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_dataframe_field.py
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_dataframe_field.py
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import logging
from typing import Literal, Optional
import numpy as np
import rich
from anndata import AnnData
from pandas.api.types import CategoricalDtype
from scvi.data import _constants
from scvi.data._utils import _make_column_categorical, get_anndata_attribute
from ._base_field import BaseAnnDataField
from ._mudata import MuDataWrapper
logger = logging.getLogger(__name__)
class BaseDataFrameField(BaseAnnDataField):
"""An abstract AnnDataField for .obs attributes in the AnnData data structure.
Parameters
----------
registry_key
Key to register field under in data registry.
attr_key
Key to access the field in the AnnData obs or var mapping. If None, defaults to `registry_key`.
field_type
Type of field. Can be either "obs" or "var".
required
If False, allows for `attr_key is None` and marks the field as `is_empty`.
"""
def __init__(
self,
registry_key: str,
attr_key: Optional[str],
field_type: Literal["obs", "var"] = None,
required: bool = True,
) -> None:
super().__init__()
if required and attr_key is None:
raise ValueError(
"`attr_key` cannot be `None` if `required=True`. Please provide an `attr_key`."
)
if field_type == "obs":
self._attr_name = _constants._ADATA_ATTRS.OBS
elif field_type == "var":
self._attr_name = _constants._ADATA_ATTRS.VAR
else:
raise ValueError("`field_type` must be either 'obs' or 'var'.")
self._registry_key = registry_key
self._attr_key = attr_key
self._is_empty = attr_key is None
@property
def registry_key(self) -> str:
return self._registry_key
@property
def attr_name(self) -> str:
return self._attr_name
@property
def attr_key(self) -> str:
return self._attr_key
@property
def is_empty(self) -> bool:
return self._is_empty
class NumericalDataFrameField(BaseDataFrameField):
"""An AnnDataField for numerical .obs or .var attributes in the AnnData data structure.
Parameters
----------
registry_key
Key to register field under in data registry.
attr_key
Key to access the field in the AnnData obs or var mapping. If None, defaults to `registry_key`.
"""
def validate_field(self, adata: AnnData) -> None:
"""Validate field."""
super().validate_field(adata)
if self.attr_key not in getattr(adata, self.attr_name):
raise KeyError(f"{self.attr_key} not found in adata.{self.attr_name}.")
def register_field(self, adata: AnnData) -> dict:
"""Register field."""
return super().register_field(adata)
def transfer_field(self, state_registry: dict, adata_target: AnnData, **kwargs) -> dict:
"""Transfer field from registry to target AnnData."""
super().transfer_field(state_registry, adata_target, **kwargs)
return self.register_field(adata_target)
def get_summary_stats(self, _state_registry: dict) -> dict:
"""Get summary stats."""
return {}
def view_state_registry(self, _state_registry: dict) -> Optional[rich.table.Table]:
"""View state registry."""
return None
class NumericalObsField(NumericalDataFrameField):
"""An AnnDataField for numerical .obs attributes in the AnnData data structure."""
def __init__(self, *args, **kwargs):
super().__init__(*args, field_type="obs", **kwargs)
class NumericalVarField(NumericalDataFrameField):
"""An AnnDataField for numerical .var attributes in the AnnData data structure."""
def __init__(self, *args, **kwargs):
super().__init__(*args, field_type="var", **kwargs)
MuDataNumericalObsField = MuDataWrapper(NumericalObsField)
MuDataNumericalVarField = MuDataWrapper(NumericalVarField)
class CategoricalDataFrameField(BaseDataFrameField):
"""An AnnDataField for categorical .obs or .var attributes in the AnnData data structure.
Parameters
----------
registry_key
Key to register field under in data registry.
attr_key
Key to access the field in the AnnData obs or var mapping. If None, defaults to `registry_key`.
field_type
Type of field. Can be either "obs" or "var".
"""
CATEGORICAL_MAPPING_KEY = "categorical_mapping"
ORIGINAL_ATTR_KEY = "original_key"
def __init__(
self,
registry_key: str,
attr_key: Optional[str],
field_type: Literal["obs", "var"] = None,
) -> None:
self.is_default = attr_key is None
self._original_attr_key = attr_key or registry_key
super().__init__(
registry_key,
f"_scvi_{registry_key}",
field_type=field_type,
)
self.count_stat_key = f"n_{self.registry_key}"
def _setup_default_attr(self, adata: AnnData) -> None:
"""Setup default attr."""
self._original_attr_key = self.attr_key
length = (
adata.shape[0] if self._attr_name == _constants._ADATA_ATTRS.OBS else adata.shape[1]
)
getattr(adata, self.attr_name)[self.attr_key] = np.zeros(length, dtype=np.int64)
def _get_original_column(self, adata: AnnData) -> np.ndarray:
"""Get original column from adata."""
return get_anndata_attribute(adata, self.attr_name, self._original_attr_key)
def validate_field(self, adata: AnnData) -> None:
"""Validate field."""
super().validate_field(adata)
if self._original_attr_key not in getattr(adata, self.attr_name):
raise KeyError(f"{self._original_attr_key} not found in adata.{self.attr_name}.")
def register_field(self, adata: AnnData) -> dict:
"""Register field."""
if self.is_default:
self._setup_default_attr(adata)
super().register_field(adata)
categorical_mapping = _make_column_categorical(
getattr(adata, self.attr_name),
self._original_attr_key,
self.attr_key,
)
return {
self.CATEGORICAL_MAPPING_KEY: categorical_mapping,
self.ORIGINAL_ATTR_KEY: self._original_attr_key,
}
def transfer_field(
self,
state_registry: dict,
adata_target: AnnData,
extend_categories: bool = False,
**kwargs,
) -> dict:
"""Transfer field from registry to target AnnData."""
super().transfer_field(state_registry, adata_target, **kwargs)
if self.is_default:
self._setup_default_attr(adata_target)
self.validate_field(adata_target)
mapping = state_registry[self.CATEGORICAL_MAPPING_KEY].copy()
# extend mapping for new categories
for c in np.unique(self._get_original_column(adata_target)):
if c not in mapping:
if extend_categories:
mapping = np.concatenate([mapping, [c]])
else:
raise ValueError(
f"Category {c} not found in source registry. "
f"Cannot transfer setup without `extend_categories = True`."
)
cat_dtype = CategoricalDtype(categories=mapping, ordered=True)
new_mapping = _make_column_categorical(
getattr(adata_target, self.attr_name),
self._original_attr_key,
self.attr_key,
categorical_dtype=cat_dtype,
)
return {
self.CATEGORICAL_MAPPING_KEY: new_mapping,
self.ORIGINAL_ATTR_KEY: self._original_attr_key,
}
def get_summary_stats(self, state_registry: dict) -> dict:
"""Get summary stats."""
categorical_mapping = state_registry[self.CATEGORICAL_MAPPING_KEY]
n_categories = len(np.unique(categorical_mapping))
return {self.count_stat_key: n_categories}
def view_state_registry(self, state_registry: dict) -> Optional[rich.table.Table]:
"""View state registry."""
source_key = state_registry[self.ORIGINAL_ATTR_KEY]
mapping = state_registry[self.CATEGORICAL_MAPPING_KEY]
t = rich.table.Table(title=f"{self.registry_key} State Registry")
t.add_column(
"Source Location",
justify="center",
style="dodger_blue1",
no_wrap=True,
overflow="fold",
)
t.add_column("Categories", justify="center", style="green", no_wrap=True, overflow="fold")
t.add_column(
"scvi-tools Encoding",
justify="center",
style="dark_violet",
no_wrap=True,
overflow="fold",
)
for i, cat in enumerate(mapping):
if i == 0:
t.add_row(f"adata.{self.attr_name}['{source_key}']", str(cat), str(i))
else:
t.add_row("", str(cat), str(i))
return t
class CategoricalObsField(CategoricalDataFrameField):
"""An AnnDataField for categorical .obs attributes in the AnnData data structure."""
def __init__(self, *args, **kwargs):
super().__init__(*args, field_type="obs", **kwargs)
class CategoricalVarField(CategoricalDataFrameField):
"""An AnnDataField for categorical .var attributes in the AnnData data structure."""
def __init__(self, *args, **kwargs):
super().__init__(*args, field_type="var", **kwargs)
MuDataCategoricalObsField = MuDataWrapper(CategoricalObsField)
MuDataCategoricalVarField = MuDataWrapper(CategoricalVarField)