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deeplabcut.core.conversion_table

Defines conversion tables mapping DeepLabCut project bodyparts to SA bodyparts.

Classes:

Name Description
ConversionTable

Maps DLC project bodyparts to the corresponding SuperAnimal bodyparts.

ConversionTable dataclass

Maps DLC project bodyparts to the corresponding SuperAnimal bodyparts.

The conversion table must satisfy the following conditions (checked by validate): - All SuperAnimal bodyparts must be valid (defined for the SuperAnimal model) - All project bodyparts must be valid (defined for the DLC project)

Methods:

Name Description
__post_init__

Validates the table.
converted_bodyparts

Returns: The project bodyparts included in this ordered
to_array

Returns:
validate

Raises:
Source code in deeplabcut/core/conversion_table.py 
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@dataclass
class ConversionTable:
    """Maps DLC project bodyparts to the corresponding SuperAnimal bodyparts.

    The conversion table must satisfy the following conditions (checked by validate):
        - All SuperAnimal bodyparts must be valid (defined for the SuperAnimal model)
        - All project bodyparts must be valid (defined for the DLC project)
    """

    super_animal: str
    project_bodyparts: list[str]
    super_animal_bodyparts: list[str]
    table: dict[str, str]

    def __post_init__(self):
        """Validates the table."""
        self.validate()

    def to_array(self) -> np.ndarray:
        """
        Returns:
            An array mapping the indices of SuperAnimal bodyparts

        Raises:
            ValueError: If the conversion table is misconfigured.
        """
        self.validate()
        sa_indices = {sa_bpt: i for i, sa_bpt in enumerate(self.super_animal_bodyparts)}
        sa_bpt_ordering = [self.table[bpt] for bpt in self.converted_bodyparts()]
        return np.array([sa_indices[sa_bpt] for sa_bpt in sa_bpt_ordering])

    def converted_bodyparts(self) -> list[str]:
        """Returns: The project bodyparts included in this ordered"""
        return [bpt for bpt in self.project_bodyparts if bpt in self.table]

    def validate(self) -> None:
        """
        Raises:
            ValueError: If the conversion table is misconfigured.
        """
        project_bpts = set(self.project_bodyparts)
        sa_bpts = set(self.super_animal_bodyparts)

        mapped_sa = set(self.table.values())
        mapped_project = set(self.table.keys())

        # check all mapped SuperAnimal bodyparts are in the config
        if len(mapped_sa.difference(sa_bpts)) != 0:
            extra_bodyparts = set(mapped_sa).difference(sa_bpts)
            raise ValueError(
                f"Some bodyparts in your mapping are not in the {self.super_animal} "
                f"model: {extra_bodyparts}. Available bodyparts are {' '.join(sa_bpts)}"
            )

        # check all given bodyparts are in the project configuration
        if len(mapped_project.difference(project_bpts)) != 0:
            extra_bodyparts = mapped_project.difference(project_bpts)
            raise ValueError(
                "Some bodyparts in your mapping are not in your project configuration: "
                f"{extra_bodyparts}. Defined bodyparts are {' '.join(project_bpts)}"
            )

__post_init__ 

__post_init__()

Validates the table.

Source code in deeplabcut/core/conversion_table.py 
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def __post_init__(self):
    """Validates the table."""
    self.validate()

converted_bodyparts 

converted_bodyparts() -> list[str]

Returns: The project bodyparts included in this ordered

Source code in deeplabcut/core/conversion_table.py 
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def converted_bodyparts(self) -> list[str]:
    """Returns: The project bodyparts included in this ordered"""
    return [bpt for bpt in self.project_bodyparts if bpt in self.table]

to_array 

to_array() -> np.ndarray

Returns:

Type Description
ndarray

An array mapping the indices of SuperAnimal bodyparts

Raises:

Type Description
ValueError

If the conversion table is misconfigured.
Source code in deeplabcut/core/conversion_table.py 
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def to_array(self) -> np.ndarray:
    """
    Returns:
        An array mapping the indices of SuperAnimal bodyparts

    Raises:
        ValueError: If the conversion table is misconfigured.
    """
    self.validate()
    sa_indices = {sa_bpt: i for i, sa_bpt in enumerate(self.super_animal_bodyparts)}
    sa_bpt_ordering = [self.table[bpt] for bpt in self.converted_bodyparts()]
    return np.array([sa_indices[sa_bpt] for sa_bpt in sa_bpt_ordering])

validate 

validate() -> None

Raises:

Type Description
ValueError

If the conversion table is misconfigured.
Source code in deeplabcut/core/conversion_table.py 
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def validate(self) -> None:
    """
    Raises:
        ValueError: If the conversion table is misconfigured.
    """
    project_bpts = set(self.project_bodyparts)
    sa_bpts = set(self.super_animal_bodyparts)

    mapped_sa = set(self.table.values())
    mapped_project = set(self.table.keys())

    # check all mapped SuperAnimal bodyparts are in the config
    if len(mapped_sa.difference(sa_bpts)) != 0:
        extra_bodyparts = set(mapped_sa).difference(sa_bpts)
        raise ValueError(
            f"Some bodyparts in your mapping are not in the {self.super_animal} "
            f"model: {extra_bodyparts}. Available bodyparts are {' '.join(sa_bpts)}"
        )

    # check all given bodyparts are in the project configuration
    if len(mapped_project.difference(project_bpts)) != 0:
        extra_bodyparts = mapped_project.difference(project_bpts)
        raise ValueError(
            "Some bodyparts in your mapping are not in your project configuration: "
            f"{extra_bodyparts}. Defined bodyparts are {' '.join(project_bpts)}"
        )