Source code for datashader.core

from __future__ import annotations

from numbers import Number
from math import log10
import warnings

import numpy as np
import pandas as pd
import dask.dataframe as dd
import dask.array as da
from xarray import DataArray, Dataset

from .utils import Dispatcher, ngjit, calc_res, calc_bbox, orient_array, \
    dshape_from_xarray_dataset
from .utils import get_indices, dshape_from_pandas, dshape_from_dask
from .utils import Expr # noqa (API import)
from .resampling import resample_2d, resample_2d_distributed
from . import reductions as rd

try:
    import cudf
except Exception:
    cudf = None

try:
    import dask_cudf
except Exception:
    dask_cudf = None

try:
    import spatialpandas
except Exception:
    spatialpandas = None

class Axis:
    """Interface for implementing axis transformations.

    Instances hold implementations of transformations to and from axis space.
    The default implementation is equivalent to:

    >>> def forward_transform(data_x):
    ...     scale * mapper(data_x) + t
    >>> def inverse_transform(axis_x):
    ...     inverse_mapper((axis_x - t)/s)

    Where ``mapper`` and ``inverse_mapper`` are elementwise functions mapping
    to and from axis-space respectively, and ``scale`` and ``transform`` are
    parameters describing a linear scale and translate transformation, computed
    by the ``compute_scale_and_translate`` method.
    """

    def compute_scale_and_translate(self, range, n):
        """Compute the scale and translate parameters for a linear transformation
        ``output = s * input + t``, mapping from data space to axis space.

        Parameters
        ----------
        range : tuple
            A tuple representing the range ``[min, max]`` along the axis, in
            data space. Both min and max are inclusive.
        n : int
            The number of bins along the axis.

        Returns
        -------
        s, t : floats
        """
        start, end = map(self.mapper, range)
        s = n/(end - start)
        t = -start * s
        return s, t

    def compute_index(self, st, n):
        """Compute a 1D array representing the axis index.

        Parameters
        ----------
        st : tuple
            A tuple of ``(scale, translate)`` parameters.
        n : int
            The number of bins along the dimension.

        Returns
        -------
        index : ndarray
        """
        px = np.arange(n)+0.5
        s, t = st
        return self.inverse_mapper((px - t)/s)

    def mapper(val):
        """A mapping from data space to axis space"""
        raise NotImplementedError

    def inverse_mapper(val):
        """A mapping from axis space to data space"""
        raise NotImplementedError

    def validate(self, range):
        """Given a range (low,high), raise an error if the range is invalid for this axis"""
        pass


class LinearAxis(Axis):
    """A linear Axis"""
    @staticmethod
    @ngjit
    def mapper(val):
        return val

    @staticmethod
    @ngjit
    def inverse_mapper(val):
        return val


class LogAxis(Axis):
    """A base-10 logarithmic Axis"""
    @staticmethod
    @ngjit
    def mapper(val):
        return log10(float(val))

    @staticmethod
    @ngjit
    def inverse_mapper(val):
        y = 10 # temporary workaround for https://github.com/numba/numba/issues/3135 (numba 0.39.0)
        return y**val

    def validate(self, range):
        if range is None:
            # Nothing to check if no range
            return
        if range[0] <= 0 or range[1] <= 0:
            raise ValueError('Range values must be >0 for logarithmic axes')


_axis_lookup = {'linear': LinearAxis(), 'log': LogAxis()}


def validate_xy_or_geometry(glyph, x, y, geometry):
    if (geometry is None and (x is None or y is None) or
            geometry is not None and (x is not None or y is not None)):
        raise ValueError("""
{glyph} coordinates may be specified by providing both the x and y arguments, or by
providing the geometry argument. Received:
    x: {x}
    y: {y}
    geometry: {geometry}
""".format(glyph=glyph, x=repr(x), y=repr(y), geometry=repr(geometry)))


[docs]class Canvas: """An abstract canvas representing the space in which to bin. Parameters ---------- plot_width, plot_height : int, optional Width and height of the output aggregate in pixels. x_range, y_range : tuple, optional A tuple representing the bounds inclusive space ``[min, max]`` along the axis. x_axis_type, y_axis_type : str, optional The type of the axis. Valid options are ``'linear'`` [default], and ``'log'``. """ def __init__(self, plot_width=600, plot_height=600, x_range=None, y_range=None, x_axis_type='linear', y_axis_type='linear'): self.plot_width = plot_width self.plot_height = plot_height self.x_range = None if x_range is None else tuple(x_range) self.y_range = None if y_range is None else tuple(y_range) self.x_axis = _axis_lookup[x_axis_type] self.y_axis = _axis_lookup[y_axis_type] def points(self, source, x=None, y=None, agg=None, geometry=None): """Compute a reduction by pixel, mapping data to pixels as points. Parameters ---------- source : pandas.DataFrame, dask.DataFrame, or xarray.DataArray/Dataset The input datasource. x, y : str Column names for the x and y coordinates of each point. If provided, the geometry argument may not also be provided. agg : Reduction, optional Reduction to compute. Default is ``count()``. geometry: str Column name of a PointsArray of the coordinates of each point. If provided, the x and y arguments may not also be provided. """ from .glyphs import Point, MultiPointGeometry from .reductions import count as count_rdn validate_xy_or_geometry('Point', x, y, geometry) if agg is None: agg = count_rdn() if geometry is None: glyph = Point(x, y) else: if spatialpandas and isinstance(source, spatialpandas.dask.DaskGeoDataFrame): # Downselect partitions to those that may contain points in viewport x_range = self.x_range if self.x_range is not None else (None, None) y_range = self.y_range if self.y_range is not None else (None, None) source = source.cx_partitions[slice(*x_range), slice(*y_range)] glyph = MultiPointGeometry(geometry) elif spatialpandas and isinstance(source, spatialpandas.GeoDataFrame): glyph = MultiPointGeometry(geometry) elif (geopandas_source := self._source_from_geopandas(source)) is not None: source = geopandas_source from datashader.glyphs.points import MultiPointGeoPandas glyph = MultiPointGeoPandas(geometry) else: raise ValueError( "source must be an instance of spatialpandas.GeoDataFrame, " "spatialpandas.dask.DaskGeoDataFrame, geopandas.GeoDataFrame, or " "dask_geopandas.GeoDataFrame. Received objects of type {typ}".format( typ=type(source))) return bypixel(source, self, glyph, agg) def line(self, source, x=None, y=None, agg=None, axis=0, geometry=None, line_width=0, antialias=False): """Compute a reduction by pixel, mapping data to pixels as one or more lines. For aggregates that take in extra fields, the interpolated bins will receive the fields from the previous point. In pseudocode: >>> for i in range(len(rows) - 1): # doctest: +SKIP ... row0 = rows[i] ... row1 = rows[i + 1] ... for xi, yi in interpolate(row0.x, row0.y, row1.x, row1.y): ... add_to_aggregate(xi, yi, row0) Parameters ---------- source : pandas.DataFrame, dask.DataFrame, or xarray.DataArray/Dataset The input datasource. x, y : str or number or list or tuple or np.ndarray Specification of the x and y coordinates of each vertex * str or number: Column labels in source * list or tuple: List or tuple of column labels in source * np.ndarray: When axis=1, a literal array of the coordinates to be used for every row agg : Reduction, optional Reduction to compute. Default is ``any()``. axis : 0 or 1, default 0 Axis in source to draw lines along * 0: Draw lines using data from the specified columns across all rows in source * 1: Draw one line per row in source using data from the specified columns geometry : str Column name of a LinesArray of the coordinates of each line. If provided, the x and y arguments may not also be provided. line_width : number, optional Width of the line to draw, in pixels. If zero, the default, lines are drawn using a simple algorithm with a blocky single-pixel width based on whether the line passes through each pixel or does not. If greater than one, lines are drawn with the specified width using a slower and more complex antialiasing algorithm with fractional values along each edge, so that lines have a more uniform visual appearance across all angles. Line widths between 0 and 1 effectively use a line_width of 1 pixel but with a proportionate reduction in the strength of each pixel, approximating the visual appearance of a subpixel line width. antialias : bool, optional This option is kept for backward compatibility only. ``True`` is equivalent to ``line_width=1`` and ``False`` (the default) to ``line_width=0``. Do not specify both ``antialias`` and ``line_width`` in the same call as a ``ValueError`` will be raised if they disagree. Examples -------- Define a canvas and a pandas DataFrame with 6 rows >>> import pandas as pd # doctest: +SKIP ... import numpy as np ... import datashader as ds ... from datashader import Canvas ... import datashader.transfer_functions as tf ... cvs = Canvas() ... df = pd.DataFrame({ ... 'A1': [1, 1.5, 2, 2.5, 3, 4], ... 'A2': [1.5, 2, 3, 3.2, 4, 5], ... 'B1': [10, 12, 11, 14, 13, 15], ... 'B2': [11, 9, 10, 7, 8, 12], ... }, dtype='float64') Aggregate one line across all rows, with coordinates df.A1 by df.B1 >>> agg = cvs.line(df, x='A1', y='B1', axis=0) # doctest: +SKIP ... tf.spread(tf.shade(agg)) Aggregate two lines across all rows. The first with coordinates df.A1 by df.B1 and the second with coordinates df.A2 by df.B2 >>> agg = cvs.line(df, x=['A1', 'A2'], y=['B1', 'B2'], axis=0) # doctest: +SKIP ... tf.spread(tf.shade(agg)) Aggregate two lines across all rows where the lines share the same x coordinates. The first line will have coordinates df.A1 by df.B1 and the second will have coordinates df.A1 by df.B2 >>> agg = cvs.line(df, x='A1', y=['B1', 'B2'], axis=0) # doctest: +SKIP ... tf.spread(tf.shade(agg)) Aggregate 6 length-2 lines, one per row, where the ith line has coordinates [df.A1[i], df.A2[i]] by [df.B1[i], df.B2[i]] >>> agg = cvs.line(df, x=['A1', 'A2'], y=['B1', 'B2'], axis=1) # doctest: +SKIP ... tf.spread(tf.shade(agg)) Aggregate 6 length-4 lines, one per row, where the x coordinates of every line are [0, 1, 2, 3] and the y coordinates of the ith line are [df.A1[i], df.A2[i], df.B1[i], df.B2[i]]. >>> agg = cvs.line(df, # doctest: +SKIP ... x=np.arange(4), ... y=['A1', 'A2', 'B1', 'B2'], ... axis=1) ... tf.spread(tf.shade(agg)) Aggregate RaggedArrays of variable length lines, one per row (requires pandas >= 0.24.0) >>> df_ragged = pd.DataFrame({ # doctest: +SKIP ... 'A1': pd.array([ ... [1, 1.5], [2, 2.5, 3], [1.5, 2, 3, 4], [3.2, 4, 5]], ... dtype='Ragged[float32]'), ... 'B1': pd.array([ ... [10, 12], [11, 14, 13], [10, 7, 9, 10], [7, 8, 12]], ... dtype='Ragged[float32]'), ... 'group': pd.Categorical([0, 1, 2, 1]) ... }) ... ... agg = cvs.line(df_ragged, x='A1', y='B1', axis=1) ... tf.spread(tf.shade(agg)) Aggregate RaggedArrays of variable length lines by group column, one per row (requires pandas >= 0.24.0) >>> agg = cvs.line(df_ragged, x='A1', y='B1', # doctest: +SKIP ... agg=ds.count_cat('group'), axis=1) ... tf.spread(tf.shade(agg)) """ from .glyphs import (LineAxis0, LinesAxis1, LinesAxis1XConstant, LinesAxis1YConstant, LineAxis0Multi, LinesAxis1Ragged, LineAxis1Geometry, LinesXarrayCommonX) validate_xy_or_geometry('Line', x, y, geometry) if agg is None: agg = rd.any() if line_width is None: line_width = 0 # Check and convert antialias kwarg to line_width. if antialias and line_width != 0: raise ValueError( "Do not specify values for both the line_width and \n" "antialias keyword arguments; use line_width instead.") if antialias: line_width = 1.0 if geometry is not None: if spatialpandas and isinstance(source, spatialpandas.dask.DaskGeoDataFrame): # Downselect partitions to those that may contain lines in viewport x_range = self.x_range if self.x_range is not None else (None, None) y_range = self.y_range if self.y_range is not None else (None, None) source = source.cx_partitions[slice(*x_range), slice(*y_range)] glyph = LineAxis1Geometry(geometry) elif spatialpandas and isinstance(source, spatialpandas.GeoDataFrame): glyph = LineAxis1Geometry(geometry) elif (geopandas_source := self._source_from_geopandas(source)) is not None: source = geopandas_source from datashader.glyphs.line import LineAxis1GeoPandas glyph = LineAxis1GeoPandas(geometry) else: raise ValueError( "source must be an instance of spatialpandas.GeoDataFrame, " "spatialpandas.dask.DaskGeoDataFrame, geopandas.GeoDataFrame, or " "dask_geopandas.GeoDataFrame. Received objects of type {typ}".format( typ=type(source))) elif isinstance(source, Dataset) and isinstance(x, str) and isinstance(y, str): x_arr = source[x] y_arr = source[y] if x_arr.ndim != 1: raise ValueError(f"x array must have 1 dimension not {x_arr.ndim}") if y_arr.ndim != 2: raise ValueError(f"y array must have 2 dimensions not {y_arr.ndim}") if x not in y_arr.dims: raise ValueError("x must be one of the coordinate dimensions of y") y_coord_dims = list(y_arr.coords.dims) x_dim_index = y_coord_dims.index(x) glyph = LinesXarrayCommonX(x, y, x_dim_index) else: # Broadcast column specifications to handle cases where # x is a list and y is a string or vice versa orig_x, orig_y = x, y x, y = _broadcast_column_specifications(x, y) if axis == 0: if (isinstance(x, (Number, str)) and isinstance(y, (Number, str))): glyph = LineAxis0(x, y) elif (isinstance(x, (list, tuple)) and isinstance(y, (list, tuple))): glyph = LineAxis0Multi(tuple(x), tuple(y)) else: raise ValueError(""" Invalid combination of x and y arguments to Canvas.line when axis=0. Received: x: {x} y: {y} See docstring for more information on valid usage""".format( x=repr(orig_x), y=repr(orig_y))) elif axis == 1: if isinstance(x, (list, tuple)) and isinstance(y, (list, tuple)): glyph = LinesAxis1(tuple(x), tuple(y)) elif (isinstance(x, np.ndarray) and isinstance(y, (list, tuple))): glyph = LinesAxis1XConstant(x, tuple(y)) elif (isinstance(x, (list, tuple)) and isinstance(y, np.ndarray)): glyph = LinesAxis1YConstant(tuple(x), y) elif (isinstance(x, (Number, str)) and isinstance(y, (Number, str))): glyph = LinesAxis1Ragged(x, y) else: raise ValueError(""" Invalid combination of x and y arguments to Canvas.line when axis=1. Received: x: {x} y: {y} See docstring for more information on valid usage""".format( x=repr(orig_x), y=repr(orig_y))) else: raise ValueError(""" The axis argument to Canvas.line must be 0 or 1 Received: {axis}""".format(axis=axis)) if (line_width > 0 and ((cudf and isinstance(source, cudf.DataFrame)) or (dask_cudf and isinstance(source, dask_cudf.DataFrame)))): warnings.warn( "Antialiased lines are not supported for CUDA-backed sources, " "so reverting to line_width=0") line_width = 0 glyph.set_line_width(line_width) if glyph.antialiased: # This is required to identify and report use of reductions that do # not yet support antialiasing. non_cat_agg = agg if isinstance(non_cat_agg, rd.by): non_cat_agg = non_cat_agg.reduction if not isinstance(non_cat_agg, ( rd.any, rd.count, rd.max, rd.min, rd.sum, rd.summary, rd._sum_zero, rd._first_or_last, rd.mean, rd.max_n, rd.min_n, rd._first_n_or_last_n, rd._max_or_min_row_index, rd._max_n_or_min_n_row_index, rd.where, )): raise NotImplementedError( f"{type(non_cat_agg)} reduction not implemented for antialiased lines") return bypixel(source, self, glyph, agg, antialias=glyph.antialiased) def area(self, source, x, y, agg=None, axis=0, y_stack=None): """Compute a reduction by pixel, mapping data to pixels as a filled area region Parameters ---------- source : pandas.DataFrame, dask.DataFrame, or xarray.DataArray/Dataset The input datasource. x, y : str or number or list or tuple or np.ndarray Specification of the x and y coordinates of each vertex of the line defining the starting edge of the area region. * str or number: Column labels in source * list or tuple: List or tuple of column labels in source * np.ndarray: When axis=1, a literal array of the coordinates to be used for every row agg : Reduction, optional Reduction to compute. Default is ``count()``. axis : 0 or 1, default 0 Axis in source to draw lines along * 0: Draw area regions using data from the specified columns across all rows in source * 1: Draw one area region per row in source using data from the specified columns y_stack: str or number or list or tuple or np.ndarray or None Specification of the y coordinates of each vertex of the line defining the ending edge of the area region, where the x coordinate is given by the x argument described above. If y_stack is None, then the area region is filled to the y=0 line If y_stack is not None, then the form of y_stack must match the form of y. Examples -------- Define a canvas and a pandas DataFrame with 6 rows >>> import pandas as pd # doctest: +SKIP ... import numpy as np ... import datashader as ds ... from datashader import Canvas ... import datashader.transfer_functions as tf ... cvs = Canvas() ... df = pd.DataFrame({ ... 'A1': [1, 1.5, 2, 2.5, 3, 4], ... 'A2': [1.6, 2.1, 2.9, 3.2, 4.2, 5], ... 'B1': [10, 12, 11, 14, 13, 15], ... 'B2': [11, 9, 10, 7, 8, 12], ... }, dtype='float64') Aggregate one area region across all rows, that starts with coordinates df.A1 by df.B1 and is filled to the y=0 line >>> agg = cvs.area(df, x='A1', y='B1', # doctest: +SKIP ... agg=ds.count(), axis=0) ... tf.shade(agg) Aggregate one area region across all rows, that starts with coordinates df.A1 by df.B1 and is filled to the line with coordinates df.A1 by df.B2 >>> agg = cvs.area(df, x='A1', y='B1', y_stack='B2', # doctest: +SKIP ... agg=ds.count(), axis=0) ... tf.shade(agg) Aggregate two area regions across all rows. The first starting with coordinates df.A1 by df.B1 and the second with coordinates df.A2 by df.B2. Both regions are filled to the y=0 line >>> agg = cvs.area(df, x=['A1', 'A2'], y=['B1', 'B2'], # doctest: +SKIP agg=ds.count(), axis=0) ... tf.shade(agg) Aggregate two area regions across all rows where the regions share the same x coordinates. The first region will start with coordinates df.A1 by df.B1 and the second will start with coordinates df.A1 by df.B2. Both regions are filled to the y=0 line >>> agg = cvs.area(df, x='A1', y=['B1', 'B2'], agg=ds.count(), axis=0) # doctest: +SKIP ... tf.shade(agg) Aggregate 6 length-2 area regions, one per row, where the ith region starts with coordinates [df.A1[i], df.A2[i]] by [df.B1[i], df.B2[i]] and is filled to the y=0 line >>> agg = cvs.area(df, x=['A1', 'A2'], y=['B1', 'B2'], # doctest: +SKIP agg=ds.count(), axis=1) ... tf.shade(agg) Aggregate 6 length-4 area regions, one per row, where the starting x coordinates of every region are [0, 1, 2, 3] and the starting y coordinates of the ith region are [df.A1[i], df.A2[i], df.B1[i], df.B2[i]]. All regions are filled to the y=0 line >>> agg = cvs.area(df, # doctest: +SKIP ... x=np.arange(4), ... y=['A1', 'A2', 'B1', 'B2'], ... agg=ds.count(), ... axis=1) ... tf.shade(agg) Aggregate RaggedArrays of variable length area regions, one per row. The starting coordinates of the ith region are df_ragged.A1 by df_ragged.B1 and the regions are filled to the y=0 line. (requires pandas >= 0.24.0) >>> df_ragged = pd.DataFrame({ # doctest: +SKIP ... 'A1': pd.array([ ... [1, 1.5], [2, 2.5, 3], [1.5, 2, 3, 4], [3.2, 4, 5]], ... dtype='Ragged[float32]'), ... 'B1': pd.array([ ... [10, 12], [11, 14, 13], [10, 7, 9, 10], [7, 8, 12]], ... dtype='Ragged[float32]'), ... 'B2': pd.array([ ... [6, 10], [9, 10, 18], [9, 5, 6, 8], [4, 5, 11]], ... dtype='Ragged[float32]'), ... 'group': pd.Categorical([0, 1, 2, 1]) ... }) ... ... agg = cvs.area(df_ragged, x='A1', y='B1', agg=ds.count(), axis=1) ... tf.shade(agg) Instead of filling regions to the y=0 line, fill to the line with coordinates df_ragged.A1 by df_ragged.B2 >>> agg = cvs.area(df_ragged, x='A1', y='B1', y_stack='B2', # doctest: +SKIP ... agg=ds.count(), axis=1) ... tf.shade(agg) (requires pandas >= 0.24.0) """ from .glyphs import ( AreaToZeroAxis0, AreaToLineAxis0, AreaToZeroAxis0Multi, AreaToLineAxis0Multi, AreaToZeroAxis1, AreaToLineAxis1, AreaToZeroAxis1XConstant, AreaToLineAxis1XConstant, AreaToZeroAxis1YConstant, AreaToLineAxis1YConstant, AreaToZeroAxis1Ragged, AreaToLineAxis1Ragged, ) from .reductions import any as any_rdn if agg is None: agg = any_rdn() # Broadcast column specifications to handle cases where # x is a list and y is a string or vice versa orig_x, orig_y, orig_y_stack = x, y, y_stack x, y, y_stack = _broadcast_column_specifications(x, y, y_stack) if axis == 0: if y_stack is None: if (isinstance(x, (Number, str)) and isinstance(y, (Number, str))): glyph = AreaToZeroAxis0(x, y) elif (isinstance(x, (list, tuple)) and isinstance(y, (list, tuple))): glyph = AreaToZeroAxis0Multi(tuple(x), tuple(y)) else: raise ValueError(""" Invalid combination of x and y arguments to Canvas.area when axis=0. Received: x: {x} y: {y} See docstring for more information on valid usage""".format( x=repr(x), y=repr(y))) else: # y_stack is not None if (isinstance(x, (Number, str)) and isinstance(y, (Number, str)) and isinstance(y_stack, (Number, str))): glyph = AreaToLineAxis0(x, y, y_stack) elif (isinstance(x, (list, tuple)) and isinstance(y, (list, tuple)) and isinstance(y_stack, (list, tuple))): glyph = AreaToLineAxis0Multi( tuple(x), tuple(y), tuple(y_stack)) else: raise ValueError(""" Invalid combination of x, y, and y_stack arguments to Canvas.area when axis=0. Received: x: {x} y: {y} y_stack: {y_stack} See docstring for more information on valid usage""".format( x=repr(orig_x), y=repr(orig_y), y_stack=repr(orig_y_stack))) elif axis == 1: if y_stack is None: if (isinstance(x, (list, tuple)) and isinstance(y, (list, tuple))): glyph = AreaToZeroAxis1(tuple(x), tuple(y)) elif (isinstance(x, np.ndarray) and isinstance(y, (list, tuple))): glyph = AreaToZeroAxis1XConstant(x, tuple(y)) elif (isinstance(x, (list, tuple)) and isinstance(y, np.ndarray)): glyph = AreaToZeroAxis1YConstant(tuple(x), y) elif (isinstance(x, (Number, str)) and isinstance(y, (Number, str))): glyph = AreaToZeroAxis1Ragged(x, y) else: raise ValueError(""" Invalid combination of x and y arguments to Canvas.area when axis=1. Received: x: {x} y: {y} See docstring for more information on valid usage""".format( x=repr(x), y=repr(y))) else: if (isinstance(x, (list, tuple)) and isinstance(y, (list, tuple)) and isinstance(y_stack, (list, tuple))): glyph = AreaToLineAxis1( tuple(x), tuple(y), tuple(y_stack)) elif (isinstance(x, np.ndarray) and isinstance(y, (list, tuple)) and isinstance(y_stack, (list, tuple))): glyph = AreaToLineAxis1XConstant( x, tuple(y), tuple(y_stack)) elif (isinstance(x, (list, tuple)) and isinstance(y, np.ndarray) and isinstance(y_stack, np.ndarray)): glyph = AreaToLineAxis1YConstant(tuple(x), y, y_stack) elif (isinstance(x, (Number, str)) and isinstance(y, (Number, str)) and isinstance(y_stack, (Number, str))): glyph = AreaToLineAxis1Ragged(x, y, y_stack) else: raise ValueError(""" Invalid combination of x, y, and y_stack arguments to Canvas.area when axis=1. Received: x: {x} y: {y} y_stack: {y_stack} See docstring for more information on valid usage""".format( x=repr(orig_x), y=repr(orig_y), y_stack=repr(orig_y_stack))) else: raise ValueError(""" The axis argument to Canvas.area must be 0 or 1 Received: {axis}""".format(axis=axis)) return bypixel(source, self, glyph, agg) def polygons(self, source, geometry, agg=None): """Compute a reduction by pixel, mapping data to pixels as one or more filled polygons. Parameters ---------- source : xarray.DataArray or Dataset The input datasource. geometry : str Column name of a PolygonsArray of the coordinates of each line. agg : Reduction, optional Reduction to compute. Default is ``any()``. Returns ------- data : xarray.DataArray Examples -------- >>> import datashader as ds # doctest: +SKIP ... import datashader.transfer_functions as tf ... from spatialpandas.geometry import PolygonArray ... from spatialpandas import GeoDataFrame ... import pandas as pd ... ... polygons = PolygonArray([ ... # First Element ... [[0, 0, 1, 0, 2, 2, -1, 4, 0, 0], # Filled quadrilateral (CCW order) ... [0.5, 1, 1, 2, 1.5, 1.5, 0.5, 1], # Triangular hole (CW order) ... [0, 2, 0, 2.5, 0.5, 2.5, 0.5, 2, 0, 2], # Rectangular hole (CW order) ... [2.5, 3, 3.5, 3, 3.5, 4, 2.5, 3], # Filled triangle ... ], ... ... # Second Element ... [[3, 0, 3, 2, 4, 2, 4, 0, 3, 0], # Filled rectangle (CCW order) ... # Rectangular hole (CW order) ... [3.25, 0.25, 3.75, 0.25, 3.75, 1.75, 3.25, 1.75, 3.25, 0.25], ... ] ... ]) ... ... df = GeoDataFrame({'polygons': polygons, 'v': range(len(polygons))}) ... ... cvs = ds.Canvas() ... agg = cvs.polygons(df, geometry='polygons', agg=ds.sum('v')) ... tf.shade(agg) """ from .glyphs import PolygonGeom from .reductions import any as any_rdn if spatialpandas and isinstance(source, spatialpandas.dask.DaskGeoDataFrame): # Downselect partitions to those that may contain polygons in viewport x_range = self.x_range if self.x_range is not None else (None, None) y_range = self.y_range if self.y_range is not None else (None, None) source = source.cx_partitions[slice(*x_range), slice(*y_range)] glyph = PolygonGeom(geometry) elif spatialpandas and isinstance(source, spatialpandas.GeoDataFrame): glyph = PolygonGeom(geometry) elif (geopandas_source := self._source_from_geopandas(source)) is not None: source = geopandas_source from .glyphs.polygon import GeopandasPolygonGeom glyph = GeopandasPolygonGeom(geometry) else: raise ValueError( "source must be an instance of spatialpandas.GeoDataFrame, " "spatialpandas.dask.DaskGeoDataFrame, geopandas.GeoDataFrame or " f"dask_geopandas.GeoDataFrame, not {type(source)}") if agg is None: agg = any_rdn() return bypixel(source, self, glyph, agg) def quadmesh(self, source, x=None, y=None, agg=None): """Samples a recti- or curvi-linear quadmesh by canvas size and bounds. Parameters ---------- source : xarray.DataArray or Dataset The input datasource. x, y : str Column names for the x and y coordinates of each point. agg : Reduction, optional Reduction to compute. Default is ``mean()``. Note that agg is ignored when upsampling. Returns ------- data : xarray.DataArray """ from .glyphs import QuadMeshRaster, QuadMeshRectilinear, QuadMeshCurvilinear # Determine reduction operation from .reductions import mean as mean_rnd if isinstance(source, Dataset): if agg is None or agg.column is None: name = list(source.data_vars)[0] else: name = agg.column # Keep as dataset so that source[agg.column] works source = source[[name]] elif isinstance(source, DataArray): # Make dataset so that source[agg.column] works name = source.name source = source.to_dataset() else: raise ValueError("Invalid input type") if agg is None: agg = mean_rnd(name) if x is None and y is None: y, x = source[name].dims elif not x or not y: raise ValueError("Either specify both x and y coordinates" "or allow them to be inferred.") yarr, xarr = source[y], source[x] if (yarr.ndim > 1 or xarr.ndim > 1) and xarr.dims != yarr.dims: raise ValueError("Ensure that x- and y-coordinate arrays " "share the same dimensions. x-coordinates " "are indexed by %s dims while " "y-coordinates are indexed by %s dims." % (xarr.dims, yarr.dims)) if (name is not None and agg.column is not None and agg.column != name): raise ValueError('DataArray name %r does not match ' 'supplied reduction %s.' % (source.name, agg)) if xarr.ndim == 1: xaxis_linear = self.x_axis is _axis_lookup["linear"] yaxis_linear = self.y_axis is _axis_lookup["linear"] even_yspacing = np.allclose( yarr, np.linspace(yarr[0], yarr[-1], len(yarr)) ) even_xspacing = np.allclose( xarr, np.linspace(xarr[0], xarr[-1], len(xarr)) ) if xaxis_linear and yaxis_linear and even_xspacing and even_yspacing: # Source is a raster, where all x and y coordinates are evenly spaced glyph = QuadMeshRaster(x, y, name) upsample_width, upsample_height = glyph.is_upsample( source, x, y, name, self.x_range, self.y_range, self.plot_width, self.plot_height ) if upsample_width and upsample_height: # Override aggregate with more efficient one for upsampling agg = rd._upsample(name) return bypixel(source, self, glyph, agg) elif not upsample_width and not upsample_height: # Downsample both width and height return bypixel(source, self, glyph, agg) else: # Mix of upsampling and downsampling # Use general rectilinear quadmesh implementation glyph = QuadMeshRectilinear(x, y, name) return bypixel(source, self, glyph, agg) else: # Source is a general rectilinear quadmesh glyph = QuadMeshRectilinear(x, y, name) return bypixel(source, self, glyph, agg) elif xarr.ndim == 2: glyph = QuadMeshCurvilinear(x, y, name) return bypixel(source, self, glyph, agg) else: raise ValueError("""\ x- and y-coordinate arrays must have 1 or 2 dimensions. Received arrays with dimensions: {dims}""".format( dims=list(xarr.dims))) # TODO re 'untested', below: Consider replacing with e.g. a 3x3 # array in the call to Canvas (plot_height=3,plot_width=3), then # show the output as a numpy array that has a compact # representation def trimesh(self, vertices, simplices, mesh=None, agg=None, interp=True, interpolate=None): """Compute a reduction by pixel, mapping data to pixels as a triangle. >>> import datashader as ds >>> verts = pd.DataFrame({'x': [0, 5, 10], ... 'y': [0, 10, 0], ... 'weight': [1, 5, 3]}, ... columns=['x', 'y', 'weight']) >>> tris = pd.DataFrame({'v0': [2], 'v1': [0], 'v2': [1]}, ... columns=['v0', 'v1', 'v2']) >>> cvs = ds.Canvas(x_range=(verts.x.min(), verts.x.max()), ... y_range=(verts.y.min(), verts.y.max())) >>> untested = cvs.trimesh(verts, tris) Parameters ---------- vertices : pandas.DataFrame, dask.DataFrame The input datasource for triangle vertex coordinates. These can be interpreted as the x/y coordinates of the vertices, with optional weights for value interpolation. Columns should be ordered corresponding to 'x', 'y', followed by zero or more (optional) columns containing vertex values. The rows need not be ordered. The column data types must be floating point or integer. simplices : pandas.DataFrame, dask.DataFrame The input datasource for triangle (simplex) definitions. These can be interpreted as rows of ``vertices``, aka positions in the ``vertices`` index. Columns should be ordered corresponding to 'vertex0', 'vertex1', and 'vertex2'. Order of the vertices can be clockwise or counter-clockwise; it does not matter as long as the data is consistent for all simplices in the dataframe. The rows need not be ordered. The data type for the first three columns in the dataframe must be integer. agg : Reduction, optional Reduction to compute. Default is ``mean()``. mesh : pandas.DataFrame, optional An ordered triangle mesh in tabular form, used for optimization purposes. This dataframe is expected to have come from ``datashader.utils.mesh()``. If this argument is not None, the first two arguments are ignored. interpolate : str, optional default=linear Method to use for interpolation between specified values. ``nearest`` means to use a single value for the whole triangle, and ``linear`` means to do bilinear interpolation of the pixels within each triangle (a weighted average of the vertex values). For backwards compatibility, also accepts ``interp=True`` for ``linear`` and ``interp=False`` for ``nearest``. """ from .glyphs import Triangles from .reductions import mean as mean_rdn from .utils import mesh as create_mesh source = mesh # 'interp' argument is deprecated as of datashader=0.6.4 if interpolate is not None: if interpolate == 'linear': interp = True elif interpolate == 'nearest': interp = False else: raise ValueError('Invalid interpolate method: options include {}'.format( ['linear','nearest'])) # Validation is done inside the [pd]d_mesh utility functions if source is None: source = create_mesh(vertices, simplices) verts_have_weights = len(vertices.columns) > 2 if verts_have_weights: weight_col = vertices.columns[2] else: weight_col = simplices.columns[3] if agg is None: agg = mean_rdn(weight_col) elif agg.column is None: agg.column = weight_col cols = source.columns x, y, weights = cols[0], cols[1], cols[2:] return bypixel(source, self, Triangles(x, y, weights, weight_type=verts_have_weights, interp=interp), agg) def raster(self, source, layer=None, upsample_method='linear', # Deprecated as of datashader=0.6.4 downsample_method=rd.mean(), # Deprecated as of datashader=0.6.4 nan_value=None, agg=None, interpolate=None, chunksize=None, max_mem=None): """Sample a raster dataset by canvas size and bounds. Handles 2D or 3D xarray DataArrays, assuming that the last two array dimensions are the y- and x-axis that are to be resampled. If a 3D array is supplied a layer may be specified to resample to select the layer along the first dimension to resample. Missing values (those having the value indicated by the "nodata" attribute of the raster) are replaced with `NaN` if floats, and 0 if int. Also supports resampling out-of-core DataArrays backed by dask Arrays. By default it will try to maintain the same chunksize in the output array but a custom chunksize may be provided. If there are memory constraints they may be defined using the max_mem parameter, which determines how large the chunks in memory may be. Parameters ---------- source : xarray.DataArray or xr.Dataset 2D or 3D labelled array (if Dataset, the agg reduction must define the data variable). layer : float For a 3D array, value along the z dimension : optional default=None ds_method : str (optional) Grid cell aggregation method for a possible downsampling. us_method : str (optional) Grid cell interpolation method for a possible upsampling. nan_value : int or float, optional Optional nan_value which will be masked out when applying the resampling. agg : Reduction, optional default=mean() Resampling mode when downsampling raster. The supported options include: first, last, mean, mode, var, std, min, The agg can be specified as either a string name or as a reduction function, but note that the function object will be used only to extract the agg type (mean, max, etc.) and the optional column name; the hardcoded raster code supports only a fixed set of reductions and ignores the actual code of the provided agg. interpolate : str, optional default=linear Resampling mode when upsampling raster. options include: nearest, linear. chunksize : tuple(int, int) (optional) Size of the output chunks. By default this the chunk size is inherited from the *src* array. max_mem : int (optional) The maximum number of bytes that should be loaded into memory during the regridding operation. Returns ------- data : xarray.Dataset """ # For backwards compatibility if agg is None: agg=downsample_method if interpolate is None: interpolate=upsample_method upsample_methods = ['nearest','linear'] downsample_methods = {'first':'first', rd.first:'first', 'last':'last', rd.last:'last', 'mode':'mode', rd.mode:'mode', 'mean':'mean', rd.mean:'mean', 'var':'var', rd.var:'var', 'std':'std', rd.std:'std', 'min':'min', rd.min:'min', 'max':'max', rd.max:'max'} if interpolate not in upsample_methods: raise ValueError('Invalid interpolate method: options include {}'.format( upsample_methods)) if not isinstance(source, (DataArray, Dataset)): raise ValueError('Expected xarray DataArray or Dataset as ' 'the data source, found %s.' % type(source).__name__) column = None if isinstance(agg, rd.Reduction): agg, column = type(agg), agg.column if (isinstance(source, DataArray) and column is not None and source.name != column): agg_repr = '%s(%r)' % (agg.__name__, column) raise ValueError('DataArray name %r does not match ' 'supplied reduction %s.' % (source.name, agg_repr)) if isinstance(source, Dataset): data_vars = list(source.data_vars) if column is None: raise ValueError('When supplying a Dataset the agg reduction ' 'must specify the variable to aggregate. ' 'Available data_vars include: %r.' % data_vars) elif column not in source.data_vars: raise KeyError('Supplied reduction column %r not found ' 'in Dataset, expected one of the following ' 'data variables: %r.' % (column, data_vars)) source = source[column] if agg not in downsample_methods.keys(): raise ValueError('Invalid aggregation method: options include {}'.format( list(downsample_methods.keys()))) ds_method = downsample_methods[agg] if source.ndim not in [2, 3]: raise ValueError('Raster aggregation expects a 2D or 3D ' 'DataArray, found %s dimensions' % source.ndim) res = calc_res(source) ydim, xdim = source.dims[-2:] xvals, yvals = source[xdim].values, source[ydim].values left, bottom, right, top = calc_bbox(xvals, yvals, res) if layer is not None: source=source.sel(**{source.dims[0]: layer}) array = orient_array(source, res) if nan_value is not None: mask = array==nan_value array = np.ma.masked_array(array, mask=mask, fill_value=nan_value) fill_value = nan_value elif np.issubdtype(source.dtype, np.integer): fill_value = 0 else: fill_value = np.nan if self.x_range is None: self.x_range = (left,right) if self.y_range is None: self.y_range = (bottom,top) # window coordinates xmin = max(self.x_range[0], left) ymin = max(self.y_range[0], bottom) xmax = min(self.x_range[1], right) ymax = min(self.y_range[1], top) width_ratio = min((xmax - xmin) / (self.x_range[1] - self.x_range[0]), 1) height_ratio = min((ymax - ymin) / (self.y_range[1] - self.y_range[0]), 1) if np.isclose(width_ratio, 0) or np.isclose(height_ratio, 0): raise ValueError('Canvas x_range or y_range values do not match closely enough ' 'with the data source to be able to accurately rasterize. ' 'Please provide ranges that are more accurate.') w = max(int(round(self.plot_width * width_ratio)), 1) h = max(int(round(self.plot_height * height_ratio)), 1) cmin, cmax = get_indices(xmin, xmax, xvals, res[0]) rmin, rmax = get_indices(ymin, ymax, yvals, res[1]) kwargs = dict(w=w, h=h, ds_method=ds_method, us_method=interpolate, fill_value=fill_value) if array.ndim == 2: source_window = array[rmin:rmax+1, cmin:cmax+1] if ds_method in ['var', 'std']: source_window = source_window.astype('f') if isinstance(source_window, da.Array): data = resample_2d_distributed( source_window, chunksize=chunksize, max_mem=max_mem, **kwargs) else: data = resample_2d(source_window, **kwargs) layers = 1 else: source_window = array[:, rmin:rmax+1, cmin:cmax+1] if ds_method in ['var', 'std']: source_window = source_window.astype('f') arrays = [] for arr in source_window: if isinstance(arr, da.Array): arr = resample_2d_distributed( arr, chunksize=chunksize, max_mem=max_mem, **kwargs) else: arr = resample_2d(arr, **kwargs) arrays.append(arr) data = np.dstack(arrays) layers = len(arrays) if w != self.plot_width or h != self.plot_height: num_height = self.plot_height - h num_width = self.plot_width - w lpad = xmin - self.x_range[0] rpad = self.x_range[1] - xmax lpct = lpad / (lpad + rpad) if lpad + rpad > 0 else 0 left = max(int(np.ceil(num_width * lpct)), 0) right = max(num_width - left, 0) lshape, rshape = (self.plot_height, left), (self.plot_height, right) if layers > 1: lshape, rshape = lshape + (layers,), rshape + (layers,) left_pad = np.full(lshape, fill_value, source_window.dtype) right_pad = np.full(rshape, fill_value, source_window.dtype) tpad = ymin - self.y_range[0] bpad = self.y_range[1] - ymax tpct = tpad / (tpad + bpad) if tpad + bpad > 0 else 0 top = max(int(np.ceil(num_height * tpct)), 0) bottom = max(num_height - top, 0) tshape, bshape = (top, w), (bottom, w) if layers > 1: tshape, bshape = tshape + (layers,), bshape + (layers,) top_pad = np.full(tshape, fill_value, source_window.dtype) bottom_pad = np.full(bshape, fill_value, source_window.dtype) concat = da.concatenate if isinstance(data, da.Array) else np.concatenate arrays = (top_pad, data) if top_pad.shape[0] > 0 else (data,) if bottom_pad.shape[0] > 0: arrays += (bottom_pad,) data = concat(arrays, axis=0) if len(arrays) > 1 else arrays[0] arrays = (left_pad, data) if left_pad.shape[1] > 0 else (data,) if right_pad.shape[1] > 0: arrays += (right_pad,) data = concat(arrays, axis=1) if len(arrays) > 1 else arrays[0] # Reorient array to original orientation if res[1] > 0: data = data[::-1] if res[0] < 0: data = data[:, ::-1] # Compute DataArray metadata # To avoid floating point representation error, # do not recompute x coords if same x_range and same plot_width, # do not recompute y coords if same y_range and same plot_height close_x = np.allclose([left, right], self.x_range) and np.size(xvals) == self.plot_width close_y = np.allclose([bottom, top], self.y_range) and np.size(yvals) == self.plot_height if close_x: xs = xvals else: x_st = self.x_axis.compute_scale_and_translate(self.x_range, self.plot_width) xs = self.x_axis.compute_index(x_st, self.plot_width) if res[0] < 0: xs = xs[::-1] if close_y: ys = yvals else: y_st = self.y_axis.compute_scale_and_translate(self.y_range, self.plot_height) ys = self.y_axis.compute_index(y_st, self.plot_height) if res[1] > 0: ys = ys[::-1] coords = {xdim: xs, ydim: ys} dims = [ydim, xdim] attrs = dict(res=res[0], x_range=self.x_range, y_range=self.y_range) # Find nodata value if available in any of the common conventional locations # See https://corteva.github.io/rioxarray/stable/getting_started/nodata_management.html # and https://github.com/holoviz/datashader/issues/990 for a in ['_FillValue', 'missing_value', 'fill_value', 'nodata', 'NODATA']: if a in source.attrs: attrs['nodata'] = source.attrs[a] break if 'nodata' not in attrs: try: attrs['nodata'] = source.attrs['nodatavals'][0] except Exception: pass # Handle DataArray with layers if data.ndim == 3: data = data.transpose([2, 0, 1]) layer_dim = source.dims[0] coords[layer_dim] = source.coords[layer_dim] dims = [layer_dim]+dims return DataArray(data, coords=coords, dims=dims, attrs=attrs) def validate_ranges(self, x_range, y_range): self.x_axis.validate(x_range) self.y_axis.validate(y_range) def validate_size(self, width, height): if width <= 0 or height <= 0: raise ValueError("Invalid size: plot_width and plot_height must be bigger than 0") def validate(self): """Check that parameter settings are valid for this object""" self.validate_ranges(self.x_range, self.y_range) self.validate_size(self.plot_width, self.plot_height) def _source_from_geopandas(self, source): """ Check if the specified source is a geopandas or dask-geopandas GeoDataFrame. If so, spatially filter the source and return it. If not, return None. """ try: import geopandas except ImportError: geopandas = None try: import dask_geopandas except ImportError: dask_geopandas = None if ((geopandas and isinstance(source, geopandas.GeoDataFrame)) or (dask_geopandas and isinstance(source, dask_geopandas.GeoDataFrame))): # Explicit shapely version check as cannot continue unless shapely >= 2 from packaging.version import Version from shapely import __version__ as shapely_version if Version(shapely_version) < Version('2.0.0'): raise ImportError("Use of GeoPandas in Datashader requires Shapely >= 2.0.0") if isinstance(source, geopandas.GeoDataFrame): x_range = self.x_range if self.x_range is not None else (-np.inf, np.inf) y_range = self.y_range if self.y_range is not None else (-np.inf, np.inf) from shapely import box query = source.sindex.query(box(x_range[0], y_range[0], x_range[1], y_range[1])) source = source.iloc[query] else: x_range = self.x_range if self.x_range is not None else (None, None) y_range = self.y_range if self.y_range is not None else (None, None) source = source.cx[slice(*x_range), slice(*y_range)] return source else: return None
def bypixel(source, canvas, glyph, agg, *, antialias=False): """Compute an aggregate grouped by pixel sized bins. Aggregate input data ``source`` into a grid with shape and axis matching ``canvas``, mapping data to bins by ``glyph``, and aggregating by reduction ``agg``. Parameters ---------- source : pandas.DataFrame, dask.DataFrame Input datasource canvas : Canvas glyph : Glyph agg : Reduction """ source, dshape = _bypixel_sanitise(source, glyph, agg) schema = dshape.measure glyph.validate(schema) agg.validate(schema) canvas.validate() # All-NaN objects (e.g. chunks of arrays with no data) are valid in Datashader with warnings.catch_warnings(): warnings.filterwarnings('ignore', r'All-NaN (slice|axis) encountered') return bypixel.pipeline(source, schema, canvas, glyph, agg, antialias=antialias) def _bypixel_sanitise(source, glyph, agg): # Convert 1D xarray DataArrays and DataSets into Dask DataFrames if isinstance(source, DataArray) and source.ndim == 1: if not source.name: source.name = 'value' source = source.reset_coords() if isinstance(source, Dataset) and len(source.dims) == 1: columns = list(source.coords.keys()) + list(source.data_vars.keys()) cols_to_keep = _cols_to_keep(columns, glyph, agg) source = source.drop_vars([col for col in columns if col not in cols_to_keep]) source = source.to_dask_dataframe() if (isinstance(source, pd.DataFrame) or (cudf and isinstance(source, cudf.DataFrame))): # Avoid datashape.Categorical instantiation bottleneck # by only retaining the necessary columns: # https://github.com/bokeh/datashader/issues/396 # Preserve column ordering without duplicates cols_to_keep = _cols_to_keep(source.columns, glyph, agg) if len(cols_to_keep) < len(source.columns): # If _sindex is set, ensure it is not dropped # https://github.com/holoviz/datashader/issues/1121 sindex = None from .glyphs.polygon import PolygonGeom if isinstance(glyph, PolygonGeom): sindex = getattr(source[glyph.geometry].array, "_sindex", None) source = source[cols_to_keep] if (sindex is not None and getattr(source[glyph.geometry].array, "_sindex", None) is None): source[glyph.geometry].array._sindex = sindex dshape = dshape_from_pandas(source) elif isinstance(source, dd.DataFrame): dshape, source = dshape_from_dask(source) elif isinstance(source, Dataset): # Multi-dimensional Dataset dshape = dshape_from_xarray_dataset(source) else: raise ValueError("source must be a pandas or dask DataFrame") return source, dshape def _cols_to_keep(columns, glyph, agg): """ Return which columns from the supplied data source are kept as they are needed by the specified agg. Excludes any SpecialColumn. """ cols_to_keep = dict({col: False for col in columns}) for col in glyph.required_columns(): cols_to_keep[col] = True def recurse(cols_to_keep, agg): if hasattr(agg, 'values'): for subagg in agg.values: recurse(cols_to_keep, subagg) elif hasattr(agg, 'columns'): for column in agg.columns: if column not in (None, rd.SpecialColumn.RowIndex): cols_to_keep[column] = True elif agg.column not in (None, rd.SpecialColumn.RowIndex): cols_to_keep[agg.column] = True recurse(cols_to_keep, agg) return [col for col, keepit in cols_to_keep.items() if keepit] def _broadcast_column_specifications(*args): lengths = {len(a) for a in args if isinstance(a, (list, tuple))} if len(lengths) != 1: # None of the inputs are lists/tuples, return them as is return args else: n = lengths.pop() return tuple( (arg,) * n if isinstance(arg, (Number, str)) else arg for arg in args ) bypixel.pipeline = Dispatcher()