thewtex / xarray-dataclasses

:zap: xarray extension for typed DataArray and Dataset creation

xarray-dataclasses

xarray extension for typed DataArray and Dataset creation

Overview

xarray-dataclasses is a Python package that makes it easy to create xarray's DataArray and Dataset objects that are "typed" (i.e. fixed dimensions, data type, coordinates, attributes, and name) using the Python's dataclass:

from dataclasses import dataclass
from typing import Literal
from xarray_dataclasses import AsDataArray, Coord, Data


X = Literal["x"]
Y = Literal["y"]


@dataclass
class Image(AsDataArray):
    """2D image as DataArray."""

    data: Data[tuple[X, Y], float]
    x: Coord[X, int] = 0
    y: Coord[Y, int] = 0

Features

• Typed DataArray or Dataset objects can easily be created:

  image = Image.new([[0, 1], [2, 3]], [0, 1], [0, 1])

• NumPy-like filled-data creation is also available:

  image = Image.zeros([2, 2], x=[0, 1], y=[0, 1])

• Support for features by the Python's dataclass (field, __post_init__, ...).
• Support for static type check by Pyright.

Installation

pip install xarray-dataclasses

Basic usage

xarray-dataclasses uses the Python's dataclass. Data (or data variables), coordinates, attributes, and a name of DataArray or Dataset objects will be defined as dataclass fields by special type hints (Data, Coord, Attr, Name), respectively. Note that the following code is supposed in the examples below.

from dataclasses import dataclass
from typing import Literal
from xarray_dataclasses import AsDataArray, AsDataset
from xarray_dataclasses import Attr, Coord, Data, Name


X = Literal["x"]
Y = Literal["y"]

Data field

Data field is a field whose value will become the data of a DataArray object or a data variable of a Dataset object. The type hint Data[TDims, TDtype] fixes the dimensions and the data type of the object. Here are some examples of how to specify them.

Type hint	Inferred dimensions
Data[tuple[()], ...]	()
Data[Literal["x"], ...]	("x",)
Data[tuple[Literal["x"]], ...]	("x",)
Data[tuple[Literal["x"], Literal["y"]], ...]	("x", "y")

Type hint	Inferred data type
Data[..., Any]	None
Data[..., None]	None
Data[..., float]	numpy.dtype("float64")
Data[..., numpy.float128]	numpy.dtype("float128")
Data[..., Literal["datetime64[ns]"]]	numpy.dtype("<M8[ns]")

Coordinate field

Coordinate field is a field whose value will become a coordinate of a DataArray or a Dataset object. The type hint Coord[TDims, TDtype] fixes the dimensions and the data type of the object.

Attribute field

Attribute field is a field whose value will become an attribute of a DataArray or a Dataset object. The type hint Attr[TAttr] specifies the type of the value, which is used only for static type check.

Name field

Name field is a field whose value will become the name of a DataArray object. The type hint Name[TName] specifies the type of the value, which is used only for static type check.

DataArray class

DataArray class is a dataclass that defines typed DataArray specifications. Exactly one data field is allowed in a DataArray class. The second and subsequent data fields are just ignored in DataArray creation.

@dataclass
class Image(AsDataArray):
    """2D image as DataArray."""

    data: Data[tuple[X, Y], float]
    x: Coord[X, int] = 0
    y: Coord[Y, int] = 0
    units: Attr[str] = "cd / m^2"
    name: Name[str] = "luminance"

A DataArray object will be created by a class method new():

Image.new([[0, 1], [2, 3]], x=[0, 1], y=[0, 1])

<xarray.DataArray "luminance" (x: 2, y: 2)>
array([[0., 1.],
       [2., 3.]])
Coordinates:
  * x        (x) int64 0 1
  * y        (y) int64 0 1
Attributes:
    units:    cd / m^2

NumPy-like class methods (zeros(), ones(), ...) are also available:

Image.ones((3, 3))

<xarray.DataArray "luminance" (x: 3, y: 3)>
array([[1., 1., 1.],
       [1., 1., 1.],
       [1., 1., 1.]])
Coordinates:
  * x        (x) int64 0 0 0
  * y        (y) int64 0 0 0
Attributes:
    units:    cd / m^2

Dataset class

Dataset class is a dataclass that defines typed Dataset specifications. Multiple data fields are allowed to define the data variables of the object.

@dataclass
class ColorImage(AsDataset):
    """2D color image as Dataset."""

    red: Data[tuple[X, Y], float]
    green: Data[tuple[X, Y], float]
    blue: Data[tuple[X, Y], float]
    x: Coord[X, int] = 0
    y: Coord[Y, int] = 0
    units: Attr[str] = "cd / m^2"

A Dataset object will be created by a class method new():

ColorImage.new(
    [[0, 0], [0, 0]],  # red
    [[1, 1], [1, 1]],  # green
    [[2, 2], [2, 2]],  # blue
)

<xarray.Dataset>
Dimensions:  (x: 2, y: 2)
Coordinates:
  * x        (x) int64 0 0
  * y        (y) int64 0 0
Data variables:
    red      (x, y) float64 0.0 0.0 0.0 0.0
    green    (x, y) float64 1.0 1.0 1.0 1.0
    blue     (x, y) float64 2.0 2.0 2.0 2.0
Attributes:
    units:    cd / m^2

Advanced usage

Coordof and Dataof type hints

xarray-dataclasses provides advanced type hints, Coordof and Dataof. Unlike Data and Coord, they specify a dataclass that defines a DataArray class. This is useful when users want to add metadata to dimensions for plotting. For example:

from xarray_dataclasses import Coordof


@dataclass
class XAxis:
    data: Data[X, int]
    long_name: Attr[str] = "x axis"
    units: Attr[str] = "pixel"


@dataclass
class YAxis:
    data: Data[Y, int]
    long_name: Attr[str] = "y axis"
    units: Attr[str] = "pixel"


@dataclass
class Image(AsDataArray):
    """2D image as DataArray."""

    data: Data[tuple[X, Y], float]
    x: Coordof[XAxis] = 0
    y: Coordof[YAxis] = 0

General data varible names in Dataset creation

Due to the limitation of Python's parameter names, it is not possible to define data variable names that contain white spaces, for example. In such cases, please define DataArray classes of each data variable so that they have name fields and specify them by Dataof in a Dataset class. Then the values of the name fields will be used as data variable names. For example:

@dataclass
class Red:
    data: Data[tuple[X, Y], float]
    name: Name[str] = "Red image"


@dataclass
class Green:
    data: Data[tuple[X, Y], float]
    name: Name[str] = "Green image"


@dataclass
class Blue:
    data: Data[tuple[X, Y], float]
    name: Name[str] = "Blue image"


@dataclass
class ColorImage(AsDataset):
    """2D color image as Dataset."""

    red: Dataof[Red]
    green: Dataof[Green]
    blue: Dataof[Blue]

ColorImage.new(
    [[0, 0], [0, 0]],
    [[1, 1], [1, 1]],
    [[2, 2], [2, 2]],
)

<xarray.Dataset>
Dimensions:      (x: 2, y: 2)
Dimensions without coordinates: x, y
Data variables:
    Red image    (x, y) float64 0.0 0.0 0.0 0.0
    Green image  (x, y) float64 1.0 1.0 1.0 1.0
    Blue image   (x, y) float64 2.0 2.0 2.0 2.0

Customization of DataArray or Dataset creation

For customization, users can add a special class attribute, __dataoptions__, to a DataArray or Dataset class. A custom factory for DataArray or Dataset creation is only supported in the current implementation.

import xarray as xr
from xarray_dataclasses import DataOptions


class Custom(xr.DataArray):
    """Custom DataArray."""

    __slots__ = ()

    def custom_method(self) -> bool:
        """Custom method."""
        return True


@dataclass
class Image(AsDataArray):
    """2D image as DataArray."""

    data: Data[tuple[X, Y], float]
    x: Coord[X, int] = 0
    y: Coord[Y, int] = 0

    __dataoptions__ = DataOptions(Custom)


image = Image.ones([3, 3])
isinstance(image, Custom)  # True
image.custom_method()  # True

DataArray and Dataset creation without shorthands

xarray-dataclasses provides functions, asdataarray and asdataset. This is useful when users do not want to inherit the mix-in class (AsDataArray or AsDataset) in a DataArray or Dataset dataclass. For example:

from xarray_dataclasses import asdataarray


@dataclass
class Image:
    """2D image as DataArray."""

    data: Data[tuple[X, Y], float]
    x: Coord[X, int] = 0
    y: Coord[Y, int] = 0


image = asdataarray(Image([[0, 1], [2, 3]], [0, 1], [0, 1]))