dlc_reader.py

read_yaml(fullpath, filename='*')

Return contents of yml in fullpath. If available, defer to DJ-saved version

Parameters:

Name	Type	Description	Default
fullpath			required
filename			'*'
Returns			required

Source code in src/spyglass/position/v1/dlc_reader.py

def read_yaml(fullpath, filename="*"):
    """Return contents of yml in fullpath. If available, defer to DJ-saved version

    Parameters
    ----------
    fullpath: String or pathlib path. Directory with yaml files
    filename: String. Filename, no extension. Permits wildcards.

    Returns filepath and contents as dict
    """
    from deeplabcut.utils.auxiliaryfunctions import read_config

    # Take the DJ-saved if there. If not, return list of available
    yml_paths = list(Path(fullpath).glob("dj_dlc_config.yaml")) or sorted(
        list(Path(fullpath).glob(f"{filename}.y*ml"))
    )

    assert (  # If more than 1 and not DJ-saved,
        len(yml_paths) == 1
    ), f"Found more yaml files than expected: {len(yml_paths)}\n{fullpath}"

    return yml_paths[0], read_config(yml_paths[0])

save_yaml(output_dir, config_dict, filename='dj_dlc_config', mkdir=True)

Save config_dict to output_path as filename.yaml. By default, preserves original.

Parameters:

Name	Type	Description	Default
output_dir			required
config_dict			required
filename		Set to 'config' to overwrite original file. If extension is included, removed and replaced with "yaml".	'dj_dlc_config'
mkdir			True

Returns:

Type	Description
str	path of saved file as string - due to DLC func preference for strings

Source code in src/spyglass/position/v1/dlc_reader.py

def save_yaml(output_dir, config_dict, filename="dj_dlc_config", mkdir=True):
    """Save config_dict to output_path as filename.yaml. By default, preserves original.

    Parameters
    ----------
    output_dir: where to save yaml file
    config_dict: dict of config params or element-deeplabcut model.Model dict
    filename: Optional, default 'dj_dlc_config' or preserve original 'config'
              Set to 'config' to overwrite original file.
              If extension is included, removed and replaced with "yaml".
    mkdir (bool): Optional, True. Make new directory if output_dir not exist

    Returns
    -------
    str
        path of saved file as string - due to DLC func preference for strings
    """
    from deeplabcut.utils.auxiliaryfunctions import write_config

    if "config_template" in config_dict:  # if passed full model.Model dict
        config_dict = config_dict["config_template"]
    if mkdir:
        Path(output_dir).mkdir(exist_ok=True)
    if "." in filename:  # if user provided extension, remove
        filename = filename.split(".")[0]

    output_filepath = Path(output_dir) / f"{filename}.yaml"
    write_config(output_filepath, config_dict)
    return str(output_filepath)

do_pose_estimation(video_filepaths, dlc_model, project_path, output_dir, videotype='', gputouse=None, save_as_csv=False, batchsize=None, cropping=None, TFGPUinference=True, dynamic=(False, 0.5, 10), robust_nframes=False, allow_growth=False, use_shelve=False)

Launch DLC's analyze_videos within element-deeplabcut

Other optional parameters may be set other than those described below. See deeplabcut.analyze_videos parameters for descriptions/defaults.

Parameters:

Name	Type	Description	Default
video_filepaths			required
dlc_model			required
project_path			required
output_dir			required

Source code in src/spyglass/position/v1/dlc_reader.py

def do_pose_estimation(
    video_filepaths,
    dlc_model,
    project_path,
    output_dir,
    videotype="",
    gputouse=None,
    save_as_csv=False,
    batchsize=None,
    cropping=None,
    TFGPUinference=True,
    dynamic=(False, 0.5, 10),
    robust_nframes=False,
    allow_growth=False,
    use_shelve=False,
):
    """Launch DLC's analyze_videos within element-deeplabcut

    Other optional parameters may be set other than those described below. See
    deeplabcut.analyze_videos parameters for descriptions/defaults.

    Parameters
    ----------
    video_filepaths: list of videos to analyze
    dlc_model: element-deeplabcut dlc.Model dict
    project_path: path to project config.yml
    output_dir: where to save output
    """
    from deeplabcut.pose_estimation_tensorflow import analyze_videos

    # ---- Build and save DLC configuration (yaml) file ----
    dlc_config = dlc_model["config_template"]
    dlc_project_path = Path(project_path)
    dlc_config["project_path"] = dlc_project_path.as_posix()

    # ---- Write config files ----
    # To output dir: Important for loading/parsing output in datajoint
    _ = save_yaml(output_dir, dlc_config)
    # To project dir: Required by DLC to run the analyze_videos
    if dlc_project_path != output_dir:
        config_filepath = save_yaml(dlc_project_path, dlc_config)
    # ---- Trigger DLC prediction job ----
    analyze_videos(
        config=config_filepath,
        videos=video_filepaths,
        shuffle=dlc_model["shuffle"],
        trainingsetindex=dlc_model["trainingsetindex"],
        destfolder=output_dir,
        modelprefix=dlc_model["model_prefix"],
        videotype=videotype,
        gputouse=gputouse,
        save_as_csv=save_as_csv,
        batchsize=batchsize,
        cropping=cropping,
        TFGPUinference=TFGPUinference,
        dynamic=dynamic,
        robust_nframes=robust_nframes,
        allow_growth=allow_growth,
        use_shelve=use_shelve,
    )