Source code for dance.transforms.base

import hashlib
import warnings
from abc import ABC, abstractmethod

from anndata import AnnData

from dance import logger
from dance.data.base import Data
from dance.typing import LogLevel, Optional, Tuple


class BaseTransform(ABC):
    """BaseTransform abstract object.

    Parameters
    ----------
    log_level
        Logging level.
    out
        Name of the obsm channel or layer where the transformed features will be saved. Use the current
        transformation name if it is not set.

    """

    _DISPLAY_ATTRS: Tuple[str] = ()

    def __init__(self, out: Optional[str] = None, log_level: LogLevel = "WARNING"):
        self.out = out or self.name

        self.logger = logger.getChild(self.name)
        self.logger.setLevel(log_level)
        self.log_level = log_level

    @property
    def name(self) -> str:
        return self.__class__.__name__

    def hexdigest(self) -> str:
        """Return MD5 hash using the representation of the transform object."""
        return hashlib.md5(repr(self).encode()).hexdigest()

    def __repr__(self) -> str:
        display_attrs_str_list = [f"{i}={getattr(self, i)!r}" for i in self._DISPLAY_ATTRS]
        display_attrs_str = ", ".join(display_attrs_str_list)
        return f"{self.name}({display_attrs_str})"

    @abstractmethod
    def __call__(self, data: Data) -> Data:
        raise NotImplementedError


class AnnDataAdaptor:
    """Adaptor for transforming AnnData instead of dance data object.

    Example
    -------
    Modify an :class:`AnnData` object inplace

        >>> AnnDataAdaptor(FilterGenes(mode="sum"))(adata)

    """

    def __init__(self, transform, **data_init_kwargs):
        warnings.warn(
            "This is a temporary patch to enable transforming AnnData, and "
            "might have potential incompatibility issues. Use cautiously.",
            UserWarning,
            stacklevel=2,
        )
        self.transform = transform
        self.data_init_kwargs = data_init_kwargs

    def __call__(self, adata: AnnData) -> AnnData:
        data = Data(adata, **self.data_init_kwargs)
        self.transform(data)
        return data.data