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
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]
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
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
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