Ejemplo n.º 1
0
def _get_shaped_data(
    adata: AnnData,
    per: str,
    annotations: Annotations,
    *,
    shape: Tuple[int, ...],
    name: Union[str, utt.Shaped],
) -> Any:
    if isinstance(name, str):
        if per == "vo" and name == "__x__":
            data = _fix_data(adata.X)
        else:
            if name not in annotations:  # type: ignore
                raise _unknown_data(adata, name, per)
            data = _fix_data(annotations[name])

        if not utt.frozen(data):
            utt.freeze(data)

    else:
        if utt.is_1d(name):
            data = utt.to_numpy_vector(name)
        else:
            data = utt.to_proper_matrix(name)  # type: ignore

    assert data.shape == shape
    return data
Ejemplo n.º 2
0
def set_vo_data(
    adata: AnnData,
    name: str,
    data: utt.ProperMatrix,
    *,
    formatter: Optional[Callable[[Any], Any]] = None,
) -> Any:
    """
    Set per-variable-per-observation (per-gene-per-cell) data.
    """
    utl.log_set(adata, "vo", name, data, formatter=formatter)

    utt.mustbe_canonical(data)
    if not utt.frozen(data):
        utt.freeze(data)

    if name == "__x__":
        adata.X = data
    else:
        adata.layers[name] = data

    if hasattr(adata, "__derived__"):
        derived = getattr(adata, "__derived__")
        for layout in ["column_major", "row_major"]:
            layout_name = f"vo:{name}:{layout}"
            if layout_name in derived:
                del derived[layout_name]
Ejemplo n.º 3
0
def set_va_data(adata: AnnData,
                name: str,
                data: utt.ProperMatrix,
                *,
                formatter: Optional[Callable[[Any], Any]] = None) -> Any:
    """
    Set per-variable-per-any (gene) data.

    If ``formatter`` is specified, its results is used when logging the operation.
    """
    utl.log_set(adata, "va", name, data, formatter=formatter)

    utt.mustbe_canonical(data)
    if not utt.frozen(data):
        utt.freeze(data)

    adata.varm[name] = data
Ejemplo n.º 4
0
def set_o_data(
    adata: AnnData,
    name: str,
    data: utt.NumpyVector,
    *,
    formatter: Optional[Callable[[Any], Any]] = None,
) -> Any:
    """
    Set per-observation (cell) data.

    If ``formatter`` is specified, its results is used when logging the operation.
    """
    utl.log_set(adata, "o", name, data, formatter=formatter)

    if not isinstance(data, list):
        utt.mustbe_canonical(data)
        if not utt.frozen(data):
            utt.freeze(data)

    adata.obs[name] = data
Ejemplo n.º 5
0
def _get_layout_data(
    adata: AnnData,
    per: str,
    annotations: Annotations,
    *,
    shape: Tuple[int, ...],
    name: Union[str, utt.Matrix],
    layout: Optional[str],
) -> Any:
    data = _get_shaped_data(adata, per, annotations, shape=shape, name=name)
    if not isinstance(name, str):
        if not utt.is_layout(data, layout):
            assert layout is not None
            data = utc.to_layout(name, layout=layout)
        return data

    if utt.is_layout(data, layout):
        return data

    assert layout in utt.LAYOUT_OF_AXIS
    layout_name = f"{per}:{name}:{layout}"

    if not hasattr(adata, "__derived__"):
        derived: Dict[str, utt.ProperMatrix] = {}
        setattr(adata, "__derived__", derived)
    else:
        derived = getattr(adata, "__derived__")

    layout_data = derived.get(layout_name)
    if layout_data is not None:
        assert layout_data.shape == shape
        assert utt.is_layout(layout_data, layout)
    else:
        layout_data = utc.to_layout(data, layout=layout)
        derived[layout_name] = layout_data

    if not utt.frozen(layout_data):
        utt.freeze(layout_data)

    return layout_data