def spatial_neighbors(
adata: AnnData,
spatial_key: str = Key.obsm.spatial,
coord_type: Optional[Union[str, CoordType]] = None,
n_rings: int = 1,
n_neigh: int = 6,
delaunay: bool = False,
radius: Optional[float] = None,
transform: Optional[Union[str, Transform]] = None,
key_added: Optional[str] = None,
) -> None:
"""
Create a graph from spatial coordinates.
Parameters
----------
%(adata)s
%(spatial_key)s
coord_type
Type of coordinate system. Valid options are:
- `{c.VISIUM!r}` - Visium coordinates.
- `{c.GENERIC!r}` - generic coordinates.
If `None`, use `{c.VISIUM!r}` if ``spatial_key`` is present in :attr:`anndata.AnnData.obsm`,
otherwise use `{c.GENERIC!r}`.
n_rings
Number of rings of neighbors for Visium data.
n_neigh
Number of neighborhoods to consider for non-Visium data.
delaunay
Whether to compute the graph from Delaunay triangulation.
radius
Radius of neighbors for non-Visium data.
transform
Type of adjacency matrix transform. Valid options are:
- `{t.SPECTRAL.s!r}` - spectral transformation of the adjacency matrix.
- `{t.COSINE.s!r}` - cosine transformation of the adjacency matrix.
- `{t.NONE.v}` - no transformation of the adjacency matrix.
key_added
Key which controls where the results are saved.
Returns
-------
Modifies the ``adata`` with the following keys:
- :attr:`anndata.AnnData.obsp` ``['{{key_added}}_connectivities']`` - spatial connectivity matrix.
- :attr:`anndata.AnnData.obsp` ``['{{key_added}}_distances']`` - spatial distances matrix.
- :attr:`anndata.AnnData.uns` ``['{{key_added}}']`` - spatial neighbors dictionary.
"""
_assert_positive(n_rings, name="n_rings")
_assert_positive(n_neigh, name="n_neigh")
_assert_spatial_basis(adata, spatial_key)
transform = Transform.NONE if transform is None else Transform(transform)
if coord_type is None:
coord_type = CoordType.VISIUM if Key.uns.spatial in adata.uns else CoordType.GENERIC
else:
coord_type = CoordType(coord_type)
start = logg.info(
f"Creating graph using `{coord_type}` coordinates and `{transform}` transform"
)
coords = adata.obsm[spatial_key]
if coord_type == CoordType.VISIUM:
if n_rings > 1:
Adj: csr_matrix = _build_connectivity(coords,
6,
neigh_correct=True,
set_diag=True,
delaunay=delaunay,
return_distance=False)
Res = Adj
Walk = Adj
for i in range(n_rings - 1):
Walk = Walk @ Adj
with warnings.catch_warnings():
warnings.simplefilter("ignore", SparseEfficiencyWarning)
Walk[Res.nonzero()] = 0.0
Walk.eliminate_zeros()
Walk.data[:] = i + 2.0
Res = Res + Walk
Adj = Res
Adj.setdiag(0.0)
Adj.eliminate_zeros()
Dst = Adj.copy()
Adj.data[:] = 1.0
else:
Adj = _build_connectivity(coords,
6,
neigh_correct=True,
delaunay=delaunay)
Dst = None
elif coord_type == CoordType.GENERIC:
Adj, Dst = _build_connectivity(coords,
n_neigh,
radius,
delaunay=delaunay,
return_distance=True)
else:
raise NotImplementedError(coord_type)
# check transform
if transform == Transform.SPECTRAL:
Adj = _transform_a_spectral(Adj)
elif transform == Transform.COSINE:
Adj = _transform_a_cosine(Adj)
elif transform == Transform.NONE:
pass
else:
raise NotImplementedError(
f"Transform `{transform}` is not yet implemented.")
neighs_key = Key.uns.spatial_neighs(key_added)
conns_key = Key.obsp.spatial_conn(key_added)
dists_key = Key.obsp.spatial_dist(key_added)
neighbors_dict = {
"connectivities_key": conns_key,
"params": {
"n_neighbors": n_neigh,
"coord_type": coord_type.v,
"radius": radius,
"transform": transform.v
},
"distances_key": dists_key,
}
_save_data(adata, attr="obsp", key=conns_key, data=Adj)
if Dst is not None:
_save_data(adata, attr="obsp", key=dists_key, data=Dst, prefix=False)
_save_data(adata,
attr="uns",
key=neighs_key,
data=neighbors_dict,
prefix=False,
time=start)
def nhood_enrichment(
adata: AnnData,
cluster_key: str,
connectivity_key: Optional[str] = None,
n_perms: int = 1000,
numba_parallel: bool = False,
seed: Optional[int] = None,
copy: bool = False,
n_jobs: Optional[int] = None,
backend: str = "loky",
show_progress_bar: bool = True,
) -> Optional[Tuple[np.ndarray, np.ndarray]]:
"""
Compute neighborhood enrichment by permutation test.
Parameters
----------
%(adata)s
%(cluster_key)s
%(conn_key)s
%(n_perms)s
%(numba_parallel)s
%(seed)s
%(copy)s
%(parallelize)s
Returns
-------
If ``copy = True``, returns a :class:`tuple` with the z-score and the enrichment count.
Otherwise, modifies the ``adata`` with the following keys:
- :attr:`anndata.AnnData.uns` ``['{cluster_key}_nhood_enrichment']['zscore']`` - the enrichment z-score.
- :attr:`anndata.AnnData.uns` ``['{cluster_key}_nhood_enrichment']['count']`` - the enrichment count.
"""
connectivity_key = Key.obsp.spatial_conn(connectivity_key)
_assert_categorical_obs(adata, cluster_key)
_assert_connectivity_key(adata, connectivity_key)
_assert_positive(n_perms, name="n_perms")
adj = adata.obsp[connectivity_key]
original_clust = adata.obs[cluster_key]
clust_map = {
v: i
for i, v in enumerate(original_clust.cat.categories.values)
} # map categories
int_clust = np.array([clust_map[c] for c in original_clust], dtype=ndt)
indices, indptr = (adj.indices.astype(ndt), adj.indptr.astype(ndt))
n_cls = len(clust_map)
_test = _create_function(n_cls, parallel=numba_parallel)
count = _test(indices, indptr, int_clust)
n_jobs = _get_n_cores(n_jobs)
start = logg.info(
f"Calculating neighborhood enrichment using `{n_jobs}` core(s)")
perms = parallelize(
_nhood_enrichment_helper,
collection=np.arange(n_perms),
extractor=np.vstack,
n_jobs=n_jobs,
backend=backend,
show_progress_bar=show_progress_bar,
)(callback=_test,
indices=indices,
indptr=indptr,
int_clust=int_clust,
n_cls=n_cls,
seed=seed)
zscore = (count - perms.mean(axis=0)) / perms.std(axis=0)
if copy:
return zscore, count
_save_data(
adata,
attr="uns",
key=Key.uns.nhood_enrichment(cluster_key),
data={
"zscore": zscore,
"count": count
},
time=start,
)
def test(
self,
cluster_key: str,
clusters: Optional[Cluster_t] = None,
n_perms: int = 1000,
threshold: float = 0.01,
seed: Optional[int] = None,
corr_method: Optional[str] = None,
corr_axis: Union[str, CorrAxis] = CorrAxis.INTERACTIONS.v,
alpha: float = 0.05,
copy: bool = False,
key_added: Optional[str] = None,
numba_parallel: Optional[bool] = None,
**kwargs: Any,
) -> Optional[Mapping[str, pd.DataFrame]]:
"""
Perform the permutation test as described in :cite:`cellphonedb`.
Parameters
----------
%(cluster_key)s
clusters
Clusters from :attr:`anndata.AnnData.obs` ``['{{cluster_key}}']``. Can be specified either as a sequence
of :class:`tuple` or just a sequence of cluster names, in which case all combinations considered.
%(n_perms)s
threshold
Do not perform permutation test if any of the interacting components is being expressed
in less than ``threshold`` percent of cells within a given cluster.
%(seed)s
%(corr_method)s
corr_axis
Axis over which to perform the FDR correction. Only used when ``corr_method != None``. Valid options are:
- `{fa.INTERACTIONS.s!r}` - correct interactions by performing FDR correction across the clusters.
- `{fa.CLUSTERS.s!r}` - correct clusters by performing FDR correction across the interactions.
alpha
Significance level for FDR correction. Only used when ``corr_method != None``.
%(copy)s
key_added
Key in :attr:`anndata.AnnData.uns` where the result is stored if ``copy = False``.
If `None`, ``'{{cluster_key}}_ligrec'`` will be used.
%(numba_parallel)s
%(parallelize)s
Returns
-------
%(ligrec_test_returns)s
"""
_assert_positive(n_perms, name="n_perms")
_assert_categorical_obs(self._adata, key=cluster_key)
if corr_method is not None:
corr_axis = CorrAxis(corr_axis)
if TYPE_CHECKING:
assert isinstance(corr_axis, CorrAxis)
if len(self._adata.obs[cluster_key].cat.categories) <= 1:
raise ValueError(
f"Expected at least `2` clusters, found `{len(self._adata.obs[cluster_key].cat.categories)}`."
)
if TYPE_CHECKING:
assert isinstance(self.interactions, pd.DataFrame)
assert isinstance(self._filtered_data, pd.DataFrame)
interactions = self.interactions[[SOURCE, TARGET]]
self._filtered_data["clusters"] = self._adata.obs[cluster_key].astype(
"string").astype("category").values
if clusters is None:
clusters = list(
map(str, self._adata.obs[cluster_key].cat.categories))
if all(isinstance(c, str) for c in clusters):
clusters = list(product(
clusters, repeat=2)) # type: ignore[no-redef,assignment]
clusters = sorted(
_check_tuple_needles(
clusters, # type: ignore[arg-type]
self._filtered_data["clusters"].cat.categories,
msg="Invalid cluster `{0!r}`.",
reraise=True,
))
clusters_flat = list({c for cs in clusters for c in cs})
data = self._filtered_data.loc[
np.isin(self._filtered_data["clusters"], clusters_flat), :]
data["clusters"] = data["clusters"].cat.remove_unused_categories()
cat = data["clusters"].cat
cluster_mapper = dict(zip(cat.categories, range(len(cat.categories))))
gene_mapper = dict(zip(data.columns[:-1],
range(len(data.columns) -
1))) # -1 for 'clusters'
data.columns = [
gene_mapper[c] if c != "clusters" else c for c in data.columns
]
clusters_ = np.array([[cluster_mapper[c1], cluster_mapper[c2]]
for c1, c2 in clusters],
dtype=np.uint32)
cat.rename_categories(cluster_mapper, inplace=True)
# much faster than applymap (tested on 1M interactions)
interactions_ = np.vectorize(lambda g: gene_mapper[g])(
interactions.values)
n_jobs = _get_n_cores(kwargs.pop("n_jobs", None))
start = logg.info(
f"Running `{n_perms}` permutations on `{len(interactions)}` interactions "
f"and `{len(clusters)}` cluster combinations using `{n_jobs}` core(s)"
)
res = _analysis(
data,
interactions_,
clusters_,
threshold=threshold,
n_perms=n_perms,
seed=seed,
n_jobs=n_jobs,
numba_parallel=numba_parallel,
**kwargs,
)
res = {
"means":
_create_sparse_df(
res.means,
index=pd.MultiIndex.from_frame(interactions,
names=[SOURCE, TARGET]),
columns=pd.MultiIndex.from_tuples(
clusters, names=["cluster_1", "cluster_2"]),
fill_value=0,
),
"pvalues":
_create_sparse_df(
res.pvalues,
index=pd.MultiIndex.from_frame(interactions,
names=[SOURCE, TARGET]),
columns=pd.MultiIndex.from_tuples(
clusters, names=["cluster_1", "cluster_2"]),
fill_value=np.nan,
),
"metadata":
self.interactions[self.interactions.columns.difference(
[SOURCE, TARGET])],
}
res["metadata"].index = res["means"].index.copy()
if TYPE_CHECKING:
assert isinstance(res, dict)
if corr_method is not None:
logg.info(f"Performing FDR correction across the `{corr_axis.v}` "
f"using method `{corr_method}` at level `{alpha}`")
res["pvalues"] = _fdr_correct(res["pvalues"],
corr_method,
corr_axis,
alpha=alpha)
if copy:
logg.info("Finish", time=start)
return res
_save_data(self._adata,
attr="uns",
key=Key.uns.ligrec(cluster_key, key_added),
data=res,
time=start)
def moran(
adata: AnnData,
connectivity_key: str = Key.obsp.spatial_conn(),
genes: Optional[Union[str, Sequence[str]]] = None,
transformation: Literal["r", "B", "D", "U", "V"] = "r",
n_perms: int = 1000,
corr_method: Optional[str] = "fdr_bh",
layer: Optional[str] = None,
seed: Optional[int] = None,
copy: bool = False,
n_jobs: Optional[int] = None,
backend: str = "loky",
show_progress_bar: bool = True,
) -> Optional[pd.DataFrame]:
"""
Calculate Moran’s I Global Autocorrelation Statistic.
Parameters
----------
%(adata)s
%(conn_key)s
genes
List of gene names, as stored in :attr:`anndata.AnnData.var_names`, used to compute Moran's I statistics
:cite:`pysal`.
If `None`, it's computed :attr:`anndata.AnnData.var` ``['highly_variable']``, if present. Otherwise,
it's computed for all genes.
transformation
Transformation to be used, as reported in :class:`esda.Moran`. Default is `"r"`, row-standardized.
%(n_perms)s
%(corr_method)s
layer
Layer in :attr:`anndata.AnnData.layers` to use. If `None`, use :attr:`anndata.AnnData.X`.
%(seed)s
%(copy)s
%(parallelize)s
Returns
-------
If ``copy = True``, returns a :class:`pandas.DataFrame` with the following keys:
- `'I'` - Moran's I statistic.
- `'pval_sim'` - p-value based on permutations.
- `'VI_sim'` - variance of `'I'` from permutations.
- `'pval_sim_{{corr_method}}'` - the corrected p-values if ``corr_method != None`` .
Otherwise, modifies the ``adata`` with the following key:
- :attr:`anndata.AnnData.uns` ``['moranI']`` - the above mentioned dataframe.
"""
if esda is None or libpysal is None:
raise ImportError(
"Please install `esda` and `libpysal` as `pip install esda libpysal`."
)
_assert_positive(n_perms, name="n_perms")
_assert_connectivity_key(adata, connectivity_key)
if genes is None:
if "highly_variable" in adata.var.columns:
genes = adata[:, adata.var.highly_variable.values].var_names.values
else:
genes = adata.var_names.values
genes = _assert_non_empty_sequence(genes, name="genes")
n_jobs = _get_n_cores(n_jobs)
start = logg.info(
f"Calculating for `{len(genes)}` genes using `{n_jobs}` core(s)")
w = _set_weight_class(adata, key=connectivity_key) # init weights
df = parallelize(
_moran_helper,
collection=genes,
extractor=pd.concat,
use_ixs=True,
n_jobs=n_jobs,
backend=backend,
show_progress_bar=show_progress_bar,
)(adata=adata,
weights=w,
transformation=transformation,
permutations=n_perms,
layer=layer,
seed=seed)
if corr_method is not None:
_, pvals_adj, _, _ = multipletests(df["pval_sim"].values,
alpha=0.05,
method=corr_method)
df[f"pval_sim_{corr_method}"] = pvals_adj
df.sort_values(by="I", ascending=False, inplace=True)
if copy:
logg.info("Finish", time=start)
return df
_save_data(adata, attr="uns", key="moranI", data=df, time=start)
def spatial_autocorr(
adata: AnnData,
connectivity_key: str = Key.obsp.spatial_conn(),
genes: Optional[Union[str, Sequence[str]]] = None,
mode: Literal[
"moran",
"geary"] = SpatialAutocorr.MORAN.s, # type: ignore[assignment]
transformation: bool = True,
n_perms: Optional[int] = None,
two_tailed: bool = False,
corr_method: Optional[str] = "fdr_bh",
layer: Optional[str] = None,
seed: Optional[int] = None,
use_raw: bool = False,
copy: bool = False,
n_jobs: Optional[int] = None,
backend: str = "loky",
show_progress_bar: bool = True,
) -> Optional[pd.DataFrame]:
"""
Calculate Global Autocorrelation Statistic (Moran’s I or Geary's C).
See :cite:`pysal` for reference.
Parameters
----------
%(adata)s
%(conn_key)s
genes
List of gene names, as stored in :attr:`anndata.AnnData.var_names`, used to compute global
spatial autocorrelation statistic.
If `None`, it's computed :attr:`anndata.AnnData.var` ``['highly_variable']``, if present. Otherwise,
it's computed for all genes.
mode
Mode of score calculation:
- `{sp.MORAN.s!r}` - `Moran's I autocorrelation <https://en.wikipedia.org/wiki/Moran%27s_I>`_.
- `{sp.GEARY.s!r}` - `Geary's C autocorrelation <https://en.wikipedia.org/wiki/Geary%27s_C>`_.
transformation
If `True`, weights in :attr:`anndata.AnnData.obsp` ``['{key}']`` are row-normalized,
advised for analytic p-value calculation.
%(n_perms)s
If `None`, only p-values under normality assumption are computed.
two_tailed
If `True`, p-values are two-tailed, otherwise they are one-tailed.
%(corr_method)s
layer
Layer in :attr:`anndata.AnnData.layers` to use. If `None`, use :attr:`anndata.AnnData.X`.
%(seed)s
%(copy)s
%(parallelize)s
Returns
-------
If ``copy = True``, returns a :class:`pandas.DataFrame` with the following keys:
- `'I' or 'C'` - Moran's I or Geary's C statistic.
- `'pval_norm'` - p-value under normality assumption.
- `'var_norm'` - variance of `'score'` under normality assumption.
- `'{{p_val}}_{{corr_method}}'` - the corrected p-values if ``corr_method != None`` .
If ``n_perms != None`` is not None, additionally returns the following columns:
- `'pval_z_sim'` - p-value based on standard normal approximation from permutations.
- `'pval_sim'` - p-value based on permutations.
- `'var_sim'` - variance of `'score'` from permutations.
Otherwise, modifies the ``adata`` with the following key:
- :attr:`anndata.AnnData.uns` ``['moranI']`` - the above mentioned dataframe, if ``mode = {sp.MORAN.s!r}``.
- :attr:`anndata.AnnData.uns` ``['gearyC']`` - the above mentioned dataframe, if ``mode = {sp.GEARY.s!r}``.
"""
_assert_connectivity_key(adata, connectivity_key)
if genes is None:
if "highly_variable" in adata.var.columns:
genes = adata[:, adata.var.highly_variable.values].var_names.values
else:
genes = adata.var_names.values
genes = _assert_non_empty_sequence(genes, name="genes")
mode = SpatialAutocorr(mode) # type: ignore[assignment]
if TYPE_CHECKING:
assert isinstance(mode, SpatialAutocorr)
params = {
"mode": mode.s,
"transformation": transformation,
"two_tailed": two_tailed
}
if mode == SpatialAutocorr.MORAN:
params["func"] = _morans_i
params["stat"] = "I"
params["expected"] = -1.0 / (adata.shape[0] - 1) # expected score
params["ascending"] = False
elif mode == SpatialAutocorr.GEARY:
params["func"] = _gearys_c
params["stat"] = "C"
params["expected"] = 1.0
params["ascending"] = True
else:
raise NotImplementedError(f"Mode `{mode}` is not yet implemented.")
n_jobs = _get_n_cores(n_jobs)
vals = _get_obs_rep(adata[:, genes], use_raw=use_raw, layer=layer).T
g = adata.obsp[connectivity_key].copy()
# row-normalize
if transformation:
normalize(g, norm="l1", axis=1, copy=False)
score = params["func"](g, vals)
start = logg.info(
f"Calculating {mode}'s statistic for `{n_perms}` permutations using `{n_jobs}` core(s)"
)
if n_perms is not None:
_assert_positive(n_perms, name="n_perms")
perms = np.arange(n_perms)
score_perms = parallelize(
_score_helper,
collection=perms,
extractor=np.concatenate,
use_ixs=True,
n_jobs=n_jobs,
backend=backend,
show_progress_bar=show_progress_bar,
)(mode=mode, g=g, vals=vals, seed=seed)
else:
score_perms = None
with np.errstate(divide="ignore"):
pval_results = _p_value_calc(score, score_perms, g, params)
results = {params["stat"]: score}
results.update(pval_results)
df = pd.DataFrame(results, index=genes)
if corr_method is not None:
for pv in filter(lambda x: "pval" in x, df.columns):
_, pvals_adj, _, _ = multipletests(df[pv].values,
alpha=0.05,
method=corr_method)
df[f"{pv}_{corr_method}"] = pvals_adj
df.sort_values(by=params["stat"],
ascending=params["ascending"],
inplace=True)
if copy:
logg.info("Finish", time=start)
return df
_save_data(adata,
attr="uns",
key=params["mode"] + params["stat"],
data=df,
time=start)
def generate_spot_crops(
self,
adata: AnnData,
library_id: Optional[str] = None,
spatial_key: str = Key.obsm.spatial,
spot_scale: float = 1.0,
obs_names: Optional[Iterable[Any]] = None,
as_array: Union[str, bool] = False,
return_obs: bool = False,
**kwargs: Any,
) -> Union[Iterator["ImageContainer"], Iterator[np.ndarray],
Iterator[Tuple[np.ndarray, ...]], Iterator[Dict[str,
np.ndarray]], ]:
"""
Iterate over :attr:`adata.obs_names` and extract crops.
Implemented for 10X spatial datasets.
Parameters
----------
%(adata)s
library_id
Key in :attr:`anndata.AnnData.uns` ``['{spatial_key}']`` used to get the spot diameter.
%(spatial_key)s
spot_scale
Scaling factor for the spot diameter. Larger values mean more context.
obs_names
Observations from :attr:`adata.obs_names` for which to generate the crops. If `None`, all names are used.
%(as_array)s
return_obs
Whether to also yield names from ``obs_names``.
kwargs
Keyword arguments for :meth:`crop_center`.
Yields
------
If ``return_obs = True``, yields a :class:`tuple` ``(crop, obs_name)``. Otherwise, yields just the crops.
The type of the crops depends on ``as_array``.
"""
self._assert_not_empty()
_assert_positive(spot_scale, name="scale")
_assert_spatial_basis(adata, spatial_key)
library_id = Key.uns.library_id(adata,
spatial_key=spatial_key,
library_id=library_id)
if obs_names is None:
obs_names = adata.obs_names
obs_names = _assert_non_empty_sequence(obs_names, name="observations")
adata = adata[obs_names, :]
spatial = adata.obsm[spatial_key][:, :2]
diameter = adata.uns[spatial_key][library_id]["scalefactors"][
"spot_diameter_fullres"]
radius = int(round(diameter // 2 * spot_scale))
for i, obs in enumerate(adata.obs_names):
crop = self.crop_center(y=spatial[i][1],
x=spatial[i][0],
radius=radius,
**kwargs)
crop.data.attrs[Key.img.obs] = obs
crop = crop._maybe_as_array(as_array)
yield (crop, obs) if return_obs else crop
def crop_corner(
self,
y: FoI_t,
x: FoI_t,
size: Optional[Union[FoI_t, Tuple[FoI_t, FoI_t]]] = None,
scale: float = 1.0,
cval: Union[int, float] = 0,
mask_circle: bool = False,
preserve_dtypes: bool = True,
) -> "ImageContainer":
"""
Extract a crop from the upper-left corner.
Parameters
----------
%(yx)s
%(size)s
scale
Rescale the crop using :func:`skimage.transform.rescale`.
cval
Fill value to use if ``mask_circle = True`` or if crop goes out of the image boundary.
mask_circle
Whether to mask out values that are not within a circle defined by this crop.
Only available if ``size`` defines a square.
preserve_dtypes
Whether to preserver the data types of underlying :class:`xarray.DataArray`, even if ``cval``
is of different type.
Returns
-------
The cropped image of size ``size * scale``.
Raises
------
ValueError
If the crop would completely lie outside of the image or if ``mask_circle = True`` and
``size`` does not define a square.
Notes
-----
If ``preserve_dtypes = True`` but ``cval`` cannot be safely cast, ``cval`` will be set to 0.
"""
self._assert_not_empty()
y, x = self._convert_to_pixel_space((y, x))
size = self._get_size(size)
size = self._convert_to_pixel_space(size)
ys, xs = size
_assert_positive(ys, name="height")
_assert_positive(xs, name="width")
_assert_positive(scale, name="scale")
orig = CropCoords(x0=x, y0=y, x1=x + xs, y1=y + ys)
ymin, xmin = self.shape
coords = CropCoords(x0=min(max(x, 0), xmin),
y0=min(max(y, 0), ymin),
x1=min(x + xs, xmin),
y1=min(y + ys, ymin))
if not coords.dy:
raise ValueError("Height of the crop is empty.")
if not coords.dx:
raise ValueError("Width of the crop is empty.")
crop = self.data.isel(x=slice(coords.x0, coords.x1),
y=slice(coords.y0, coords.y1)).copy(deep=False)
crop.attrs[Key.img.coords] = coords
if orig != coords:
padding = orig - coords
# because padding does not change dtype by itself
for key, arr in crop.items():
if preserve_dtypes:
if not np.can_cast(cval, arr.dtype, casting="safe"):
cval = 0
else:
crop[key] = crop[key].astype(np.dtype(type(cval)),
copy=False)
crop = crop.pad(
y=(padding.y_pre, padding.y_post),
x=(padding.x_pre, padding.x_post),
mode="constant",
constant_values=cval,
)
crop.attrs["padding"] = padding
else:
crop.attrs["padding"] = _NULL_PADDING
return self._from_dataset(
self._post_process(data=crop,
scale=scale,
cval=cval,
mask_circle=mask_circle,
preserve_dtypes=preserve_dtypes))