#!/usr/bin/env python
# -*- coding: utf-8 -*-
from collections.abc import Sequence as seq
from typing import Collection, ItemsView, Sequence, Tuple, Union
###############################################################################
[docs]class DimensionNames:
Time = "T"
Channel = "C"
SpatialZ = "Z"
SpatialY = "Y"
SpatialX = "X"
Samples = "S"
MosaicTile = "M"
DEFAULT_DIMENSION_ORDER_LIST = [
DimensionNames.Time,
DimensionNames.Channel,
DimensionNames.SpatialZ,
DimensionNames.SpatialY,
DimensionNames.SpatialX,
]
DEFAULT_DIMENSION_ORDER_LIST_WITH_SAMPLES = DEFAULT_DIMENSION_ORDER_LIST + [
DimensionNames.Samples
]
DEFAULT_DIMENSION_ORDER_LIST_WITH_MOSAIC_TILES = [
DimensionNames.MosaicTile
] + DEFAULT_DIMENSION_ORDER_LIST
DEFAULT_DIMENSION_ORDER_LIST_WITH_MOSAIC_TILES_AND_SAMPLES = (
[DimensionNames.MosaicTile]
+ DEFAULT_DIMENSION_ORDER_LIST
+ [DimensionNames.Samples]
)
DEFAULT_DIMENSION_ORDER = "".join(DEFAULT_DIMENSION_ORDER_LIST)
DEFAULT_DIMENSION_ORDER_WITH_SAMPLES = "".join(
DEFAULT_DIMENSION_ORDER_LIST_WITH_SAMPLES
)
DEFAULT_DIMENSION_ORDER_WITH_MOSAIC_TILES = "".join(
DEFAULT_DIMENSION_ORDER_LIST_WITH_MOSAIC_TILES
)
DEFAULT_DIMENSION_ORDER_WITH_MOSAIC_TILES_AND_SAMPLES = "".join(
DEFAULT_DIMENSION_ORDER_LIST_WITH_MOSAIC_TILES_AND_SAMPLES
)
DEFAULT_CHUNK_DIMS = [
DimensionNames.SpatialZ,
DimensionNames.SpatialY,
DimensionNames.SpatialX,
DimensionNames.Samples,
]
REQUIRED_CHUNK_DIMS = [
DimensionNames.SpatialY,
DimensionNames.SpatialX,
DimensionNames.Samples,
]
###############################################################################
[docs]class Dimensions:
def __init__(self, dims: Collection[str], shape: Tuple[int, ...]):
"""
A general object for managing the pairing of dimension name and dimension size.
Parameters
----------
dims: Collection[str]
An ordered string or collection of the dimensions to pair with their sizes.
shape: Tuple[int, ...]
An ordered tuple of the dimensions sizes to pair with their names.
Examples
--------
>>> dims = Dimensions("TCZYX", (1, 4, 75, 624, 924))
... dims.X
... dims['T', 'X']
"""
# zip(strict=True) only in Python 3.10
# Check equal length dims and shape
if len(dims) != len(shape):
raise ValueError(
f"Number of dimensions provided ({len(dims)} -- '{dims}') "
f"does not match shape size provided ({len(shape)} -- '{shape}')."
)
# Make dims a string
if not isinstance(dims, str):
if any([len(c) != 1 for c in dims]):
raise ValueError(
f"When providing a list of dimension strings, "
f"each dimension may only be a single character long "
f"(received: '{dims}')."
)
dims = "".join(dims)
# Store order and shape
self._order = dims
self._shape = shape
# Create attributes
self._dims_shape = dict(zip(dims, shape))
for dim, size in self._dims_shape.items():
setattr(self, dim, size)
@property
def order(self) -> str:
"""
Returns
-------
order: str
The natural order of the dimensions as a single string.
"""
return self._order
@property
def shape(self) -> Tuple[int, ...]:
"""
Returns
-------
shape: Tuple[int, ...]
The dimension sizes in their natural order.
"""
return self._shape
[docs] def items(self) -> ItemsView[str, int]:
return self._dims_shape.items()
def __str__(self) -> str:
dims_string = ", ".join([f"{dim}: {size}" for dim, size in self.items()])
return f"<Dimensions [{dims_string}]>"
def __repr__(self) -> str:
return str(self)
def __getitem__(self, key: Union[str, Sequence[str]]) -> Tuple[int, ...]:
if isinstance(key, str):
if key not in self._order:
raise IndexError(f"{key} not in {self._order}")
return (self._dims_shape[key],)
elif isinstance(key, seq) and all(isinstance(k, str) for k in key):
invalid_dims = []
for k in key:
if k not in self._order:
invalid_dims.append(k)
if len(invalid_dims) == 0:
return tuple(self._dims_shape[k] for k in key)
else:
raise IndexError(f"{', '.join(invalid_dims)} not in {self._order}")
else:
raise TypeError(
f"Key must be a string or list of strings but got type {type(key)}"
)
def __setattr__(self, __name: str, __value: int) -> None:
super().__setattr__(__name, __value)
def __getattr__(self, __name: str) -> int:
# TODO: Py310 __match_args__ for better typing
return super().__getattribute__(__name)