From f32a684839dc4b58ee2521b4bc08b39e4f98a433 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:07:34 -0400
Subject: [PATCH 01/22] port over dlc utils

---
 .../behavior/deeplabcut/_dlc_utils.py         | 314 ++++++++++++++++++
 1 file changed, 314 insertions(+)
 create mode 100644 src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
new file mode 100644
index 000000000..01a10de62
--- /dev/null
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -0,0 +1,314 @@
+import datetime
+import os
+import pickle
+import warnings
+from pathlib import Path
+from platform import python_version
+import importlib
+
+import cv2
+import yaml
+import numpy as np
+import pandas as pd
+from hdmf.build.warnings import DtypeConversionWarning
+from packaging.version import Version  # Installed with setuptools
+from pynwb import NWBFile, NWBHDF5IO
+from ndx_pose import PoseEstimationSeries, PoseEstimation
+from ruamel.yaml import YAML
+
+
+def _read_config(configname):
+    """
+    Reads structured config file defining a project.
+    """
+    ruamelFile = YAML()
+    path = Path(configname)
+    if os.path.exists(path):
+        try:
+            with open(path, "r") as f:
+                cfg = ruamelFile.load(f)
+                curr_dir = os.path.dirname(configname)
+                if cfg["project_path"] != curr_dir:
+                    cfg["project_path"] = curr_dir
+        except Exception as err:
+            if len(err.args) > 2:
+                if (
+                    err.args[2]
+                    == "could not determine a constructor for the tag '!!python/tuple'"
+                ):
+                    with open(path, "r") as ymlfile:
+                        cfg = yaml.load(ymlfile, Loader=yaml.SafeLoader)
+                else:
+                    raise
+
+    else:
+        raise FileNotFoundError(
+            "Config file is not found. Please make sure that the file exists and/or that you passed the path of the config file correctly!"
+        )
+    return cfg
+
+
+
+def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=True):
+    """
+    Return numpy array of the timestamps for a video.
+
+    Parameters
+    ----------
+    movie_file : str
+        Path to movie_file
+    """
+    # TODO: consider moving this to DLC, and actually extract alongside video analysis!
+
+    reader = cv2.VideoCapture(movie_file)
+    timestamps = []
+    for _ in range(len(reader)):
+        _ = reader.read()
+        timestamps.append(reader.get(cv2.CAP_PROP_POS_MSEC))
+
+    timestamps = np.array(timestamps) / 1000  # Convert to seconds
+
+    if np.nanvar(np.diff(timestamps)) < 1.0 / reader.fps * 1.0 / VARIABILITYBOUND:
+        warnings.warn(
+            "Variability of timestamps suspiciously small. See: https://github.com/DeepLabCut/DLC2NWB/issues/1"
+        )
+
+    if any(timestamps[1:] == 0):
+        # Infers times when OpenCV provides 0s
+        warning_msg = "Removing"
+        timestamp_zero_count = np.count_nonzero(timestamps == 0)
+        timestamps[1:][timestamps[1:] == 0] = np.nan # replace 0s with nan
+
+        if infer_timestamps:
+            warning_msg = "Replacing"
+            timestamps = _infer_nan_timestamps(timestamps)
+
+        warnings.warn( # warns user of percent of 0 frames
+            "%s cv2 timestamps returned as 0: %f%%"
+            % (warning_msg, ( timestamp_zero_count / len(timestamps) * 100))
+        )
+
+    return timestamps
+
+
+def _infer_nan_timestamps(timestamps):
+    """Given np.array, interpolate nan values using index * sampling rate"""
+    bad_timestamps_mask = np.isnan(timestamps)
+    # Runs of good timestamps
+    good_run_indices = np.where( 
+        np.diff(np.hstack(([False], bad_timestamps_mask == False, [False])))
+    )[0].reshape(-1, 2)
+    
+    # For each good run, get the diff and append to cumulative array
+    sampling_diffs = np.array([])
+    for idx in good_run_indices: 
+        sampling_diffs = np.append(sampling_diffs, np.diff(timestamps[idx[0]:idx[1]]))
+    estimated_sampling_rate = np.mean(sampling_diffs) # Average over diffs
+    
+    # Infer timestamps with avg sampling rate
+    bad_timestamps_indexes = np.argwhere(bad_timestamps_mask)[:, 0]
+    inferred_timestamps = bad_timestamps_indexes * estimated_sampling_rate
+    timestamps[bad_timestamps_mask] = inferred_timestamps
+
+    return timestamps
+
+
+def _ensure_individuals_in_header(df, dummy_name):
+    if "individuals" not in df.columns.names:
+        # Single animal project -> add individual row to
+        # the header of single animal projects.
+        temp = pd.concat({dummy_name: df}, names=["individuals"], axis=1)
+        df = temp.reorder_levels(
+            ["scorer", "individuals", "bodyparts", "coords"], axis=1
+        )
+    return df
+
+
+def _get_pes_args(config_file, h5file, individual_name, infer_timestamps=True):
+    if "DLC" not in h5file or not h5file.endswith(".h5"):
+        raise IOError("The file passed in is not a DeepLabCut h5 data file.")
+
+    cfg = _read_config(config_file)
+
+    vidname, scorer = os.path.split(h5file)[-1].split("DLC")
+    scorer = "DLC" + os.path.splitext(scorer)[0]
+    video = None
+
+    df = _ensure_individuals_in_header(pd.read_hdf(h5file), individual_name)
+
+    # Fetch the corresponding metadata pickle file
+    paf_graph = []
+    filename, _ = os.path.splitext(h5file)
+    for i, c in enumerate(filename[::-1]):
+        if c.isnumeric():
+            break
+    if i > 0:
+        filename = filename[:-i]
+    metadata_file = filename + "_meta.pickle"
+    if os.path.isfile(metadata_file):
+        with open(metadata_file, "rb") as file:
+            metadata = pickle.load(file)
+        test_cfg = metadata["data"]["DLC-model-config file"]
+        paf_graph = test_cfg.get("partaffinityfield_graph", [])
+        if paf_graph:
+            paf_inds = test_cfg.get("paf_best")
+            if paf_inds is not None:
+                paf_graph = [paf_graph[i] for i in paf_inds]
+    else:
+        warnings.warn("Metadata not found...")
+
+    for video_path, params in cfg["video_sets"].items():
+        if vidname in video_path:
+            video = video_path, params["crop"]
+            break
+
+    if video is None:
+        warnings.warn(f"The video file corresponding to {h5file} could not be found...")
+        video = "fake_path", "0, 0, 0, 0"
+
+        timestamps = (
+            df.index.tolist()
+        )  # setting timestamps to dummy TODO: extract timestamps in DLC?
+    else:
+        timestamps = _get_movie_timestamps(video[0], infer_timestamps=infer_timestamps)
+    return scorer, df, video, paf_graph, timestamps, cfg
+
+
+def _write_pes_to_nwbfile(
+    nwbfile,
+    animal,
+    df_animal,
+    scorer,
+    video,  # Expects this to be a tuple; first index is string path, second is the image shape as "0, width, 0, height"
+    paf_graph,
+    timestamps,
+    exclude_nans,
+):  
+    pose_estimation_series = []
+    for kpt, xyp in df_animal.groupby(level="bodyparts", axis=1, sort=False):
+        data = xyp.to_numpy()
+
+        if exclude_nans: 
+            # exclude_nans is inverse infer_timestamps. if not infer, there may be nans
+            data = data[~np.isnan(timestamps)]
+            timestamps_cleaned = timestamps[~np.isnan(timestamps)] 
+        else:
+            timestamps_cleaned = timestamps
+
+        pes = PoseEstimationSeries(
+            name=f"{animal}_{kpt}",
+            description=f"Keypoint {kpt} from individual {animal}.",
+            data=data[:, :2],
+            unit="pixels",
+            reference_frame="(0,0) corresponds to the bottom left corner of the video.",
+            timestamps=timestamps_cleaned,
+            confidence=data[:, 2],
+            confidence_definition="Softmax output of the deep neural network.",
+        )
+        pose_estimation_series.append(pes)
+
+    deeplabcut_version = None
+    is_deeplabcut_installed = importlib.util.find_spec(name="deeplabcut") is not None
+    if is_deeplabcut_installed:
+        deeplabcut_version = importlib.metadata.version(distribution_name="deeplabcut")
+    pe = PoseEstimation(
+        pose_estimation_series=pose_estimation_series,
+        description="2D keypoint coordinates estimated using DeepLabCut.",
+        original_videos=[video[0]],
+        # TODO check if this is a mandatory arg in ndx-pose (can skip if video is not found_
+        dimensions=[list(map(int, video[1].split(",")))[1::2]],
+        scorer=scorer,
+        source_software="DeepLabCut",
+        source_software_version=deeplabcut_version,
+        nodes=[pes.name for pes in pose_estimation_series],
+        edges=paf_graph if paf_graph else None,
+    )
+    if 'behavior' in nwbfile.processing:
+        behavior_pm = nwbfile.processing["behavior"]
+    else:
+        behavior_pm = nwbfile.create_processing_module(
+            name="behavior", description="processed behavioral data"
+        )
+    behavior_pm.add(pe)
+    return nwbfile
+
+
+def write_subject_to_nwb(nwbfile, h5file, individual_name, config_file):
+    """
+    Given, subject name, write h5file to an existing nwbfile.
+
+    Parameters
+    ----------
+    nwbfile: pynwb.NWBFile
+        nwbfile to write the subject specific pose estimation series.
+    h5file : str
+        Path to a h5 data file
+    individual_name : str
+        Name of the subject (whose pose is predicted) for single-animal DLC project.
+        For multi-animal projects, the names from the DLC project will be used directly.
+    config_file : str
+        Path to a project config.yaml file
+    config_dict : dict
+        dict containing configuration options. Provide this as alternative to config.yml file.
+
+    Returns
+    -------
+    nwbfile: pynwb.NWBFile
+        nwbfile with pes written in the behavior module
+    """
+    scorer, df, video, paf_graph, timestamps, _ = _get_pes_args(config_file, h5file, individual_name)
+    df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
+    return _write_pes_to_nwbfile(nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps)
+
+
+def convert_h5_to_nwb(config, h5file, individual_name="ind1", infer_timestamps=True):
+    """
+    Convert a DeepLabCut (DLC) video prediction, h5 data file to Neurodata Without Borders (NWB). Also
+    takes project config, to store relevant metadata.
+
+    Parameters
+    ----------
+    config : str
+        Path to a project config.yaml file
+
+    h5file : str
+        Path to a h5 data file
+
+    individual_name : str
+        Name of the subject (whose pose is predicted) for single-animal DLC project.
+        For multi-animal projects, the names from the DLC project will be used directly.
+
+    infer_timestamps : bool
+        Default True. Uses framerate to infer the timestamps returned as 0 from OpenCV.
+        If False, exclude these frames from resulting NWB file.
+
+    TODO: allow one to overwrite those names, with a mapping?
+
+    Returns
+    -------
+    list of str
+        List of paths to the newly created NWB data files.
+        By default NWB files are stored in the same folder as the h5file.
+
+    """
+    scorer, df, video, paf_graph, timestamps, cfg = _get_pes_args(config, h5file, individual_name, 
+                                                                  infer_timestamps=infer_timestamps)
+    output_paths = []
+    for animal, df_ in df.groupby(level="individuals", axis=1):
+        nwbfile = NWBFile(
+            session_description=cfg["Task"],
+            experimenter=cfg["scorer"],
+            identifier=scorer,
+            session_start_time=datetime.datetime.now(datetime.timezone.utc),
+        )
+
+        # TODO Store the test_pose_config as well?
+        nwbfile = _write_pes_to_nwbfile(nwbfile, animal, df_, scorer, video, paf_graph, timestamps,
+                                        exclude_nans=(not infer_timestamps))
+        output_path = h5file.replace(".h5", f"_{animal}.nwb")
+        with warnings.catch_warnings(), NWBHDF5IO(output_path, mode="w") as io:
+            warnings.filterwarnings("ignore", category=DtypeConversionWarning)
+            io.write(nwbfile)
+        output_paths.append(output_path)
+
+    return output_paths

From 76726b5270b4541561ad7fa139618109009917b6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 18:11:49 +0000
Subject: [PATCH 02/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../behavior/deeplabcut/_dlc_utils.py         | 65 ++++++++-----------
 1 file changed, 27 insertions(+), 38 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 01a10de62..f1d8d7b64 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -1,19 +1,19 @@
 import datetime
+import importlib
 import os
 import pickle
 import warnings
 from pathlib import Path
 from platform import python_version
-import importlib
 
 import cv2
-import yaml
 import numpy as np
 import pandas as pd
+import yaml
 from hdmf.build.warnings import DtypeConversionWarning
+from ndx_pose import PoseEstimation, PoseEstimationSeries
 from packaging.version import Version  # Installed with setuptools
-from pynwb import NWBFile, NWBHDF5IO
-from ndx_pose import PoseEstimationSeries, PoseEstimation
+from pynwb import NWBHDF5IO, NWBFile
 from ruamel.yaml import YAML
 
 
@@ -32,10 +32,7 @@ def _read_config(configname):
                     cfg["project_path"] = curr_dir
         except Exception as err:
             if len(err.args) > 2:
-                if (
-                    err.args[2]
-                    == "could not determine a constructor for the tag '!!python/tuple'"
-                ):
+                if err.args[2] == "could not determine a constructor for the tag '!!python/tuple'":
                     with open(path, "r") as ymlfile:
                         cfg = yaml.load(ymlfile, Loader=yaml.SafeLoader)
                 else:
@@ -48,7 +45,6 @@ def _read_config(configname):
     return cfg
 
 
-
 def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=True):
     """
     Return numpy array of the timestamps for a video.
@@ -77,15 +73,14 @@ def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=Tr
         # Infers times when OpenCV provides 0s
         warning_msg = "Removing"
         timestamp_zero_count = np.count_nonzero(timestamps == 0)
-        timestamps[1:][timestamps[1:] == 0] = np.nan # replace 0s with nan
+        timestamps[1:][timestamps[1:] == 0] = np.nan  # replace 0s with nan
 
         if infer_timestamps:
             warning_msg = "Replacing"
             timestamps = _infer_nan_timestamps(timestamps)
 
-        warnings.warn( # warns user of percent of 0 frames
-            "%s cv2 timestamps returned as 0: %f%%"
-            % (warning_msg, ( timestamp_zero_count / len(timestamps) * 100))
+        warnings.warn(  # warns user of percent of 0 frames
+            "%s cv2 timestamps returned as 0: %f%%" % (warning_msg, (timestamp_zero_count / len(timestamps) * 100))
         )
 
     return timestamps
@@ -95,16 +90,14 @@ def _infer_nan_timestamps(timestamps):
     """Given np.array, interpolate nan values using index * sampling rate"""
     bad_timestamps_mask = np.isnan(timestamps)
     # Runs of good timestamps
-    good_run_indices = np.where( 
-        np.diff(np.hstack(([False], bad_timestamps_mask == False, [False])))
-    )[0].reshape(-1, 2)
-    
+    good_run_indices = np.where(np.diff(np.hstack(([False], bad_timestamps_mask == False, [False]))))[0].reshape(-1, 2)
+
     # For each good run, get the diff and append to cumulative array
     sampling_diffs = np.array([])
-    for idx in good_run_indices: 
-        sampling_diffs = np.append(sampling_diffs, np.diff(timestamps[idx[0]:idx[1]]))
-    estimated_sampling_rate = np.mean(sampling_diffs) # Average over diffs
-    
+    for idx in good_run_indices:
+        sampling_diffs = np.append(sampling_diffs, np.diff(timestamps[idx[0] : idx[1]]))
+    estimated_sampling_rate = np.mean(sampling_diffs)  # Average over diffs
+
     # Infer timestamps with avg sampling rate
     bad_timestamps_indexes = np.argwhere(bad_timestamps_mask)[:, 0]
     inferred_timestamps = bad_timestamps_indexes * estimated_sampling_rate
@@ -118,9 +111,7 @@ def _ensure_individuals_in_header(df, dummy_name):
         # Single animal project -> add individual row to
         # the header of single animal projects.
         temp = pd.concat({dummy_name: df}, names=["individuals"], axis=1)
-        df = temp.reorder_levels(
-            ["scorer", "individuals", "bodyparts", "coords"], axis=1
-        )
+        df = temp.reorder_levels(["scorer", "individuals", "bodyparts", "coords"], axis=1)
     return df
 
 
@@ -166,9 +157,7 @@ def _get_pes_args(config_file, h5file, individual_name, infer_timestamps=True):
         warnings.warn(f"The video file corresponding to {h5file} could not be found...")
         video = "fake_path", "0, 0, 0, 0"
 
-        timestamps = (
-            df.index.tolist()
-        )  # setting timestamps to dummy TODO: extract timestamps in DLC?
+        timestamps = df.index.tolist()  # setting timestamps to dummy TODO: extract timestamps in DLC?
     else:
         timestamps = _get_movie_timestamps(video[0], infer_timestamps=infer_timestamps)
     return scorer, df, video, paf_graph, timestamps, cfg
@@ -183,15 +172,15 @@ def _write_pes_to_nwbfile(
     paf_graph,
     timestamps,
     exclude_nans,
-):  
+):
     pose_estimation_series = []
     for kpt, xyp in df_animal.groupby(level="bodyparts", axis=1, sort=False):
         data = xyp.to_numpy()
 
-        if exclude_nans: 
+        if exclude_nans:
             # exclude_nans is inverse infer_timestamps. if not infer, there may be nans
             data = data[~np.isnan(timestamps)]
-            timestamps_cleaned = timestamps[~np.isnan(timestamps)] 
+            timestamps_cleaned = timestamps[~np.isnan(timestamps)]
         else:
             timestamps_cleaned = timestamps
 
@@ -223,12 +212,10 @@ def _write_pes_to_nwbfile(
         nodes=[pes.name for pes in pose_estimation_series],
         edges=paf_graph if paf_graph else None,
     )
-    if 'behavior' in nwbfile.processing:
+    if "behavior" in nwbfile.processing:
         behavior_pm = nwbfile.processing["behavior"]
     else:
-        behavior_pm = nwbfile.create_processing_module(
-            name="behavior", description="processed behavioral data"
-        )
+        behavior_pm = nwbfile.create_processing_module(name="behavior", description="processed behavioral data")
     behavior_pm.add(pe)
     return nwbfile
 
@@ -291,8 +278,9 @@ def convert_h5_to_nwb(config, h5file, individual_name="ind1", infer_timestamps=T
         By default NWB files are stored in the same folder as the h5file.
 
     """
-    scorer, df, video, paf_graph, timestamps, cfg = _get_pes_args(config, h5file, individual_name, 
-                                                                  infer_timestamps=infer_timestamps)
+    scorer, df, video, paf_graph, timestamps, cfg = _get_pes_args(
+        config, h5file, individual_name, infer_timestamps=infer_timestamps
+    )
     output_paths = []
     for animal, df_ in df.groupby(level="individuals", axis=1):
         nwbfile = NWBFile(
@@ -303,8 +291,9 @@ def convert_h5_to_nwb(config, h5file, individual_name="ind1", infer_timestamps=T
         )
 
         # TODO Store the test_pose_config as well?
-        nwbfile = _write_pes_to_nwbfile(nwbfile, animal, df_, scorer, video, paf_graph, timestamps,
-                                        exclude_nans=(not infer_timestamps))
+        nwbfile = _write_pes_to_nwbfile(
+            nwbfile, animal, df_, scorer, video, paf_graph, timestamps, exclude_nans=(not infer_timestamps)
+        )
         output_path = h5file.replace(".h5", f"_{animal}.nwb")
         with warnings.catch_warnings(), NWBHDF5IO(output_path, mode="w") as io:
             warnings.filterwarnings("ignore", category=DtypeConversionWarning)

From 0ab7fe77870e733dc76412a063138846917d8d3c Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:12:55 -0400
Subject: [PATCH 03/22] remove from requirements

---
 .../datainterfaces/behavior/deeplabcut/requirements.txt         | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt b/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
index 17d8300fb..29659c517 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
@@ -1,4 +1,2 @@
-dlc2nwb>=0.3
-tables<3.9.0;python_version<'3.9'  # imported by package but not included in pip setup (is included in setup.cfg)
 tables<3.9.2;sys_platform=="darwin"
 tables;sys_platform=="linux" or sys_platform=="win32"

From 3882cdb9a0615acbd6ef3647c1a244751fb3216b Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:14:34 -0400
Subject: [PATCH 04/22] adjust lazy import

---
 .../behavior/deeplabcut/deeplabcutdatainterface.py        | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index 8fa1d3cf1..f946e00fc 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -37,14 +37,14 @@ def write_subject_to_nwb(
     nwbfile : pynwb.NWBFile
         nwbfile with pes written in the behavior module
     """
-    dlc2nwb = get_package(package_name="dlc2nwb")
+    from ._dlc_utils import _get_pes_args, _write_pes_to_nwbfile
 
-    scorer, df, video, paf_graph, dlc_timestamps, _ = dlc2nwb.utils._get_pes_args(config_file, h5file, individual_name)
+    scorer, df, video, paf_graph, dlc_timestamps, _ = _get_pes_args(config_file, h5file, individual_name)
     if timestamps is None:
         timestamps = dlc_timestamps
 
     df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
-    return dlc2nwb.utils._write_pes_to_nwbfile(
+    return _write_pes_to_nwbfile(
         nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False
     )
 
@@ -126,7 +126,6 @@ def set_aligned_timestamps(self, aligned_timestamps: Union[List, np.ndarray]):
         aligned_timestamps : list, np.ndarray
             alternative timestamps vector.
         """
-
         self._timestamps = np.array(aligned_timestamps)
 
     def add_to_nwbfile(
@@ -144,7 +143,6 @@ def add_to_nwbfile(
         metadata: dict
             metadata info for constructing the nwb file (optional).
         """
-
         write_subject_to_nwb(
             nwbfile=nwbfile,
             h5file=str(self.source_data["file_path"]),

From 82555a53fff0815260377c48e9fac0b5ad504a85 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:14:54 -0400
Subject: [PATCH 05/22] remove 3.8 classifier

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1af10b6c3..e06c90077 100644
--- a/setup.py
+++ b/setup.py
@@ -88,7 +88,6 @@
     license="BSD-3-Clause",
     classifiers=[
         "Intended Audience :: Science/Research",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",

From 2696417ae4f6b7c83cc172d097e2b0106c168617 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:18:54 -0400
Subject: [PATCH 06/22] Update CHANGELOG.md

---
 CHANGELOG.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04e10f6a7..14ec72857 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,8 +19,7 @@
 * Make annotations from the raw format available on `IntanRecordingInterface`. [PR #934](https://github.com/catalystneuro/neuroconv/pull/943)
 * Add an option to suppress display the progress bar (tqdm) in `VideoContext`  [PR #937](https://github.com/catalystneuro/neuroconv/pull/937)
 * Automatic compression of data in the `LightnignPoseDataInterface` has been disabled - users should refer to the new `configure_backend` method for a general approach for setting compression. [PR #942](https://github.com/catalystneuro/neuroconv/pull/942)
-
-
+* Port over `dlc2nwb` utility functions for ease of maintenance. [PR #946](https://github.com/catalystneuro/neuroconv/pull/946)
 
 
 

From 5d42589571141142390b3b35b89f69dabb03cb0e Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:27:23 -0400
Subject: [PATCH 07/22] remove unused functions, move over essential piece

---
 .../behavior/deeplabcut/_dlc_utils.py         | 104 +++++++-----------
 1 file changed, 37 insertions(+), 67 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index f1d8d7b64..b546922ad 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -5,6 +5,7 @@
 import warnings
 from pathlib import Path
 from platform import python_version
+from typing import Optional, Union, List
 
 import cv2
 import numpy as np
@@ -16,6 +17,7 @@
 from pynwb import NWBHDF5IO, NWBFile
 from ruamel.yaml import YAML
 
+from ....utils import FilePathType
 
 def _read_config(configname):
     """
@@ -58,13 +60,20 @@ def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=Tr
 
     reader = cv2.VideoCapture(movie_file)
     timestamps = []
+    n_frames = int(reader.get(cv2.CAP_PROP_FRAME_COUNT))
+    fps = reader.get(cv2.CAP_PROP_FPS)
+
+    for _ in range(n_frames):
+        _ = reader.read()
+        timestamps.append(reader.get(cv2.CAP_PROP_POS_MSEC))
+    
     for _ in range(len(reader)):
         _ = reader.read()
         timestamps.append(reader.get(cv2.CAP_PROP_POS_MSEC))
 
     timestamps = np.array(timestamps) / 1000  # Convert to seconds
 
-    if np.nanvar(np.diff(timestamps)) < 1.0 / reader.fps * 1.0 / VARIABILITYBOUND:
+    if np.nanvar(np.diff(timestamps)) < 1.0 / fps * 1.0 / VARIABILITYBOUND:
         warnings.warn(
             "Variability of timestamps suspiciously small. See: https://github.com/DeepLabCut/DLC2NWB/issues/1"
         )
@@ -172,7 +181,10 @@ def _write_pes_to_nwbfile(
     paf_graph,
     timestamps,
     exclude_nans,
+    pose_estimation_container_kwargs: Optional[dict] = None,
 ):
+    pose_estimation_container_kwargs = pose_estimation_container_kwargs or dict()
+
     pose_estimation_series = []
     for kpt, xyp in df_animal.groupby(level="bodyparts", axis=1, sort=False):
         data = xyp.to_numpy()
@@ -211,6 +223,7 @@ def _write_pes_to_nwbfile(
         source_software_version=deeplabcut_version,
         nodes=[pes.name for pes in pose_estimation_series],
         edges=paf_graph if paf_graph else None,
+        **pose_estimation_container_kwargs,
     )
     if "behavior" in nwbfile.processing:
         behavior_pm = nwbfile.processing["behavior"]
@@ -220,84 +233,41 @@ def _write_pes_to_nwbfile(
     return nwbfile
 
 
-def write_subject_to_nwb(nwbfile, h5file, individual_name, config_file):
+def add_subject_to_nwbfile(
+    nwbfile: NWBFile,
+    h5file: FilePathType,
+    individual_name: str,
+    config_file: FilePathType,
+    timestamps: Optional[Union[List, np.ndarray]] = None,
+) -> NWBFile:
     """
-    Given, subject name, write h5file to an existing nwbfile.
+    Given the subject name, add the DLC .h5 file to an in-memory NWBFile object.
 
     Parameters
     ----------
-    nwbfile: pynwb.NWBFile
-        nwbfile to write the subject specific pose estimation series.
-    h5file : str
-        Path to a h5 data file
+    nwbfile : pynwb.NWBFile
+        The in-memory nwbfile object to which the subject specific pose estimation series will be added.
+    h5file : str or path
+        Path to the DeepLabCut .h5 output file.
     individual_name : str
         Name of the subject (whose pose is predicted) for single-animal DLC project.
         For multi-animal projects, the names from the DLC project will be used directly.
-    config_file : str
+    config_file : str or path
         Path to a project config.yaml file
-    config_dict : dict
-        dict containing configuration options. Provide this as alternative to config.yml file.
+    timestamps : list, np.ndarray or None, default: None
+        Alternative timestamps vector. If None, then use the inferred timestamps from DLC2NWB
 
     Returns
     -------
-    nwbfile: pynwb.NWBFile
+    nwbfile : pynwb.NWBFile
         nwbfile with pes written in the behavior module
     """
-    scorer, df, video, paf_graph, timestamps, _ = _get_pes_args(config_file, h5file, individual_name)
-    df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
-    return _write_pes_to_nwbfile(nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps)
-
-
-def convert_h5_to_nwb(config, h5file, individual_name="ind1", infer_timestamps=True):
-    """
-    Convert a DeepLabCut (DLC) video prediction, h5 data file to Neurodata Without Borders (NWB). Also
-    takes project config, to store relevant metadata.
-
-    Parameters
-    ----------
-    config : str
-        Path to a project config.yaml file
-
-    h5file : str
-        Path to a h5 data file
-
-    individual_name : str
-        Name of the subject (whose pose is predicted) for single-animal DLC project.
-        For multi-animal projects, the names from the DLC project will be used directly.
-
-    infer_timestamps : bool
-        Default True. Uses framerate to infer the timestamps returned as 0 from OpenCV.
-        If False, exclude these frames from resulting NWB file.
-
-    TODO: allow one to overwrite those names, with a mapping?
-
-    Returns
-    -------
-    list of str
-        List of paths to the newly created NWB data files.
-        By default NWB files are stored in the same folder as the h5file.
+    scorer, df, video, paf_graph, dlc_timestamps, _ = _get_pes_args(config_file, h5file, individual_name)
+    if timestamps is None:
+        timestamps = dlc_timestamps
 
-    """
-    scorer, df, video, paf_graph, timestamps, cfg = _get_pes_args(
-        config, h5file, individual_name, infer_timestamps=infer_timestamps
+    df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
+    
+    return _write_pes_to_nwbfile(
+        nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False
     )
-    output_paths = []
-    for animal, df_ in df.groupby(level="individuals", axis=1):
-        nwbfile = NWBFile(
-            session_description=cfg["Task"],
-            experimenter=cfg["scorer"],
-            identifier=scorer,
-            session_start_time=datetime.datetime.now(datetime.timezone.utc),
-        )
-
-        # TODO Store the test_pose_config as well?
-        nwbfile = _write_pes_to_nwbfile(
-            nwbfile, animal, df_, scorer, video, paf_graph, timestamps, exclude_nans=(not infer_timestamps)
-        )
-        output_path = h5file.replace(".h5", f"_{animal}.nwb")
-        with warnings.catch_warnings(), NWBHDF5IO(output_path, mode="w") as io:
-            warnings.filterwarnings("ignore", category=DtypeConversionWarning)
-            io.write(nwbfile)
-        output_paths.append(output_path)
-
-    return output_paths

From 4c504f1a29dc6ba118ab2ff3fd3bfe4665861461 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 18:27:34 +0000
Subject: [PATCH 08/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py       | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index b546922ad..fe487f6c5 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -5,7 +5,7 @@
 import warnings
 from pathlib import Path
 from platform import python_version
-from typing import Optional, Union, List
+from typing import List, Optional, Union
 
 import cv2
 import numpy as np
@@ -19,6 +19,7 @@
 
 from ....utils import FilePathType
 
+
 def _read_config(configname):
     """
     Reads structured config file defining a project.
@@ -66,7 +67,7 @@ def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=Tr
     for _ in range(n_frames):
         _ = reader.read()
         timestamps.append(reader.get(cv2.CAP_PROP_POS_MSEC))
-    
+
     for _ in range(len(reader)):
         _ = reader.read()
         timestamps.append(reader.get(cv2.CAP_PROP_POS_MSEC))
@@ -267,7 +268,7 @@ def add_subject_to_nwbfile(
         timestamps = dlc_timestamps
 
     df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
-    
+
     return _write_pes_to_nwbfile(
         nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False
     )

From e09a4fa466dcf1fab6000a37c8c2b882afb25c55 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:28:01 -0400
Subject: [PATCH 09/22] simplify interface

---
 .../deeplabcut/deeplabcutdatainterface.py     | 44 ++-----------------
 1 file changed, 3 insertions(+), 41 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index f946e00fc..4d70f32db 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -9,46 +9,6 @@
 from ....utils import FilePathType
 
 
-def write_subject_to_nwb(
-    nwbfile: NWBFile,
-    h5file: FilePathType,
-    individual_name: str,
-    config_file: FilePathType,
-    timestamps: Optional[Union[List, np.ndarray]] = None,
-):
-    """
-    Given, subject name, write h5file to an existing nwbfile.
-
-    Parameters
-    ----------
-    nwbfile : pynwb.NWBFile
-        The in-memory nwbfile object to which the subject specific pose estimation series will be added.
-    h5file : str or path
-        Path to the DeepLabCut .h5 output file.
-    individual_name : str
-        Name of the subject (whose pose is predicted) for single-animal DLC project.
-        For multi-animal projects, the names from the DLC project will be used directly.
-    config_file : str or path
-        Path to a project config.yaml file
-    timestamps : list, np.ndarray or None, default: None
-        Alternative timestamps vector. If None, then use the inferred timestamps from DLC2NWB
-    Returns
-    -------
-    nwbfile : pynwb.NWBFile
-        nwbfile with pes written in the behavior module
-    """
-    from ._dlc_utils import _get_pes_args, _write_pes_to_nwbfile
-
-    scorer, df, video, paf_graph, dlc_timestamps, _ = _get_pes_args(config_file, h5file, individual_name)
-    if timestamps is None:
-        timestamps = dlc_timestamps
-
-    df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
-    return _write_pes_to_nwbfile(
-        nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False
-    )
-
-
 class DeepLabCutInterface(BaseTemporalAlignmentInterface):
     """Data interface for DeepLabCut datasets."""
 
@@ -143,7 +103,9 @@ def add_to_nwbfile(
         metadata: dict
             metadata info for constructing the nwb file (optional).
         """
-        write_subject_to_nwb(
+        from ._dlc_utils import add_subject_to_nwbfile
+        
+        add_subject_to_nwbfile(
             nwbfile=nwbfile,
             h5file=str(self.source_data["file_path"]),
             individual_name=self.subject_name,

From 4d3f422dbaa4d3aa1b654400d898094b15116f48 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 18:28:14 +0000
Subject: [PATCH 10/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../behavior/deeplabcut/deeplabcutdatainterface.py              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index 4d70f32db..5af93c07c 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -104,7 +104,7 @@ def add_to_nwbfile(
             metadata info for constructing the nwb file (optional).
         """
         from ._dlc_utils import add_subject_to_nwbfile
-        
+
         add_subject_to_nwbfile(
             nwbfile=nwbfile,
             h5file=str(self.source_data["file_path"]),

From 58f57afa636ebb1b39789b6ea402e814bad64ce1 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 14:34:42 -0400
Subject: [PATCH 11/22] expose to new public helper

---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py         | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index fe487f6c5..39d9c696a 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -240,6 +240,7 @@ def add_subject_to_nwbfile(
     individual_name: str,
     config_file: FilePathType,
     timestamps: Optional[Union[List, np.ndarray]] = None,
+    pose_estimation_container_kwargs: Optional[dict] = None,
 ) -> NWBFile:
     """
     Given the subject name, add the DLC .h5 file to an in-memory NWBFile object.
@@ -257,6 +258,8 @@ def add_subject_to_nwbfile(
         Path to a project config.yaml file
     timestamps : list, np.ndarray or None, default: None
         Alternative timestamps vector. If None, then use the inferred timestamps from DLC2NWB
+    pose_estimation_container_kwargs : dict, optional
+        Dictionary of keyword argument pairs to pass to the PoseEstimation container.
 
     Returns
     -------
@@ -270,5 +273,5 @@ def add_subject_to_nwbfile(
     df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
 
     return _write_pes_to_nwbfile(
-        nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False
+        nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False, pose_estimation_container_kwargs=pose_estimation_container_kwargs,
     )

From 21812fb88a5a7bd4a3779cc71cd936eb0cbf02b6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 18:34:54 +0000
Subject: [PATCH 12/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py   | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 39d9c696a..f80d1855a 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -273,5 +273,13 @@ def add_subject_to_nwbfile(
     df_animal = df.groupby(level="individuals", axis=1).get_group(individual_name)
 
     return _write_pes_to_nwbfile(
-        nwbfile, individual_name, df_animal, scorer, video, paf_graph, timestamps, exclude_nans=False, pose_estimation_container_kwargs=pose_estimation_container_kwargs,
+        nwbfile,
+        individual_name,
+        df_animal,
+        scorer,
+        video,
+        paf_graph,
+        timestamps,
+        exclude_nans=False,
+        pose_estimation_container_kwargs=pose_estimation_container_kwargs,
     )

From 8f4b18476b9357aa46622111aa69131ebed71539 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 16:43:32 -0400
Subject: [PATCH 13/22] fix init

---
 .../behavior/deeplabcut/deeplabcutdatainterface.py          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index 5af93c07c..95a55161c 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -47,13 +47,13 @@ def __init__(
         verbose: bool, default: True
             controls verbosity.
         """
-        dlc2nwb = get_package(package_name="dlc2nwb")
-
+        from ._dlc_utils import _read_config
+        
         file_path = Path(file_path)
         if "DLC" not in file_path.stem or ".h5" not in file_path.suffixes:
             raise IOError("The file passed in is not a DeepLabCut h5 data file.")
 
-        self._config_file = dlc2nwb.utils.read_config(config_file_path)
+        self._config_file = _read_config(config_file_path=config_file_path)
         self.subject_name = subject_name
         self.verbose = verbose
         super().__init__(file_path=file_path, config_file_path=config_file_path)

From 8b9a50dd0a8caf5ec7661dea66d5b799316e62d3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Jul 2024 20:43:44 +0000
Subject: [PATCH 14/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../behavior/deeplabcut/deeplabcutdatainterface.py              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index 95a55161c..8484f66f6 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -48,7 +48,7 @@ def __init__(
             controls verbosity.
         """
         from ._dlc_utils import _read_config
-        
+
         file_path = Path(file_path)
         if "DLC" not in file_path.stem or ".h5" not in file_path.suffixes:
             raise IOError("The file passed in is not a DeepLabCut h5 data file.")

From b4f07c37b1a485733ac74a56d56344e6b8b0634a Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 16:45:29 -0400
Subject: [PATCH 15/22] update requirements

---
 .../datainterfaces/behavior/deeplabcut/requirements.txt         | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt b/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
index 29659c517..03e0ee0b0 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt
@@ -1,2 +1,4 @@
 tables<3.9.2;sys_platform=="darwin"
 tables;sys_platform=="linux" or sys_platform=="win32"
+ndx-pose==0.1.1
+neuroconv[video]

From 94584257a45b5b4c28faf352f6799a117185193b Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 20:42:03 -0400
Subject: [PATCH 16/22] synch kwarg

---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index f80d1855a..751e17c53 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -20,17 +20,17 @@
 from ....utils import FilePathType
 
 
-def _read_config(configname):
+def _read_config(config_file_path):
     """
     Reads structured config file defining a project.
     """
     ruamelFile = YAML()
-    path = Path(configname)
+    path = Path(config_file_path)
     if os.path.exists(path):
         try:
             with open(path, "r") as f:
                 cfg = ruamelFile.load(f)
-                curr_dir = os.path.dirname(configname)
+                curr_dir = os.path.dirname(config_file_path)
                 if cfg["project_path"] != curr_dir:
                     cfg["project_path"] = curr_dir
         except Exception as err:

From 165588e310f68267801c11a95badfea14708dae0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jul 2024 02:12:31 +0000
Subject: [PATCH 17/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py        | 6 +-----
 .../behavior/deeplabcut/deeplabcutdatainterface.py          | 1 -
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 751e17c53..675741a2a 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -1,20 +1,16 @@
-import datetime
 import importlib
 import os
 import pickle
 import warnings
 from pathlib import Path
-from platform import python_version
 from typing import List, Optional, Union
 
 import cv2
 import numpy as np
 import pandas as pd
 import yaml
-from hdmf.build.warnings import DtypeConversionWarning
 from ndx_pose import PoseEstimation, PoseEstimationSeries
-from packaging.version import Version  # Installed with setuptools
-from pynwb import NWBHDF5IO, NWBFile
+from pynwb import NWBFile
 from ruamel.yaml import YAML
 
 from ....utils import FilePathType
diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index 8484f66f6..f5aea74aa 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -5,7 +5,6 @@
 from pynwb.file import NWBFile
 
 from ....basetemporalalignmentinterface import BaseTemporalAlignmentInterface
-from ....tools import get_package
 from ....utils import FilePathType
 
 

From 92abc4bde930477af53dd7f307e55c1290627549 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 22:16:15 -0400
Subject: [PATCH 18/22] lazy imports in utils

---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 675741a2a..67339ab1f 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -5,11 +5,9 @@
 from pathlib import Path
 from typing import List, Optional, Union
 
-import cv2
 import numpy as np
 import pandas as pd
 import yaml
-from ndx_pose import PoseEstimation, PoseEstimationSeries
 from pynwb import NWBFile
 from ruamel.yaml import YAML
 
@@ -53,7 +51,7 @@ def _get_movie_timestamps(movie_file, VARIABILITYBOUND=1000, infer_timestamps=Tr
     movie_file : str
         Path to movie_file
     """
-    # TODO: consider moving this to DLC, and actually extract alongside video analysis!
+    import cv2
 
     reader = cv2.VideoCapture(movie_file)
     timestamps = []
@@ -180,6 +178,8 @@ def _write_pes_to_nwbfile(
     exclude_nans,
     pose_estimation_container_kwargs: Optional[dict] = None,
 ):
+    from ndx_pose import PoseEstimation, PoseEstimationSeries
+    
     pose_estimation_container_kwargs = pose_estimation_container_kwargs or dict()
 
     pose_estimation_series = []

From b76425215eeaf16b5535121bc9e267cafbd3d1d8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jul 2024 02:16:50 +0000
Subject: [PATCH 19/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 67339ab1f..99a29fc39 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -179,7 +179,7 @@ def _write_pes_to_nwbfile(
     pose_estimation_container_kwargs: Optional[dict] = None,
 ):
     from ndx_pose import PoseEstimation, PoseEstimationSeries
-    
+
     pose_estimation_container_kwargs = pose_estimation_container_kwargs or dict()
 
     pose_estimation_series = []

From c18819eba27dacdbf9c0b3d76876ec1c06923b35 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 10 Jul 2024 22:19:57 -0400
Subject: [PATCH 20/22] generalize container kwarg passing

---
 .../behavior/deeplabcut/_dlc_utils.py             | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 99a29fc39..669a745e2 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -209,7 +209,8 @@ def _write_pes_to_nwbfile(
     is_deeplabcut_installed = importlib.util.find_spec(name="deeplabcut") is not None
     if is_deeplabcut_installed:
         deeplabcut_version = importlib.metadata.version(distribution_name="deeplabcut")
-    pe = PoseEstimation(
+
+    pose_estimation_default_kwargs = dict(
         pose_estimation_series=pose_estimation_series,
         description="2D keypoint coordinates estimated using DeepLabCut.",
         original_videos=[video[0]],
@@ -222,11 +223,15 @@ def _write_pes_to_nwbfile(
         edges=paf_graph if paf_graph else None,
         **pose_estimation_container_kwargs,
     )
-    if "behavior" in nwbfile.processing:
-        behavior_pm = nwbfile.processing["behavior"]
+    pose_estimation_default_kwargs.update(pose_estimation_container_kwargs)
+    pose_estimation_container = PoseEstimation(**pose_estimation_default_kwargs)
+    
+    if "behavior" in nwbfile.processing:  # TODO: replace with get_module
+        behavior_processing_module = nwbfile.processing["behavior"]
     else:
-        behavior_pm = nwbfile.create_processing_module(name="behavior", description="processed behavioral data")
-    behavior_pm.add(pe)
+        behavior_processing_module = nwbfile.create_processing_module(name="behavior", description="processed behavioral data")
+    behavior_processing_module.add(pose_estimation_container)
+    
     return nwbfile
 
 

From 61a56bd8880f3aba88a386aaa484cd69598f4090 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jul 2024 02:20:47 +0000
Subject: [PATCH 21/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../datainterfaces/behavior/deeplabcut/_dlc_utils.py      | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
index 669a745e2..72ddafe28 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/_dlc_utils.py
@@ -225,13 +225,15 @@ def _write_pes_to_nwbfile(
     )
     pose_estimation_default_kwargs.update(pose_estimation_container_kwargs)
     pose_estimation_container = PoseEstimation(**pose_estimation_default_kwargs)
-    
+
     if "behavior" in nwbfile.processing:  # TODO: replace with get_module
         behavior_processing_module = nwbfile.processing["behavior"]
     else:
-        behavior_processing_module = nwbfile.create_processing_module(name="behavior", description="processed behavioral data")
+        behavior_processing_module = nwbfile.create_processing_module(
+            name="behavior", description="processed behavioral data"
+        )
     behavior_processing_module.add(pose_estimation_container)
-    
+
     return nwbfile
 
 

From d3ea2a1fcff90500943538a02851f8146be36e14 Mon Sep 17 00:00:00 2001
From: Luigi Petrucco <luigi.petrucco@gmail.com>
Date: Thu, 11 Jul 2024 17:34:03 +0200
Subject: [PATCH 22/22] add name parameter to the `DeepLabCutInterface` (#917)

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 .../deeplabcut/deeplabcutdatainterface.py       |  2 ++
 tests/test_on_data/test_behavior_interfaces.py  | 17 +++++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
index f5aea74aa..e053e88fa 100644
--- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
+++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py
@@ -91,6 +91,7 @@ def add_to_nwbfile(
         self,
         nwbfile: NWBFile,
         metadata: Optional[dict] = None,
+        container_name: str = "PoseEstimation",
     ):
         """
         Conversion from DLC output files to nwb. Derived from dlc2nwb library.
@@ -110,4 +111,5 @@ def add_to_nwbfile(
             individual_name=self.subject_name,
             config_file=str(self.source_data["config_file_path"]),
             timestamps=self._timestamps,
+            pose_estimation_container_kwargs=dict(name=container_name),
         )
diff --git a/tests/test_on_data/test_behavior_interfaces.py b/tests/test_on_data/test_behavior_interfaces.py
index 155b32d72..36011da92 100644
--- a/tests/test_on_data/test_behavior_interfaces.py
+++ b/tests/test_on_data/test_behavior_interfaces.py
@@ -335,6 +335,7 @@ class TestDeepLabCutInterface(DeepLabCutInterfaceMixin, unittest.TestCase):
 
     def run_custom_checks(self):
         self.check_custom_timestamps(nwbfile_path=self.nwbfile_path)
+        self.check_renaming_instance(nwbfile_path=self.nwbfile_path)
 
     def check_custom_timestamps(self, nwbfile_path: str):
         # TODO: Peel out into separate test class and replace this part with check_read_nwb
@@ -361,6 +362,22 @@ def check_custom_timestamps(self, nwbfile_path: str):
                 pose_timestamps = pose_estimation.timestamps
                 np.testing.assert_array_equal(pose_timestamps, self._custom_timestamps_case_1)
 
+    def check_renaming_instance(self, nwbfile_path: str):
+        custom_container_name = "TestPoseEstimation"
+
+        metadata = self.interface.get_metadata()
+        metadata["NWBFile"].update(session_start_time=datetime.now().astimezone())
+
+        self.interface.run_conversion(
+            nwbfile_path=nwbfile_path, overwrite=True, metadata=metadata, container_name=custom_container_name
+        )
+
+        with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
+            nwbfile = io.read()
+            assert "behavior" in nwbfile.processing
+            assert "PoseEstimation" not in nwbfile.processing["behavior"].data_interfaces
+            assert custom_container_name in nwbfile.processing["behavior"].data_interfaces
+
     def check_read_nwb(self, nwbfile_path: str):
         # TODO: move this to the upstream mixin
         with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io: