",
-                            "Medial geniculate body, medial division (MG-m)",
-                            "Medial geniculate body, suprageniculate nucleus (MG-sg)",
-                            "Hypothalamus (HY)",
-                            "Hypothalamic region, unspecified (HTh-u)",
-                            "Pretectum (PreT)",
-                            "Pretectal region (PRT)",
-                            "Nucleus sagulum (Sag)",
-                            "Mesencephalon (Mes)",
-                            "Midbrain (MB)",
-                            "Tectum (Tc)",
-                            "Inferior colliculus (IC)",
-                            "Inferior colliculus, dorsal cortex (DCIC)",
-                            "Inferior colliculus, central nucleus (CNIC)",
-                            "Inferior colliculus, external cortex (ECIC)",
-                            "Superior colliculus (Su)",
-                            "Superficial gray layer of the superior colliculus (SuG)",
-                            "Deeper layers of the superior colliculus (SuD)",
-                            "Tegmentum (Tg)",
-                            "Substantia nigra (SN)",
-                            "Substantia nigra, reticular part (SN-r)",
-                            "Substantia nigra, compact part (SN-c)",
-                            "Substantia nigra, lateral part (SN-l)",
-                            "Ventral tegmental area (VTA)",
-                            "Peripeduncular nucleus (PP)",
-                            "Interpeduncular nucleus (IP)",
-                            "Periaqueductal gray (PAG)",
-                            "Brainstem, unspecified (BS-u)",
-                            "Rhombencephalon (Rho)",
-                            "Metencephalon (Met)",
-                            "Pontine nuclei (Pn)",
-                            "Cerebellum (Cb)",
-                            "Molecular cell layer of the cerebellum (Cb-m)",
-                            "Cerebellum, unspecified (Cb-u)",
-                            "Myelencephalon (Myel)",
-                            "Cochlear nucleus, ventral part (VCN)",
-                            "Ventral cochlear nucleus, anterior part (AVCN)",
-                            "Ventral cochlear nucleus, posterior part (PVCN)",
-                            "Ventral cochlear nucleus, cap area (Cap)",
-                            "Ventral cochlear nucleus, granule cell layer (GCL)",
-                            "Cochlear nucleus, dorsal part (DCN)",
-                            "Dorsal cochlear nucleus, molecular layer (DCNM)",
-                            "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)",
-                            "Dorsal cochlear nucleus, deep core (DCND)",
-                            "Spinal trigeminal nucleus (Sp5n)",
-                            "Periventricular gray (PVG)",
-                            "Superior olivary complex (SO)",
-                            "Nucleus of the trapezoid body (NTB)",
-                            "Superior paraolivary nucleus (SPN)",
-                            "Medial superior olive (MSO)",
-                            "Lateral superior olive (LSO)",
-                            "Superior periolivary region (SPR)",
-                            "Ventral periolivary nuclei (VPO)",
-                            "Nuclei of the lateral lemniscus (NLL)",
-                            "Lateral lemniscus, ventral nucleus (VLL)",
-                            "Lateral lemniscus, intermediate nucleus (ILL)",
-                            "Lateral lemniscus, dorsal nucleus (DLL)",
-                            "Inferior olive (IO)",
-                            "Ventricular system (V)",
-                            "ventricular system, unspecified (V-u)",
-                            "4th ventricle (4V)",
-                            "central canal (CC)",
-                            "spinal cord (SpC)",
-                            "Inner ear (IE)",
-                            "vestibular apparatus (VeA)",
-                            "cochlea (Co)",
-                            "cochlear nerve (8cn)",
-                            "vestibular nerve (8vn)",
-                            "spiral ganglion (SpG)"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    },
-                    "targeted_x": {
-                        "$id": "#root/electrode_groups/items/targeted_x",
-                        "title": "targeted_x",
-                        "type": "number",
-                        "description": "Medial/Latetal",
-                        "examples": [
-                            2.6
-                        ],
-                        "default": 0.0
-                    },
-                    "targeted_y": {
-                        "$id": "#root/electrode_groups/items/targeted_y",
-                        "title": "targeted_y",
-                        "type": "number",
-                        "description": "Anterior/Posterior",
-                        "examples": [
-                            -3.8
-                        ],
-                        "default": 0.0
-                    },
-                    "targeted_z": {
-                        "$id": "#root/electrode_groups/items/targeted_z",
-                        "title": "targeted_z",
-                        "type": "number",
-                        "description": "Ventral/Dorsal",
-                        "examples": [
-                            0
-                        ],
-                        "default": 0
-                    },
-                    "units": {
-                        "$id": "#root/electrode_groups/items/units",
-                        "title": "units",
-                        "type": "string",
-                        "default": "mm",
-                        "examples": [
-                            "pm",
-                            "nm",
-                            "μm",
-                            "mm",
-                            "cm",
-                            "in",
-                            "yd",
-                            "ft"
-                        ],
-                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
-                    }
-                }
-            }
-        },
-        "ntrode_electrode_group_channel_map": {
-            "$id": "#root/ntrode_electrode_group_channel_map",
-            "title": "ntrode_electrode_group_channel_map",
-            "type": "array",
-            "default": [],
-            "items": {
-                "$id": "#root/ntrode_electrode_group_channel_map/items",
-                "title": "Items",
-                "type": "object",
-                "required": [
-                    "ntrode_id",
-                    "electrode_group_id",
-                    "bad_channels",
-                    "map"
-                ],
-                "properties": {
-                    "ntrode_id": {
-                        "$id": "#root/ntrode_electrode_group_channel_map/items/ntrode_id",
-                        "title": "ntrode_id",
-                        "type": "integer",
-                        "examples": [
-                            1
-                        ],
-                        "default": 0
-                    },
-                    "electrode_group_id": {
-                        "$id": "#root/ntrode_electrode_group_channel_map/items/electrode_group_id",
-                        "title": "electrode_group_id",
-                        "type": "integer",
-                        "examples": [
-                            0
-                        ],
-                        "default": 0
-                    },
-                    "bad_channels": {
-                        "$id": "#root/ntrode_electrode_group_channel_map/items/bad_channels",
-                        "title": "bad_channels",
-                        "type": "array",
-                        "default": [],
-                        "examples": [],
-                        "uniqueItems": true,
-                        "description": "Comma separated list of bad channels",
-                        "items": {
-                            "$id": "#root/ntrode_electrode_group_channel_map/items/bad_channels/items",
-                            "title": "Items",
-                            "type": "integer",
-                            "examples": [
-                                0
-                            ],
-                            "default": 0
-                        }
-                    },
-                    "map": {
-                        "$id": "#root/ntrode_electrode_group_channel_map/items/map",
-                        "title": "map",
-                        "type": "object",
-                        "properties": {
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-                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/0",
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-                                    2,
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-                                    91,
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-                                    93,
-                                    94,
-                                    95,
-                                    96,
-                                    97,
-                                    98,
-                                    99,
-                                    100,
-                                    101,
-                                    102,
-                                    103,
-                                    104,
-                                    105,
-                                    106,
-                                    107,
-                                    108,
-                                    109,
-                                    110,
-                                    111,
-                                    112,
-                                    113,
-                                    114,
-                                    115,
-                                    116,
-                                    117,
-                                    118,
-                                    119,
-                                    120,
-                                    121,
-                                    122,
-                                    123,
-                                    124,
-                                    125,
-                                    126,
-                                    127
-                                ],
-                                "enum": [
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-                                    1,
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-                                    99,
-                                    100,
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-                                    103,
-                                    104,
-                                    105,
-                                    106,
-                                    107,
-                                    108,
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-                                    110,
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-                                    112,
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-                                    114,
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-                                    116,
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-                                    121,
-                                    122,
-                                    123,
-                                    124,
-                                    125,
-                                    126,
-                                    127
-                                ],
-                                "minimum": 0,
-                                "default": 0
-                            },
-                            "1": {
-                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/1",
-                                "title": "1",
-                                "type": "integer",
-                                "examples": [
-                                    0,
-                                    1,
-                                    2,
-                                    3,
-                                    4,
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-                                    76,
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-                                    78,
-                                    79,
-                                    80,
-                                    81,
-                                    82,
-                                    83,
-                                    84,
-                                    85,
-                                    86,
-                                    87,
-                                    88,
-                                    89,
-                                    90,
-                                    91,
-                                    92,
-                                    93,
-                                    94,
-                                    95,
-                                    96,
-                                    97,
-                                    98,
-                                    99,
-                                    100,
-                                    101,
-                                    102,
-                                    103,
-                                    104,
-                                    105,
-                                    106,
-                                    107,
-                                    108,
-                                    109,
-                                    110,
-                                    111,
-                                    112,
-                                    113,
-                                    114,
-                                    115,
-                                    116,
-                                    117,
-                                    118,
-                                    119,
-                                    120,
-                                    121,
-                                    122,
-                                    123,
-                                    124,
-                                    125,
-                                    126,
-                                    127
-                                ],
-                                "minimum": 0,
-                                "default": 126
-                            },
-                            "127": {
-                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/127",
-                                "title": "127",
-                                "type": "integer",
-                                "examples": [
-                                    0,
-                                    1,
-                                    2,
-                                    3,
-                                    4,
-                                    5,
-                                    6,
-                                    7,
-                                    8,
-                                    9,
-                                    10,
-                                    11,
-                                    12,
-                                    13,
-                                    14,
-                                    15,
-                                    16,
-                                    17,
-                                    18,
-                                    19,
-                                    20,
-                                    21,
-                                    22,
-                                    23,
-                                    24,
-                                    25,
-                                    26,
-                                    27,
-                                    28,
-                                    29,
-                                    30,
-                                    31,
-                                    32,
-                                    33,
-                                    34,
-                                    35,
-                                    36,
-                                    37,
-                                    38,
-                                    39,
-                                    40,
-                                    41,
-                                    42,
-                                    43,
-                                    44,
-                                    45,
-                                    46,
-                                    47,
-                                    48,
-                                    49,
-                                    50,
-                                    51,
-                                    52,
-                                    53,
-                                    54,
-                                    55,
-                                    56,
-                                    57,
-                                    58,
-                                    59,
-                                    60,
-                                    61,
-                                    62,
-                                    63,
-                                    64,
-                                    65,
-                                    66,
-                                    67,
-                                    68,
-                                    69,
-                                    70,
-                                    71,
-                                    72,
-                                    73,
-                                    74,
-                                    75,
-                                    76,
-                                    77,
-                                    78,
-                                    79,
-                                    80,
-                                    81,
-                                    82,
-                                    83,
-                                    84,
-                                    85,
-                                    86,
-                                    87,
-                                    88,
-                                    89,
-                                    90,
-                                    91,
-                                    92,
-                                    93,
-                                    94,
-                                    95,
-                                    96,
-                                    97,
-                                    98,
-                                    99,
-                                    100,
-                                    101,
-                                    102,
-                                    103,
-                                    104,
-                                    105,
-                                    106,
-                                    107,
-                                    108,
-                                    109,
-                                    110,
-                                    111,
-                                    112,
-                                    113,
-                                    114,
-                                    115,
-                                    116,
-                                    117,
-                                    118,
-                                    119,
-                                    120,
-                                    121,
-                                    122,
-                                    123,
-                                    124,
-                                    125,
-                                    126,
-                                    127
-                                ],
-                                "enum": [
-                                    0,
-                                    1,
-                                    2,
-                                    3,
-                                    4,
-                                    5,
-                                    6,
-                                    7,
-                                    8,
-                                    9,
-                                    10,
-                                    11,
-                                    12,
-                                    13,
-                                    14,
-                                    15,
-                                    16,
-                                    17,
-                                    18,
-                                    19,
-                                    20,
-                                    21,
-                                    22,
-                                    23,
-                                    24,
-                                    25,
-                                    26,
-                                    27,
-                                    28,
-                                    29,
-                                    30,
-                                    31,
-                                    32,
-                                    33,
-                                    34,
-                                    35,
-                                    36,
-                                    37,
-                                    38,
-                                    39,
-                                    40,
-                                    41,
-                                    42,
-                                    43,
-                                    44,
-                                    45,
-                                    46,
-                                    47,
-                                    48,
-                                    49,
-                                    50,
-                                    51,
-                                    52,
-                                    53,
-                                    54,
-                                    55,
-                                    56,
-                                    57,
-                                    58,
-                                    59,
-                                    60,
-                                    61,
-                                    62,
-                                    63,
-                                    64,
-                                    65,
-                                    66,
-                                    67,
-                                    68,
-                                    69,
-                                    70,
-                                    71,
-                                    72,
-                                    73,
-                                    74,
-                                    75,
-                                    76,
-                                    77,
-                                    78,
-                                    79,
-                                    80,
-                                    81,
-                                    82,
-                                    83,
-                                    84,
-                                    85,
-                                    86,
-                                    87,
-                                    88,
-                                    89,
-                                    90,
-                                    91,
-                                    92,
-                                    93,
-                                    94,
-                                    95,
-                                    96,
-                                    97,
-                                    98,
-                                    99,
-                                    100,
-                                    101,
-                                    102,
-                                    103,
-                                    104,
-                                    105,
-                                    106,
-                                    107,
-                                    108,
-                                    109,
-                                    110,
-                                    111,
-                                    112,
-                                    113,
-                                    114,
-                                    115,
-                                    116,
-                                    117,
-                                    118,
-                                    119,
-                                    120,
-                                    121,
-                                    122,
-                                    123,
-                                    124,
-                                    125,
-                                    126,
-                                    127
-                                ],
-                                "minimum": 0,
-                                "default": 127
-                            }
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
\ No newline at end of file
diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index 0ce43fe..bbf9d71 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -687,7 +687,7 @@ def get_digitalsignal(self, stream_id, channel_id):
         if self.sysClock_byte:
             timestamps = self.get_regressed_systime(i_start, i_stop)
         else:
-            timestamps = self.get_systime_from_trodes_timestamps(i_start, i_stop)
+            timestamps = self.get_analogsignal_timestamps(i_start, i_stop)
         dio_change_times = timestamps[np.where(change_dir)[0] + 1]
 
         # insert the first timestamp with the first value
@@ -701,7 +701,6 @@ def get_digitalsignal(self, stream_id, channel_id):
 
         return dio_change_times, change_dir_trim
 
-    @functools.lru_cache(maxsize=1)
     def get_regressed_systime(self, i_start, i_stop=None):
         NANOSECONDS_PER_SECOND = 1e9
         # get values
@@ -714,15 +713,13 @@ def get_regressed_systime(self, i_start, i_stop=None):
         adjusted_timestamps = intercept + slope * trodestime_index
         return (adjusted_timestamps) / NANOSECONDS_PER_SECOND
 
-    @functools.lru_cache(maxsize=1)
     def get_systime_from_trodes_timestamps(self, i_start, i_stop=None):
         MILLISECONDS_PER_SECOND = 1e3
         # get values
         trodestime = self.get_analogsignal_timestamps(i_start, i_stop)
-        initial_time = self.get_analogsignal_timestamps(0, 1)[0]
-        return (trodestime - initial_time) * (1.0 / self._sampling_rate) + int(
-            self.system_time_at_creation
-        ) / MILLISECONDS_PER_SECOND
+        return (trodestime - int(self.timestamp_at_creation)) * (
+            1.0 / self._sampling_rate
+        ) + int(self.system_time_at_creation) / MILLISECONDS_PER_SECOND
 
     def _interpolate_raw_memmap(
         self,
diff --git a/src/spikegadgets_to_nwb/tests/integration-tests/__init__.py b/src/spikegadgets_to_nwb/tests/integration-tests/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py b/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
deleted file mode 100644
index 4d9d904..0000000
--- a/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
+++ /dev/null
@@ -1,190 +0,0 @@
-import pytest
-import os
-from spikegadgets_to_nwb.metadata_validation import (
-    validate,
-)
-from spikegadgets_to_nwb.tests.test_data.test_metadata_dict_samples import (
-    basic_data,
-    basic_data_with_optional_arrays,
-    empty_experimenter_name,
-    string_as_experimenter_name,
-    empty_lab,
-    empty_institution,
-    empty_experiment_description,
-    empty_session_description,
-    empty_session_id,
-    empty_keywords,
-    keywords_array_with_empty_item,
-    not_array_keywords,
-    empty_subject,
-    subject_with_empty_values,
-    subject_with_invalid_sex,
-    subject_with_invalid_date,
-    empty_data_acq_device,
-    data_acq_device_with_no_values,
-    empty_units,
-    invalid_times_period_multiplier,
-    invalid_raw_data_to_volts,
-    invalid_default_header_file_path,
-    empty_device_name,
-    basic_ntrode_electrode_group_channel_map,
-)
-
-
-@pytest.mark.parametrize("metadata", [(None), ("")])
-def test_metadata_validation_only_accepts_right_data_type(metadata):
-    with pytest.raises(AssertionError) as e:
-        validate(metadata)
-
-
-@pytest.mark.parametrize("metadata", [(basic_data), (basic_data_with_optional_arrays)])
-def test_metadata_validation_verification_on_valid_data(metadata):
-    is_valid, errors = validate(metadata)
-
-    assert is_valid, "".join(errors)
-
-
-@pytest.mark.parametrize(
-    "metadata, key, expected",
-    [
-        (empty_experimenter_name, "experimenter_name", ["[] is too short"]),
-        (
-            string_as_experimenter_name,
-            "experimenter_name",
-            [
-                "'' is not of type 'array'",
-            ],
-        ),
-        (empty_lab, "lab", ["does not match"]),
-        (empty_institution, "institution", ["does not match"]),
-        (
-            empty_experiment_description,
-            "experiment_description",
-            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
-        ),
-        (
-            empty_session_description,
-            "session_description",
-            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
-        ),
-        (
-            empty_session_id,
-            "session_id",
-            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
-        ),
-        (
-            empty_keywords,
-            "keywords",
-            [
-                "[] is too short",
-            ],
-        ),
-        (
-            keywords_array_with_empty_item,
-            "keywords",
-            [
-                "",
-            ],
-        ),
-        (not_array_keywords, "keywords", ["is not of type 'array'"]),
-        (
-            subject_with_empty_values,
-            "subject1",
-            [
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "is not one of ['M', 'F', 'U', 'O']",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "-1 is less than the minimum of 0",
-                "does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'",
-            ],
-        ),
-        (
-            empty_subject,
-            "subject",
-            [
-                "'description' is a required property",
-                "'genotype' is a required property",
-                "'sex' is a required property",
-                "'species' is a required property",
-                "'subject_id' is a required property",
-                "'weight' is a required property",
-                "'date_of_birth' is a required property",
-            ],
-        ),
-        (subject_with_invalid_sex, "subject", ["is not one of ['M', 'F', 'U', 'O']"]),
-        (
-            subject_with_invalid_date,
-            "subject",
-            [
-                "'2023-01-04' does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'"
-            ],
-        ),
-        (
-            data_acq_device_with_no_values,
-            "data_acq_device1",
-            [
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
-            ],
-        ),
-        (empty_data_acq_device, "data_acq_device", ["[] is too short"]),
-        (
-            empty_units,
-            "units",
-            [
-                "'analog' is a required property",
-                "'behavioral_events' is a required property",
-            ],
-        ),
-        (
-            invalid_times_period_multiplier,
-            "times_period_multiplier",
-            [
-                "'a' is not of type 'number'",
-            ],
-        ),
-        (
-            invalid_raw_data_to_volts,
-            "raw_data_to_volts",
-            ["'a' is not of type 'number'"],
-        ),
-        (
-            invalid_default_header_file_path,
-            "default_header_file_path",
-            ["None is not of type 'string'"],
-        ),
-        (empty_device_name, "device_name", ["'name' is a required property"]),
-        (
-            basic_ntrode_electrode_group_channel_map,
-            "ntrode_electrode_group_channel_map",
-            (
-                [
-                    "'a' is not of type 'integer'",
-                    "'z' is not of type 'integer'",
-                    "'z' is not of type 'integer'",
-                    "'0' is not of type 'integer'",
-                    "'0' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
-                    "'t' is not of type 'integer'",
-                    "'t' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
-                    "'a' is not of type 'integer'",
-                    "'a' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
-                    "-3 is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
-                    "-3 is less than the minimum of 0",
-                ]
-            ),
-        ),
-    ],
-)
-def test_metadata_validation_verification_on_invalid_data(metadata, key, expected):
-    is_valid, errors = validate(metadata)
-
-    assert len(errors) == len(expected), f"Not all the errors are occurring in - {key}"
-    assert not is_valid, f"{key} should be invalid"
-    for index, error in enumerate(errors):
-        assert (
-            expected[index] in error
-        ), f"Expected error not found - ${expected[index]}"
diff --git a/src/spikegadgets_to_nwb/tests/test_convert.py b/src/spikegadgets_to_nwb/tests/test_convert.py
index 7206ed9..5861158 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert.py
@@ -1,17 +1,25 @@
-import numpy as np
 import os
 from pathlib import Path
+
+import numpy as np
+import pandas as pd
 from pynwb import NWBHDF5IO
-import shutil
 
 from spikegadgets_to_nwb.convert import _create_nwb, get_included_probe_metadata_paths
 from spikegadgets_to_nwb.data_scanner import get_file_info
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 MICROVOLTS_PER_VOLT = 1e6
 
 
 def test_get_file_info():
+    try:
+        # running on github
+        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
+    except (TypeError, FileNotFoundError):
+        # running locally
+        data_path = Path(path)
     path_df = get_file_info(data_path)
     path_df = path_df[
         path_df.animal == "sample"
@@ -46,41 +54,53 @@ def test_get_included_probe_metadat_paths():
 
 
 def test_convert():
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    try:
+        # running on github
+        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
+        yml_data_path = Path(path + "/test_data")
+        yml_path_df = get_file_info(yml_data_path)
+        yml_path_df = yml_path_df[yml_path_df.file_extension == ".yml"]
+        append_yml_df = True
+    except (TypeError, FileNotFoundError):
+        # running locally
+        data_path = Path(path + "/test_data")
+        append_yml_df = False
+    probe_metadata = [Path(path + "/test_data/tetrode_12.5.yml")]
+
     # make session_df
     path_df = get_file_info(data_path)
-    # exclude the reconfig yaml file
-    path_df = path_df[
-        path_df.full_path
-        != str(data_path / "20230622_sample_metadataProbeReconfig.yml")
-    ]
+    if append_yml_df:
+        path_df = path_df[
+            path_df.file_extension != ".yml"
+        ]  # strip ymls, fixes github runner issue where yamls only sometimes present between jobs
+        path_df = pd.concat([path_df, yml_path_df])
+        path_df = path_df[
+            path_df.full_path
+            != yml_data_path.as_posix() + "/20230622_sample_metadataProbeReconfig.yml"
+        ]
+    else:
+        path_df = path_df[
+            path_df.full_path
+            != data_path.as_posix() + "/20230622_sample_metadataProbeReconfig.yml"
+        ]
     session_df = path_df[(path_df.animal == "sample")]
     assert len(session_df[session_df.file_extension == ".yml"]) == 1
-    # make temporary directory for video files
-    video_directory = data_path / "temp_video_directory_full_convert"
-    if not os.path.exists(video_directory):
-        os.makedirs(video_directory)
-
     _create_nwb(
         session=("20230622", "sample", "1"),
         session_df=session_df,
         probe_metadata_paths=probe_metadata,
         output_dir=str(data_path),
-        video_directory=str(video_directory),
     )
-
-    output_file_path = data_path / "sample20230622.nwb"
-    assert output_file_path.exists()
-    rec_to_nwb_file = data_path / "minirec20230622_.nwb"
-    with NWBHDF5IO(output_file_path) as io:
+    assert "sample20230622.nwb" in os.listdir(str(data_path))
+    with NWBHDF5IO(str(data_path) + "/sample20230622.nwb") as io:
         nwbfile = io.read()
-        with NWBHDF5IO(rec_to_nwb_file) as io2:
+        with NWBHDF5IO(str(data_path) + "/minirec20230622_.nwb") as io2:
             old_nwbfile = io2.read()
+
             # run nwb comparison
             compare_nwbfiles(nwbfile, old_nwbfile)
     # cleanup
-    os.remove(output_file_path)
-    shutil.rmtree(video_directory)
+    os.remove(str(data_path) + "/sample20230622.nwb")
 
 
 def check_module_entries(test, reference):
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_analog.py b/src/spikegadgets_to_nwb/tests/test_convert_analog.py
index 9df75c9..7111a82 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_analog.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_analog.py
@@ -1,19 +1,30 @@
 import os
+
 import pynwb
 
 from spikegadgets_to_nwb import convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.convert_analog import add_analog_data, get_analog_channel_names
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_add_analog_data():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    rec_file = data_path / "20230622_sample_01_a1.rec"
-    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
-    rec_header = convert_rec_header.read_header(rec_file)
+    nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
+
+    try:
+        # running on github
+        rec_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        rec_header = convert_rec_header.read_header(rec_file)
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
+    except:
+        # running locally
+        rec_file = path + "/test_data/20230622_sample_01_a1.rec"
+        rec_header = convert_rec_header.read_header(rec_file)
+        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
     # make file with data
     nwbfile = convert_yaml.initialize_nwb(metadata, rec_header)
     analog_channel_names = get_analog_channel_names(rec_header)
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_dios.py b/src/spikegadgets_to_nwb/tests/test_convert_dios.py
index 3c0b66f..8d566e3 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_dios.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_dios.py
@@ -1,22 +1,32 @@
-import numpy as np
 import os
+
+import numpy as np
 import pynwb
 
 from spikegadgets_to_nwb import convert_yaml
 from spikegadgets_to_nwb.convert_dios import add_dios
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_add_dios_single_rec():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, _ = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
-    recfile = [data_path / "20230622_sample_01_a1.rec"]
-    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
+    try:
+        # running on github
+        recfile = [os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"]
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = [path + "/test_data/20230622_sample_01_a1.rec"]
+        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
 
     add_dios(nwbfile, recfile, metadata)
 
@@ -61,16 +71,27 @@ def test_add_dios_single_rec():
 
 def test_add_dios_two_epoch():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, _ = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
-    recfile = [
-        data_path / "20230622_sample_01_a1.rec",
-        data_path / "20230622_sample_02_a1.rec",
-    ]
-    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
+    try:
+        # running on github
+        recfile = [
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = [
+            path + "/test_data/20230622_sample_01_a1.rec",
+            path + "/test_data/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
 
     add_dios(nwbfile, recfile, metadata)
 
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py b/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
index bf0ef0b..aac211c 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
@@ -1,27 +1,38 @@
-import numpy as np
 import os
-from pathlib import Path
+
+import numpy as np
 import pynwb
 
 from spikegadgets_to_nwb import convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.convert_ephys import add_raw_ephys
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-from spikegadgets_to_nwb.tests.utils import data_path
 
 MICROVOLTS_PER_VOLT = 1e6
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_add_raw_ephys_single_rec():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
-    # "reconfig_probeDevice.trodesconf"
-    rec_header = convert_rec_header.read_header(trodesconf_file)
+    try:
+        # running on github
+        trodesconf_file = (
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        )  # "/test_data/reconfig_probeDevice.trodesconf"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
+    except:
+        # running locally
+        trodesconf_file = (
+            path + "/test_data/20230622_sample_01_a1.rec"
+        )  # "/test_data/reconfig_probeDevice.trodesconf"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -34,14 +45,22 @@ def test_add_raw_ephys_single_rec():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    recfile = [data_path / "20230622_sample_01_a1.rec"]
-    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
+    try:
+        # running on github
+        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = path + "/test_data/20230622_sample_01_a1.rec"
+        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
 
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
         nwbfile,
-        recfile,
+        [
+            recfile,
+        ],
         map_row_ephys_data_to_row_electrodes_table,
     )
 
@@ -90,13 +109,15 @@ def test_add_raw_ephys_single_rec():
 
 def test_add_raw_ephys_single_rec_probe_configuration():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadataProbeReconfig.yml"
-    probe_metadata = [data_path / "128c-4s6mm6cm-15um-26um-sl.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadataProbeReconfig.yml"
+    probe_metadata = [
+        path + "/test_data/128c-4s6mm6cm-15um-26um-sl.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = data_path / "reconfig_probeDevice.trodesconf"
+    trodesconf_file = path + "/test_data/reconfig_probeDevice.trodesconf"
     rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
@@ -110,16 +131,24 @@ def test_add_raw_ephys_single_rec_probe_configuration():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    recfile = [data_path / "20230622_sample_01_a1.rec"]
-    rec_to_nwb_file = (
-        data_path / "probe_reconfig_20230622_155936.nwb"
-    )  # comparison file
+    try:
+        # running on github
+        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        rec_to_nwb_file = (
+            os.environ.get("DOWNLOAD_DIR") + "/probe_reconfig_20230622_155936.nwb"
+        )
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = path + "/test_data/20230622_sample_01_a1.rec"
+        rec_to_nwb_file = path + "/test_data/probe_reconfig_20230622_155936.nwb"
 
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
         nwbfile,
-        recfile,
+        [
+            recfile,
+        ],
         map_row_ephys_data_to_row_electrodes_table,
     )
 
@@ -169,14 +198,22 @@ def test_add_raw_ephys_single_rec_probe_configuration():
 
 def test_add_raw_ephys_two_epoch():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
-    rec_header = convert_rec_header.read_header(trodesconf_file)
+    try:
+        # running on github
+        trodesconf_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
+    except:
+        # running locally
+        trodesconf_file = path + "/test_data/20230622_sample_01_a1.rec"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -189,12 +226,20 @@ def test_add_raw_ephys_two_epoch():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    recfile = [
-        data_path / "20230622_sample_01_a1.rec",
-        data_path / "20230622_sample_02_a1.rec",
-    ]
-    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
-
+    try:
+        # running on github
+        recfile = [
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = [
+            path + "/test_data/20230622_sample_01_a1.rec",
+            path + "/test_data/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index 83a13d9..31d0bb3 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -1,5 +1,7 @@
-import numpy as np
 import os
+from pathlib import Path
+
+import numpy as np
 from pynwb import NWBHDF5IO
 
 from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator
@@ -8,27 +10,34 @@
 from spikegadgets_to_nwb.data_scanner import get_file_info
 from spikegadgets_to_nwb.spike_gadgets_raw_io import SpikeGadgetsRawIO
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_add_epochs():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = load_metadata(metadata_path, [])
     nwbfile = initialize_nwb(metadata, default_test_xml_tree())
-    file_info = get_file_info(data_path)
-    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
-    # get all streams for all files
-    neo_io = [
-        SpikeGadgetsRawIO(filename=file)
-        for file in file_info[file_info.file_extension == ".rec"].full_path
-    ]
-    [neo_io.parse_header() for neo_io in neo_io]
-
+    try:
+        # running on github
+        file_info = get_file_info(Path(os.environ.get("DOWNLOAD_DIR")))
+        rec_to_nwb_file = (
+            os.environ.get("DOWNLOAD_DIR") + "/probe_reconfig_20230622_155936.nwb"
+        )
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        file_info = get_file_info(Path(path))
+        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
     file_info = file_info[file_info.animal == "sample"]
-    file_info = file_info[file_info.date == 20230622]
-    add_epochs(nwbfile, file_info, neo_io)
+    # assert file_info[file_info.file_extension == ".rec"].full_path.to_list() == []
+    # get all streams for all files
+    rec_dci = RecFileDataChunkIterator(
+        file_info[file_info.file_extension == ".rec"].full_path.to_list()
+    )
+    add_epochs(nwbfile, file_info, 20230622, "sample", rec_dci.neo_io)
     epochs_df = nwbfile.epochs.to_dataframe()
-    # load old nwb version
+    # load old nwb versio
     io = NWBHDF5IO(rec_to_nwb_file, "r")
     old_nwbfile = io.read()
     old_epochs_df = old_nwbfile.epochs.to_dataframe()
@@ -41,14 +50,23 @@ def test_add_epochs():
 
 
 def test_add_sample_count():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = load_metadata(metadata_path, [])
     nwbfile = initialize_nwb(metadata, default_test_xml_tree())
-    recfile = [
-        data_path / "20230622_sample_01_a1.rec",
-        data_path / "20230622_sample_02_a1.rec",
-    ]
-    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
+    try:
+        # running on github
+        recfile = [
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = [
+            path + "/test_data/20230622_sample_01_a1.rec",
+            path + "/test_data/20230622_sample_02_a1.rec",
+        ]
+        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
 
     # make recfile data chunk iterator
     rec_dci = RecFileDataChunkIterator(recfile)
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_position.py b/src/spikegadgets_to_nwb/tests/test_convert_position.py
index bada810..6a32276 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_position.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_position.py
@@ -4,13 +4,9 @@
 import numpy as np
 import pandas as pd
 import pytest
-from pynwb import NWBHDF5IO, TimeSeries
+from pynwb import NWBHDF5IO
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
-from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator
-from spikegadgets_to_nwb.convert_intervals import add_sample_count
-from spikegadgets_to_nwb.convert_dios import add_dios
-from spikegadgets_to_nwb.convert_intervals import add_epochs
 from spikegadgets_to_nwb.convert_position import (
     add_position,
     correct_timestamps_for_camera_to_mcu_lag,
@@ -24,10 +20,10 @@
     parse_dtype,
     read_trodes_datafile,
     remove_acquisition_timing_pause_non_ptp,
-    find_camera_dio_channel,
 )
 from spikegadgets_to_nwb.data_scanner import get_file_info
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_parse_dtype_standard():
@@ -198,15 +194,23 @@ def test_correct_timestamps_for_camera_to_mcu_lag():
 
 
 def test_add_position():
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    try:
+        # running on github
+        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
+    except (TypeError, FileNotFoundError):
+        # running locally
+        data_path = Path(path + "/test_data")
+    probe_metadata = [Path(path + "/test_data/tetrode_12.5.yml")]
 
     # make session_df
     path_df = get_file_info(data_path)
     session_df = path_df[(path_df.animal == "sample")]
 
     # get metadata
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     rec_file = session_df[
         (session_df.epoch == 1) & (session_df.file_extension == ".rec")
@@ -218,10 +222,11 @@ def test_add_position():
 
     # run add_position and prerequisite functions
     convert_yaml.add_cameras(nwbfile, metadata)
-    add_position(nwbfile, metadata, session_df, rec_header)
+    add_position(nwbfile, metadata, session_df, rec_header, video_directory="")
 
     # Check that the objects were properly added
     assert "position" in nwbfile.processing["behavior"].data_interfaces
+    assert "video_files" in nwbfile.processing
     assert "non_repeat_timestamp_labels" in nwbfile.processing
     assert "position_frame_index" in nwbfile.processing
 
@@ -282,66 +287,3 @@ def test_add_position():
                 assert validated, f"Could not find matching series for {series}"
     # cleanup
     os.remove(filename)
-
-
-from spikegadgets_to_nwb.convert_position import read_trodes_datafile
-
-
-def test_add_position_non_ptp():
-    # make session_df
-    path_df = get_file_info(data_path)
-    session_df = path_df[(path_df.animal == "ginny")]
-    # get metadata
-    metadata_path = data_path / "nonptp_metadata.yml"
-    metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    # load the prepped non-ptp nwbfile
-    with NWBHDF5IO(data_path / "non_ptp_prep.nwb", "a", load_namespaces=True) as io:
-        nwbfile = io.read()
-        add_position(
-            nwbfile,
-            metadata,
-            session_df,
-            ptp_enabled=False,
-            rec_dci_timestamps=nwbfile.processing["sample_count"][
-                "sample_count"
-            ].timestamps[:]
-            / 1e9,
-            sample_count=nwbfile.processing["sample_count"]
-            .data_interfaces["sample_count"]
-            .data[:],
-        )
-        # read in position data to compare to
-        ref_pos = pd.read_pickle(data_path / "position_df.pkl")
-        # check that the data is the same
-        for series in [
-            "led_0_series_1",
-            "led_0_series_2",
-            "led_1_series_1",
-            "led_1_series_2",
-        ]:
-            # check series in new nwbfile
-            assert (
-                series
-                in nwbfile.processing["behavior"]["position"].spatial_series.keys()
-            )
-            # get the data for this series
-            t_new = nwbfile.processing["behavior"]["position"][series].timestamps[:]
-            pos_new = nwbfile.processing["behavior"]["position"][series].data[:]
-            assert t_new.size == pos_new.shape[0]
-            assert pos_new.shape[1] == 2
-            validated = False
-            for name in ref_pos.name.to_list():
-                t_ref = ref_pos[ref_pos.name == name].timestamps.values[0]
-
-                if t_new.size == t_ref.size and np.allclose(
-                    t_ref, t_new, atol=1, rtol=0
-                ):
-                    pos_ref = ref_pos[ref_pos.name == name].data.to_list()[0]
-                    if np.allclose(
-                        pos_ref[:100, :2], pos_new[:100], atol=1e-6, rtol=0
-                    ) or np.allclose(
-                        pos_ref[:100, 2:], pos_new[:100], atol=1e-6, rtol=0
-                    ):
-                        validated = True
-                        break
-            assert validated, f"Could not find matching series for {series}"
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py b/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
index b39f776..0c5da8c 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
@@ -5,7 +5,8 @@
 from ndx_franklab_novela import HeaderDevice
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def default_test_xml_tree() -> ElementTree:
@@ -16,23 +17,39 @@ def default_test_xml_tree() -> ElementTree:
     ElementTree
         root xml tree for intial nwb generation
     """
-    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
-    # "reconfig_probeDevice.trodesconf"
-    rec_header = convert_rec_header.read_header(trodesconf_file)
+    try:
+        # running on github
+        trodesconf_file = (
+            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        )  # "/test_data/reconfig_probeDevice.trodesconf"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
+    except:
+        # running locally
+        trodesconf_file = (
+            path + "/test_data/20230622_sample_01_a1.rec"
+        )  # "/test_data/reconfig_probeDevice.trodesconf"
+        rec_header = convert_rec_header.read_header(trodesconf_file)
     return rec_header
 
 
 def test_add_header_device():
     # Set up test data
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
-    recfile = data_path / "20230622_sample_01_a1.rec"
-
     # Call the function to be tested
-    convert_rec_header.add_header_device(
-        nwbfile, convert_rec_header.read_header(recfile)
-    )
+    try:
+        # running on github
+        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+        convert_rec_header.add_header_device(
+            nwbfile, convert_rec_header.read_header(recfile)
+        )
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = path + "/test_data/20230622_sample_01_a1.rec"
+        convert_rec_header.add_header_device(
+            nwbfile, convert_rec_header.read_header(recfile)
+        )
 
     # Perform assertions to check the results
     # Check if the device was added correctly
@@ -63,7 +80,7 @@ def test_add_header_device():
     assert header_device.file_path == ""
 
     # Check if error raised if improper header file is passed
-    recfile = data_path / "bad_header.trodesconf"
+    recfile = path + "/test_data/bad_header.trodesconf"
     with pytest.raises(
         ValueError,
         match="SpikeGadgets: the xml header does not contain '</Configuration>'",
@@ -78,9 +95,14 @@ def test_detect_ptp():
 
 def test_validate_yaml_header_electrode_map():
     # get metadata and rec_header
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    recfile = data_path / "20230622_sample_01_a1.rec"
+    try:
+        # running on github
+        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = path + "/test_data/20230622_sample_01_a1.rec"
     rec_header = convert_rec_header.read_header(recfile)
 
     # correct matching
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py b/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
index ce44d36..d68f8ad 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
@@ -1,7 +1,6 @@
-from datetime import datetime
 import logging
 import os
-import shutil
+from datetime import datetime
 
 from hdmf.common.table import DynamicTable, VectorData
 from ndx_franklab_novela import Probe, Shank, ShanksElectrode
@@ -9,15 +8,12 @@
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-from spikegadgets_to_nwb.data_scanner import get_file_info
-from spikegadgets_to_nwb.convert_position import add_associated_video_files
-from spikegadgets_to_nwb.tests.utils import data_path
 
-from ndx_franklab_novela import CameraDevice
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_initial_nwb_creation():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     # check that things were added in
@@ -38,7 +34,7 @@ def test_initial_nwb_creation():
 
 
 def test_subject_creation():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_subject(nwb_file, metadata)
@@ -54,7 +50,7 @@ def test_subject_creation():
 
 
 def test_camera_creation():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_cameras(nwb_file, metadata)
@@ -68,7 +64,7 @@ def test_camera_creation():
 
 
 def test_acq_device_creation():
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_acquisition_devices(nwb_file, metadata)
@@ -82,13 +78,20 @@ def test_acq_device_creation():
 
 def test_electrode_creation():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    probe_metadata = [data_path / "tetrode_12.5.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    probe_metadata = [
+        path + "/test_data/tetrode_12.5.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using rec data
-    recfile = data_path / "20230622_sample_01_a1.rec"
+    try:
+        # running on github
+        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
+    except (TypeError, FileNotFoundError):
+        # running locally
+        recfile = path + "/test_data/20230622_sample_01_a1.rec"
     rec_header = convert_rec_header.read_header(recfile)
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -153,8 +156,10 @@ def test_electrode_creation():
 
 def test_electrode_creation_reconfigured():
     # load metadata yml and make nwb file
-    metadata_path = data_path / "20230622_sample_metadataProbeReconfig.yml"
-    probe_metadata = [data_path / "128c-4s6mm6cm-15um-26um-sl.yml"]
+    metadata_path = path + "/test_data/20230622_sample_metadataProbeReconfig.yml"
+    probe_metadata = [
+        path + "/test_data/128c-4s6mm6cm-15um-26um-sl.yml",
+    ]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
@@ -163,7 +168,7 @@ def test_electrode_creation_reconfigured():
     metadata["ntrode_electrode_group_channel_map"][-1]["map"]["31"] = 126
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = data_path / "reconfig_probeDevice.trodesconf"
+    trodesconf_file = path + "/test_data/reconfig_probeDevice.trodesconf"
     rec_header = convert_rec_header.read_header(trodesconf_file)
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -230,7 +235,7 @@ def test_electrode_creation_reconfigured():
 
 def test_add_tasks():
     # Set up test data
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
@@ -284,12 +289,12 @@ def test_add_associated_files(capsys):
     # Create a logger
     logger = convert.setup_logger("convert", "testing.log")
     # Set up test data
-    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     # Change path of files to be relative to this directory
     for assoc_meta in metadata["associated_files"]:
-        assoc_meta["path"] = str(data_path / assoc_meta["name"])
+        assoc_meta["path"] = path + "/test_data/"
     # call the function to test
     convert_yaml.add_associated_files(nwbfile, metadata)
     assert "associated_files" in nwbfile.processing
@@ -311,7 +316,7 @@ def test_add_associated_files(capsys):
 
     # Test printed errormessage for missing file
     # Change path of files to be relative to this directory
-    metadata["associated_files"][0]["path"] = "bad_path.txt"
+    metadata["associated_files"][0]["path"] = ""
     metadata["associated_files"][0]["name"] = "bad_path.txt"
     metadata["associated_files"].pop(1)
     convert_yaml.add_associated_files(nwbfile, metadata)
@@ -326,42 +331,9 @@ def test_add_associated_files(capsys):
                     break
     assert printed_warning
 
-
-def test_add_associated_video_files():
-    # Set up test data
-    metadata_path = data_path / "20230622_sample_metadata.yml"
-    metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
-    convert_yaml.add_cameras(nwbfile, metadata)
-
-    # make session_df
-    path_df = get_file_info(data_path)
-    session_df = path_df[(path_df.animal == "sample")]
-
-    # make temp video directory
-    video_directory = data_path / "temp_video_directory"
-    if not os.path.exists(video_directory):
-        os.makedirs(video_directory)
-
-    # Call the function to be tested
-    add_associated_video_files(
-        nwbfile, metadata, session_df, video_directory=str(video_directory)
-    )
-    assert "video_files" in nwbfile.processing
-    assert "video" in nwbfile.processing["video_files"].data_interfaces
-    assert len(nwbfile.processing["video_files"]["video"].time_series) == 2
-
-    for video, video_meta in zip(
-        nwbfile.processing["video_files"]["video"].time_series,
-        metadata["associated_video_files"],
-    ):
-        video = nwbfile.processing["video_files"]["video"][video]
-        assert video.name == video_meta["name"]
-        assert video.format == "external"
-        assert video.timestamps_unit == "seconds"
-        assert video.timestamps is not None
-        assert isinstance(video.device, CameraDevice)
-        assert (video_directory / video.external_file[0]).exists()
-
-    # cleanup
-    shutil.rmtree(video_directory)
+    def test_add_associated_video_files():
+        # Set up test data
+        metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+        metadata, _ = convert_yaml.load_metadata(metadata_path, [])
+        nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
+        return
diff --git a/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml b/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
index 990c3f8..9531e6b 100644
--- a/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
+++ b/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
@@ -62,11 +62,20 @@ associated_files:
     path: path/
     task_epochs: 2
 associated_video_files:
-  - name: 20230622_sample_01_a1.1.h264
+  - name: video1
     camera_id: 0
     task_epochs: 1
-  - name: 20230622_sample_02_a1.1.h264
+  - name: video3
     camera_id: 0
+    task_epochs: 3
+  - name: video5
+    camera_id: 0
+    task_epochs: 5
+  - name: video2
+    camera_id: 1
+    task_epochs: 2
+  - name: video4
+    camera_id: 1
     task_epochs: 2
 units:
   analog: "-1"
diff --git a/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml b/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
deleted file mode 100644
index f0a8663..0000000
--- a/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
+++ /dev/null
@@ -1,1225 +0,0 @@
-
-experiment_description: Hippocampus content feedback
-experimenter_name: Michael Coulter
-institution: University of California, San Francisco
-lab: Loren Frank
-raw_data_to_volts: 1.95e-07
-session_description: Hippocampus content feedback
-session_id: ginny_20211027
-subject:
-  description: Long Evans Rat
-  genotype: Wild Type
-  sex: Male
-  species: Rat
-  subject_id: ginny
-  weight: Unknown
-  date_of_birth: 2000-01-01T00:00:00.000Z
-
-associated_files:
-- description: Statescript log run 1
-  name: statescript_r1
-  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_02_r1.stateScriptLog
-  task_epochs:
-  - 2
-- description: Statescript log run 2
-  name: statescript_r2
-  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_04_r2.stateScriptLog
-  task_epochs:
-  - 4
-- description: Statescript log run 3
-  name: statescript_r3
-  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_06_r3.stateScriptLog
-  task_epochs:
-  - 6
-
-associated_video_files:
-- name: 20211027_ginny_01_s1.1.h264
-  camera_id : 0
-  task_epochs: 1
-- name: 20211027_ginny_03_s2.1.h264
-  camera_id : 0
-  task_epochs: 3
-- name: 20211027_ginny_05_s3.1.h264
-  camera_id : 0
-  task_epochs: 5
-- name: 20211027_ginny_07_s4.1.h264
-  camera_id : 0
-  task_epochs: 7
-- name: 20211027_ginny_02_r1.1.h264
-  camera_id : 1
-  task_epochs: 2
-- name: 20211027_ginny_04_r2.1.h264
-  camera_id : 1
-  task_epochs: 4
-- name: 20211027_ginny_06_r3.1.h264
-  camera_id : 1
-  task_epochs: 6
-
-tasks:
-- camera_id:
-  - 1
-  task_description: training session
-  task_epochs:
-  - 2
-  - 4
-  - 6
-  task_name: Content feedback
-  task_environment: n/a
-- camera_id:
-  - 0
-  task_description: sleep
-  task_epochs:
-  - 1
-  - 3
-  - 5
-  - 7
-  task_name: Sleep
-  task_environment: n/a
-times_period_multiplier: 1.5
-units:
-  analog: unspecified
-  behavioral_events: unspecified
-
-cameras:
-- camera_name: MEC_sleep_camera
-  id: 0
-  lens: unknown2
-  manufacturer: unknown2
-  meters_per_pixel: 0.00055
-  model: unknown2
-- camera_name: MEC_run_camera
-  id: 1
-  lens: unknown
-  manufacturer: unknown
-  meters_per_pixel: 0.0022
-  model: unknown
-
-behavioral_events:
-- name: Arm1_poke
-  description: Din13
-- name: Arm2_poke
-  description: Din9
-- name: CenterWell_poke
-  description: Din7
-- name: BackWell_poke
-  description: Din10
-- name: Arm1_light
-  description: Dout13
-- name: Arm2_light
-  description: Dout9
-- name: CenterWell_light
-  description: Dout7
-- name: BackWell_light
-  description: Dout10
-- name: Arm1_milk_pump
-  description: Dout11
-- name: Arm2_milk_pump
-  description: Dout12
-- name: CenterWell_milk_pump
-  description: Dout14
-- name: BackWell_milk_pump
-  description: Dout8
-- name: CamerasyncRun camera ticks
-  description: Din15
-- name: CamerasyncSleep camera ticks
-  description: Din16
-
-data_acq_device:
-- adc_circuit: Intan
-  amplifier: Intan
-  system: SpikeGadgets
-default_header_file_path: default_header.xml
-device:
-  name:
-  - Trodes
-electrode_groups:
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 0
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 1
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 2
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 3
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 4
-  location: ''
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 5
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 6
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 7
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 8
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 9
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 10
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 11
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 12
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 13
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 14
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 15
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 16
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 17
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 18
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 19
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 20
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 21
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 22
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 23
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 24
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 25
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 26
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 27
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 28
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 29
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 30
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 31
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 32
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 33
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 34
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 35
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 36
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 37
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 38
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 39
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 40
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 41
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 42
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 43
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 44
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 45
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 46
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 47
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 48
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 49
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 50
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 51
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 52
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 53
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 54
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 55
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 56
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 57
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 58
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 59
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 60
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 61
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 62
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-- description: tetrode
-  device_type: tetrode_12.5
-  id: 63
-  location: ca1
-  targeted_location: CA1
-  targeted_x: 0.0
-  targeted_y: 0.0
-  targeted_z: 0.0
-  units: um
-
-ntrode_electrode_group_channel_map:
-- bad_channels: []
-  electrode_group_id: 0
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 1
-- bad_channels: [0]
-  electrode_group_id: 1
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 2
-- bad_channels: []
-  electrode_group_id: 2
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 3
-- bad_channels: []
-  electrode_group_id: 3
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 4
-- bad_channels: []
-  electrode_group_id: 4
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 5
-- bad_channels: []
-  electrode_group_id: 5
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 6
-- bad_channels: []
-  electrode_group_id: 6
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 7
-- bad_channels: []
-  electrode_group_id: 7
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 8
-- bad_channels: []
-  electrode_group_id: 8
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 9
-- bad_channels: []
-  electrode_group_id: 9
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 10
-- bad_channels: []
-  electrode_group_id: 10
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 11
-- bad_channels: []
-  electrode_group_id: 11
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 12
-- bad_channels: []
-  electrode_group_id: 12
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 13
-- bad_channels: []
-  electrode_group_id: 13
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 14
-- bad_channels: []
-  electrode_group_id: 14
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 15
-- bad_channels: []
-  electrode_group_id: 15
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 16
-- bad_channels: []
-  electrode_group_id: 16
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 17
-- bad_channels: []
-  electrode_group_id: 17
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 18
-- bad_channels: []
-  electrode_group_id: 18
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 19
-- bad_channels: []
-  electrode_group_id: 19
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 20
-- bad_channels: []
-  electrode_group_id: 20
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 21
-- bad_channels: []
-  electrode_group_id: 21
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 22
-- bad_channels: []
-  electrode_group_id: 22
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 23
-- bad_channels: []
-  electrode_group_id: 23
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 24
-- bad_channels: []
-  electrode_group_id: 24
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 25
-- bad_channels: []
-  electrode_group_id: 25
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 26
-- bad_channels: []
-  electrode_group_id: 26
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 27
-- bad_channels: []
-  electrode_group_id: 27
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 28
-- bad_channels: []
-  electrode_group_id: 28
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 29
-- bad_channels: []
-  electrode_group_id: 29
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 30
-- bad_channels: []
-  electrode_group_id: 30
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 31
-- bad_channels: []
-  electrode_group_id: 31
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 32
-- bad_channels: []
-  electrode_group_id: 32
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 33
-- bad_channels: []
-  electrode_group_id: 33
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 34
-- bad_channels: []
-  electrode_group_id: 34
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 35
-- bad_channels: []
-  electrode_group_id: 35
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 36
-- bad_channels: [0]
-  electrode_group_id: 36
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 37
-- bad_channels: []
-  electrode_group_id: 37
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 38
-- bad_channels: []
-  electrode_group_id: 38
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 39
-- bad_channels: []
-  electrode_group_id: 39
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 40
-- bad_channels: [2]
-  electrode_group_id: 40
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 41
-- bad_channels: []
-  electrode_group_id: 41
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 42
-- bad_channels: []
-  electrode_group_id: 42
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 43
-- bad_channels: []
-  electrode_group_id: 43
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 44
-- bad_channels: []
-  electrode_group_id: 44
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 45
-- bad_channels: []
-  electrode_group_id: 45
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 46
-- bad_channels: []
-  electrode_group_id: 46
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 47
-- bad_channels: []
-  electrode_group_id: 47
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 48
-- bad_channels: []
-  electrode_group_id: 48
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 49
-- bad_channels: []
-  electrode_group_id: 49
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 50
-- bad_channels: []
-  electrode_group_id: 50
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 51
-- bad_channels: []
-  electrode_group_id: 51
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 52
-- bad_channels: []
-  electrode_group_id: 52
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 53
-- bad_channels: []
-  electrode_group_id: 53
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 54
-- bad_channels: []
-  electrode_group_id: 54
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 55
-- bad_channels: []
-  electrode_group_id: 55
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 56
-- bad_channels: []
-  electrode_group_id: 56
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 57
-- bad_channels: []
-  electrode_group_id: 57
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 58
-- bad_channels: []
-  electrode_group_id: 58
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 59
-- bad_channels: []
-  electrode_group_id: 59
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 60
-- bad_channels: []
-  electrode_group_id: 60
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 61
-- bad_channels: []
-  electrode_group_id: 61
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 62
-- bad_channels: []
-  electrode_group_id: 62
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 63
-- bad_channels: []
-  electrode_group_id: 63
-  map:
-    '0': 0
-    '1': 1
-    '2': 2
-    '3': 3
-  ntrode_id: 64
diff --git a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
deleted file mode 100644
index 6cad848..0000000
--- a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
+++ /dev/null
@@ -1,212 +0,0 @@
-import pytest
-import copy
-
-basic_data = {
-    "experimenter_name": ["michael jackson"],
-    "lab": "Loren Frank Lab",
-    "institution": "University of California, San Francisco",
-    "experiment_description": "making of thriller",
-    "session_description": "make an album like the nutcracker",
-    "session_id": "6",
-    "keywords": ["best"],
-    "subject": {
-        "description": "Long-Evans Rat",
-        "genotype": "Wild Type",
-        "sex": "M",
-        "species": "Rattus norvegicus",
-        "subject_id": "1",
-        "date_of_birth": "2023-07-24T00:00:00.000Z",
-        "weight": 100,
-    },
-    "data_acq_device": [
-        {
-            "name": "SpikeGadgets",
-            "system": "SpikeGadgets",
-            "amplifier": "Intan",
-            "adc_circuit": "Intan",
-        }
-    ],
-    "cameras": [],
-    "tasks": [],
-    "associated_files": [],
-    "associated_video_files": [],
-    "units": {"analog": "1", "behavioral_events": "1"},
-    "times_period_multiplier": 1,
-    "raw_data_to_volts": 1,
-    "default_header_file_path": "epic/michaeljackson/thriller",
-    "behavioral_events": [],
-    "device": {"name": ["Trodes"]},
-    "electrode_groups": [],
-    "ntrode_electrode_group_channel_map": [],
-}
-
-basic_data_with_optional_arrays = {
-    "experimenter_name": ["michael jackson"],
-    "lab": "Loren Frank Lab",
-    "institution": "University of California, San Francisco",
-    "experiment_description": "making of thriller",
-    "session_description": "make an album like the nutcracker",
-    "session_id": "6",
-    "keywords": ["best"],
-    "subject": {
-        "description": "Long-Evans Rat",
-        "genotype": "Wild Type",
-        "sex": "M",
-        "species": "Rattus norvegicus",
-        "subject_id": "1",
-        "date_of_birth": "2023-07-24T00:00:00.000Z",
-        "weight": 100,
-    },
-    "data_acq_device": [
-        {
-            "name": "SpikeGadgets",
-            "system": "SpikeGadgets",
-            "amplifier": "Intan",
-            "adc_circuit": "Intan",
-        }
-    ],
-    "cameras": [
-        {
-            "id": 10,
-            "meters_per_pixel": 1,
-            "manufacturer": "Epic Record",
-            "model": "555",
-            "lens": "MJ lens",
-            "camera_name": "MJ cam",
-        },
-    ],
-    "tasks": [],
-    "associated_files": [
-        {
-            "name": "Michael Jackson",
-            "description": "Thriller25",
-            "path": "Hard work",
-            "task_epochs": 0,
-        },
-        {
-            "name": "Michael Jackson2",
-            "description": "HIStory",
-            "path": "Making/a/statement",
-            "task_epochs": 1,
-        },
-    ],
-    "associated_video_files": [
-        {
-            "name": "Michael Jackson",
-            "camera_id": 1,
-            "task_epochs": 1,
-        }
-    ],
-    "units": {"analog": "1", "behavioral_events": "1"},
-    "times_period_multiplier": 1,
-    "raw_data_to_volts": 1,
-    "default_header_file_path": "epic/michaeljackson/thriller",
-    "behavioral_events": [
-        {
-            "description": "Din555",
-            "name": "M. Joe Jackson",
-        }
-    ],
-    "device": {"name": ["Trodes"]},
-    "electrode_groups": [],
-    "ntrode_electrode_group_channel_map": [],
-}
-
-empty_experimenter_name = copy.deepcopy(basic_data)
-empty_experimenter_name["experimenter_name"] = []
-
-string_as_experimenter_name = copy.deepcopy(basic_data)
-string_as_experimenter_name["experimenter_name"] = ""
-
-empty_lab = copy.deepcopy(basic_data)
-empty_lab["lab"] = ""
-
-empty_institution = copy.deepcopy(basic_data)
-empty_institution["institution"] = ""
-
-empty_experiment_description = copy.deepcopy(basic_data)
-empty_experiment_description["experiment_description"] = ""
-
-empty_session_description = copy.deepcopy(basic_data)
-empty_session_description["session_description"] = ""
-
-empty_session_id = copy.deepcopy(basic_data)
-empty_session_id["session_id"] = ""
-
-empty_keywords = copy.deepcopy(basic_data)
-empty_keywords["keywords"] = []
-
-keywords_array_with_empty_item = copy.deepcopy(basic_data)
-keywords_array_with_empty_item["keywords"] = [""]
-
-not_array_keywords = copy.deepcopy(basic_data)
-not_array_keywords["keywords"] = "test"
-
-subject_with_empty_values = copy.deepcopy(basic_data)
-subject_with_empty_values["subject"] = {
-    "description": "",
-    "genotype": "",
-    "sex": "",
-    "species": "",
-    "subject_id": "",
-    "date_of_birth": "",
-    "weight": -1,
-}
-
-empty_subject = copy.deepcopy(basic_data)
-empty_subject["subject"] = {}
-
-subject_with_invalid_sex = copy.deepcopy(basic_data)
-subject_with_invalid_sex["subject"] = {
-    "description": "Long-Evans Rat",
-    "genotype": "Wild Type",
-    "sex": "m",
-    "species": "Rattus norvegicus",
-    "subject_id": "1",
-    "date_of_birth": "2023-07-24T00:00:00.000Z",
-    "weight": 100,
-}
-
-subject_with_invalid_date = copy.deepcopy(basic_data)
-subject_with_invalid_date["subject"] = {
-    "description": "Long-Evans Rat",
-    "genotype": "Wild Type",
-    "sex": "M",
-    "species": "Rattus norvegicus",
-    "subject_id": "1",
-    "date_of_birth": "2023-01-04",
-    "weight": 100,
-}
-
-data_acq_device_with_no_values = copy.deepcopy(basic_data)
-data_acq_device_with_no_values["data_acq_device"] = [
-    {"name": "", "system": "", "amplifier": "", "adc_circuit": ""}
-]
-
-empty_data_acq_device = copy.deepcopy(basic_data)
-empty_data_acq_device["data_acq_device"] = []
-
-empty_units = copy.deepcopy(basic_data)
-empty_units["units"] = {}
-
-invalid_times_period_multiplier = copy.deepcopy(basic_data)
-invalid_times_period_multiplier["times_period_multiplier"] = "a"
-
-invalid_raw_data_to_volts = copy.deepcopy(basic_data)
-invalid_raw_data_to_volts["raw_data_to_volts"] = "a"
-
-invalid_default_header_file_path = copy.deepcopy(basic_data)
-invalid_default_header_file_path["default_header_file_path"] = None
-
-empty_device_name = copy.deepcopy(basic_data)
-empty_device_name["device"] = {}
-
-basic_ntrode_electrode_group_channel_map = copy.deepcopy(basic_data)
-basic_ntrode_electrode_group_channel_map["ntrode_electrode_group_channel_map"] = [
-    {
-        "ntrode_id": "a",
-        "electrode_group_id": "z",
-        "bad_channels": ["z"],
-        "map": {"0": "0", "1": "t", "2": "a", "3": -3},
-    }
-]
diff --git a/src/spikegadgets_to_nwb/tests/test_metadata_validation.py b/src/spikegadgets_to_nwb/tests/test_metadata_validation.py
deleted file mode 100644
index 003e858..0000000
--- a/src/spikegadgets_to_nwb/tests/test_metadata_validation.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import copy
-import datetime
-from unittest.mock import MagicMock, patch
-from spikegadgets_to_nwb.metadata_validation import (
-    validate,
-    _get_nwb_json_schema_path,
-)
-from spikegadgets_to_nwb.tests.test_data import test_metadata_dict_samples
-
-
-def test_path_to_json_schema_is_correct():
-    path = _get_nwb_json_schema_path()
-    json_schema_file = "nwb_schema.json"
-
-    assert json_schema_file in path
-
-
-@patch("spikegadgets_to_nwb.metadata_validation._get_json_schema")
-@patch("jsonschema.Draft202012Validator")
-def test_verify_validation_called(jsonValidator, getSchema):
-    basic_test_data = copy.deepcopy(test_metadata_dict_samples.basic_data)
-    basic_test_data["subject"]["date_of_birth"] = datetime.datetime.now().isoformat()
-    validate(basic_test_data)
-    assert getSchema.call_count == 1
-    assert jsonValidator.call_count == 1
diff --git a/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py b/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
index 4aff4a5..7054c1f 100644
--- a/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
+++ b/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
@@ -1,13 +1,23 @@
+import os
+from pathlib import Path
+
 import numpy as np
 
 from spikegadgets_to_nwb.spike_gadgets_raw_io import InsertedMemmap, SpikeGadgetsRawIO
-from spikegadgets_to_nwb.tests.utils import data_path
+
+path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_spikegadgets_raw_io_interpolation():
     # Interpolation of dropped timestamp only done for ephys data and systime
 
     # get the path to the rec file
+    try:
+        # running on github
+        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
+    except (TypeError, FileNotFoundError):
+        # running locally
+        data_path = Path(path + "/test_data")
     rec_file = data_path / "20230622_sample_01_a1.rec"
 
     # create the SpikeGadgetsRawIO object
diff --git a/src/spikegadgets_to_nwb/tests/utils.py b/src/spikegadgets_to_nwb/tests/utils.py
deleted file mode 100644
index f97acbf..0000000
--- a/src/spikegadgets_to_nwb/tests/utils.py
+++ /dev/null
@@ -1,23 +0,0 @@
-"""Set the path to the bulk test data dir and copies the yaml/config files there"""
-import os
-from pathlib import Path
-import shutil
-
-
-yaml_path = Path(__file__).resolve().parent / "test_data"
-
-data_path = os.environ.get("DOWNLOAD_DIR", None)
-if data_path is not None:
-    # running from the GitHub Action workflow
-    data_path = Path(data_path)
-    shutil.copytree(
-        yaml_path,
-        data_path,
-        dirs_exist_ok=True,
-        ignore=shutil.ignore_patterns(*os.listdir(data_path)),  # ignore existing
-    )
-else:
-    # running locally -- bulk test data is the same directory as the test yaml files
-    data_path = yaml_path
-
-del yaml_path

From 173534ab721072eef6b96727be135cbee088178b Mon Sep 17 00:00:00 2001
From: Eric Denovellis <edeno@bu.edu>
Date: Fri, 27 Oct 2023 14:57:02 -0700
Subject: [PATCH 08/16] Revert "Revert "Merge branch 'main' into
 split_iterator""

This reverts commit cb52f19631e2e1f7277e40d93396ae738c374018.
---
 .github/workflows/test_package_build.yml      |     9 +-
 environment.yml                               |     3 +-
 pyproject.toml                                |     3 +-
 src/spikegadgets_to_nwb/convert.py            |    75 +-
 src/spikegadgets_to_nwb/convert_analog.py     |     1 -
 src/spikegadgets_to_nwb/convert_dios.py       |    24 +-
 src/spikegadgets_to_nwb/convert_intervals.py  |    16 +-
 src/spikegadgets_to_nwb/convert_position.py   |   390 +-
 src/spikegadgets_to_nwb/convert_yaml.py       |    21 +-
 .../metadata_validation.py                    |    75 +
 src/spikegadgets_to_nwb/nwb_schema.json       | 35971 ++++++++++++++++
 .../spike_gadgets_raw_io.py                   |    11 +-
 .../tests/integration-tests/__init__.py       |     0
 .../test_metadata_validation_it.py            |   190 +
 src/spikegadgets_to_nwb/tests/test_convert.py |    66 +-
 .../tests/test_convert_analog.py              |    21 +-
 .../tests/test_convert_dios.py                |    47 +-
 .../tests/test_convert_ephys.py               |   103 +-
 .../tests/test_convert_intervals.py           |    60 +-
 .../tests/test_convert_position.py            |    90 +-
 .../tests/test_convert_rec_header.py          |    48 +-
 .../tests/test_convert_yaml.py                |    90 +-
 .../test_data/20230622_sample_metadata.yml    |    13 +-
 .../tests/test_data/nonptp_metadata.yml       |  1225 +
 .../test_data/test_metadata_dict_samples.py   |   212 +
 .../tests/test_metadata_validation.py         |    25 +
 .../tests/test_spikegadgets_io.py             |    12 +-
 src/spikegadgets_to_nwb/tests/utils.py        |    23 +
 28 files changed, 38351 insertions(+), 473 deletions(-)
 create mode 100644 src/spikegadgets_to_nwb/metadata_validation.py
 create mode 100644 src/spikegadgets_to_nwb/nwb_schema.json
 create mode 100644 src/spikegadgets_to_nwb/tests/integration-tests/__init__.py
 create mode 100644 src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
 create mode 100644 src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
 create mode 100644 src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
 create mode 100644 src/spikegadgets_to_nwb/tests/test_metadata_validation.py
 create mode 100644 src/spikegadgets_to_nwb/tests/utils.py

diff --git a/.github/workflows/test_package_build.yml b/.github/workflows/test_package_build.yml
index a49a53e..880a840 100644
--- a/.github/workflows/test_package_build.yml
+++ b/.github/workflows/test_package_build.yml
@@ -46,6 +46,8 @@ jobs:
     strategy:
       matrix:
         package: ['wheel', 'sdist', 'archive', 'editable']
+    env:
+      DOWNLOAD_DIR: ${{ github.workspace }}/test_data
     steps:
       - name: Download sdist and wheel artifacts
         if: matrix.package != 'archive'
@@ -66,7 +68,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: 3
+          python-version: "3.11"
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Update pip
@@ -90,19 +92,14 @@ jobs:
           UCSF_BOX_TOKEN: ${{ secrets.UCSF_BOX_TOKEN }}
           UCSF_BOX_USER: ${{ secrets.UCSF_BOX_USER }}
           WEBSITE: ftps://ftp.box.com/spikegadgets_to_nwb_test_data/
-          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: |
           wget --recursive --no-verbose --no-host-directories --no-directories --user $UCSF_BOX_USER --password $UCSF_BOX_TOKEN -P $DOWNLOAD_DIR $WEBSITE
           tree $DOWNLOAD_DIR
       - name: Run tests without coverage
         if: matrix.package != 'editable'
-        env:
-          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: pytest --doctest-modules -v --pyargs spikegadgets_to_nwb
       - name: Run tests with coverage
         if: matrix.package == 'editable'
-        env:
-          DOWNLOAD_DIR: ${{ github.workspace }}/src/spikegadgets_to_nwb/tests/test_data
         run: pytest --cov=src --cov-report=xml --doctest-modules -v --pyargs spikegadgets_to_nwb
       - name: Upload coverage reports to Codecov
         if: matrix.package == 'editable'
diff --git a/environment.yml b/environment.yml
index 63dcffa..95ccd1b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,8 +15,9 @@ dependencies:
 - pytest-cov
 - pip
 - pyyaml
+- jsonschema
 - ffmpeg
 - pip:
     - ndx-franklab-novela
     - neo
-    - hdmf=3.8.1
+    - hdmf==3.8.1
diff --git a/pyproject.toml b/pyproject.toml
index 4d3b5b8..04f93e3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,8 +10,9 @@ requires-python = ">=3.8"
 license = { file = "LICENSE" }
 authors = [
     { name = "Sam Bray", email = "sam.bray@ucsf.edu" },
-    { name = "Ryan Ly", email = "rly@lbl.gov" },
     { name = "Eric Denovellis", email = "eric.denovellis@ucsf.edu" },
+    { name = "Ryan Ly", email = "rly@lbl.gov" },
+    { name = "Philip Adenekan", email = "phil.adenekan@ucsf.edu" },
     { name = "Loren Frank", email = "loren.frank@ucsf.edu" },
 ]
 classifiers = [
diff --git a/src/spikegadgets_to_nwb/convert.py b/src/spikegadgets_to_nwb/convert.py
index 6318a61..e2ec922 100644
--- a/src/spikegadgets_to_nwb/convert.py
+++ b/src/spikegadgets_to_nwb/convert.py
@@ -10,9 +10,13 @@
 from spikegadgets_to_nwb.convert_dios import add_dios
 from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator, add_raw_ephys
 from spikegadgets_to_nwb.convert_intervals import add_epochs, add_sample_count
-from spikegadgets_to_nwb.convert_position import add_position
+from spikegadgets_to_nwb.convert_position import (
+    add_associated_video_files,
+    add_position,
+)
 from spikegadgets_to_nwb.convert_rec_header import (
     add_header_device,
+    detect_ptp_from_header,
     make_hw_channel_map,
     make_ref_electrode_map,
     read_header,
@@ -105,7 +109,34 @@ def create_nwbs(
     video_directory: str = "",
     convert_video: bool = False,
     n_workers: int = 1,
+    query_expression: str | None = None,
 ):
+    """
+    Convert SpikeGadgets data to NWB format.
+
+    Parameters
+    ----------
+    path : Path
+        Path to the SpikeGadgets data file.
+    header_reconfig_path : Path, optional
+        Path to the header reconfiguration file, by default None.
+    probe_metadata_paths : list[Path], optional
+        List of paths to the probe metadata files, by default None.
+    output_dir : str, optional
+        Output directory for the NWB files, by default "/home/stelmo/nwb/raw".
+    video_directory : str, optional
+        Directory containing the video files, by default "".
+    convert_video : bool, optional
+        Whether to convert the video files, by default False.
+    n_workers : int, optional
+        Number of workers to use for parallel processing, by default 1.
+    query_expression : str, optional
+        Pandas query expression to filter the data, by default None.
+        e.g. "animal == 'sample' and epoch == 1"
+        See https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html.
+
+    """
+
     if not isinstance(path, Path):
         path = Path(path)
 
@@ -115,6 +146,9 @@ def create_nwbs(
 
     file_info = get_file_info(path)
 
+    if query_expression is not None:
+        file_info = file_info.query(query_expression)
+
     if n_workers > 1:
 
         def pass_func(args):
@@ -225,6 +259,9 @@ def _create_nwb(
         nwb_file, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
     add_header_device(nwb_file, rec_header)
+    add_associated_video_files(
+        nwb_file, metadata, session_df, video_directory, convert_video
+    )
 
     logger.info("ADDING EPHYS DATA")
     ### add rec file data ###
@@ -243,26 +280,32 @@ def _create_nwb(
     add_analog_data(nwb_file, rec_filepaths, timestamps=rec_dci_timestamps)
     logger.info("ADDING SAMPLE COUNTS")
     add_sample_count(nwb_file, rec_dci)
-    logger.info("ADDING POSITION")
-    ### add position ###
-    add_position(
-        nwb_file,
-        metadata,
-        session_df,
-        rec_header,
-        video_directory=video_directory,
-        convert_video=convert_video,
-    )
-
-    # add epochs
     logger.info("ADDING EPOCHS")
     add_epochs(
         nwbfile=nwb_file,
-        file_info=session_df,
-        date=session[0],
-        animal=session[1],
+        session_df=session_df,
         neo_io=rec_dci.neo_io,
     )
+    logger.info("ADDING POSITION")
+    ### add position ###
+    ptp_enabled = detect_ptp_from_header(rec_header)
+    if ptp_enabled:
+        add_position(
+            nwb_file,
+            metadata,
+            session_df,
+        )
+    else:
+        add_position(
+            nwb_file,
+            metadata,
+            session_df,
+            ptp_enabled=ptp_enabled,
+            rec_dci_timestamps=rec_dci_timestamps,
+            sample_count=nwb_file.processing["sample_count"]
+            .data_interfaces["sample_count"]
+            .data,
+        )
 
     # write file
     logger.info(f"WRITING: {output_dir}/{session[1]}{session[0]}.nwb")
diff --git a/src/spikegadgets_to_nwb/convert_analog.py b/src/spikegadgets_to_nwb/convert_analog.py
index 0bdfb3e..f0c2ad1 100644
--- a/src/spikegadgets_to_nwb/convert_analog.py
+++ b/src/spikegadgets_to_nwb/convert_analog.py
@@ -1,4 +1,3 @@
-from warnings import warn
 from xml.etree import ElementTree
 
 import numpy as np
diff --git a/src/spikegadgets_to_nwb/convert_dios.py b/src/spikegadgets_to_nwb/convert_dios.py
index 8161c53..b28341e 100644
--- a/src/spikegadgets_to_nwb/convert_dios.py
+++ b/src/spikegadgets_to_nwb/convert_dios.py
@@ -70,26 +70,24 @@ def add_dios(nwbfile: NWBFile, recfile: list[str], metadata: dict) -> None:
             prefix = "ECU_"
             break
 
-    for channel_name in channel_name_map:
-        # merge streams from multiple files
-        all_timestamps = []
-        all_state_changes = []
-        for io in neo_io:
+    # compile data for all dio channels in all files
+    all_timestamps = [np.array([], dtype=np.float64) for i in channel_name_map]
+    all_state_changes = [np.array([], dtype=np.float64) for i in channel_name_map]
+    for io in neo_io:
+        for i, channel_name in enumerate(channel_name_map):
             timestamps, state_changes = io.get_digitalsignal(
                 stream_name, prefix + channel_name
             )
-            all_timestamps.append(timestamps)
-            all_state_changes.append(state_changes)
-        all_timestamps = np.concatenate(all_timestamps)
-        all_state_changes = np.concatenate(all_state_changes)
-        assert isinstance(all_timestamps[0], np.float64)
-        assert isinstance(all_timestamps, np.ndarray)
+            all_timestamps[i] = np.concatenate((all_timestamps[i], timestamps))
+            all_state_changes[i] = np.concatenate((all_state_changes[i], state_changes))
+    # Add each channel as a behavioral event time series
+    for i, channel_name in enumerate(channel_name_map):
         ts = TimeSeries(
             name=channel_name_map[channel_name],
             description=channel_name,
-            data=all_state_changes,
+            data=all_state_changes[i],
             unit="-1",  # TODO change to "N/A",
-            timestamps=all_timestamps,  # TODO adjust timestamps
+            timestamps=all_timestamps[i],  # TODO adjust timestamps
         )
         beh_events.add_timeseries(ts)
 
diff --git a/src/spikegadgets_to_nwb/convert_intervals.py b/src/spikegadgets_to_nwb/convert_intervals.py
index 709d76b..e76843a 100644
--- a/src/spikegadgets_to_nwb/convert_intervals.py
+++ b/src/spikegadgets_to_nwb/convert_intervals.py
@@ -14,9 +14,7 @@
 
 def add_epochs(
     nwbfile: NWBFile,
-    file_info: pd.DataFrame,
-    date: int,
-    animal: str,
+    session_df: pd.DataFrame,
     neo_io: List[SpikeGadgetsRawIO],
 ):
     """add epochs to nwbfile
@@ -35,11 +33,13 @@ def add_epochs(
         neo_io iterators for each rec file. Contains time information
     """
     logger = logging.getLogger("convert")
-    session_info = file_info[(file_info.date == date) & (file_info.animal == animal)]
-    for epoch in set(session_info.epoch):
-        rec_file_list = session_info[
-            (session_info.epoch == epoch) & (session_info.file_extension == ".rec")
+    for epoch in set(session_df.epoch):
+        rec_file_list = session_df[
+            (session_df.epoch == epoch) & (session_df.file_extension == ".rec")
         ]
+        if len(rec_file_list) == 0:
+            logger.info(f"no rec files for epoch {epoch}, No epoch interval created")
+            continue
         start_time = None
         end_time = None
         logger.info(list(rec_file_list.full_path))
@@ -58,7 +58,7 @@ def add_epochs(
                     )
                 else:
                     file_end_time = np.max(
-                        io._get_systime_from_trodes_timestamps(n_time - 1, n_time)
+                        io.get_systime_from_trodes_timestamps(n_time - 1, n_time)
                     )
                 if end_time is None or file_end_time > end_time:
                     end_time = float(file_end_time)
diff --git a/src/spikegadgets_to_nwb/convert_position.py b/src/spikegadgets_to_nwb/convert_position.py
index a2ae0d8..eedbc58 100644
--- a/src/spikegadgets_to_nwb/convert_position.py
+++ b/src/spikegadgets_to_nwb/convert_position.py
@@ -3,7 +3,6 @@
 import re
 import subprocess
 from pathlib import Path
-from xml.etree import ElementTree
 
 import numpy as np
 import pandas as pd
@@ -13,8 +12,6 @@
 from scipy.ndimage import label
 from scipy.stats import linregress
 
-from spikegadgets_to_nwb.convert_rec_header import detect_ptp_from_header
-
 NANOSECONDS_PER_SECOND = 1e9
 
 
@@ -127,7 +124,7 @@ def get_framerate(timestamps: np.ndarray) -> float:
     Parameters
     ----------
     timestamps : np.ndarray
-        An array of timestamps for each frame in the video.
+        An array of timestamps for each frame in the video, units = nanoseconds.
 
     Returns
     -------
@@ -150,7 +147,7 @@ def find_acquisition_timing_pause(
     Parameters
     ----------
     timestamps : np.ndarray
-        An array of timestamps for each frame in the video.
+        An array of timestamps for each frame in the video. Expects units=nanoseconds.
     min_duration : float, optional
         The minimum duration of the pause in seconds, by default 0.4.
     max_duration : float, optional
@@ -161,7 +158,7 @@ def find_acquisition_timing_pause(
     Returns
     -------
     pause_mid_time : float
-        The midpoint time of the timing pause.
+        The midpoint time of the timing pause in nanoseconds.
 
     """
     timestamps = np.asarray(timestamps)
@@ -374,20 +371,69 @@ def correct_timestamps_for_camera_to_mcu_lag(
     corrected_camera_systime = (
         regression_result.intercept + frame_count * regression_result.slope
     )
-    corrected_camera_systime /= NANOSECONDS_PER_SECOND
+    # corrected_camera_systime /= NANOSECONDS_PER_SECOND
 
     return corrected_camera_systime
 
 
-def find_camera_dio_channel(dios):
-    raise NotImplementedError
+def find_camera_dio_channel(nwb_file):
+    dio_camera_name = [
+        key
+        for key in nwb_file.processing["behavior"]
+        .data_interfaces["behavioral_events"]
+        .time_series
+        if "camera ticks" in key
+    ]
+    if len(dio_camera_name) > 1:
+        raise ValueError(
+            "Multiple camera dio channels found by name. Not implemented for multiple cameras without PTP yet."
+        )
+
+    if len(dio_camera_name) == 0:
+        raise ValueError(
+            "No camera dio channel found by name. Check metadata YAML. Name must contain 'camera ticks'"
+        )
+
+    return (
+        nwb_file.processing["behavior"]
+        .data_interfaces["behavioral_events"]
+        .time_series[dio_camera_name[0]]
+        .timestamps
+    )
+
+
+def get_video_timestamps(video_timestamps_filepath: Path) -> np.ndarray:
+    """
+    Get video timestamps.
+
+    Parameters
+    ----------
+    video_timestamps_filepath : Path
+        Path to the video timestamps file.
+
+    Returns
+    -------
+    np.ndarray
+        An array of video timestamps.
+    """
+    # Get video timestamps
+    video_timestamps = (
+        pd.DataFrame(read_trodes_datafile(video_timestamps_filepath)["data"])
+        .set_index("PosTimestamp")
+        .rename(columns={"frameCount": "HWframeCount"})
+    )
+    return (
+        np.asarray(video_timestamps.HWTimestamp, dtype=np.float64)
+        / NANOSECONDS_PER_SECOND
+    )
 
 
 def get_position_timestamps(
     position_timestamps_filepath: Path,
     position_tracking_filepath=None | Path,
-    mcu_neural_timestamps=None | np.ndarray,
-    dios=None,
+    rec_dci_timestamps=None | np.ndarray,
+    dio_camera_timestamps=None | np.ndarray,
+    sample_count=None | np.ndarray,
     ptp_enabled: bool = True,
 ):
     logger = logging.getLogger("convert")
@@ -461,57 +507,57 @@ def get_position_timestamps(
             )[0][0]
             + 1
         )
-        original_video_timestamps = video_timestamps.copy()
         video_timestamps = video_timestamps.iloc[pause_mid_ind:]
         logger.info(
             "Camera frame rate estimated from MCU timestamps:"
             f" {1 / np.median(np.diff(video_timestamps.index)):0.1f} frames/s"
         )
-        return video_timestamps, original_video_timestamps
+        return video_timestamps
     else:
-        dio_camera_ticks = find_camera_dio_channel(dios)
-        is_valid_tick = np.isin(dio_camera_ticks, mcu_neural_timestamps.index)
-        dio_systime = np.asarray(
-            mcu_neural_timestamps.loc[dio_camera_ticks[is_valid_tick]]
-        )
-        # The DIOs and camera frames are initially unaligned. There is a
-        # half second pause at the start to allow for alignment.
-        pause_mid_time = find_acquisition_timing_pause(dio_systime)
+        try:
+            pause_mid_time = (
+                find_acquisition_timing_pause(
+                    dio_camera_timestamps * NANOSECONDS_PER_SECOND
+                )
+                / NANOSECONDS_PER_SECOND
+            )
+            frame_rate_from_dio = get_framerate(
+                dio_camera_timestamps[dio_camera_timestamps > pause_mid_time]
+            )
+            logger.info(
+                "Camera frame rate estimated from DIO camera ticks:"
+                f" {frame_rate_from_dio:0.1f} frames/s"
+            )
+        except IndexError:
+            pause_mid_time = -1
 
-        # Estimate the frame rate from the DIO camera ticks as a sanity check.
-        frame_rate_from_dio = get_framerate(dio_systime[dio_systime > pause_mid_time])
-        logger.info(
-            "Camera frame rate estimated from DIO camera ticks:"
-            f" {frame_rate_from_dio:0.1f} frames/s"
-        )
         frame_count = np.asarray(video_timestamps.HWframeCount)
 
-        camera_systime, is_valid_camera_time = estimate_camera_time_from_mcu_time(
-            video_timestamps, mcu_neural_timestamps
-        )
+        is_valid_camera_time = np.isin(video_timestamps.index, sample_count)
+
+        camera_systime = rec_dci_timestamps[
+            np.digitize(video_timestamps.index[is_valid_camera_time], sample_count)
+        ]
         (
-            dio_systime,
+            dio_camera_timestamps,
             frame_count,
             is_valid_camera_time,
             camera_systime,
         ) = remove_acquisition_timing_pause_non_ptp(
-            dio_systime,
+            dio_camera_timestamps,
             frame_count,
             camera_systime,
             is_valid_camera_time,
             pause_mid_time,
         )
-        original_video_timestamps = video_timestamps.copy()
         video_timestamps = video_timestamps.iloc[is_valid_camera_time]
-
         frame_rate_from_camera_systime = get_framerate(camera_systime)
         logger.info(
-            "Camera frame rate estimated from MCU timestamps:"
+            "Camera frame rate estimated from camera sys time:"
             f" {frame_rate_from_camera_systime:0.1f} frames/s"
         )
-
         camera_to_mcu_lag = estimate_camera_to_mcu_lag(
-            camera_systime, dio_systime, len(non_repeat_timestamp_labels_id)
+            camera_systime, dio_camera_timestamps, len(non_repeat_timestamp_labels_id)
         )
         corrected_camera_systime = []
         for id in non_repeat_timestamp_labels_id:
@@ -524,22 +570,73 @@ def get_position_timestamps(
                 )
             )
         corrected_camera_systime = np.concatenate(corrected_camera_systime)
-        video_timestamps.iloc[
-            is_valid_camera_time
-        ].index = corrected_camera_systime.index
-        return (
-            video_timestamps.set_index(pd.Index(corrected_camera_systime, name="time")),
-            original_video_timestamps,
+
+        video_timestamps = video_timestamps.set_index(
+            pd.Index(corrected_camera_systime, name="time")
+        )
+        return video_timestamps.groupby(
+            video_timestamps.index
+        ).first()  # TODO: Figure out why duplicate timesteps make it to this point and why this line is necessary
+
+
+def find_camera_dio_channel_per_epoch(
+    nwb_file: NWBFile, epoch_start: float, epoch_end: float
+):
+    """Find the camera dio channel for a given epoch.
+    Searches through dio channels with "camera ticks" in the name.
+    Selects first one with at least 100 ticks in the epoch.
+
+    Parameters
+    ----------
+    nwb_file : NWBFile
+        The NWBFile to find the dio channel in.
+    epoch_start : float
+        timestamp of the start of the epoch
+    epoch_end : float
+        timestamp of the end of the epoch
+
+    Returns
+    -------
+    dio_camera_timestamps : np.ndarray
+        The dio timestamps for the camera restricted to the epoch of interest
+
+    Raises
+    ------
+    ValueError
+        Error if dio's  are not added to the nwbfile
+    ValueError
+        Error if no camera dio channel is found
+    """
+    dio_camera_list = [
+        key
+        for key in nwb_file.processing["behavior"]["behavioral_events"].time_series
+        if "camera ticks" in key
+    ]
+    if not dio_camera_list:
+        raise ValueError(
+            "No camera dio channel found by name. Check metadata YAML. Name must contain 'camera ticks'"
         )
+    for camera in dio_camera_list:
+        dio_camera_timestamps = (
+            nwb_file.processing["behavior"]["behavioral_events"]
+            .time_series[camera]
+            .timestamps
+        )
+        epoch_ind = np.logical_and(
+            dio_camera_timestamps >= epoch_start, dio_camera_timestamps <= epoch_end
+        )
+        if np.sum(epoch_ind) > 100:
+            return dio_camera_timestamps[epoch_ind]
+    raise ValueError("No camera dio has sufficient ticks for this epoch")
 
 
 def add_position(
     nwb_file: NWBFile,
     metadata: dict,
     session_df: pd.DataFrame,
-    rec_header: ElementTree.ElementTree,
-    video_directory: str,
-    convert_video: bool = False,
+    ptp_enabled: bool = True,
+    rec_dci_timestamps: np.ndarray | None = None,
+    sample_count: np.ndarray | None = None,
 ):
     """
     Add position data to an NWBFile.
@@ -552,12 +649,12 @@ def add_position(
         Metadata about the experiment.
     session_df : pd.DataFrame
         A DataFrame containing information about the session.
-    rec_header : ElementTree.ElementTree
-        The recording header.
-    video_directory : str
-        The directory containing the video files.
-    convert_video : bool, optional
-        Whether to convert the video files to NWB format, by default False.
+    ptp_enabled : bool, optional
+        Whether PTP was enabled, by default True.
+    rec_dci_timestamps : np.ndarray, optional
+        The recording timestamps, by default None. Only used if ptp not enabled.
+    sample_count : np.ndarray, optional
+        The trodes sample count, by default None. Only used if ptp not enabled.
     """
     logger = logging.getLogger("convert")
 
@@ -588,29 +685,21 @@ def add_position(
     epoch_to_camera_ids = pd.concat(df).set_index("epoch").sort_index()
 
     position = Position(name="position")
-    ptp_enabled = detect_ptp_from_header(rec_header)
 
     # Make a processing module for behavior and add to the nwbfile
     if not "behavior" in nwb_file.processing:
         nwb_file.create_processing_module(
             name="behavior", description="Contains all behavior-related data"
         )
-
-    # make processing module for video files
-    nwb_file.create_processing_module(
-        name="video_files", description="Contains all associated video files data"
-    )
-    # make a behavioral Event object to hold videos
-    video = BehavioralEvents(name="video")
+    # get epoch data to seperate dio timestamps into epochs
+    if (not ptp_enabled) and (not len(nwb_file.epochs)):
+        raise ValueError(
+            "add_epochs() must be run before add_position() for non-ptp data"
+        )
+    if not ptp_enabled:
+        epoch_df = nwb_file.epochs.to_dataframe()
 
     for epoch in session_df.epoch.unique():
-        position_timestamps_filepath = session_df.loc[
-            np.logical_and(
-                session_df.epoch == epoch,
-                session_df.file_extension == ".cameraHWSync",
-            )
-        ].full_path.to_list()[0]
-
         try:
             position_tracking_filepath = session_df.loc[
                 np.logical_and(
@@ -618,6 +707,21 @@ def add_position(
                     session_df.file_extension == ".videoPositionTracking",
                 )
             ].full_path.to_list()[0]
+            # find the matching hw timestamps filepath
+            video_index = position_tracking_filepath.split(".")[-2]
+            video_hw_df = session_df.loc[
+                np.logical_and(
+                    session_df.epoch == epoch,
+                    session_df.file_extension == ".cameraHWSync",
+                )
+            ]
+            position_timestamps_filepath = video_hw_df[
+                [
+                    full_path.split(".")[-3] == video_index
+                    for full_path in video_hw_df.full_path
+                ]
+            ].full_path.to_list()[0]
+
         except IndexError:
             position_tracking_filepath = None
 
@@ -625,10 +729,23 @@ def add_position(
         logger.info(f"\tposition_timestamps_filepath: {position_timestamps_filepath}")
         logger.info(f"\tposition_tracking_filepath: {position_tracking_filepath}")
 
-        position_df, original_video_timestamps = get_position_timestamps(
+        # restrict dio camera timestamps to the current epoch
+        if not ptp_enabled:
+            epoch_start = epoch_df[epoch_df.index == epoch - 1]["start_time"].iloc[0]
+            epoch_end = epoch_df[epoch_df.index == epoch - 1]["stop_time"].iloc[0]
+            dio_camera_timestamps_epoch = find_camera_dio_channel_per_epoch(
+                nwb_file=nwb_file, epoch_start=epoch_start, epoch_end=epoch_end
+            )
+        else:
+            dio_camera_timestamps_epoch = None
+
+        position_df = get_position_timestamps(
             position_timestamps_filepath,
             position_tracking_filepath,
             ptp_enabled=ptp_enabled,
+            rec_dci_timestamps=rec_dci_timestamps,
+            dio_camera_timestamps=dio_camera_timestamps_epoch,
+            sample_count=sample_count,
         )
 
         # TODO: Doesn't handle multiple cameras currently
@@ -650,14 +767,7 @@ def add_position(
                         timestamps=np.asarray(position_df.index),
                     )
         else:
-            position.create_spatial_series(
-                name=f"series_{epoch}",
-                description=", ".join(["xloc", "yloc"]),
-                data=np.asarray([]),
-                conversion=meters_per_pixel,
-                reference_frame="Upper left corner of video frame",
-                timestamps=np.asarray(position_df.index),
-            )
+            logging.warning(f"No position tracking data found for epoch {epoch}")
 
         # add the video frame index as a new processing module
         if "position_frame_index" not in nwb_file.processing:
@@ -690,41 +800,10 @@ def add_position(
             )
         )
 
-        # add the video file data
-        # find the video metadata for this epoch
-        video_metadata = None
-        for vid_ in metadata["associated_video_files"]:
-            if vid_["task_epochs"][0] == epoch:
-                video_metadata = vid_
-                break
-        if video_metadata is None:
-            raise KeyError(f"Missing video metadata for epoch {epoch}")
-
-        if convert_video:
-            video_file_name = convert_h264_to_mp4(
-                os.path.join(video_directory, video_metadata["name"])
-            )
-        else:
-            video_file_name = os.path.join(video_directory, video_metadata["name"])
-
-        video.add_timeseries(
-            ImageSeries(
-                device=nwb_file.devices[
-                    "camera_device " + str(video_metadata["camera_id"])
-                ],
-                name=video_metadata["name"],
-                timestamps=np.asarray(position_df.index),
-                external_file=[video_file_name],
-                format="external",
-                starting_frame=[0],
-                description="video of animal behavior from epoch",
-            )
-        )
     nwb_file.processing["behavior"].add(position)
-    nwb_file.processing["video_files"].add(video)
 
 
-def convert_h264_to_mp4(file: str) -> str:
+def convert_h264_to_mp4(file: str, video_directory: str) -> str:
     """
     Converts h264 file to mp4 file using ffmpeg.
 
@@ -732,6 +811,8 @@ def convert_h264_to_mp4(file: str) -> str:
     ----------
     file : str
         The path to the input h264 file.
+    video_directory : str
+        Where to save the output mp4 file.
 
     Returns
     -------
@@ -745,6 +826,7 @@ def convert_h264_to_mp4(file: str) -> str:
 
     """
     new_file_name = file.replace(".h264", ".mp4")
+    new_file_name = video_directory + "/" + new_file_name.split("/")[-1]
     logger = logging.getLogger("convert")
     if os.path.exists(new_file_name):
         return new_file_name
@@ -760,3 +842,95 @@ def convert_h264_to_mp4(file: str) -> str:
             f"Video conversion FAILED. {file} has NOT been converted to {new_file_name}"
         )
         raise e
+
+
+def copy_video_to_directory(file: str, video_directory: str) -> str:
+    """Copies video file to video directory without conversion"""
+    new_file_name = video_directory + "/" + file.split("/")[-1]
+    logger = logging.getLogger("convert")
+    if os.path.exists(new_file_name):
+        return new_file_name
+    try:
+        # Construct the ffmpeg command
+        subprocess.run(f"cp {file} {new_file_name}", shell=True)
+        logger.info(f"Video copy completed. {file} has been copied to {new_file_name}")
+        return new_file_name
+    except subprocess.CalledProcessError as e:
+        logger.error(
+            f"Video copy FAILED. {file} has NOT been copied to {new_file_name}"
+        )
+        raise e
+
+
+def add_associated_video_files(
+    nwb_file: NWBFile,
+    metadata: dict,
+    session_df: pd.DataFrame,
+    video_directory: str,
+    convert_video: bool = False,
+):
+    # make processing module for video files
+    nwb_file.create_processing_module(
+        name="video_files", description="Contains all associated video files data"
+    )
+    # make a behavioral Event object to hold videos
+    video = BehavioralEvents(name="video")
+    # add the video file data
+    for video_metadata in metadata["associated_video_files"]:
+        epoch = video_metadata["task_epochs"][0]
+        # get the video file path
+        video_path = None
+        for file in session_df[session_df.file_extension == ".h264"].full_path:
+            if video_metadata["name"].rsplit(".", 1)[0] in file:
+                video_path = file
+                break
+        if video_path is None:
+            raise FileNotFoundError(
+                f"Could not find video file {video_metadata['name']} in session_df"
+            )
+
+        # get timestamps for this video
+        # find the matching hw timestamps filepath
+        video_index = video_path.split(".")[-2]
+        video_hw_df = session_df.loc[
+            np.logical_and(
+                session_df.epoch == epoch,
+                session_df.file_extension == ".cameraHWSync",
+            )
+        ]
+        if not len(video_hw_df):
+            raise ValueError(
+                f"No cameraHWSync found for epoch {epoch}, video {video_index} in session_df"
+            )
+        video_timestamps_filepath = video_hw_df[
+            [
+                full_path.split(".")[-3] == video_index
+                for full_path in video_hw_df.full_path
+            ]
+        ].full_path.to_list()[0]
+        # get the timestamps
+        video_timestamps = get_video_timestamps(video_timestamps_filepath)
+
+        if convert_video:
+            video_file_name = convert_h264_to_mp4(video_path, video_directory)
+        else:
+            video_file_name = copy_video_to_directory(video_path, video_directory)
+
+        video.add_timeseries(
+            ImageSeries(
+                device=nwb_file.devices[
+                    "camera_device " + str(video_metadata["camera_id"])
+                ],
+                name=video_metadata["name"],
+                timestamps=video_timestamps,
+                external_file=[video_file_name.split("/")[-1]],
+                format="external",
+                starting_frame=[0],
+                description="video of animal behavior from epoch",
+            )
+        )
+    if video_metadata is None:
+        raise KeyError(f"Missing video metadata for epoch {epoch}")
+
+    nwb_file.processing["video_files"].add(video)
+    return
diff --git a/src/spikegadgets_to_nwb/convert_yaml.py b/src/spikegadgets_to_nwb/convert_yaml.py
index c0bd4a0..6cd4d1e 100644
--- a/src/spikegadgets_to_nwb/convert_yaml.py
+++ b/src/spikegadgets_to_nwb/convert_yaml.py
@@ -20,6 +20,9 @@
 from pynwb.ecephys import ElectrodeGroup
 from pynwb.file import ProcessingModule, Subject
 
+import spikegadgets_to_nwb.metadata_validation
+from spikegadgets_to_nwb import __version__
+
 
 def load_metadata(
     metadata_path: str, probe_metadata_paths: list[str]
@@ -38,8 +41,16 @@ def load_metadata(
     tuple[dict, list[dict]]
         the yaml generator metadata and list of probe metadatas
     """
+    metadata = None
     with open(metadata_path, "r") as stream:
         metadata = yaml.safe_load(stream)
+    (
+        is_metadata_valid,
+        metadata_errors,
+    ) = spikegadgets_to_nwb.metadata_validation.validate(metadata)
+    if not is_metadata_valid:
+        logger = logging.getLogger("convert")
+        logger.exception("".join(metadata_errors))
     probe_metadata = []
     for path in probe_metadata_paths:
         with open(path, "r") as stream:
@@ -82,6 +93,8 @@ def initialize_nwb(metadata: dict, first_epoch_config: ElementTree) -> NWBFile:
         session_id=metadata["session_id"],
         # notes=self.link_to_notes, TODO
         experiment_description=metadata["experiment_description"],
+        source_script="spikegadgets_to_nwb " + __version__,
+        source_script_file_name="convert.py",
     )
     return nwbfile
 
@@ -392,15 +405,13 @@ def add_associated_files(nwbfile: NWBFile, metadata: dict) -> None:
         # read file content
         content = ""
         try:
-            with open(file["path"] + file["name"], "r") as open_file:
+            with open(file["path"], "r") as open_file:
                 content = open_file.read()
         except FileNotFoundError as err:
-            logger.info(
-                f"ERROR: associated file {file['path']+file['name']} does not exist"
-            )
+            logger.info(f"ERROR: associated file {file['path']} does not exist")
             logger.info(str(err))
         except IOError as err:
-            logger.info(f"ERROR: Cannot read file at {file['path']+file['name']}")
+            logger.info(f"ERROR: Cannot read file at {file['path']}")
             logger.info(str(err))
         # convert task epoch values into strings
         task_epochs = "".join([str(element) + ", " for element in file["task_epochs"]])
diff --git a/src/spikegadgets_to_nwb/metadata_validation.py b/src/spikegadgets_to_nwb/metadata_validation.py
new file mode 100644
index 0000000..8856e8e
--- /dev/null
+++ b/src/spikegadgets_to_nwb/metadata_validation.py
@@ -0,0 +1,75 @@
+import copy
+import datetime
+import os
+
+import jsonschema
+import yaml
+
+
+def _get_nwb_json_schema_path() -> str:
+    """Get the NWB JSON Schema file path
+
+    Returns
+    -------
+    str
+        NWB Schema file Path
+    """
+    current_path = os.path.dirname(os.path.abspath(__file__))
+    json_schema_file = "/./nwb_schema.json"
+    return f"{current_path}{os.path.normpath(json_schema_file)}"
+
+
+def _get_json_schema() -> str:
+    """Get JSON Schema
+
+    Returns
+    -------
+    str
+        JSON Schema content
+    """
+    json_schema = None
+    json_schema_path = _get_nwb_json_schema_path()
+    with open(json_schema_path, "r") as stream:
+        json_schema = yaml.safe_load(stream)
+    return json_schema
+
+
+def validate(metadata: dict) -> tuple:
+    """Validates metadata
+
+    Parameters
+    ----------
+    metadata : dict
+        metadata documenting the particulars of a session
+
+    Returns
+    -------
+    tuple
+        information of the validity of the metadata data and any errors
+    """
+    assert metadata is not None  # metadata cannot be null
+    assert isinstance(metadata, dict)  # cannot proceed if metadata is not a dictionary
+
+    # date_of_birth is set to a datetime by the YAML-to-dict converter.
+    # This code converts date_of_birth  to string
+    metadata_content = copy.deepcopy(metadata) or {}
+    if (
+        metadata_content["subject"]
+        and metadata_content["subject"]["date_of_birth"]
+        and type(metadata_content["subject"]["date_of_birth"]) is datetime.datetime
+    ):
+        metadata_content["subject"]["date_of_birth"] = (
+            metadata_content["subject"]["date_of_birth"].utcnow().isoformat()
+        )
+
+    schema = _get_json_schema()
+    validator = jsonschema.Draft202012Validator(schema)
+    metadata_validation_errors = validator.iter_errors(metadata_content)
+    errors = []
+
+    for metadata_validation_error in metadata_validation_errors:
+        errors.append(metadata_validation_error.message)
+
+    is_valid = len(errors) == 0
+
+    return is_valid, errors
diff --git a/src/spikegadgets_to_nwb/nwb_schema.json b/src/spikegadgets_to_nwb/nwb_schema.json
new file mode 100644
index 0000000..f7f82f4
--- /dev/null
+++ b/src/spikegadgets_to_nwb/nwb_schema.json
@@ -0,0 +1,35971 @@
+{
+    "definitions": {},
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "https://lorenfranklab.github.io/rec_to_nwb_yaml_creator/v1.0.0",
+    "title": "Spikegadgets to NWB Validator",
+    "type": "object",
+    "description": "Spikegadgets to NWB Validator YAML schema version",
+    "required": [
+        "experimenter_name",
+        "lab",
+        "institution",
+        "data_acq_device",
+        "times_period_multiplier",
+        "raw_data_to_volts"
+    ],
+    "properties": {
+        "experimenter_name": {
+            "$id": "#root/experimenter_name",
+            "title": "experimenter_name",
+            "type": "array",
+            "default": [],
+            "examples": [
+                "Jennifer Guidera",
+                "Alison Comrie"
+            ],
+            "minItems": 1,
+            "uniqueItems": true,
+            "description": "Name of experimenter performing current session",
+            "items": {
+                "$id": "#root/experimenter_name/items",
+                "title": "items",
+                "type": "string",
+                "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+            }
+        },
+        "lab": {
+            "$id": "#root/lab",
+            "title": "lab",
+            "type": "string",
+            "default": "",
+            "examples": [
+                "Frank"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+            "description": "Laboratory where the experiment is conducted"
+        },
+        "institution": {
+            "$id": "#root/institution",
+            "title": "institution",
+            "type": "string",
+            "default": "University of California, San Francisco",
+            "examples": [
+                "Air Force Institute of Technology Graduate School of Engineering & Management",
+                "Albert Einstein College of Medicine",
+                "American University",
+                "Arizona State University Campus Immersion",
+                "Arizona State University Digital Immersion",
+                "Arkansas State University",
+                "Augusta University",
+                "Auburn University",
+                "Azusa Pacific University",
+                "Ball State University",
+                "Baylor College of Medicine",
+                "Baylor University",
+                "Binghamton University",
+                "Boise State University",
+                "Boston College",
+                "Boston University",
+                "Bowling Green State University",
+                "Brandeis University",
+                "Brigham Young University",
+                "Brown University",
+                "California Institute of Technology",
+                "California State University, East Bay",
+                "California State University, Fresno",
+                "California State University, Fullerton",
+                "California State University, Long Beach",
+                "California State University, San Bernardino",
+                "Carnegie Mellon University",
+                "Case Western Reserve University",
+                "Catholic University of America",
+                "Central Michigan University",
+                "Chapman University",
+                "Claremont Graduate University",
+                "Clark Atlanta University",
+                "Clark University",
+                "Clarkson University",
+                "Clemson University",
+                "Cleveland State University",
+                "College of William and Mary",
+                "Colorado School of Mines",
+                "Colorado State University",
+                "Columbia University",
+                "Cornell University",
+                "Creighton University",
+                "CUNY City College",
+                "Dartmouth College",
+                "DePaul University",
+                "Drexel University",
+                "Duke University",
+                "Duquesne University",
+                "East Carolina University",
+                "East Tennessee State University",
+                "Eastern Michigan University",
+                "Eastern Virginia Medical School",
+                "Emory University",
+                "Florida Agricultural and Mechanical University",
+                "Florida Atlantic University",
+                "Florida Institute of Technology",
+                "Florida International University",
+                "Florida State University",
+                "Fordham University",
+                "George Mason University",
+                "George Washington University",
+                "Georgetown University",
+                "Georgia Institute of Technology",
+                "Georgia Southern University",
+                "Georgia State University",
+                "Graduate Center, CUNY",
+                "Harvard University",
+                "Howard University",
+                "Icahn School of Medicine at Mount Sinai",
+                "Idaho State University",
+                "Illinois Institute of Technology",
+                "Illinois State University",
+                "Indiana University – Purdue University Indianapolis",
+                "Indiana University Bloomington",
+                "Indiana University of Pennsylvania",
+                "Iowa State University",
+                "Jackson State University",
+                "James Madison University",
+                "Johns Hopkins University",
+                "Kansas State University",
+                "Kennesaw State University",
+                "Kent State University",
+                "Lehigh University",
+                "Loma Linda University",
+                "Long Island University",
+                "Louisiana State University",
+                "Louisiana Tech University",
+                "Loyola Marymount University",
+                "Loyola University Chicago",
+                "Marquette University",
+                "Marshall University",
+                "Massachusetts Institute of Technology",
+                "Mayo Clinic College of Medicine and Science",
+                "Medical College of Wisconsin",
+                "Medical University of South Carolina",
+                "Mercer University",
+                "Miami University",
+                "Michigan State University",
+                "Michigan Technological University",
+                "Middle Tennessee State University",
+                "Mississippi State University",
+                "Missouri University of Science and Technology",
+                "Montana State University",
+                "Montclair State University",
+                "Morgan State University",
+                "New Jersey Institute of Technology",
+                "New Mexico State University",
+                "New York University",
+                "North Carolina A & T State University",
+                "North Carolina State University",
+                "North Dakota State University",
+                "Northeastern University",
+                "Northern Arizona University",
+                "Northern Illinois University",
+                "Northwestern University",
+                "Nova Southeastern University",
+                "Oakland University",
+                "Ohio State University",
+                "Ohio University",
+                "Oklahoma State University–Stillwater",
+                "Old Dominion University",
+                "Oregon Health & Science University",
+                "Oregon State University",
+                "Pennsylvania State University",
+                "Portland State University",
+                "Prairie View A&M University",
+                "Princeton University",
+                "Purdue University",
+                "Rensselaer Polytechnic Institute",
+                "Rice University",
+                "Rochester Institute of Technology",
+                "Rockefeller University",
+                "Rowan University",
+                "Rutgers University–Camden",
+                "Rutgers University–New Brunswick",
+                "Rutgers University–Newark",
+                "Saint Louis University",
+                "Sam Houston State University",
+                "San Diego State University",
+                "San Francisco State University",
+                "Seton Hall University",
+                "South Dakota State University",
+                "Southern Illinois University Carbondale",
+                "Southern Methodist University",
+                "Southern University",
+                "Stanford University",
+                "Stevens Institute of Technology",
+                "Stony Brook University",
+                "SUNY College of Environmental Science and Forestry",
+                "Syracuse University",
+                "Tarleton State University",
+                "Teachers College at Columbia University",
+                "Temple University",
+                "Tennessee State University",
+                "Tennessee Technological University",
+                "Texas A&M University",
+                "Texas A&M University–Corpus Christi",
+                "Texas A&M University–Kingsville",
+                "Texas Christian University",
+                "Texas Southern University",
+                "Texas State University",
+                "Texas Tech University",
+                "Texas Tech University Health Sciences Center",
+                "The New School",
+                "Thomas Jefferson University",
+                "Tufts University",
+                "Tulane University",
+                "Uniformed Services University of the Health Sciences",
+                "University at Albany, SUNY",
+                "University at Buffalo",
+                "University of Akron Main Campus",
+                "University of Alabama",
+                "University of Alabama at Birmingham",
+                "University of Alabama in Huntsville",
+                "University of Alaska Fairbanks",
+                "University of Arizona",
+                "University of Arkansas",
+                "University of Arkansas at Little Rock",
+                "University of Arkansas for Medical Sciences",
+                "University of California, Berkeley",
+                "University of California, Davis",
+                "University of California, Irvine",
+                "University of California, Los Angeles",
+                "University of California, Merced",
+                "University of California, Riverside",
+                "University of California, San Diego",
+                "University of California, San Francisco",
+                "University of California, Santa Barbara",
+                "University of California, Santa Cruz",
+                "University of Central Florida",
+                "University of Chicago",
+                "University of Cincinnati",
+                "University of Colorado Boulder",
+                "University of Colorado Colorado Springs",
+                "University of Colorado Denver",
+                "University of Connecticut",
+                "University of Dayton",
+                "University of Delaware",
+                "University of Denver",
+                "University of Florida",
+                "University of Georgia",
+                "University of Hawaii at Manoa",
+                "University of Houston",
+                "University of Idaho",
+                "University of Illinois Chicago",
+                "University of Illinois Urbana-Champaign",
+                "University of Iowa",
+                "University of Kansas",
+                "University of Kentucky",
+                "University of Louisiana at Lafayette",
+                "University of Louisville",
+                "University of Maine",
+                "University of Maryland, Baltimore",
+                "University of Maryland, Baltimore County",
+                "University of Maryland, College Park",
+                "University of Maryland, Eastern Shore",
+                "University of Massachusetts Amherst",
+                "University of Massachusetts Boston",
+                "University of Massachusetts Chan Medical School",
+                "University of Massachusetts Dartmouth",
+                "University of Massachusetts Lowell",
+                "University of Memphis",
+                "University of Miami",
+                "University of Michigan",
+                "University of Minnesota",
+                "University of Mississippi",
+                "University of Missouri",
+                "University of Missouri–Kansas City",
+                "University of Missouri–St. Louis",
+                "University of Montana",
+                "University of Nebraska at Omaha",
+                "University of Nebraska Medical Center",
+                "University of Nebraska–Lincoln",
+                "University of Nevada, Las Vegas",
+                "University of Nevada, Reno",
+                "University of New England",
+                "University of New Hampshire",
+                "University of New Mexico",
+                "University of New Orleans",
+                "University of North Carolina at Chapel Hill",
+                "University of North Carolina at Charlotte",
+                "University of North Carolina at Greensboro",
+                "University of North Carolina Wilmington",
+                "University of North Dakota",
+                "University of North Florida",
+                "University of North Texas",
+                "University of Notre Dame",
+                "University of Oklahoma",
+                "University of Oklahoma Health Sciences Center",
+                "University of Oregon",
+                "University of Pennsylvania",
+                "University of Pittsburgh",
+                "University of Puerto Rico at Río Piedras",
+                "University of Rhode Island",
+                "University of Rochester",
+                "University of San Diego",
+                "University of South Alabama",
+                "University of South Carolina",
+                "University of South Dakota",
+                "University of South Florida",
+                "University of Southern California",
+                "University of Southern Mississippi",
+                "University of Tennessee",
+                "University of Tennessee Health Science Center",
+                "University of Texas at Arlington",
+                "University of Texas at Austin",
+                "University of Texas at Dallas",
+                "University of Texas at El Paso",
+                "University of Texas at San Antonio",
+                "University of Texas Health Science Center at Houston",
+                "University of Texas Health Science Center at San Antonio",
+                "University of Texas Medical Branch",
+                "University of Texas Southwestern Medical Center",
+                "University of Toledo",
+                "University of Tulsa",
+                "University of Utah",
+                "University of Vermont",
+                "University of Virginia",
+                "University of Washington",
+                "University of Wisconsin–Madison",
+                "University of Wisconsin–Milwaukee",
+                "University of Wyoming",
+                "Utah State University",
+                "Vanderbilt University",
+                "Villanova University",
+                "Virginia Commonwealth University",
+                "Virginia Tech",
+                "Wake Forest University",
+                "Washington State University",
+                "Washington University in St. Louis",
+                "Wayne State University",
+                "Weill Cornell Medicine",
+                "West Chester University of Pennsylvania",
+                "West Virginia University",
+                "Western Michigan University",
+                "Wichita State University",
+                "Worcester Polytechnic Institute",
+                "Wright State University",
+                "Yale University"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+            "description": "Type to search for institution ..."
+        },
+        "experiment_description": {
+            "$id": "#root/experiment_description",
+            "title": "experiment_description",
+            "type": "string",
+            "default": "",
+            "examples": [
+                "spatial alternation memory task"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+            "description": "Research work being conducted"
+        },
+        "session_description": {
+            "$id": "#root/session_description",
+            "title": "session_description",
+            "type": "string",
+            "default": "",
+            "examples": [
+                "spatial alternation memory task"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+            "description": "Aspect of research being conducted"
+        },
+        "session_id": {
+            "$id": "#root/session_id",
+            "title": "session_id",
+            "type": "string",
+            "default": "",
+            "examples": [
+                "J16_20210606"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+            "description": "Current session's identification code/number"
+        },
+        "keywords": {
+            "$id": "#root/keywords",
+            "title": "keywords",
+            "type": "array",
+            "default": [],
+            "examples": [
+                "J16_20210606"
+            ],
+            "minItems": 1,
+            "uniqueItems": true,
+            "description": "keywords",
+            "items": {
+                "$id": "#root/keywords/items",
+                "title": "items",
+                "type": "string",
+                "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+            }
+        },
+        "subject": {
+            "$id": "#root/subject",
+            "title": "subject",
+            "type": "object",
+            "required": [
+                "description",
+                "genotype",
+                "sex",
+                "species",
+                "subject_id",
+                "weight",
+                "date_of_birth"
+            ],
+            "properties": {
+                "description": {
+                    "$id": "#root/subject/description",
+                    "title": "description",
+                    "type": "string",
+                    "default": "",
+                    "examples": [
+                        "Long Evans Rat"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                    "description": "Summary of animal model/patient/specimen being examined"
+                },
+                "genotype": {
+                    "$id": "#root/subject/genotype",
+                    "title": "genotype",
+                    "type": "string",
+                    "default": "",
+                    "examples": [
+                        "Wild Type"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                    "description": "Genetic summary of animal model/patient/specimen"
+                },
+                "sex": {
+                    "$id": "#root/subject/sex",
+                    "title": "sex",
+                    "type": "string",
+                    "enum": [
+                        "M",
+                        "F",
+                        "U",
+                        "O"
+                    ],
+                    "default": "M",
+                    "examples": [
+                        "M",
+                        "F",
+                        "U",
+                        "O"
+                    ],
+                    "description": "Gender of animal model/patient"
+                },
+                "species": {
+                    "$id": "#root/subject/species",
+                    "title": "species",
+                    "type": "string",
+                    "default": "",
+                    "examples": [
+                        "Rat"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                    "description": "Category of animal model/patient"
+                },
+                "subject_id": {
+                    "$id": "#root/subject/subject_id",
+                    "title": "subject_id",
+                    "type": "string",
+                    "default": "",
+                    "examples": [
+                        "J16"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                    "description": "Identification code/number of animal model/patient"
+                },
+                "weight": {
+                    "$id": "#root/subject/weight",
+                    "title": "weight",
+                    "type": "number",
+                    "default": "100",
+                    "minimum": 0,
+                    "description": "Mass of animal model/patient in grams"
+                },
+                "date_of_birth": {
+                    "$id": "#root/subject/date_of_birth",
+                    "title": "date_of_birth",
+                    "type": "string",
+                    "default": "",
+                    "pattern": "(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d\\.\\d+)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d:[0-5]\\d)|(\\d{4}-[01]\\d-[0-3]\\dT[0-2]\\d:[0-5]\\d)",
+                    "description": "date of birth of animal model/patient, in ISO 8061 format"
+                }
+            }
+        },
+        "data_acq_device": {
+            "$id": "#root/data_acq_device",
+            "title": "data_acq_device",
+            "type": "array",
+            "minItems": 1,
+            "default": [],
+            "items": {
+                "$id": "#root/data_acq_device/items",
+                "title": "items",
+                "type": "object",
+                "required": [
+                    "name",
+                    "system",
+                    "amplifier",
+                    "adc_circuit"
+                ],
+                "properties": {
+                    "name": {
+                        "$id": "#root/data_acq_device/items/name",
+                        "title": "name",
+                        "type": "string",
+                        "default": "",
+                        "description": "Data acquisition device name",
+                        "examples": [
+                            "Spike Gadgets"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "system": {
+                        "$id": "#root/data_acq_device/items/system",
+                        "title": "system",
+                        "type": "string",
+                        "default": "",
+                        "description": "Data acquisition  information like version or id",
+                        "examples": [
+                            "MCU"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "amplifier": {
+                        "$id": "#root/data_acq_device/items/amplifier",
+                        "title": "amplifier",
+                        "type": "string",
+                        "default": "",
+                        "description": "Amplifier device",
+                        "examples": [
+                            "intan"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "adc_circuit": {
+                        "$id": "#root/data_acq_device/items/adc_circuit",
+                        "title": "adc_circuit",
+                        "type": "string",
+                        "default": "",
+                        "description": "adc circuit",
+                        "examples": [
+                            "intan"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    }
+                }
+            }
+        },
+        "associated_files": {
+            "$id": "#root/associated_files",
+            "title": "associated_files",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/associated_files/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "name",
+                    "description",
+                    "path",
+                    "task_epochs"
+                ],
+                "properties": {
+                    "name": {
+                        "$id": "#root/associated_files/items/name",
+                        "title": "name",
+                        "type": "string",
+                        "default": "",
+                        "description": "File name",
+                        "examples": [
+                            "stateScriptLog_r1"
+                        ],
+                        "pattern": "(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "description": {
+                        "$id": "#root/associated_files/items/description",
+                        "title": "description",
+                        "type": "string",
+                        "default": "",
+                        "description": "Purpose of file",
+                        "examples": [
+                            "stateScriptLog epoch r1"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "path": {
+                        "$id": "#root/associated_files/items/path",
+                        "title": "path",
+                        "type": "string",
+                        "default": "",
+                        "description": "File location",
+                        "examples": [
+                            "/nimbus/jguidera/J16/raw/20210606/20210606_J16_02_r1.stateScriptLog"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "task_epochs": {
+                        "$id": "#root/associated_files/items/task_epochs",
+                        "title": "task_epochs",
+                        "type": "integer",
+                        "default": 0,
+                        "description": "task epoch"
+                    }
+                }
+            }
+        },
+        "units": {
+            "$id": "#root/units",
+            "title": "units",
+            "type": "object",
+            "required": [
+                "analog",
+                "behavioral_events"
+            ],
+            "properties": {
+                "analog": {
+                    "$id": "#root/units/analog",
+                    "title": "analog",
+                    "type": "string",
+                    "default": "",
+                    "description": "analog",
+                    "examples": [
+                        "unspecified"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                },
+                "behavioral_events": {
+                    "$id": "#root/units/behavioral_events",
+                    "title": "behavioral_events",
+                    "type": "string",
+                    "default": "",
+                    "description": "behavioral_events",
+                    "examples": [
+                        "unspecified"
+                    ],
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                }
+            }
+        },
+        "times_period_multiplier": {
+            "$id": "#root/times_period_multiplier",
+            "title": "times_period_multiplier",
+            "type": "number",
+            "examples": [
+                1.5
+            ],
+            "default": 0.0
+        },
+        "raw_data_to_volts": {
+            "$id": "#root/raw_data_to_volts",
+            "title": "raw_data_to_volts",
+            "type": "number",
+            "examples": [
+                1.95e-7
+            ],
+            "default": 0.0
+        },
+        "default_header_file_path": {
+            "$id": "#root/default_header_file_path",
+            "title": "default_header_file_path",
+            "type": "string",
+            "default": "",
+            "examples": [
+                "default_header.xml"
+            ],
+            "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+        },
+        "cameras": {
+            "$id": "#root/cameras",
+            "title": "cameras",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/cameras/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "id",
+                    "meters_per_pixel",
+                    "manufacturer",
+                    "model",
+                    "lens",
+                    "camera_name"
+                ],
+                "properties": {
+                    "id": {
+                        "$id": "#root/cameras/items/id",
+                        "title": "id",
+                        "type": "integer",
+                        "examples": [
+                            0
+                        ],
+                        "default": 0,
+                        "description": "camera id"
+                    },
+                    "meters_per_pixel": {
+                        "$id": "#root/cameras/items/meters_per_pixel",
+                        "title": "meters_per_pixel",
+                        "type": "number",
+                        "examples": [
+                            0.000842
+                        ],
+                        "default": 0.0,
+                        "description": "meter per pixel"
+                    },
+                    "manufacturer": {
+                        "$id": "#root/cameras/items/manufacturer",
+                        "title": "manufacturer",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "Manta"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Manufacturer"
+                    },
+                    "model": {
+                        "$id": "#root/cameras/items/model",
+                        "title": "model",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "unknown"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Model"
+                    },
+                    "lens": {
+                        "$id": "#root/cameras/items/lens",
+                        "title": "lens",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "unknown"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Len"
+                    },
+                    "camera_name": {
+                        "$id": "#root/cameras/items/camera_name",
+                        "title": "camera_name",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "HomeBox_camera"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Camera Name"
+                    }
+                }
+            }
+        },
+        "tasks": {
+            "$id": "#root/tasks",
+            "title": "tasks",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/tasks/items",
+                "title": "items",
+                "type": "object",
+                "required": [
+                    "task_name",
+                    "task_description",
+                    "task_environment",
+                    "camera_id",
+                    "task_epochs"
+                ],
+                "properties": {
+                    "task_name": {
+                        "$id": "#root/tasks/items/task_name",
+                        "title": "task_name",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "home"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Task name"
+                    },
+                    "task_description": {
+                        "$id": "#root/tasks/items/task_description",
+                        "title": "task_description",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "The animal rests in a box"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Task description"
+                    },
+                    "task_environment": {
+                        "$id": "#root/tasks/items/task_environment",
+                        "title": "task_environment",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "HomeBox"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "description": "Task environment"
+                    },
+                    "camera_id": {
+                        "$id": "#root/tasks/items/camera_id",
+                        "title": "camera_id",
+                        "type": "array",
+                        "description": "Comma separated camera ids, from camera list",
+                        "examples": [],
+                        "default": [],
+                        "items": {
+                            "$id": "#root/tasks/items/camera_id/items",
+                            "title": "Items",
+                            "uniqueItems": true,
+                            "type": "integer",
+                            "examples": [
+                                0
+                            ],
+                            "default": 0
+                        }
+                    },
+                    "task_epochs": {
+                        "$id": "#root/tasks/items/task_epochs",
+                        "title": "task_epochs",
+                        "type": "array",
+                        "description": "Comma separated numbers of task epochs",
+                        "examples": [],
+                        "default": [],
+                        "items": {
+                            "$id": "#root/tasks/items/task_epochs/items",
+                            "title": "Items",
+                            "type": "integer",
+                            "uniqueItems": true,
+                            "examples": [
+                                18
+                            ],
+                            "default": 0
+                        }
+                    }
+                }
+            }
+        },
+        "associated_video_files": {
+            "$id": "#root/associated_video_files",
+            "title": "associated_video_files",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/associated_video_files/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "name",
+                    "camera_id",
+                    "task_epochs"
+                ],
+                "properties": {
+                    "name": {
+                        "$id": "#root/associated_video_files/items/name",
+                        "title": "name",
+                        "type": "string",
+                        "default": "",
+                        "description": "File name",
+                        "examples": [
+                            "20210606_J16_01_s1.1.h264"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "camera_id": {
+                        "$id": "#root/associated_video_files/items/camera_id",
+                        "title": "camera_id",
+                        "type": "integer",
+                        "description": "camera id from camera list",
+                        "default": 0
+                    },
+                    "task_epochs": {
+                        "$id": "#root/associated_video_files/items/task_epochs",
+                        "title": "task_epochs",
+                        "type": "integer",
+                        "default": 0,
+                        "description": "task epoch"
+                    }
+                }
+            }
+        },
+        "behavioral_events": {
+            "$id": "#root/behavioral_events",
+            "title": "behavioral_events",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/behavioral_events/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "description",
+                    "name"
+                ],
+                "properties": {
+                    "description": {
+                        "$id": "#root/behavioral_events/items/description",
+                        "title": "description",
+                        "type": "string",
+                        "default": "Din1",
+                        "examples": [
+                            "Din",
+                            "Dout",
+                            "Accel",
+                            "Gyro",
+                            "Mag"
+                        ],
+                        "description": "Behavioral Events",
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "name": {
+                        "$id": "#root/behavioral_events/items/name",
+                        "title": "name",
+                        "type": "string",
+                        "default": "Home box camera",
+                        "examples": [
+                            "Home box camera",
+                            "Poke",
+                            "Light",
+                            "Pump",
+                            "Run Camera Ticks",
+                            "Sleep"
+                        ],
+                        "description": "Type of behavioral events",
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    }
+                }
+            }
+        },
+        "device": {
+            "$id": "#root/device",
+            "title": "device",
+            "type": "object",
+            "required": [
+                "name"
+            ],
+            "properties": {
+                "name": {
+                    "$id": "#root/device/items/name",
+                    "title": "name",
+                    "type": "array",
+                    "minItems": 1,
+                    "default": "Trodes",
+                    "description": "Selected recording device",
+                    "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                }
+            }
+        },
+        "electrode_groups": {
+            "$id": "#root/electrode_groups",
+            "title": "electrode_groups",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/electrode_groups/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "id",
+                    "location",
+                    "device_type",
+                    "description",
+                    "targeted_location",
+                    "targeted_x",
+                    "targeted_y",
+                    "targeted_z",
+                    "units"
+                ],
+                "properties": {
+                    "id": {
+                        "$id": "#root/electrode_groups/items/id",
+                        "title": "id",
+                        "type": "integer",
+                        "examples": [
+                            0
+                        ],
+                        "default": 0,
+                        "minimum": 0,
+                        "description": "electrode/probe identification code/number"
+                    },
+                    "location": {
+                        "$id": "#root/electrode_groups/items/location",
+                        "title": "location",
+                        "type": "string",
+                        "default": "Cornu ammonis 1 (CA1)",
+                        "description": "Exact location of electrode/probe",
+                        "examples": [
+                            "Brain (Brain)",
+                            "White matter (wmt)",
+                            "Olfactory white matter (olf)",
+                            "lateral olfactory tract (lot)",
+                            "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)",
+                            "Anterior commissure (ac)",
+                            "anterior commissure, anterior limb (aca)",
+                            "anterior commissure, posterior limb (acp)",
+                            "anterior commissure, intrabulbar part (aci)",
+                            "Hippocampal white matter (hiw)",
+                            "alveus of the hippocampus (alv)",
+                            "ventral hippocampal commissure (vhc)",
+                            "fornix (f)",
+                            "fimbria of the hippocampus (fi)",
+                            "Corticofugal pathways (cfp)",
+                            "corticofugal tract and corona radiata (ic-cp-lfp-py)",
+                            "pyramidal decussation (pyx)",
+                            "Medial lemniscus (ml)",
+                            "medial lemniscus, unspecified (ml-u)",
+                            "medial lemniscus decussation (mlx)",
+                            "Thalamic tracts (tht)",
+                            "External medullary lamina (eml)",
+                            "external medullary lamina, unspecified (eml-u)",
+                            "external medullary lamina, auditory radiation (eml-ar)",
+                            "internal medullary lamina (iml)",
+                            "intramedullary thalamic area (ima)",
+                            "superior cerebellar peduncle and prerubral field (scp-pr)",
+                            "pretectothalamic lamina (ptl)",
+                            "mammillotegmental tract (mtg)",
+                            "commissural stria terminalis (cst)",
+                            "fasciculus retroflexus (fr)",
+                            "stria medullaris thalami (sm)",
+                            "stria terminalis (st)",
+                            "habenular commissure (hbc)",
+                            "posterior commissure (pc)",
+                            "Facial nerve (7n)",
+                            "facial nerve, unspecified (7n-u)",
+                            "ascending fibers of the facial nerve (asc7)",
+                            "genu of the facial nerve (g7)",
+                            "Optic fiber system and supraoptic decussation (ofs)",
+                            "optic nerve (2n)",
+                            "optic tract and optic chiasm (opt-och)",
+                            "supraoptic decussation (sox)",
+                            "White matter of the tectum (tew)",
+                            "commissure of the superior colliculus (csc)",
+                            "brachium of the superior colliculus (bsc)",
+                            "inferior colliculus, commissure (cic)",
+                            "inferior colliculus, brachium (bic)",
+                            "Cerebellar and precerebellar white matter (cbt)",
+                            "inferior cerebellar peduncle (icp)",
+                            "middle cerebellar peduncle (mcp)",
+                            "transverse fibers of the pons (tfp)",
+                            "White matter of the brainstem (bsw)",
+                            "Lateral lemniscus (ll)",
+                            "lateral lemniscus, commissure (ll-c)",
+                            "lateral lemniscus, unspecified (ll-u)",
+                            "acoustic striae (as)",
+                            "trapezoid body (tz)",
+                            "spinal trigeminal tract (sp5t)",
+                            "Gray matter (GM)",
+                            "Telencephalon (Tel)",
+                            "Laminated pallium (LamP)",
+                            "Olfactory bulb (OB)",
+                            "Glomerular layer of the accessory olfactory bulb (GlA)",
+                            "Glomerular layer of the olfactory bulb (Gl)",
+                            "Olfactory bulb, unspecified (OB-u)",
+                            "Nucleus of the lateral olfactory tract (NLOT)",
+                            "Cerebral cortex (Cx)",
+                            "Hippocampal region (HR)",
+                            "Hippocampal formation (HF)",
+                            "Fasciola cinereum (FC)",
+                            "Subiculum (SUB)",
+                            "Cornu Ammonis (CA)",
+                            "Cornu ammonis 1 (CA1)",
+                            "Cornu ammonis 2 (CA2)",
+                            "Cornu ammonis 3 (CA3)",
+                            "Dentate gyrus (DG)",
+                            "Parahippocampal region (PHR)",
+                            "Postrhinal cortex (POR)",
+                            "Presubiculum (PrS)",
+                            "Parasubiculum (PaS)",
+                            "Perirhinal cortex (PER)",
+                            "Perirhinal area 35 (PER35)",
+                            "Perirhinal area 36 (PER36)",
+                            "Entorhinal cortex (EC)",
+                            "Medial entorhinal cortex (MEC)",
+                            "Lateral entorhinal cortex (LEC)",
+                            "Piriform cortex (PIR)",
+                            "Piriform cortex, layer 1 (PIR1)",
+                            "Piriform cortex, layer 2 (PIR2)",
+                            "Piriform cortex, layer 3 (PIR3)",
+                            "Cingulate region (CgR)",
+                            "Cingulate cortex (Cg)",
+                            "Cingulate area 1 (Cg1)",
+                            "Cingulate area 2 (Cg2)",
+                            "Retrosplenial cortex (RS)",
+                            "Retrosplenial dysgranular area (RSD)",
+                            "Retrosplenial granular area (RSG)",
+                            "Insular region (INS)",
+                            "Agranular insular cortex (AI)",
+                            "Agranular insular cortex, ventral area (AI-v)",
+                            "Agranular insular cortex dorsal area  (AI-d)",
+                            "Agranular insular cortex, posterior area  (AI-p)",
+                            "Dysgranular insular cortex (DI)",
+                            "Granular insular cortex (GI)",
+                            "Frontal region (Front)",
+                            "Frontal association cortex (FrA)",
+                            "Orbitofrontal cortex (Orb)",
+                            "Medial orbital area (MO)",
+                            "Ventral orbital area (VO)",
+                            "Ventrolateral orbital area (VLO)",
+                            "Lateral orbital area (LO)",
+                            "Dorsolateral orbital area (DLO)",
+                            "Mediofrontal cortex (MFC)",
+                            "Prelimbic area (PrL)",
+                            "Infralimbic area (IL)",
+                            "Motor cortex (M)",
+                            "Primary motor area (M1)",
+                            "Secondary motor area (M2)",
+                            "Frontal association area 3 (Fr3)",
+                            "Parietal region (Par)",
+                            "Somatosensory cortex (SS)",
+                            "Primary somatosensory area (S1)",
+                            "Primary somatosensory area, face representation (S1-f)",
+                            "Primary somatosensory area, barrel field (S1-bf)",
+                            "Primary somatosensory area, dysgranular zone (S1-dz)",
+                            "Primary somatosensory area, forelimb representation (S1-fl)",
+                            "Primary somatosensory area, hindlimb representation (S1-hl)",
+                            "Primary somatosensory area, trunk representation (S1-tr)",
+                            "Secondary somatosensory area (S2)",
+                            "Posterior parietal cortex (PPC)",
+                            "Parietal association cortex, medial area (mPPC)",
+                            "Parietal association cortex, lateral area (lPPC)",
+                            "Parietal association cortex, posterior area  (PtP)",
+                            "Occipital region (Oc)",
+                            "Visual cortex (Vis)",
+                            "Primary visual area (V1)",
+                            "Secondary visual area (V2)",
+                            "Secondary visual area, medial part (V2M)",
+                            "Secondary visual area, lateral part (V2L)",
+                            "Temporal region (Te)",
+                            "Temporal association cortex (TeA)",
+                            "Auditory cortex (Au)",
+                            "Primary auditory area (Au1)",
+                            "Secondary auditory area (Au2)",
+                            "Secondary auditory area, dorsal part (Au2-d)",
+                            "Secondary auditory area, ventral part (Au2-v)",
+                            "Non-laminated pallium (N-LamP)",
+                            "Claustrum (CLA)",
+                            "Endopiriform nucleus (Endo)",
+                            "Amygdaloid area, unspecified (Am-u)",
+                            " Subpallium (SubPAL)",
+                            "Striatum (Str)",
+                            "Caudate putamen (CPu)",
+                            "Nucleus accumbens (NAc)",
+                            "Nucleus accumbens, core (NAc-c)",
+                            "Nucleus accumbens, shell (NAc-sh)",
+                            "Ventral striatal region, unspecified (VSR-u)",
+                            "Pallidum (PAL)",
+                            "Globus pallidus external (GPe)",
+                            "Globus pallidus external, medial part (GPe-m)",
+                            "Globus pallidus external, lateral part (GPe-l)",
+                            "Entopeduncular nucleus (EP)",
+                            "Ventral pallidum (VP)",
+                            "Basal forebrain region  (BRF)",
+                            "Basal forebrain region, unspecified (BFR-u)",
+                            "Bed nucleus of the stria terminalis (BNST)",
+                            "Septal region (Sep)",
+                            "Subthalamic nucleus (STh)",
+                            "Diencephalon (Dien)",
+                            "Prethalamus (Thal-Pre)",
+                            "Reticular (pre)thalamic nucleus (RT)",
+                            "Reticular (pre)thalamic nucleus, unspecified (RT-u)",
+                            "Reticular (pre)thalamic nucleus, auditory segment (RT-a)",
+                            "Zona incerta (ZI)",
+                            "Zona incerta, dorsal part (ZI-d)",
+                            "Zona incerta, ventral part (ZI-v)",
+                            "Zona incerta, rostral part (ZI-r)",
+                            "Zona incerta, caudal part (ZI-c)",
+                            "Zona incerta, A13 dopamine cells (ZI-A13)",
+                            "Zona incerta, A11 dopamine cells (ZI-A11)",
+                            "Fields of Forel (FoF)",
+                            "Pregeniculate nucleus (PrG)",
+                            "Subgeniculate nucleus (SubG)",
+                            "Intergeniculate leaflet (IGL)",
+                            "Epithalamus (Thal-EPI)",
+                            "Lateral habenular nucleus (LHb)",
+                            "Medial habenular nucleus (MHb)",
+                            "Nucleus of the stria medullaris (SMn)",
+                            "Pineal gland (PG)",
+                            "Dorsal thalamus (Thal-D)",
+                            "Anterior nuclei of the dorsal thalamus (ANT)",
+                            "Anterodorsal thalamic nucleus (AD)",
+                            "Anteroventral thalamic nucleus (AV)",
+                            "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)",
+                            "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)",
+                            "Anteromedial thalamic nucleus (AM)",
+                            "Interanteromedial thalamic nucleus (IAM)",
+                            "Paraventricular thalamic nuclei (anterior and posterior) (PV)",
+                            "Intermediodorsal thalamic nucleus (IMD)",
+                            "Parataenial thalamic nucleus (PT)",
+                            "Subparafascicular nucleus (SPF)",
+                            "Posterior intralaminar nucleus (PIL)",
+                            "Ventral midline group of the dorsal thalamus (V-MID)",
+                            "Rhomboid thalamic nucleus (Rh)",
+                            "Reuniens thalamic nucleus (Re)",
+                            "Retroreuniens thalamic nucleus (RRe)",
+                            "Xiphoid thalamic nucleus (Xi)",
+                            "Mediodorsal nucleus of the dorsal thalamus (MD)",
+                            "Mediodorsal thalamic nucleus, lateral part (MD-l)",
+                            "Mediodorsal thalamic nucleus, central part (MD-c)",
+                            "Mediodorsal thalamic nucleus, medial part (MD-m)",
+                            "Ventral nuclei of the dorsal thalamus (VENT)",
+                            "Ventral anterior thalamic nucleus (VA)",
+                            "Ventromedial thalamic nucleus (VM)",
+                            "Ventrolateral thalamic nucleus (VL)",
+                            "Angular thalamic nucleus (Ang)",
+                            "Ventral posterior thalamic nucleus (VPN)",
+                            "Ventral posteromedial thalamic nucleus (VPM)",
+                            "Ventral posterolateral thalamic nucleus (VPL)",
+                            "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)",
+                            "Submedius thalamic nucleus (SMT)",
+                            "Intralaminar nuclei of the dorsal thalamus (ILM)",
+                            "Paracentral thalamic nucleus (PCN)",
+                            "Central medial thalamic nucleus (CM)",
+                            "Central lateral thalamic nucleus (CL)",
+                            "Parafascicular thalamic nucleus (PF)",
+                            "Ethmoid-Limitans nucleus (Eth)",
+                            "Posterior complex of the dorsal thalamus (PoC)",
+                            "Posterior thalamic nucleus (Po)",
+                            "Posterior thalamic nuclear group, triangular part (Po-t)",
+                            "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)",
+                            "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)",
+                            "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)",
+                            "Lateral posterior thalamic nucleus, lateral part (LP-l)",
+                            "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)",
+                            "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)",
+                            "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)",
+                            "Dorsal lateral geniculate nucleus (DLG)",
+                            "Medial geniculate complex of the dorsal thalamus (MG)",
+                            "Medial geniculate body, ventral division (MG-v)",
+                            "Medial geniculate body, dorsal division (MG-d)",
+                            "Medial geniculate body, marginal zone (MG-mz)",
+                            "Medial geniculate body, medial division (MG-m)",
+                            "Medial geniculate body, suprageniculate nucleus (MG-sg)",
+                            "Hypothalamus (HY)",
+                            "Hypothalamic region, unspecified (HTh-u)",
+                            "Pretectum (PreT)",
+                            "Pretectal region (PRT)",
+                            "Nucleus sagulum (Sag)",
+                            "Mesencephalon (Mes)",
+                            "Midbrain (MB)",
+                            "Tectum (Tc)",
+                            "Inferior colliculus (IC)",
+                            "Inferior colliculus, dorsal cortex (DCIC)",
+                            "Inferior colliculus, central nucleus (CNIC)",
+                            "Inferior colliculus, external cortex (ECIC)",
+                            "Superior colliculus (Su)",
+                            "Superficial gray layer of the superior colliculus (SuG)",
+                            "Deeper layers of the superior colliculus (SuD)",
+                            "Tegmentum (Tg)",
+                            "Substantia nigra (SN)",
+                            "Substantia nigra, reticular part (SN-r)",
+                            "Substantia nigra, compact part (SN-c)",
+                            "Substantia nigra, lateral part (SN-l)",
+                            "Ventral tegmental area (VTA)",
+                            "Peripeduncular nucleus (PP)",
+                            "Interpeduncular nucleus (IP)",
+                            "Periaqueductal gray (PAG)",
+                            "Brainstem, unspecified (BS-u)",
+                            "Rhombencephalon (Rho)",
+                            "Metencephalon (Met)",
+                            "Pontine nuclei (Pn)",
+                            "Cerebellum (Cb)",
+                            "Molecular cell layer of the cerebellum (Cb-m)",
+                            "Cerebellum, unspecified (Cb-u)",
+                            "Myelencephalon (Myel)",
+                            "Cochlear nucleus, ventral part (VCN)",
+                            "Ventral cochlear nucleus, anterior part (AVCN)",
+                            "Ventral cochlear nucleus, posterior part (PVCN)",
+                            "Ventral cochlear nucleus, cap area (Cap)",
+                            "Ventral cochlear nucleus, granule cell layer (GCL)",
+                            "Cochlear nucleus, dorsal part (DCN)",
+                            "Dorsal cochlear nucleus, molecular layer (DCNM)",
+                            "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)",
+                            "Dorsal cochlear nucleus, deep core (DCND)",
+                            "Spinal trigeminal nucleus (Sp5n)",
+                            "Periventricular gray (PVG)",
+                            "Superior olivary complex (SO)",
+                            "Nucleus of the trapezoid body (NTB)",
+                            "Superior paraolivary nucleus (SPN)",
+                            "Medial superior olive (MSO)",
+                            "Lateral superior olive (LSO)",
+                            "Superior periolivary region (SPR)",
+                            "Ventral periolivary nuclei (VPO)",
+                            "Nuclei of the lateral lemniscus (NLL)",
+                            "Lateral lemniscus, ventral nucleus (VLL)",
+                            "Lateral lemniscus, intermediate nucleus (ILL)",
+                            "Lateral lemniscus, dorsal nucleus (DLL)",
+                            "Inferior olive (IO)",
+                            "Ventricular system (V)",
+                            "ventricular system, unspecified (V-u)",
+                            "4th ventricle (4V)",
+                            "central canal (CC)",
+                            "spinal cord (SpC)",
+                            "Inner ear (IE)",
+                            "vestibular apparatus (VeA)",
+                            "cochlea (Co)",
+                            "cochlear nerve (8cn)",
+                            "vestibular nerve (8vn)",
+                            "spiral ganglion (SpG)"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "device_type": {
+                        "$id": "#root/electrode_groups/items/device_type",
+                        "title": "device_type",
+                        "type": "string",
+                        "default": "",
+                        "examples": [
+                            "",
+                            "tetrode_12.5",
+                            "A1x32-6mm-50-177-H32_21mm",
+                            "128c-4s8mm6cm-20um-40um-sl",
+                            "128c-4s6mm6cm-15um-26um-sl",
+                            "32c-2s8mm6cm-20um-40um-dl",
+                            "64c-4s6mm6cm-20um-40um-dl",
+                            "64c-3s6mm6cm-20um-40um-sl"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$",
+                        "enum": [
+                            "tetrode_12.5",
+                            "A1x32-6mm-50-177-H32_21mm",
+                            "128c-4s8mm6cm-20um-40um-sl",
+                            "128c-4s6mm6cm-15um-26um-sl",
+                            "32c-2s8mm6cm-20um-40um-dl",
+                            "64c-4s6mm6cm-20um-40um-dl",
+                            "64c-3s6mm6cm-20um-40um-sl"
+                        ]
+                    },
+                    "description": {
+                        "$id": "#root/electrode_groups/items/description",
+                        "title": "description",
+                        "type": "string",
+                        "default": "",
+                        "description": "electrode groups description",
+                        "examples": [
+                            "tetrode"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "targeted_location": {
+                        "$id": "#root/electrode_groups/items/targeted_location",
+                        "title": "targeted_location",
+                        "type": "string",
+                        "default": "Cornu ammonis 1 (CA1)",
+                        "description": "Planned location of electrode/probe",
+                        "examples": [
+                            "Brain (Brain)",
+                            "White matter (wmt)",
+                            "Olfactory white matter (olf)",
+                            "lateral olfactory tract (lot)",
+                            "corpus callosum and associated subcortical white matter (cc-ec-cing-dwm)",
+                            "Anterior commissure (ac)",
+                            "anterior commissure, anterior limb (aca)",
+                            "anterior commissure, posterior limb (acp)",
+                            "anterior commissure, intrabulbar part (aci)",
+                            "Hippocampal white matter (hiw)",
+                            "alveus of the hippocampus (alv)",
+                            "ventral hippocampal commissure (vhc)",
+                            "fornix (f)",
+                            "fimbria of the hippocampus (fi)",
+                            "Corticofugal pathways (cfp)",
+                            "corticofugal tract and corona radiata (ic-cp-lfp-py)",
+                            "pyramidal decussation (pyx)",
+                            "Medial lemniscus (ml)",
+                            "medial lemniscus, unspecified (ml-u)",
+                            "medial lemniscus decussation (mlx)",
+                            "Thalamic tracts (tht)",
+                            "External medullary lamina (eml)",
+                            "external medullary lamina, unspecified (eml-u)",
+                            "external medullary lamina, auditory radiation (eml-ar)",
+                            "internal medullary lamina (iml)",
+                            "intramedullary thalamic area (ima)",
+                            "superior cerebellar peduncle and prerubral field (scp-pr)",
+                            "pretectothalamic lamina (ptl)",
+                            "mammillotegmental tract (mtg)",
+                            "commissural stria terminalis (cst)",
+                            "fasciculus retroflexus (fr)",
+                            "stria medullaris thalami (sm)",
+                            "stria terminalis (st)",
+                            "habenular commissure (hbc)",
+                            "posterior commissure (pc)",
+                            "Facial nerve (7n)",
+                            "facial nerve, unspecified (7n-u)",
+                            "ascending fibers of the facial nerve (asc7)",
+                            "genu of the facial nerve (g7)",
+                            "Optic fiber system and supraoptic decussation (ofs)",
+                            "optic nerve (2n)",
+                            "optic tract and optic chiasm (opt-och)",
+                            "supraoptic decussation (sox)",
+                            "White matter of the tectum (tew)",
+                            "commissure of the superior colliculus (csc)",
+                            "brachium of the superior colliculus (bsc)",
+                            "inferior colliculus, commissure (cic)",
+                            "inferior colliculus, brachium (bic)",
+                            "Cerebellar and precerebellar white matter (cbt)",
+                            "inferior cerebellar peduncle (icp)",
+                            "middle cerebellar peduncle (mcp)",
+                            "transverse fibers of the pons (tfp)",
+                            "White matter of the brainstem (bsw)",
+                            "Lateral lemniscus (ll)",
+                            "lateral lemniscus, commissure (ll-c)",
+                            "lateral lemniscus, unspecified (ll-u)",
+                            "acoustic striae (as)",
+                            "trapezoid body (tz)",
+                            "spinal trigeminal tract (sp5t)",
+                            "Gray matter (GM)",
+                            "Telencephalon (Tel)",
+                            "Laminated pallium (LamP)",
+                            "Olfactory bulb (OB)",
+                            "Glomerular layer of the accessory olfactory bulb (GlA)",
+                            "Glomerular layer of the olfactory bulb (Gl)",
+                            "Olfactory bulb, unspecified (OB-u)",
+                            "Nucleus of the lateral olfactory tract (NLOT)",
+                            "Cerebral cortex (Cx)",
+                            "Hippocampal region (HR)",
+                            "Hippocampal formation (HF)",
+                            "Fasciola cinereum (FC)",
+                            "Subiculum (SUB)",
+                            "Cornu Ammonis (CA)",
+                            "Cornu ammonis 1 (CA1)",
+                            "Cornu ammonis 2 (CA2)",
+                            "Cornu ammonis 3 (CA3)",
+                            "Dentate gyrus (DG)",
+                            "Parahippocampal region (PHR)",
+                            "Postrhinal cortex (POR)",
+                            "Presubiculum (PrS)",
+                            "Parasubiculum (PaS)",
+                            "Perirhinal cortex (PER)",
+                            "Perirhinal area 35 (PER35)",
+                            "Perirhinal area 36 (PER36)",
+                            "Entorhinal cortex (EC)",
+                            "Medial entorhinal cortex (MEC)",
+                            "Lateral entorhinal cortex (LEC)",
+                            "Piriform cortex (PIR)",
+                            "Piriform cortex, layer 1 (PIR1)",
+                            "Piriform cortex, layer 2 (PIR2)",
+                            "Piriform cortex, layer 3 (PIR3)",
+                            "Cingulate region (CgR)",
+                            "Cingulate cortex (Cg)",
+                            "Cingulate area 1 (Cg1)",
+                            "Cingulate area 2 (Cg2)",
+                            "Retrosplenial cortex (RS)",
+                            "Retrosplenial dysgranular area (RSD)",
+                            "Retrosplenial granular area (RSG)",
+                            "Insular region (INS)",
+                            "Agranular insular cortex (AI)",
+                            "Agranular insular cortex, ventral area (AI-v)",
+                            "Agranular insular cortex dorsal area  (AI-d)",
+                            "Agranular insular cortex, posterior area  (AI-p)",
+                            "Dysgranular insular cortex (DI)",
+                            "Granular insular cortex (GI)",
+                            "Frontal region (Front)",
+                            "Frontal association cortex (FrA)",
+                            "Orbitofrontal cortex (Orb)",
+                            "Medial orbital area (MO)",
+                            "Ventral orbital area (VO)",
+                            "Ventrolateral orbital area (VLO)",
+                            "Lateral orbital area (LO)",
+                            "Dorsolateral orbital area (DLO)",
+                            "Mediofrontal cortex (MFC)",
+                            "Prelimbic area (PrL)",
+                            "Infralimbic area (IL)",
+                            "Motor cortex (M)",
+                            "Primary motor area (M1)",
+                            "Secondary motor area (M2)",
+                            "Frontal association area 3 (Fr3)",
+                            "Parietal region (Par)",
+                            "Somatosensory cortex (SS)",
+                            "Primary somatosensory area (S1)",
+                            "Primary somatosensory area, face representation (S1-f)",
+                            "Primary somatosensory area, barrel field (S1-bf)",
+                            "Primary somatosensory area, dysgranular zone (S1-dz)",
+                            "Primary somatosensory area, forelimb representation (S1-fl)",
+                            "Primary somatosensory area, hindlimb representation (S1-hl)",
+                            "Primary somatosensory area, trunk representation (S1-tr)",
+                            "Secondary somatosensory area (S2)",
+                            "Posterior parietal cortex (PPC)",
+                            "Parietal association cortex, medial area (mPPC)",
+                            "Parietal association cortex, lateral area (lPPC)",
+                            "Parietal association cortex, posterior area  (PtP)",
+                            "Occipital region (Oc)",
+                            "Visual cortex (Vis)",
+                            "Primary visual area (V1)",
+                            "Secondary visual area (V2)",
+                            "Secondary visual area, medial part (V2M)",
+                            "Secondary visual area, lateral part (V2L)",
+                            "Temporal region (Te)",
+                            "Temporal association cortex (TeA)",
+                            "Auditory cortex (Au)",
+                            "Primary auditory area (Au1)",
+                            "Secondary auditory area (Au2)",
+                            "Secondary auditory area, dorsal part (Au2-d)",
+                            "Secondary auditory area, ventral part (Au2-v)",
+                            "Non-laminated pallium (N-LamP)",
+                            "Claustrum (CLA)",
+                            "Endopiriform nucleus (Endo)",
+                            "Amygdaloid area, unspecified (Am-u)",
+                            " Subpallium (SubPAL)",
+                            "Striatum (Str)",
+                            "Caudate putamen (CPu)",
+                            "Nucleus accumbens (NAc)",
+                            "Nucleus accumbens, core (NAc-c)",
+                            "Nucleus accumbens, shell (NAc-sh)",
+                            "Ventral striatal region, unspecified (VSR-u)",
+                            "Pallidum (PAL)",
+                            "Globus pallidus external (GPe)",
+                            "Globus pallidus external, medial part (GPe-m)",
+                            "Globus pallidus external, lateral part (GPe-l)",
+                            "Entopeduncular nucleus (EP)",
+                            "Ventral pallidum (VP)",
+                            "Basal forebrain region  (BRF)",
+                            "Basal forebrain region, unspecified (BFR-u)",
+                            "Bed nucleus of the stria terminalis (BNST)",
+                            "Septal region (Sep)",
+                            "Subthalamic nucleus (STh)",
+                            "Diencephalon (Dien)",
+                            "Prethalamus (Thal-Pre)",
+                            "Reticular (pre)thalamic nucleus (RT)",
+                            "Reticular (pre)thalamic nucleus, unspecified (RT-u)",
+                            "Reticular (pre)thalamic nucleus, auditory segment (RT-a)",
+                            "Zona incerta (ZI)",
+                            "Zona incerta, dorsal part (ZI-d)",
+                            "Zona incerta, ventral part (ZI-v)",
+                            "Zona incerta, rostral part (ZI-r)",
+                            "Zona incerta, caudal part (ZI-c)",
+                            "Zona incerta, A13 dopamine cells (ZI-A13)",
+                            "Zona incerta, A11 dopamine cells (ZI-A11)",
+                            "Fields of Forel (FoF)",
+                            "Pregeniculate nucleus (PrG)",
+                            "Subgeniculate nucleus (SubG)",
+                            "Intergeniculate leaflet (IGL)",
+                            "Epithalamus (Thal-EPI)",
+                            "Lateral habenular nucleus (LHb)",
+                            "Medial habenular nucleus (MHb)",
+                            "Nucleus of the stria medullaris (SMn)",
+                            "Pineal gland (PG)",
+                            "Dorsal thalamus (Thal-D)",
+                            "Anterior nuclei of the dorsal thalamus (ANT)",
+                            "Anterodorsal thalamic nucleus (AD)",
+                            "Anteroventral thalamic nucleus (AV)",
+                            "Anteroventral thalamic nucleus, dorsomedial part (AV-dm)",
+                            "Anteroventral thalamic nucleus, ventrolateral part (AV-vl)",
+                            "Anteromedial thalamic nucleus (AM)",
+                            "Interanteromedial thalamic nucleus (IAM)",
+                            "Paraventricular thalamic nuclei (anterior and posterior) (PV)",
+                            "Intermediodorsal thalamic nucleus (IMD)",
+                            "Parataenial thalamic nucleus (PT)",
+                            "Subparafascicular nucleus (SPF)",
+                            "Posterior intralaminar nucleus (PIL)",
+                            "Ventral midline group of the dorsal thalamus (V-MID)",
+                            "Rhomboid thalamic nucleus (Rh)",
+                            "Reuniens thalamic nucleus (Re)",
+                            "Retroreuniens thalamic nucleus (RRe)",
+                            "Xiphoid thalamic nucleus (Xi)",
+                            "Mediodorsal nucleus of the dorsal thalamus (MD)",
+                            "Mediodorsal thalamic nucleus, lateral part (MD-l)",
+                            "Mediodorsal thalamic nucleus, central part (MD-c)",
+                            "Mediodorsal thalamic nucleus, medial part (MD-m)",
+                            "Ventral nuclei of the dorsal thalamus (VENT)",
+                            "Ventral anterior thalamic nucleus (VA)",
+                            "Ventromedial thalamic nucleus (VM)",
+                            "Ventrolateral thalamic nucleus (VL)",
+                            "Angular thalamic nucleus (Ang)",
+                            "Ventral posterior thalamic nucleus (VPN)",
+                            "Ventral posteromedial thalamic nucleus (VPM)",
+                            "Ventral posterolateral thalamic nucleus (VPL)",
+                            "Ventral posterior nucleus of the thalamus, parvicellular part (VP-pc)",
+                            "Submedius thalamic nucleus (SMT)",
+                            "Intralaminar nuclei of the dorsal thalamus (ILM)",
+                            "Paracentral thalamic nucleus (PCN)",
+                            "Central medial thalamic nucleus (CM)",
+                            "Central lateral thalamic nucleus (CL)",
+                            "Parafascicular thalamic nucleus (PF)",
+                            "Ethmoid-Limitans nucleus (Eth)",
+                            "Posterior complex of the dorsal thalamus (PoC)",
+                            "Posterior thalamic nucleus (Po)",
+                            "Posterior thalamic nuclear group, triangular part (Po-t)",
+                            "Lateral posterior (pulvinar) complex of the dorsal thalamus (LP)",
+                            "Lateral posterior thalamic nucleus, mediorostral part (LP-mr)",
+                            "Lateral posterior thalamic nucleus, mediocaudal part (LP-mc)",
+                            "Lateral posterior thalamic nucleus, lateral part (LP-l)",
+                            "Laterodorsal thalamic nuclei of the dorsal thalamus (LD)",
+                            "Laterodorsal thalamic nucleus, dorsomedial part (LD-dm)",
+                            "Laterodorsal thalamic nucleus, ventrolateral part (LD-vl)",
+                            "Dorsal lateral geniculate nucleus (DLG)",
+                            "Medial geniculate complex of the dorsal thalamus (MG)",
+                            "Medial geniculate body, ventral division (MG-v)",
+                            "Medial geniculate body, dorsal division (MG-d)",
+                            "Medial geniculate body, marginal zone (MG-mz)",
+                            "Medial geniculate body, medial division (MG-m)",
+                            "Medial geniculate body, suprageniculate nucleus (MG-sg)",
+                            "Hypothalamus (HY)",
+                            "Hypothalamic region, unspecified (HTh-u)",
+                            "Pretectum (PreT)",
+                            "Pretectal region (PRT)",
+                            "Nucleus sagulum (Sag)",
+                            "Mesencephalon (Mes)",
+                            "Midbrain (MB)",
+                            "Tectum (Tc)",
+                            "Inferior colliculus (IC)",
+                            "Inferior colliculus, dorsal cortex (DCIC)",
+                            "Inferior colliculus, central nucleus (CNIC)",
+                            "Inferior colliculus, external cortex (ECIC)",
+                            "Superior colliculus (Su)",
+                            "Superficial gray layer of the superior colliculus (SuG)",
+                            "Deeper layers of the superior colliculus (SuD)",
+                            "Tegmentum (Tg)",
+                            "Substantia nigra (SN)",
+                            "Substantia nigra, reticular part (SN-r)",
+                            "Substantia nigra, compact part (SN-c)",
+                            "Substantia nigra, lateral part (SN-l)",
+                            "Ventral tegmental area (VTA)",
+                            "Peripeduncular nucleus (PP)",
+                            "Interpeduncular nucleus (IP)",
+                            "Periaqueductal gray (PAG)",
+                            "Brainstem, unspecified (BS-u)",
+                            "Rhombencephalon (Rho)",
+                            "Metencephalon (Met)",
+                            "Pontine nuclei (Pn)",
+                            "Cerebellum (Cb)",
+                            "Molecular cell layer of the cerebellum (Cb-m)",
+                            "Cerebellum, unspecified (Cb-u)",
+                            "Myelencephalon (Myel)",
+                            "Cochlear nucleus, ventral part (VCN)",
+                            "Ventral cochlear nucleus, anterior part (AVCN)",
+                            "Ventral cochlear nucleus, posterior part (PVCN)",
+                            "Ventral cochlear nucleus, cap area (Cap)",
+                            "Ventral cochlear nucleus, granule cell layer (GCL)",
+                            "Cochlear nucleus, dorsal part (DCN)",
+                            "Dorsal cochlear nucleus, molecular layer (DCNM)",
+                            "Dorsal cochlear nucleus, fusiform and granule layer (DCNFG)",
+                            "Dorsal cochlear nucleus, deep core (DCND)",
+                            "Spinal trigeminal nucleus (Sp5n)",
+                            "Periventricular gray (PVG)",
+                            "Superior olivary complex (SO)",
+                            "Nucleus of the trapezoid body (NTB)",
+                            "Superior paraolivary nucleus (SPN)",
+                            "Medial superior olive (MSO)",
+                            "Lateral superior olive (LSO)",
+                            "Superior periolivary region (SPR)",
+                            "Ventral periolivary nuclei (VPO)",
+                            "Nuclei of the lateral lemniscus (NLL)",
+                            "Lateral lemniscus, ventral nucleus (VLL)",
+                            "Lateral lemniscus, intermediate nucleus (ILL)",
+                            "Lateral lemniscus, dorsal nucleus (DLL)",
+                            "Inferior olive (IO)",
+                            "Ventricular system (V)",
+                            "ventricular system, unspecified (V-u)",
+                            "4th ventricle (4V)",
+                            "central canal (CC)",
+                            "spinal cord (SpC)",
+                            "Inner ear (IE)",
+                            "vestibular apparatus (VeA)",
+                            "cochlea (Co)",
+                            "cochlear nerve (8cn)",
+                            "vestibular nerve (8vn)",
+                            "spiral ganglion (SpG)"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    },
+                    "targeted_x": {
+                        "$id": "#root/electrode_groups/items/targeted_x",
+                        "title": "targeted_x",
+                        "type": "number",
+                        "description": "Medial/Latetal",
+                        "examples": [
+                            2.6
+                        ],
+                        "default": 0.0
+                    },
+                    "targeted_y": {
+                        "$id": "#root/electrode_groups/items/targeted_y",
+                        "title": "targeted_y",
+                        "type": "number",
+                        "description": "Anterior/Posterior",
+                        "examples": [
+                            -3.8
+                        ],
+                        "default": 0.0
+                    },
+                    "targeted_z": {
+                        "$id": "#root/electrode_groups/items/targeted_z",
+                        "title": "targeted_z",
+                        "type": "number",
+                        "description": "Ventral/Dorsal",
+                        "examples": [
+                            0
+                        ],
+                        "default": 0
+                    },
+                    "units": {
+                        "$id": "#root/electrode_groups/items/units",
+                        "title": "units",
+                        "type": "string",
+                        "default": "mm",
+                        "examples": [
+                            "pm",
+                            "nm",
+                            "μm",
+                            "mm",
+                            "cm",
+                            "in",
+                            "yd",
+                            "ft"
+                        ],
+                        "pattern": "^(.|\\s)*\\S(.|\\s)*$"
+                    }
+                }
+            }
+        },
+        "ntrode_electrode_group_channel_map": {
+            "$id": "#root/ntrode_electrode_group_channel_map",
+            "title": "ntrode_electrode_group_channel_map",
+            "type": "array",
+            "default": [],
+            "items": {
+                "$id": "#root/ntrode_electrode_group_channel_map/items",
+                "title": "Items",
+                "type": "object",
+                "required": [
+                    "ntrode_id",
+                    "electrode_group_id",
+                    "bad_channels",
+                    "map"
+                ],
+                "properties": {
+                    "ntrode_id": {
+                        "$id": "#root/ntrode_electrode_group_channel_map/items/ntrode_id",
+                        "title": "ntrode_id",
+                        "type": "integer",
+                        "examples": [
+                            1
+                        ],
+                        "default": 0
+                    },
+                    "electrode_group_id": {
+                        "$id": "#root/ntrode_electrode_group_channel_map/items/electrode_group_id",
+                        "title": "electrode_group_id",
+                        "type": "integer",
+                        "examples": [
+                            0
+                        ],
+                        "default": 0
+                    },
+                    "bad_channels": {
+                        "$id": "#root/ntrode_electrode_group_channel_map/items/bad_channels",
+                        "title": "bad_channels",
+                        "type": "array",
+                        "default": [],
+                        "examples": [],
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+                                ],
+                                "minimum": 0,
+                                "default": 124
+                            },
+                            "125": {
+                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/125",
+                                "title": "125",
+                                "type": "integer",
+                                "examples": [
+                                    0,
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+                                ],
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+                                    124,
+                                    125,
+                                    126,
+                                    127
+                                ],
+                                "minimum": 0,
+                                "default": 125
+                            },
+                            "126": {
+                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/126",
+                                "title": "126",
+                                "type": "integer",
+                                "examples": [
+                                    0,
+                                    1,
+                                    2,
+                                    3,
+                                    4,
+                                    5,
+                                    6,
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+                                    127
+                                ],
+                                "enum": [
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+                                    115,
+                                    116,
+                                    117,
+                                    118,
+                                    119,
+                                    120,
+                                    121,
+                                    122,
+                                    123,
+                                    124,
+                                    125,
+                                    126,
+                                    127
+                                ],
+                                "minimum": 0,
+                                "default": 126
+                            },
+                            "127": {
+                                "$id": "#root/ntrode_electrode_group_channel_map/items/map/127",
+                                "title": "127",
+                                "type": "integer",
+                                "examples": [
+                                    0,
+                                    1,
+                                    2,
+                                    3,
+                                    4,
+                                    5,
+                                    6,
+                                    7,
+                                    8,
+                                    9,
+                                    10,
+                                    11,
+                                    12,
+                                    13,
+                                    14,
+                                    15,
+                                    16,
+                                    17,
+                                    18,
+                                    19,
+                                    20,
+                                    21,
+                                    22,
+                                    23,
+                                    24,
+                                    25,
+                                    26,
+                                    27,
+                                    28,
+                                    29,
+                                    30,
+                                    31,
+                                    32,
+                                    33,
+                                    34,
+                                    35,
+                                    36,
+                                    37,
+                                    38,
+                                    39,
+                                    40,
+                                    41,
+                                    42,
+                                    43,
+                                    44,
+                                    45,
+                                    46,
+                                    47,
+                                    48,
+                                    49,
+                                    50,
+                                    51,
+                                    52,
+                                    53,
+                                    54,
+                                    55,
+                                    56,
+                                    57,
+                                    58,
+                                    59,
+                                    60,
+                                    61,
+                                    62,
+                                    63,
+                                    64,
+                                    65,
+                                    66,
+                                    67,
+                                    68,
+                                    69,
+                                    70,
+                                    71,
+                                    72,
+                                    73,
+                                    74,
+                                    75,
+                                    76,
+                                    77,
+                                    78,
+                                    79,
+                                    80,
+                                    81,
+                                    82,
+                                    83,
+                                    84,
+                                    85,
+                                    86,
+                                    87,
+                                    88,
+                                    89,
+                                    90,
+                                    91,
+                                    92,
+                                    93,
+                                    94,
+                                    95,
+                                    96,
+                                    97,
+                                    98,
+                                    99,
+                                    100,
+                                    101,
+                                    102,
+                                    103,
+                                    104,
+                                    105,
+                                    106,
+                                    107,
+                                    108,
+                                    109,
+                                    110,
+                                    111,
+                                    112,
+                                    113,
+                                    114,
+                                    115,
+                                    116,
+                                    117,
+                                    118,
+                                    119,
+                                    120,
+                                    121,
+                                    122,
+                                    123,
+                                    124,
+                                    125,
+                                    126,
+                                    127
+                                ],
+                                "enum": [
+                                    0,
+                                    1,
+                                    2,
+                                    3,
+                                    4,
+                                    5,
+                                    6,
+                                    7,
+                                    8,
+                                    9,
+                                    10,
+                                    11,
+                                    12,
+                                    13,
+                                    14,
+                                    15,
+                                    16,
+                                    17,
+                                    18,
+                                    19,
+                                    20,
+                                    21,
+                                    22,
+                                    23,
+                                    24,
+                                    25,
+                                    26,
+                                    27,
+                                    28,
+                                    29,
+                                    30,
+                                    31,
+                                    32,
+                                    33,
+                                    34,
+                                    35,
+                                    36,
+                                    37,
+                                    38,
+                                    39,
+                                    40,
+                                    41,
+                                    42,
+                                    43,
+                                    44,
+                                    45,
+                                    46,
+                                    47,
+                                    48,
+                                    49,
+                                    50,
+                                    51,
+                                    52,
+                                    53,
+                                    54,
+                                    55,
+                                    56,
+                                    57,
+                                    58,
+                                    59,
+                                    60,
+                                    61,
+                                    62,
+                                    63,
+                                    64,
+                                    65,
+                                    66,
+                                    67,
+                                    68,
+                                    69,
+                                    70,
+                                    71,
+                                    72,
+                                    73,
+                                    74,
+                                    75,
+                                    76,
+                                    77,
+                                    78,
+                                    79,
+                                    80,
+                                    81,
+                                    82,
+                                    83,
+                                    84,
+                                    85,
+                                    86,
+                                    87,
+                                    88,
+                                    89,
+                                    90,
+                                    91,
+                                    92,
+                                    93,
+                                    94,
+                                    95,
+                                    96,
+                                    97,
+                                    98,
+                                    99,
+                                    100,
+                                    101,
+                                    102,
+                                    103,
+                                    104,
+                                    105,
+                                    106,
+                                    107,
+                                    108,
+                                    109,
+                                    110,
+                                    111,
+                                    112,
+                                    113,
+                                    114,
+                                    115,
+                                    116,
+                                    117,
+                                    118,
+                                    119,
+                                    120,
+                                    121,
+                                    122,
+                                    123,
+                                    124,
+                                    125,
+                                    126,
+                                    127
+                                ],
+                                "minimum": 0,
+                                "default": 127
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index bbf9d71..0ce43fe 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -687,7 +687,7 @@ def get_digitalsignal(self, stream_id, channel_id):
         if self.sysClock_byte:
             timestamps = self.get_regressed_systime(i_start, i_stop)
         else:
-            timestamps = self.get_analogsignal_timestamps(i_start, i_stop)
+            timestamps = self.get_systime_from_trodes_timestamps(i_start, i_stop)
         dio_change_times = timestamps[np.where(change_dir)[0] + 1]
 
         # insert the first timestamp with the first value
@@ -701,6 +701,7 @@ def get_digitalsignal(self, stream_id, channel_id):
 
         return dio_change_times, change_dir_trim
 
+    @functools.lru_cache(maxsize=1)
     def get_regressed_systime(self, i_start, i_stop=None):
         NANOSECONDS_PER_SECOND = 1e9
         # get values
@@ -713,13 +714,15 @@ def get_regressed_systime(self, i_start, i_stop=None):
         adjusted_timestamps = intercept + slope * trodestime_index
         return (adjusted_timestamps) / NANOSECONDS_PER_SECOND
 
+    @functools.lru_cache(maxsize=1)
     def get_systime_from_trodes_timestamps(self, i_start, i_stop=None):
         MILLISECONDS_PER_SECOND = 1e3
         # get values
         trodestime = self.get_analogsignal_timestamps(i_start, i_stop)
-        return (trodestime - int(self.timestamp_at_creation)) * (
-            1.0 / self._sampling_rate
-        ) + int(self.system_time_at_creation) / MILLISECONDS_PER_SECOND
+        initial_time = self.get_analogsignal_timestamps(0, 1)[0]
+        return (trodestime - initial_time) * (1.0 / self._sampling_rate) + int(
+            self.system_time_at_creation
+        ) / MILLISECONDS_PER_SECOND
 
     def _interpolate_raw_memmap(
         self,
diff --git a/src/spikegadgets_to_nwb/tests/integration-tests/__init__.py b/src/spikegadgets_to_nwb/tests/integration-tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py b/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
new file mode 100644
index 0000000..4d9d904
--- /dev/null
+++ b/src/spikegadgets_to_nwb/tests/integration-tests/test_metadata_validation_it.py
@@ -0,0 +1,190 @@
+import pytest
+import os
+from spikegadgets_to_nwb.metadata_validation import (
+    validate,
+)
+from spikegadgets_to_nwb.tests.test_data.test_metadata_dict_samples import (
+    basic_data,
+    basic_data_with_optional_arrays,
+    empty_experimenter_name,
+    string_as_experimenter_name,
+    empty_lab,
+    empty_institution,
+    empty_experiment_description,
+    empty_session_description,
+    empty_session_id,
+    empty_keywords,
+    keywords_array_with_empty_item,
+    not_array_keywords,
+    empty_subject,
+    subject_with_empty_values,
+    subject_with_invalid_sex,
+    subject_with_invalid_date,
+    empty_data_acq_device,
+    data_acq_device_with_no_values,
+    empty_units,
+    invalid_times_period_multiplier,
+    invalid_raw_data_to_volts,
+    invalid_default_header_file_path,
+    empty_device_name,
+    basic_ntrode_electrode_group_channel_map,
+)
+
+
+@pytest.mark.parametrize("metadata", [(None), ("")])
+def test_metadata_validation_only_accepts_right_data_type(metadata):
+    with pytest.raises(AssertionError) as e:
+        validate(metadata)
+
+
+@pytest.mark.parametrize("metadata", [(basic_data), (basic_data_with_optional_arrays)])
+def test_metadata_validation_verification_on_valid_data(metadata):
+    is_valid, errors = validate(metadata)
+
+    assert is_valid, "".join(errors)
+
+
+@pytest.mark.parametrize(
+    "metadata, key, expected",
+    [
+        (empty_experimenter_name, "experimenter_name", ["[] is too short"]),
+        (
+            string_as_experimenter_name,
+            "experimenter_name",
+            [
+                "'' is not of type 'array'",
+            ],
+        ),
+        (empty_lab, "lab", ["does not match"]),
+        (empty_institution, "institution", ["does not match"]),
+        (
+            empty_experiment_description,
+            "experiment_description",
+            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
+        ),
+        (
+            empty_session_description,
+            "session_description",
+            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
+        ),
+        (
+            empty_session_id,
+            "session_id",
+            ["does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'"],
+        ),
+        (
+            empty_keywords,
+            "keywords",
+            [
+                "[] is too short",
+            ],
+        ),
+        (
+            keywords_array_with_empty_item,
+            "keywords",
+            [
+                "",
+            ],
+        ),
+        (not_array_keywords, "keywords", ["is not of type 'array'"]),
+        (
+            subject_with_empty_values,
+            "subject1",
+            [
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "is not one of ['M', 'F', 'U', 'O']",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "-1 is less than the minimum of 0",
+                "does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'",
+            ],
+        ),
+        (
+            empty_subject,
+            "subject",
+            [
+                "'description' is a required property",
+                "'genotype' is a required property",
+                "'sex' is a required property",
+                "'species' is a required property",
+                "'subject_id' is a required property",
+                "'weight' is a required property",
+                "'date_of_birth' is a required property",
+            ],
+        ),
+        (subject_with_invalid_sex, "subject", ["is not one of ['M', 'F', 'U', 'O']"]),
+        (
+            subject_with_invalid_date,
+            "subject",
+            [
+                "'2023-01-04' does not match '(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d\\\\.\\\\d+)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d:[0-5]\\\\d)|(\\\\d{4}-[01]\\\\d-[0-3]\\\\dT[0-2]\\\\d:[0-5]\\\\d)'"
+            ],
+        ),
+        (
+            data_acq_device_with_no_values,
+            "data_acq_device1",
+            [
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+                "does not match '^(.|\\\\s)*\\\\S(.|\\\\s)*$'",
+            ],
+        ),
+        (empty_data_acq_device, "data_acq_device", ["[] is too short"]),
+        (
+            empty_units,
+            "units",
+            [
+                "'analog' is a required property",
+                "'behavioral_events' is a required property",
+            ],
+        ),
+        (
+            invalid_times_period_multiplier,
+            "times_period_multiplier",
+            [
+                "'a' is not of type 'number'",
+            ],
+        ),
+        (
+            invalid_raw_data_to_volts,
+            "raw_data_to_volts",
+            ["'a' is not of type 'number'"],
+        ),
+        (
+            invalid_default_header_file_path,
+            "default_header_file_path",
+            ["None is not of type 'string'"],
+        ),
+        (empty_device_name, "device_name", ["'name' is a required property"]),
+        (
+            basic_ntrode_electrode_group_channel_map,
+            "ntrode_electrode_group_channel_map",
+            (
+                [
+                    "'a' is not of type 'integer'",
+                    "'z' is not of type 'integer'",
+                    "'z' is not of type 'integer'",
+                    "'0' is not of type 'integer'",
+                    "'0' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
+                    "'t' is not of type 'integer'",
+                    "'t' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
+                    "'a' is not of type 'integer'",
+                    "'a' is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
+                    "-3 is not one of [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127]",
+                    "-3 is less than the minimum of 0",
+                ]
+            ),
+        ),
+    ],
+)
+def test_metadata_validation_verification_on_invalid_data(metadata, key, expected):
+    is_valid, errors = validate(metadata)
+
+    assert len(errors) == len(expected), f"Not all the errors are occurring in - {key}"
+    assert not is_valid, f"{key} should be invalid"
+    for index, error in enumerate(errors):
+        assert (
+            expected[index] in error
+        ), f"Expected error not found - ${expected[index]}"
diff --git a/src/spikegadgets_to_nwb/tests/test_convert.py b/src/spikegadgets_to_nwb/tests/test_convert.py
index 5861158..7206ed9 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert.py
@@ -1,25 +1,17 @@
+import numpy as np
 import os
 from pathlib import Path
-
-import numpy as np
-import pandas as pd
 from pynwb import NWBHDF5IO
+import shutil
 
 from spikegadgets_to_nwb.convert import _create_nwb, get_included_probe_metadata_paths
 from spikegadgets_to_nwb.data_scanner import get_file_info
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 MICROVOLTS_PER_VOLT = 1e6
 
 
 def test_get_file_info():
-    try:
-        # running on github
-        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
-    except (TypeError, FileNotFoundError):
-        # running locally
-        data_path = Path(path)
     path_df = get_file_info(data_path)
     path_df = path_df[
         path_df.animal == "sample"
@@ -54,53 +46,41 @@ def test_get_included_probe_metadat_paths():
 
 
 def test_convert():
-    try:
-        # running on github
-        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
-        yml_data_path = Path(path + "/test_data")
-        yml_path_df = get_file_info(yml_data_path)
-        yml_path_df = yml_path_df[yml_path_df.file_extension == ".yml"]
-        append_yml_df = True
-    except (TypeError, FileNotFoundError):
-        # running locally
-        data_path = Path(path + "/test_data")
-        append_yml_df = False
-    probe_metadata = [Path(path + "/test_data/tetrode_12.5.yml")]
-
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     # make session_df
     path_df = get_file_info(data_path)
-    if append_yml_df:
-        path_df = path_df[
-            path_df.file_extension != ".yml"
-        ]  # strip ymls, fixes github runner issue where yamls only sometimes present between jobs
-        path_df = pd.concat([path_df, yml_path_df])
-        path_df = path_df[
-            path_df.full_path
-            != yml_data_path.as_posix() + "/20230622_sample_metadataProbeReconfig.yml"
-        ]
-    else:
-        path_df = path_df[
-            path_df.full_path
-            != data_path.as_posix() + "/20230622_sample_metadataProbeReconfig.yml"
-        ]
+    # exclude the reconfig yaml file
+    path_df = path_df[
+        path_df.full_path
+        != str(data_path / "20230622_sample_metadataProbeReconfig.yml")
+    ]
     session_df = path_df[(path_df.animal == "sample")]
     assert len(session_df[session_df.file_extension == ".yml"]) == 1
+    # make temporary directory for video files
+    video_directory = data_path / "temp_video_directory_full_convert"
+    if not os.path.exists(video_directory):
+        os.makedirs(video_directory)
+
     _create_nwb(
         session=("20230622", "sample", "1"),
         session_df=session_df,
         probe_metadata_paths=probe_metadata,
         output_dir=str(data_path),
+        video_directory=str(video_directory),
     )
-    assert "sample20230622.nwb" in os.listdir(str(data_path))
-    with NWBHDF5IO(str(data_path) + "/sample20230622.nwb") as io:
+
+    output_file_path = data_path / "sample20230622.nwb"
+    assert output_file_path.exists()
+    rec_to_nwb_file = data_path / "minirec20230622_.nwb"
+    with NWBHDF5IO(output_file_path) as io:
         nwbfile = io.read()
-        with NWBHDF5IO(str(data_path) + "/minirec20230622_.nwb") as io2:
+        with NWBHDF5IO(rec_to_nwb_file) as io2:
             old_nwbfile = io2.read()
-
             # run nwb comparison
             compare_nwbfiles(nwbfile, old_nwbfile)
     # cleanup
-    os.remove(str(data_path) + "/sample20230622.nwb")
+    os.remove(output_file_path)
+    shutil.rmtree(video_directory)
 
 
 def check_module_entries(test, reference):
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_analog.py b/src/spikegadgets_to_nwb/tests/test_convert_analog.py
index 7111a82..9df75c9 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_analog.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_analog.py
@@ -1,30 +1,19 @@
 import os
-
 import pynwb
 
 from spikegadgets_to_nwb import convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.convert_analog import add_analog_data, get_analog_channel_names
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def test_add_analog_data():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
-
-    try:
-        # running on github
-        rec_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        rec_header = convert_rec_header.read_header(rec_file)
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
-    except:
-        # running locally
-        rec_file = path + "/test_data/20230622_sample_01_a1.rec"
-        rec_header = convert_rec_header.read_header(rec_file)
-        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
+    rec_file = data_path / "20230622_sample_01_a1.rec"
+    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
+    rec_header = convert_rec_header.read_header(rec_file)
     # make file with data
     nwbfile = convert_yaml.initialize_nwb(metadata, rec_header)
     analog_channel_names = get_analog_channel_names(rec_header)
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_dios.py b/src/spikegadgets_to_nwb/tests/test_convert_dios.py
index 8d566e3..3c0b66f 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_dios.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_dios.py
@@ -1,32 +1,22 @@
-import os
-
 import numpy as np
+import os
 import pynwb
 
 from spikegadgets_to_nwb import convert_yaml
 from spikegadgets_to_nwb.convert_dios import add_dios
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def test_add_dios_single_rec():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, _ = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
-    try:
-        # running on github
-        recfile = [os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"]
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = [path + "/test_data/20230622_sample_01_a1.rec"]
-        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
+    recfile = [data_path / "20230622_sample_01_a1.rec"]
+    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
 
     add_dios(nwbfile, recfile, metadata)
 
@@ -71,27 +61,16 @@ def test_add_dios_single_rec():
 
 def test_add_dios_two_epoch():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, _ = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
-    try:
-        # running on github
-        recfile = [
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = [
-            path + "/test_data/20230622_sample_01_a1.rec",
-            path + "/test_data/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
+    recfile = [
+        data_path / "20230622_sample_01_a1.rec",
+        data_path / "20230622_sample_02_a1.rec",
+    ]
+    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
 
     add_dios(nwbfile, recfile, metadata)
 
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py b/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
index aac211c..bf0ef0b 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_ephys.py
@@ -1,38 +1,27 @@
-import os
-
 import numpy as np
+import os
+from pathlib import Path
 import pynwb
 
 from spikegadgets_to_nwb import convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.convert_ephys import add_raw_ephys
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
+from spikegadgets_to_nwb.tests.utils import data_path
 
 MICROVOLTS_PER_VOLT = 1e6
-path = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_add_raw_ephys_single_rec():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    try:
-        # running on github
-        trodesconf_file = (
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        )  # "/test_data/reconfig_probeDevice.trodesconf"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
-    except:
-        # running locally
-        trodesconf_file = (
-            path + "/test_data/20230622_sample_01_a1.rec"
-        )  # "/test_data/reconfig_probeDevice.trodesconf"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
+    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
+    # "reconfig_probeDevice.trodesconf"
+    rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -45,22 +34,14 @@ def test_add_raw_ephys_single_rec():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    try:
-        # running on github
-        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_155936.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = path + "/test_data/20230622_sample_01_a1.rec"
-        rec_to_nwb_file = path + "/test_data/20230622_155936.nwb"
+    recfile = [data_path / "20230622_sample_01_a1.rec"]
+    rec_to_nwb_file = data_path / "20230622_155936.nwb"  # comparison file
 
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
         nwbfile,
-        [
-            recfile,
-        ],
+        recfile,
         map_row_ephys_data_to_row_electrodes_table,
     )
 
@@ -109,15 +90,13 @@ def test_add_raw_ephys_single_rec():
 
 def test_add_raw_ephys_single_rec_probe_configuration():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadataProbeReconfig.yml"
-    probe_metadata = [
-        path + "/test_data/128c-4s6mm6cm-15um-26um-sl.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadataProbeReconfig.yml"
+    probe_metadata = [data_path / "128c-4s6mm6cm-15um-26um-sl.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = path + "/test_data/reconfig_probeDevice.trodesconf"
+    trodesconf_file = data_path / "reconfig_probeDevice.trodesconf"
     rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
@@ -131,24 +110,16 @@ def test_add_raw_ephys_single_rec_probe_configuration():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    try:
-        # running on github
-        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        rec_to_nwb_file = (
-            os.environ.get("DOWNLOAD_DIR") + "/probe_reconfig_20230622_155936.nwb"
-        )
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = path + "/test_data/20230622_sample_01_a1.rec"
-        rec_to_nwb_file = path + "/test_data/probe_reconfig_20230622_155936.nwb"
+    recfile = [data_path / "20230622_sample_01_a1.rec"]
+    rec_to_nwb_file = (
+        data_path / "probe_reconfig_20230622_155936.nwb"
+    )  # comparison file
 
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
         nwbfile,
-        [
-            recfile,
-        ],
+        recfile,
         map_row_ephys_data_to_row_electrodes_table,
     )
 
@@ -198,22 +169,14 @@ def test_add_raw_ephys_single_rec_probe_configuration():
 
 def test_add_raw_ephys_two_epoch():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using the reconfig header
-    try:
-        # running on github
-        trodesconf_file = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
-    except:
-        # running locally
-        trodesconf_file = path + "/test_data/20230622_sample_01_a1.rec"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
+    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
+    rec_header = convert_rec_header.read_header(trodesconf_file)
 
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -226,20 +189,12 @@ def test_add_raw_ephys_two_epoch():
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )
 
-    try:
-        # running on github
-        recfile = [
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = [
-            path + "/test_data/20230622_sample_01_a1.rec",
-            path + "/test_data/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
+    recfile = [
+        data_path / "20230622_sample_01_a1.rec",
+        data_path / "20230622_sample_02_a1.rec",
+    ]
+    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
+
     map_row_ephys_data_to_row_electrodes_table = list(range(len(nwbfile.electrodes)))
 
     add_raw_ephys(
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index 31d0bb3..83a13d9 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -1,7 +1,5 @@
-import os
-from pathlib import Path
-
 import numpy as np
+import os
 from pynwb import NWBHDF5IO
 
 from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator
@@ -10,34 +8,27 @@
 from spikegadgets_to_nwb.data_scanner import get_file_info
 from spikegadgets_to_nwb.spike_gadgets_raw_io import SpikeGadgetsRawIO
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def test_add_epochs():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = load_metadata(metadata_path, [])
     nwbfile = initialize_nwb(metadata, default_test_xml_tree())
-    try:
-        # running on github
-        file_info = get_file_info(Path(os.environ.get("DOWNLOAD_DIR")))
-        rec_to_nwb_file = (
-            os.environ.get("DOWNLOAD_DIR") + "/probe_reconfig_20230622_155936.nwb"
-        )
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        file_info = get_file_info(Path(path))
-        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
-    file_info = file_info[file_info.animal == "sample"]
-    # assert file_info[file_info.file_extension == ".rec"].full_path.to_list() == []
+    file_info = get_file_info(data_path)
+    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
     # get all streams for all files
-    rec_dci = RecFileDataChunkIterator(
-        file_info[file_info.file_extension == ".rec"].full_path.to_list()
-    )
-    add_epochs(nwbfile, file_info, 20230622, "sample", rec_dci.neo_io)
+    neo_io = [
+        SpikeGadgetsRawIO(filename=file)
+        for file in file_info[file_info.file_extension == ".rec"].full_path
+    ]
+    [neo_io.parse_header() for neo_io in neo_io]
+
+    file_info = file_info[file_info.animal == "sample"]
+    file_info = file_info[file_info.date == 20230622]
+    add_epochs(nwbfile, file_info, neo_io)
     epochs_df = nwbfile.epochs.to_dataframe()
-    # load old nwb versio
+    # load old nwb version
     io = NWBHDF5IO(rec_to_nwb_file, "r")
     old_nwbfile = io.read()
     old_epochs_df = old_nwbfile.epochs.to_dataframe()
@@ -50,23 +41,14 @@ def test_add_epochs():
 
 
 def test_add_sample_count():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = load_metadata(metadata_path, [])
     nwbfile = initialize_nwb(metadata, default_test_xml_tree())
-    try:
-        # running on github
-        recfile = [
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec",
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = os.environ.get("DOWNLOAD_DIR") + "/minirec20230622_.nwb"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = [
-            path + "/test_data/20230622_sample_01_a1.rec",
-            path + "/test_data/20230622_sample_02_a1.rec",
-        ]
-        rec_to_nwb_file = path + "/test_data/minirec20230622_.nwb"
+    recfile = [
+        data_path / "20230622_sample_01_a1.rec",
+        data_path / "20230622_sample_02_a1.rec",
+    ]
+    rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
 
     # make recfile data chunk iterator
     rec_dci = RecFileDataChunkIterator(recfile)
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_position.py b/src/spikegadgets_to_nwb/tests/test_convert_position.py
index 6a32276..bada810 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_position.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_position.py
@@ -4,9 +4,13 @@
 import numpy as np
 import pandas as pd
 import pytest
-from pynwb import NWBHDF5IO
+from pynwb import NWBHDF5IO, TimeSeries
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
+from spikegadgets_to_nwb.convert_ephys import RecFileDataChunkIterator
+from spikegadgets_to_nwb.convert_intervals import add_sample_count
+from spikegadgets_to_nwb.convert_dios import add_dios
+from spikegadgets_to_nwb.convert_intervals import add_epochs
 from spikegadgets_to_nwb.convert_position import (
     add_position,
     correct_timestamps_for_camera_to_mcu_lag,
@@ -20,10 +24,10 @@
     parse_dtype,
     read_trodes_datafile,
     remove_acquisition_timing_pause_non_ptp,
+    find_camera_dio_channel,
 )
 from spikegadgets_to_nwb.data_scanner import get_file_info
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def test_parse_dtype_standard():
@@ -194,23 +198,15 @@ def test_correct_timestamps_for_camera_to_mcu_lag():
 
 
 def test_add_position():
-    try:
-        # running on github
-        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
-    except (TypeError, FileNotFoundError):
-        # running locally
-        data_path = Path(path + "/test_data")
-    probe_metadata = [Path(path + "/test_data/tetrode_12.5.yml")]
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
 
     # make session_df
     path_df = get_file_info(data_path)
     session_df = path_df[(path_df.animal == "sample")]
 
     # get metadata
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     rec_file = session_df[
         (session_df.epoch == 1) & (session_df.file_extension == ".rec")
@@ -222,11 +218,10 @@ def test_add_position():
 
     # run add_position and prerequisite functions
     convert_yaml.add_cameras(nwbfile, metadata)
-    add_position(nwbfile, metadata, session_df, rec_header, video_directory="")
+    add_position(nwbfile, metadata, session_df, rec_header)
 
     # Check that the objects were properly added
     assert "position" in nwbfile.processing["behavior"].data_interfaces
-    assert "video_files" in nwbfile.processing
     assert "non_repeat_timestamp_labels" in nwbfile.processing
     assert "position_frame_index" in nwbfile.processing
 
@@ -287,3 +282,66 @@ def test_add_position():
                 assert validated, f"Could not find matching series for {series}"
     # cleanup
     os.remove(filename)
+
+
+from spikegadgets_to_nwb.convert_position import read_trodes_datafile
+
+
+def test_add_position_non_ptp():
+    # make session_df
+    path_df = get_file_info(data_path)
+    session_df = path_df[(path_df.animal == "ginny")]
+    # get metadata
+    metadata_path = data_path / "nonptp_metadata.yml"
+    metadata, _ = convert_yaml.load_metadata(metadata_path, [])
+    # load the prepped non-ptp nwbfile
+    with NWBHDF5IO(data_path / "non_ptp_prep.nwb", "a", load_namespaces=True) as io:
+        nwbfile = io.read()
+        add_position(
+            nwbfile,
+            metadata,
+            session_df,
+            ptp_enabled=False,
+            rec_dci_timestamps=nwbfile.processing["sample_count"][
+                "sample_count"
+            ].timestamps[:]
+            / 1e9,
+            sample_count=nwbfile.processing["sample_count"]
+            .data_interfaces["sample_count"]
+            .data[:],
+        )
+        # read in position data to compare to
+        ref_pos = pd.read_pickle(data_path / "position_df.pkl")
+        # check that the data is the same
+        for series in [
+            "led_0_series_1",
+            "led_0_series_2",
+            "led_1_series_1",
+            "led_1_series_2",
+        ]:
+            # check series in new nwbfile
+            assert (
+                series
+                in nwbfile.processing["behavior"]["position"].spatial_series.keys()
+            )
+            # get the data for this series
+            t_new = nwbfile.processing["behavior"]["position"][series].timestamps[:]
+            pos_new = nwbfile.processing["behavior"]["position"][series].data[:]
+            assert t_new.size == pos_new.shape[0]
+            assert pos_new.shape[1] == 2
+            validated = False
+            for name in ref_pos.name.to_list():
+                t_ref = ref_pos[ref_pos.name == name].timestamps.values[0]
+
+                if t_new.size == t_ref.size and np.allclose(
+                    t_ref, t_new, atol=1, rtol=0
+                ):
+                    pos_ref = ref_pos[ref_pos.name == name].data.to_list()[0]
+                    if np.allclose(
+                        pos_ref[:100, :2], pos_new[:100], atol=1e-6, rtol=0
+                    ) or np.allclose(
+                        pos_ref[:100, 2:], pos_new[:100], atol=1e-6, rtol=0
+                    ):
+                        validated = True
+                        break
+            assert validated, f"Could not find matching series for {series}"
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py b/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
index 0c5da8c..b39f776 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_rec_header.py
@@ -5,8 +5,7 @@
 from ndx_franklab_novela import HeaderDevice
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def default_test_xml_tree() -> ElementTree:
@@ -17,39 +16,23 @@ def default_test_xml_tree() -> ElementTree:
     ElementTree
         root xml tree for intial nwb generation
     """
-    try:
-        # running on github
-        trodesconf_file = (
-            os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        )  # "/test_data/reconfig_probeDevice.trodesconf"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
-    except:
-        # running locally
-        trodesconf_file = (
-            path + "/test_data/20230622_sample_01_a1.rec"
-        )  # "/test_data/reconfig_probeDevice.trodesconf"
-        rec_header = convert_rec_header.read_header(trodesconf_file)
+    trodesconf_file = data_path / "20230622_sample_01_a1.rec"
+    # "reconfig_probeDevice.trodesconf"
+    rec_header = convert_rec_header.read_header(trodesconf_file)
     return rec_header
 
 
 def test_add_header_device():
     # Set up test data
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
+    recfile = data_path / "20230622_sample_01_a1.rec"
+
     # Call the function to be tested
-    try:
-        # running on github
-        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-        convert_rec_header.add_header_device(
-            nwbfile, convert_rec_header.read_header(recfile)
-        )
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = path + "/test_data/20230622_sample_01_a1.rec"
-        convert_rec_header.add_header_device(
-            nwbfile, convert_rec_header.read_header(recfile)
-        )
+    convert_rec_header.add_header_device(
+        nwbfile, convert_rec_header.read_header(recfile)
+    )
 
     # Perform assertions to check the results
     # Check if the device was added correctly
@@ -80,7 +63,7 @@ def test_add_header_device():
     assert header_device.file_path == ""
 
     # Check if error raised if improper header file is passed
-    recfile = path + "/test_data/bad_header.trodesconf"
+    recfile = data_path / "bad_header.trodesconf"
     with pytest.raises(
         ValueError,
         match="SpikeGadgets: the xml header does not contain '</Configuration>'",
@@ -95,14 +78,9 @@ def test_detect_ptp():
 
 def test_validate_yaml_header_electrode_map():
     # get metadata and rec_header
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-    try:
-        # running on github
-        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = path + "/test_data/20230622_sample_01_a1.rec"
+    recfile = data_path / "20230622_sample_01_a1.rec"
     rec_header = convert_rec_header.read_header(recfile)
 
     # correct matching
diff --git a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py b/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
index d68f8ad..ce44d36 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_yaml.py
@@ -1,6 +1,7 @@
+from datetime import datetime
 import logging
 import os
-from datetime import datetime
+import shutil
 
 from hdmf.common.table import DynamicTable, VectorData
 from ndx_franklab_novela import Probe, Shank, ShanksElectrode
@@ -8,12 +9,15 @@
 
 from spikegadgets_to_nwb import convert, convert_rec_header, convert_yaml
 from spikegadgets_to_nwb.tests.test_convert_rec_header import default_test_xml_tree
+from spikegadgets_to_nwb.data_scanner import get_file_info
+from spikegadgets_to_nwb.convert_position import add_associated_video_files
+from spikegadgets_to_nwb.tests.utils import data_path
 
-path = os.path.dirname(os.path.abspath(__file__))
+from ndx_franklab_novela import CameraDevice
 
 
 def test_initial_nwb_creation():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     # check that things were added in
@@ -34,7 +38,7 @@ def test_initial_nwb_creation():
 
 
 def test_subject_creation():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_subject(nwb_file, metadata)
@@ -50,7 +54,7 @@ def test_subject_creation():
 
 
 def test_camera_creation():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_cameras(nwb_file, metadata)
@@ -64,7 +68,7 @@ def test_camera_creation():
 
 
 def test_acq_device_creation():
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwb_file = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     convert_yaml.add_acquisition_devices(nwb_file, metadata)
@@ -78,20 +82,13 @@ def test_acq_device_creation():
 
 def test_electrode_creation():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-    probe_metadata = [
-        path + "/test_data/tetrode_12.5.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    probe_metadata = [data_path / "tetrode_12.5.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
     # create the hw_channel map using rec data
-    try:
-        # running on github
-        recfile = os.environ.get("DOWNLOAD_DIR") + "/20230622_sample_01_a1.rec"
-    except (TypeError, FileNotFoundError):
-        # running locally
-        recfile = path + "/test_data/20230622_sample_01_a1.rec"
+    recfile = data_path / "20230622_sample_01_a1.rec"
     rec_header = convert_rec_header.read_header(recfile)
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -156,10 +153,8 @@ def test_electrode_creation():
 
 def test_electrode_creation_reconfigured():
     # load metadata yml and make nwb file
-    metadata_path = path + "/test_data/20230622_sample_metadataProbeReconfig.yml"
-    probe_metadata = [
-        path + "/test_data/128c-4s6mm6cm-15um-26um-sl.yml",
-    ]
+    metadata_path = data_path / "20230622_sample_metadataProbeReconfig.yml"
+    probe_metadata = [data_path / "128c-4s6mm6cm-15um-26um-sl.yml"]
     metadata, probe_metadata = convert_yaml.load_metadata(metadata_path, probe_metadata)
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
@@ -168,7 +163,7 @@ def test_electrode_creation_reconfigured():
     metadata["ntrode_electrode_group_channel_map"][-1]["map"]["31"] = 126
 
     # create the hw_channel map using the reconfig header
-    trodesconf_file = path + "/test_data/reconfig_probeDevice.trodesconf"
+    trodesconf_file = data_path / "reconfig_probeDevice.trodesconf"
     rec_header = convert_rec_header.read_header(trodesconf_file)
     hw_channel_map = convert_rec_header.make_hw_channel_map(
         metadata, rec_header.find("SpikeConfiguration")
@@ -235,7 +230,7 @@ def test_electrode_creation_reconfigured():
 
 def test_add_tasks():
     # Set up test data
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
 
@@ -289,12 +284,12 @@ def test_add_associated_files(capsys):
     # Create a logger
     logger = convert.setup_logger("convert", "testing.log")
     # Set up test data
-    metadata_path = path + "/test_data/20230622_sample_metadata.yml"
+    metadata_path = data_path / "20230622_sample_metadata.yml"
     metadata, _ = convert_yaml.load_metadata(metadata_path, [])
     nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
     # Change path of files to be relative to this directory
     for assoc_meta in metadata["associated_files"]:
-        assoc_meta["path"] = path + "/test_data/"
+        assoc_meta["path"] = str(data_path / assoc_meta["name"])
     # call the function to test
     convert_yaml.add_associated_files(nwbfile, metadata)
     assert "associated_files" in nwbfile.processing
@@ -316,7 +311,7 @@ def test_add_associated_files(capsys):
 
     # Test printed errormessage for missing file
     # Change path of files to be relative to this directory
-    metadata["associated_files"][0]["path"] = ""
+    metadata["associated_files"][0]["path"] = "bad_path.txt"
     metadata["associated_files"][0]["name"] = "bad_path.txt"
     metadata["associated_files"].pop(1)
     convert_yaml.add_associated_files(nwbfile, metadata)
@@ -331,9 +326,42 @@ def test_add_associated_files(capsys):
                     break
     assert printed_warning
 
-    def test_add_associated_video_files():
-        # Set up test data
-        metadata_path = path + "/test_data/20230622_sample_metadata.yml"
-        metadata, _ = convert_yaml.load_metadata(metadata_path, [])
-        nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
-        return
+
+def test_add_associated_video_files():
+    # Set up test data
+    metadata_path = data_path / "20230622_sample_metadata.yml"
+    metadata, _ = convert_yaml.load_metadata(metadata_path, [])
+    nwbfile = convert_yaml.initialize_nwb(metadata, default_test_xml_tree())
+    convert_yaml.add_cameras(nwbfile, metadata)
+
+    # make session_df
+    path_df = get_file_info(data_path)
+    session_df = path_df[(path_df.animal == "sample")]
+
+    # make temp video directory
+    video_directory = data_path / "temp_video_directory"
+    if not os.path.exists(video_directory):
+        os.makedirs(video_directory)
+
+    # Call the function to be tested
+    add_associated_video_files(
+        nwbfile, metadata, session_df, video_directory=str(video_directory)
+    )
+    assert "video_files" in nwbfile.processing
+    assert "video" in nwbfile.processing["video_files"].data_interfaces
+    assert len(nwbfile.processing["video_files"]["video"].time_series) == 2
+
+    for video, video_meta in zip(
+        nwbfile.processing["video_files"]["video"].time_series,
+        metadata["associated_video_files"],
+    ):
+        video = nwbfile.processing["video_files"]["video"][video]
+        assert video.name == video_meta["name"]
+        assert video.format == "external"
+        assert video.timestamps_unit == "seconds"
+        assert video.timestamps is not None
+        assert isinstance(video.device, CameraDevice)
+        assert (video_directory / video.external_file[0]).exists()
+
+    # cleanup
+    shutil.rmtree(video_directory)
diff --git a/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml b/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
index 9531e6b..990c3f8 100644
--- a/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
+++ b/src/spikegadgets_to_nwb/tests/test_data/20230622_sample_metadata.yml
@@ -62,20 +62,11 @@ associated_files:
     path: path/
     task_epochs: 2
 associated_video_files:
-  - name: video1
+  - name: 20230622_sample_01_a1.1.h264
     camera_id: 0
     task_epochs: 1
-  - name: video3
+  - name: 20230622_sample_02_a1.1.h264
     camera_id: 0
-    task_epochs: 3
-  - name: video5
-    camera_id: 0
-    task_epochs: 5
-  - name: video2
-    camera_id: 1
-    task_epochs: 2
-  - name: video4
-    camera_id: 1
     task_epochs: 2
 units:
   analog: "-1"
diff --git a/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml b/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
new file mode 100644
index 0000000..f0a8663
--- /dev/null
+++ b/src/spikegadgets_to_nwb/tests/test_data/nonptp_metadata.yml
@@ -0,0 +1,1225 @@
+
+experiment_description: Hippocampus content feedback
+experimenter_name: Michael Coulter
+institution: University of California, San Francisco
+lab: Loren Frank
+raw_data_to_volts: 1.95e-07
+session_description: Hippocampus content feedback
+session_id: ginny_20211027
+subject:
+  description: Long Evans Rat
+  genotype: Wild Type
+  sex: Male
+  species: Rat
+  subject_id: ginny
+  weight: Unknown
+  date_of_birth: 2000-01-01T00:00:00.000Z
+
+associated_files:
+- description: Statescript log run 1
+  name: statescript_r1
+  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_02_r1.stateScriptLog
+  task_epochs:
+  - 2
+- description: Statescript log run 2
+  name: statescript_r2
+  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_04_r2.stateScriptLog
+  task_epochs:
+  - 4
+- description: Statescript log run 3
+  name: statescript_r3
+  path: /cumulus/mcoulter/ginny/raw/20211027/20211027_ginny_06_r3.stateScriptLog
+  task_epochs:
+  - 6
+
+associated_video_files:
+- name: 20211027_ginny_01_s1.1.h264
+  camera_id : 0
+  task_epochs: 1
+- name: 20211027_ginny_03_s2.1.h264
+  camera_id : 0
+  task_epochs: 3
+- name: 20211027_ginny_05_s3.1.h264
+  camera_id : 0
+  task_epochs: 5
+- name: 20211027_ginny_07_s4.1.h264
+  camera_id : 0
+  task_epochs: 7
+- name: 20211027_ginny_02_r1.1.h264
+  camera_id : 1
+  task_epochs: 2
+- name: 20211027_ginny_04_r2.1.h264
+  camera_id : 1
+  task_epochs: 4
+- name: 20211027_ginny_06_r3.1.h264
+  camera_id : 1
+  task_epochs: 6
+
+tasks:
+- camera_id:
+  - 1
+  task_description: training session
+  task_epochs:
+  - 2
+  - 4
+  - 6
+  task_name: Content feedback
+  task_environment: n/a
+- camera_id:
+  - 0
+  task_description: sleep
+  task_epochs:
+  - 1
+  - 3
+  - 5
+  - 7
+  task_name: Sleep
+  task_environment: n/a
+times_period_multiplier: 1.5
+units:
+  analog: unspecified
+  behavioral_events: unspecified
+
+cameras:
+- camera_name: MEC_sleep_camera
+  id: 0
+  lens: unknown2
+  manufacturer: unknown2
+  meters_per_pixel: 0.00055
+  model: unknown2
+- camera_name: MEC_run_camera
+  id: 1
+  lens: unknown
+  manufacturer: unknown
+  meters_per_pixel: 0.0022
+  model: unknown
+
+behavioral_events:
+- name: Arm1_poke
+  description: Din13
+- name: Arm2_poke
+  description: Din9
+- name: CenterWell_poke
+  description: Din7
+- name: BackWell_poke
+  description: Din10
+- name: Arm1_light
+  description: Dout13
+- name: Arm2_light
+  description: Dout9
+- name: CenterWell_light
+  description: Dout7
+- name: BackWell_light
+  description: Dout10
+- name: Arm1_milk_pump
+  description: Dout11
+- name: Arm2_milk_pump
+  description: Dout12
+- name: CenterWell_milk_pump
+  description: Dout14
+- name: BackWell_milk_pump
+  description: Dout8
+- name: CamerasyncRun camera ticks
+  description: Din15
+- name: CamerasyncSleep camera ticks
+  description: Din16
+
+data_acq_device:
+- adc_circuit: Intan
+  amplifier: Intan
+  system: SpikeGadgets
+default_header_file_path: default_header.xml
+device:
+  name:
+  - Trodes
+electrode_groups:
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 0
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 1
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 2
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 3
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 4
+  location: ''
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 5
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 6
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 7
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 8
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 9
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 10
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 11
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 12
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 13
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 14
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 15
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 16
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 17
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 18
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 19
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 20
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 21
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 22
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 23
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 24
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 25
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 26
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 27
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 28
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 29
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 30
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 31
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 32
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 33
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 34
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 35
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 36
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 37
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 38
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 39
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 40
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 41
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 42
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 43
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 44
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 45
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 46
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 47
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 48
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 49
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 50
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 51
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 52
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 53
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 54
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 55
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 56
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 57
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 58
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 59
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 60
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 61
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 62
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+- description: tetrode
+  device_type: tetrode_12.5
+  id: 63
+  location: ca1
+  targeted_location: CA1
+  targeted_x: 0.0
+  targeted_y: 0.0
+  targeted_z: 0.0
+  units: um
+
+ntrode_electrode_group_channel_map:
+- bad_channels: []
+  electrode_group_id: 0
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 1
+- bad_channels: [0]
+  electrode_group_id: 1
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 2
+- bad_channels: []
+  electrode_group_id: 2
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 3
+- bad_channels: []
+  electrode_group_id: 3
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 4
+- bad_channels: []
+  electrode_group_id: 4
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 5
+- bad_channels: []
+  electrode_group_id: 5
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 6
+- bad_channels: []
+  electrode_group_id: 6
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 7
+- bad_channels: []
+  electrode_group_id: 7
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 8
+- bad_channels: []
+  electrode_group_id: 8
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 9
+- bad_channels: []
+  electrode_group_id: 9
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 10
+- bad_channels: []
+  electrode_group_id: 10
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 11
+- bad_channels: []
+  electrode_group_id: 11
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 12
+- bad_channels: []
+  electrode_group_id: 12
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 13
+- bad_channels: []
+  electrode_group_id: 13
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 14
+- bad_channels: []
+  electrode_group_id: 14
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 15
+- bad_channels: []
+  electrode_group_id: 15
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 16
+- bad_channels: []
+  electrode_group_id: 16
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 17
+- bad_channels: []
+  electrode_group_id: 17
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 18
+- bad_channels: []
+  electrode_group_id: 18
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 19
+- bad_channels: []
+  electrode_group_id: 19
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 20
+- bad_channels: []
+  electrode_group_id: 20
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 21
+- bad_channels: []
+  electrode_group_id: 21
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 22
+- bad_channels: []
+  electrode_group_id: 22
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 23
+- bad_channels: []
+  electrode_group_id: 23
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 24
+- bad_channels: []
+  electrode_group_id: 24
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 25
+- bad_channels: []
+  electrode_group_id: 25
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 26
+- bad_channels: []
+  electrode_group_id: 26
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 27
+- bad_channels: []
+  electrode_group_id: 27
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 28
+- bad_channels: []
+  electrode_group_id: 28
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 29
+- bad_channels: []
+  electrode_group_id: 29
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 30
+- bad_channels: []
+  electrode_group_id: 30
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 31
+- bad_channels: []
+  electrode_group_id: 31
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 32
+- bad_channels: []
+  electrode_group_id: 32
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 33
+- bad_channels: []
+  electrode_group_id: 33
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 34
+- bad_channels: []
+  electrode_group_id: 34
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 35
+- bad_channels: []
+  electrode_group_id: 35
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 36
+- bad_channels: [0]
+  electrode_group_id: 36
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 37
+- bad_channels: []
+  electrode_group_id: 37
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 38
+- bad_channels: []
+  electrode_group_id: 38
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 39
+- bad_channels: []
+  electrode_group_id: 39
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 40
+- bad_channels: [2]
+  electrode_group_id: 40
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 41
+- bad_channels: []
+  electrode_group_id: 41
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 42
+- bad_channels: []
+  electrode_group_id: 42
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 43
+- bad_channels: []
+  electrode_group_id: 43
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 44
+- bad_channels: []
+  electrode_group_id: 44
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 45
+- bad_channels: []
+  electrode_group_id: 45
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 46
+- bad_channels: []
+  electrode_group_id: 46
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 47
+- bad_channels: []
+  electrode_group_id: 47
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 48
+- bad_channels: []
+  electrode_group_id: 48
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 49
+- bad_channels: []
+  electrode_group_id: 49
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 50
+- bad_channels: []
+  electrode_group_id: 50
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 51
+- bad_channels: []
+  electrode_group_id: 51
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 52
+- bad_channels: []
+  electrode_group_id: 52
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 53
+- bad_channels: []
+  electrode_group_id: 53
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 54
+- bad_channels: []
+  electrode_group_id: 54
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 55
+- bad_channels: []
+  electrode_group_id: 55
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 56
+- bad_channels: []
+  electrode_group_id: 56
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 57
+- bad_channels: []
+  electrode_group_id: 57
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 58
+- bad_channels: []
+  electrode_group_id: 58
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 59
+- bad_channels: []
+  electrode_group_id: 59
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 60
+- bad_channels: []
+  electrode_group_id: 60
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 61
+- bad_channels: []
+  electrode_group_id: 61
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 62
+- bad_channels: []
+  electrode_group_id: 62
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 63
+- bad_channels: []
+  electrode_group_id: 63
+  map:
+    '0': 0
+    '1': 1
+    '2': 2
+    '3': 3
+  ntrode_id: 64
diff --git a/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
new file mode 100644
index 0000000..6cad848
--- /dev/null
+++ b/src/spikegadgets_to_nwb/tests/test_data/test_metadata_dict_samples.py
@@ -0,0 +1,212 @@
+import pytest
+import copy
+
+basic_data = {
+    "experimenter_name": ["michael jackson"],
+    "lab": "Loren Frank Lab",
+    "institution": "University of California, San Francisco",
+    "experiment_description": "making of thriller",
+    "session_description": "make an album like the nutcracker",
+    "session_id": "6",
+    "keywords": ["best"],
+    "subject": {
+        "description": "Long-Evans Rat",
+        "genotype": "Wild Type",
+        "sex": "M",
+        "species": "Rattus norvegicus",
+        "subject_id": "1",
+        "date_of_birth": "2023-07-24T00:00:00.000Z",
+        "weight": 100,
+    },
+    "data_acq_device": [
+        {
+            "name": "SpikeGadgets",
+            "system": "SpikeGadgets",
+            "amplifier": "Intan",
+            "adc_circuit": "Intan",
+        }
+    ],
+    "cameras": [],
+    "tasks": [],
+    "associated_files": [],
+    "associated_video_files": [],
+    "units": {"analog": "1", "behavioral_events": "1"},
+    "times_period_multiplier": 1,
+    "raw_data_to_volts": 1,
+    "default_header_file_path": "epic/michaeljackson/thriller",
+    "behavioral_events": [],
+    "device": {"name": ["Trodes"]},
+    "electrode_groups": [],
+    "ntrode_electrode_group_channel_map": [],
+}
+
+basic_data_with_optional_arrays = {
+    "experimenter_name": ["michael jackson"],
+    "lab": "Loren Frank Lab",
+    "institution": "University of California, San Francisco",
+    "experiment_description": "making of thriller",
+    "session_description": "make an album like the nutcracker",
+    "session_id": "6",
+    "keywords": ["best"],
+    "subject": {
+        "description": "Long-Evans Rat",
+        "genotype": "Wild Type",
+        "sex": "M",
+        "species": "Rattus norvegicus",
+        "subject_id": "1",
+        "date_of_birth": "2023-07-24T00:00:00.000Z",
+        "weight": 100,
+    },
+    "data_acq_device": [
+        {
+            "name": "SpikeGadgets",
+            "system": "SpikeGadgets",
+            "amplifier": "Intan",
+            "adc_circuit": "Intan",
+        }
+    ],
+    "cameras": [
+        {
+            "id": 10,
+            "meters_per_pixel": 1,
+            "manufacturer": "Epic Record",
+            "model": "555",
+            "lens": "MJ lens",
+            "camera_name": "MJ cam",
+        },
+    ],
+    "tasks": [],
+    "associated_files": [
+        {
+            "name": "Michael Jackson",
+            "description": "Thriller25",
+            "path": "Hard work",
+            "task_epochs": 0,
+        },
+        {
+            "name": "Michael Jackson2",
+            "description": "HIStory",
+            "path": "Making/a/statement",
+            "task_epochs": 1,
+        },
+    ],
+    "associated_video_files": [
+        {
+            "name": "Michael Jackson",
+            "camera_id": 1,
+            "task_epochs": 1,
+        }
+    ],
+    "units": {"analog": "1", "behavioral_events": "1"},
+    "times_period_multiplier": 1,
+    "raw_data_to_volts": 1,
+    "default_header_file_path": "epic/michaeljackson/thriller",
+    "behavioral_events": [
+        {
+            "description": "Din555",
+            "name": "M. Joe Jackson",
+        }
+    ],
+    "device": {"name": ["Trodes"]},
+    "electrode_groups": [],
+    "ntrode_electrode_group_channel_map": [],
+}
+
+empty_experimenter_name = copy.deepcopy(basic_data)
+empty_experimenter_name["experimenter_name"] = []
+
+string_as_experimenter_name = copy.deepcopy(basic_data)
+string_as_experimenter_name["experimenter_name"] = ""
+
+empty_lab = copy.deepcopy(basic_data)
+empty_lab["lab"] = ""
+
+empty_institution = copy.deepcopy(basic_data)
+empty_institution["institution"] = ""
+
+empty_experiment_description = copy.deepcopy(basic_data)
+empty_experiment_description["experiment_description"] = ""
+
+empty_session_description = copy.deepcopy(basic_data)
+empty_session_description["session_description"] = ""
+
+empty_session_id = copy.deepcopy(basic_data)
+empty_session_id["session_id"] = ""
+
+empty_keywords = copy.deepcopy(basic_data)
+empty_keywords["keywords"] = []
+
+keywords_array_with_empty_item = copy.deepcopy(basic_data)
+keywords_array_with_empty_item["keywords"] = [""]
+
+not_array_keywords = copy.deepcopy(basic_data)
+not_array_keywords["keywords"] = "test"
+
+subject_with_empty_values = copy.deepcopy(basic_data)
+subject_with_empty_values["subject"] = {
+    "description": "",
+    "genotype": "",
+    "sex": "",
+    "species": "",
+    "subject_id": "",
+    "date_of_birth": "",
+    "weight": -1,
+}
+
+empty_subject = copy.deepcopy(basic_data)
+empty_subject["subject"] = {}
+
+subject_with_invalid_sex = copy.deepcopy(basic_data)
+subject_with_invalid_sex["subject"] = {
+    "description": "Long-Evans Rat",
+    "genotype": "Wild Type",
+    "sex": "m",
+    "species": "Rattus norvegicus",
+    "subject_id": "1",
+    "date_of_birth": "2023-07-24T00:00:00.000Z",
+    "weight": 100,
+}
+
+subject_with_invalid_date = copy.deepcopy(basic_data)
+subject_with_invalid_date["subject"] = {
+    "description": "Long-Evans Rat",
+    "genotype": "Wild Type",
+    "sex": "M",
+    "species": "Rattus norvegicus",
+    "subject_id": "1",
+    "date_of_birth": "2023-01-04",
+    "weight": 100,
+}
+
+data_acq_device_with_no_values = copy.deepcopy(basic_data)
+data_acq_device_with_no_values["data_acq_device"] = [
+    {"name": "", "system": "", "amplifier": "", "adc_circuit": ""}
+]
+
+empty_data_acq_device = copy.deepcopy(basic_data)
+empty_data_acq_device["data_acq_device"] = []
+
+empty_units = copy.deepcopy(basic_data)
+empty_units["units"] = {}
+
+invalid_times_period_multiplier = copy.deepcopy(basic_data)
+invalid_times_period_multiplier["times_period_multiplier"] = "a"
+
+invalid_raw_data_to_volts = copy.deepcopy(basic_data)
+invalid_raw_data_to_volts["raw_data_to_volts"] = "a"
+
+invalid_default_header_file_path = copy.deepcopy(basic_data)
+invalid_default_header_file_path["default_header_file_path"] = None
+
+empty_device_name = copy.deepcopy(basic_data)
+empty_device_name["device"] = {}
+
+basic_ntrode_electrode_group_channel_map = copy.deepcopy(basic_data)
+basic_ntrode_electrode_group_channel_map["ntrode_electrode_group_channel_map"] = [
+    {
+        "ntrode_id": "a",
+        "electrode_group_id": "z",
+        "bad_channels": ["z"],
+        "map": {"0": "0", "1": "t", "2": "a", "3": -3},
+    }
+]
diff --git a/src/spikegadgets_to_nwb/tests/test_metadata_validation.py b/src/spikegadgets_to_nwb/tests/test_metadata_validation.py
new file mode 100644
index 0000000..003e858
--- /dev/null
+++ b/src/spikegadgets_to_nwb/tests/test_metadata_validation.py
@@ -0,0 +1,25 @@
+import copy
+import datetime
+from unittest.mock import MagicMock, patch
+from spikegadgets_to_nwb.metadata_validation import (
+    validate,
+    _get_nwb_json_schema_path,
+)
+from spikegadgets_to_nwb.tests.test_data import test_metadata_dict_samples
+
+
+def test_path_to_json_schema_is_correct():
+    path = _get_nwb_json_schema_path()
+    json_schema_file = "nwb_schema.json"
+
+    assert json_schema_file in path
+
+
+@patch("spikegadgets_to_nwb.metadata_validation._get_json_schema")
+@patch("jsonschema.Draft202012Validator")
+def test_verify_validation_called(jsonValidator, getSchema):
+    basic_test_data = copy.deepcopy(test_metadata_dict_samples.basic_data)
+    basic_test_data["subject"]["date_of_birth"] = datetime.datetime.now().isoformat()
+    validate(basic_test_data)
+    assert getSchema.call_count == 1
+    assert jsonValidator.call_count == 1
diff --git a/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py b/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
index 7054c1f..4aff4a5 100644
--- a/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
+++ b/src/spikegadgets_to_nwb/tests/test_spikegadgets_io.py
@@ -1,23 +1,13 @@
-import os
-from pathlib import Path
-
 import numpy as np
 
 from spikegadgets_to_nwb.spike_gadgets_raw_io import InsertedMemmap, SpikeGadgetsRawIO
-
-path = os.path.dirname(os.path.abspath(__file__))
+from spikegadgets_to_nwb.tests.utils import data_path
 
 
 def test_spikegadgets_raw_io_interpolation():
     # Interpolation of dropped timestamp only done for ephys data and systime
 
     # get the path to the rec file
-    try:
-        # running on github
-        data_path = Path(os.environ.get("DOWNLOAD_DIR"))
-    except (TypeError, FileNotFoundError):
-        # running locally
-        data_path = Path(path + "/test_data")
     rec_file = data_path / "20230622_sample_01_a1.rec"
 
     # create the SpikeGadgetsRawIO object
diff --git a/src/spikegadgets_to_nwb/tests/utils.py b/src/spikegadgets_to_nwb/tests/utils.py
new file mode 100644
index 0000000..f97acbf
--- /dev/null
+++ b/src/spikegadgets_to_nwb/tests/utils.py
@@ -0,0 +1,23 @@
+"""Set the path to the bulk test data dir and copies the yaml/config files there"""
+import os
+from pathlib import Path
+import shutil
+
+
+yaml_path = Path(__file__).resolve().parent / "test_data"
+
+data_path = os.environ.get("DOWNLOAD_DIR", None)
+if data_path is not None:
+    # running from the GitHub Action workflow
+    data_path = Path(data_path)
+    shutil.copytree(
+        yaml_path,
+        data_path,
+        dirs_exist_ok=True,
+        ignore=shutil.ignore_patterns(*os.listdir(data_path)),  # ignore existing
+    )
+else:
+    # running locally -- bulk test data is the same directory as the test yaml files
+    data_path = yaml_path
+
+del yaml_path

From b2c4bdfd04e68a2dce1760d39c1119c1808e2f1d Mon Sep 17 00:00:00 2001
From: Eric Denovellis <edeno@bu.edu>
Date: Fri, 27 Oct 2023 14:57:27 -0700
Subject: [PATCH 09/16] Fix merge

---
 src/spikegadgets_to_nwb/convert_dios.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/spikegadgets_to_nwb/convert_dios.py b/src/spikegadgets_to_nwb/convert_dios.py
index b28341e..8161c53 100644
--- a/src/spikegadgets_to_nwb/convert_dios.py
+++ b/src/spikegadgets_to_nwb/convert_dios.py
@@ -70,24 +70,26 @@ def add_dios(nwbfile: NWBFile, recfile: list[str], metadata: dict) -> None:
             prefix = "ECU_"
             break
 
-    # compile data for all dio channels in all files
-    all_timestamps = [np.array([], dtype=np.float64) for i in channel_name_map]
-    all_state_changes = [np.array([], dtype=np.float64) for i in channel_name_map]
-    for io in neo_io:
-        for i, channel_name in enumerate(channel_name_map):
+    for channel_name in channel_name_map:
+        # merge streams from multiple files
+        all_timestamps = []
+        all_state_changes = []
+        for io in neo_io:
             timestamps, state_changes = io.get_digitalsignal(
                 stream_name, prefix + channel_name
             )
-            all_timestamps[i] = np.concatenate((all_timestamps[i], timestamps))
-            all_state_changes[i] = np.concatenate((all_state_changes[i], state_changes))
-    # Add each channel as a behavioral event time series
-    for i, channel_name in enumerate(channel_name_map):
+            all_timestamps.append(timestamps)
+            all_state_changes.append(state_changes)
+        all_timestamps = np.concatenate(all_timestamps)
+        all_state_changes = np.concatenate(all_state_changes)
+        assert isinstance(all_timestamps[0], np.float64)
+        assert isinstance(all_timestamps, np.ndarray)
         ts = TimeSeries(
             name=channel_name_map[channel_name],
             description=channel_name,
-            data=all_state_changes[i],
+            data=all_state_changes,
             unit="-1",  # TODO change to "N/A",
-            timestamps=all_timestamps[i],  # TODO adjust timestamps
+            timestamps=all_timestamps,  # TODO adjust timestamps
         )
         beh_events.add_timeseries(ts)
 

From f51ee5b349431c52695842eddb70a46f7451af10 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Fri, 27 Oct 2023 16:14:39 -0700
Subject: [PATCH 10/16] Use split iterators in add_epochs test

---
 .../tests/test_convert_intervals.py                   | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index 83a13d9..5cfcef6 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -18,15 +18,12 @@ def test_add_epochs():
     file_info = get_file_info(data_path)
     rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
     # get all streams for all files
-    neo_io = [
-        SpikeGadgetsRawIO(filename=file)
-        for file in file_info[file_info.file_extension == ".rec"].full_path
-    ]
-    [neo_io.parse_header() for neo_io in neo_io]
-
+    rec_dci = RecFileDataChunkIterator(
+        file_info[file_info.file_extension == ".rec"].full_path.to_list()
+    )
     file_info = file_info[file_info.animal == "sample"]
     file_info = file_info[file_info.date == 20230622]
-    add_epochs(nwbfile, file_info, neo_io)
+    add_epochs(nwbfile, file_info, rec_dci.neo_io)
     epochs_df = nwbfile.epochs.to_dataframe()
     # load old nwb version
     io = NWBHDF5IO(rec_to_nwb_file, "r")

From 8a4daf39918b5a7fcbb622b4ea844be514497847 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Fri, 27 Oct 2023 16:35:50 -0700
Subject: [PATCH 11/16] Restrict epochs before creating rec_dci in
 test_add_epochs

---
 src/spikegadgets_to_nwb/tests/test_convert_intervals.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
index 5cfcef6..e30e765 100644
--- a/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
+++ b/src/spikegadgets_to_nwb/tests/test_convert_intervals.py
@@ -16,13 +16,13 @@ def test_add_epochs():
     metadata, _ = load_metadata(metadata_path, [])
     nwbfile = initialize_nwb(metadata, default_test_xml_tree())
     file_info = get_file_info(data_path)
+    file_info = file_info[file_info.animal == "sample"]
+    file_info = file_info[file_info.date == 20230622]
     rec_to_nwb_file = data_path / "minirec20230622_.nwb"  # comparison file
     # get all streams for all files
     rec_dci = RecFileDataChunkIterator(
         file_info[file_info.file_extension == ".rec"].full_path.to_list()
     )
-    file_info = file_info[file_info.animal == "sample"]
-    file_info = file_info[file_info.date == 20230622]
     add_epochs(nwbfile, file_info, rec_dci.neo_io)
     epochs_df = nwbfile.epochs.to_dataframe()
     # load old nwb version

From 139777edfe08af5f7473251c56d02f057dd43915 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 1 Nov 2023 08:03:33 -0700
Subject: [PATCH 12/16] Log print statement

---
 src/spikegadgets_to_nwb/convert_ephys.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikegadgets_to_nwb/convert_ephys.py b/src/spikegadgets_to_nwb/convert_ephys.py
index 4104d6d..162b936 100644
--- a/src/spikegadgets_to_nwb/convert_ephys.py
+++ b/src/spikegadgets_to_nwb/convert_ephys.py
@@ -120,7 +120,7 @@ def __init__(
                     j += MAXIMUM_ITERATOR_SIZE
                 self.neo_io.pop(iterator_loc)
                 self.neo_io[iterator_loc:iterator_loc] = sub_iterators
-        print("# iterators:", len(self.neo_io))
+        logger.info("# iterators:", len(self.neo_io))
         # NOTE: this will read all the timestamps from the rec file, which can be slow
         if timestamps is not None:
             self.timestamps = timestamps

From cadf02492c33b07f72f1143a947a02cb7b33addf Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 1 Nov 2023 08:03:59 -0700
Subject: [PATCH 13/16] Log print statement

---
 src/spikegadgets_to_nwb/convert_ephys.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikegadgets_to_nwb/convert_ephys.py b/src/spikegadgets_to_nwb/convert_ephys.py
index 162b936..53f2171 100644
--- a/src/spikegadgets_to_nwb/convert_ephys.py
+++ b/src/spikegadgets_to_nwb/convert_ephys.py
@@ -120,7 +120,7 @@ def __init__(
                     j += MAXIMUM_ITERATOR_SIZE
                 self.neo_io.pop(iterator_loc)
                 self.neo_io[iterator_loc:iterator_loc] = sub_iterators
-        logger.info("# iterators:", len(self.neo_io))
+        logger.info(f"# iterators: {len(self.neo_io)}")
         # NOTE: this will read all the timestamps from the rec file, which can be slow
         if timestamps is not None:
             self.timestamps = timestamps

From ea8346f1c4a09eabc191d9c1490468b3fa2823a4 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 1 Nov 2023 08:11:09 -0700
Subject: [PATCH 14/16] Name int 16 conversion constant

---
 src/spikegadgets_to_nwb/spike_gadgets_raw_io.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index 0ce43fe..5d21874 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -13,7 +13,7 @@
     _spike_channel_dtype,
 )
 from scipy.stats import linregress
-
+INT_16_CONVERSION = 256
 
 class SpikeGadgetsRawIO(BaseRawIO):
     extensions = ["rec"]
@@ -526,7 +526,7 @@ def get_analogsignal_multiplexed(self, channel_names=None) -> np.ndarray:
         # read the data into int16
         data = (
             self._raw_memmap[:, data_offsets[:, 0]]
-            + self._raw_memmap[:, data_offsets[:, 0] + 1] * 256
+            + self._raw_memmap[:, data_offsets[:, 0] + 1] * INT_16_CONVERSION
         )
         # initialize the first row
         analog_multiplexed_data[0] = data[0]

From 15cd4b3d6ca2107bc4f6b27589a8909dd3aea4f0 Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 1 Nov 2023 08:16:08 -0700
Subject: [PATCH 15/16] Fix linting

---
 src/spikegadgets_to_nwb/spike_gadgets_raw_io.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index 5d21874..91858f3 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -13,8 +13,10 @@
     _spike_channel_dtype,
 )
 from scipy.stats import linregress
+
 INT_16_CONVERSION = 256
 
+
 class SpikeGadgetsRawIO(BaseRawIO):
     extensions = ["rec"]
     rawmode = "one-file"

From d859f902c924de85964c593a61cd1dd743cfcfef Mon Sep 17 00:00:00 2001
From: Sam Bray <sam.bray@ucsf.edu>
Date: Wed, 1 Nov 2023 08:29:59 -0700
Subject: [PATCH 16/16] Use int 16 conversion variable

---
 src/spikegadgets_to_nwb/spike_gadgets_raw_io.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
index 91858f3..be06d1f 100644
--- a/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
+++ b/src/spikegadgets_to_nwb/spike_gadgets_raw_io.py
@@ -614,7 +614,8 @@ def get_analogsignal_multiplexed_partial(
         # read the data into int16
         data = (
             self._raw_memmap[i_start:i_stop, data_offsets[:, 0]]
-            + self._raw_memmap[i_start:i_stop, data_offsets[:, 0] + 1] * 256
+            + self._raw_memmap[i_start:i_stop, data_offsets[:, 0] + 1]
+            * INT_16_CONVERSION
         )
         # initialize the first row
         analog_multiplexed_data[0] = data[0]
@@ -920,7 +921,7 @@ def get_analogsignal_multiplexed(self, channel_names=None) -> np.ndarray:
         # read the data into int16
         data = (
             self._raw_memmap[:, data_offsets[:, 0]]
-            + self._raw_memmap[:, data_offsets[:, 0] + 1] * 256
+            + self._raw_memmap[:, data_offsets[:, 0] + 1] * INT_16_CONVERSION
         )
         # initialize the first row
         # if no previous state, assume first segment. Default to superclass behavior