Deduplicate shared logic between _render_shapes and _render_points (#551)

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: timtreis

src/spatialdata_plot/pl/_datashader.py

@@ -0,0 +1,342 @@
+"""Datashader aggregation, shading, and rendering helpers.
+
+Shared by ``_render_shapes`` and ``_render_points`` in ``render.py``.
+"""
+
+from __future__ import annotations
+
+from typing import Any, Literal
+
+import dask.dataframe as dd
+import datashader as ds
+import matplotlib
+import matplotlib.colors
+import numpy as np
+import pandas as pd
+from matplotlib.cm import ScalarMappable
+from matplotlib.colors import Normalize
+
+from spatialdata_plot._logging import logger
+from spatialdata_plot.pl.render_params import Color, FigParams, ShapesRenderParams
+from spatialdata_plot.pl.utils import (
+    _ax_show_and_transform,
+    _convert_alpha_to_datashader_range,
+    _create_image_from_datashader_result,
+    _datashader_aggregate_with_function,
+    _datashader_map_aggregate_to_color,
+    _datshader_get_how_kw_for_spread,
+    _hex_no_alpha,
+)
+
+# ---------------------------------------------------------------------------
+# Type aliases and constants
+# ---------------------------------------------------------------------------
+
+_DsReduction = Literal["sum", "mean", "any", "count", "std", "var", "max", "min"]
+
+# Sentinel category name used in datashader categorical paths to represent
+# missing (NaN) values.  Must not collide with realistic user category names.
+_DS_NAN_CATEGORY = "ds_nan"
+
+# ---------------------------------------------------------------------------
+# Low-level helpers
+# ---------------------------------------------------------------------------
+
+
+def _coerce_categorical_source(series: pd.Series | dd.Series) -> pd.Categorical:
+    """Return a ``pd.Categorical`` from a pandas or dask Series."""
+    if isinstance(series, dd.Series):
+        if isinstance(series.dtype, pd.CategoricalDtype) and getattr(series.cat, "known", True) is False:
+            series = series.cat.as_known()
+        series = series.compute()
+    if isinstance(series.dtype, pd.CategoricalDtype):
+        return series.array
+    return pd.Categorical(series)
+
+
+def _build_datashader_color_key(
+    cat_series: pd.Categorical,
+    color_vector: Any,
+    na_color_hex: str,
+) -> dict[str, str]:
+    """Build a datashader ``color_key`` dict from a categorical series and its color vector."""
+    na_hex = _hex_no_alpha(na_color_hex) if na_color_hex.startswith("#") else na_color_hex
+    colors_arr = np.asarray(color_vector, dtype=object)
+    first_color: dict[str, str] = {}
+    for code, color in zip(cat_series.codes, colors_arr, strict=False):
+        if code < 0:
+            continue
+        cat_name = str(cat_series.categories[code])
+        if cat_name not in first_color:
+            first_color[cat_name] = _hex_no_alpha(color) if isinstance(color, str) and color.startswith("#") else color
+    return {str(c): first_color.get(str(c), na_hex) for c in cat_series.categories}
+
+
+def _inject_ds_nan_sentinel(series: pd.Series, sentinel: str = _DS_NAN_CATEGORY) -> pd.Series:
+    """Add a sentinel category for NaN values in a categorical series.
+
+    Safely handles series that are not yet categorical, dask-backed
+    categoricals that need ``as_known()``, and series that already
+    contain the sentinel.
+    """
+    if not isinstance(series.dtype, pd.CategoricalDtype):
+        series = series.astype("category")
+    if hasattr(series.cat, "as_known"):
+        series = series.cat.as_known()
+    if sentinel not in series.cat.categories:
+        series = series.cat.add_categories(sentinel)
+    return series.fillna(sentinel)
+
+
+# ---------------------------------------------------------------------------
+# Pipeline helpers (aggregate -> norm -> shade -> render)
+# ---------------------------------------------------------------------------
+
+
+def _ds_aggregate(
+    cvs: Any,
+    transformed_element: Any,
+    col_for_color: str | None,
+    color_by_categorical: bool,
+    ds_reduction: _DsReduction | None,
+    default_reduction: _DsReduction,
+    geom_type: Literal["points", "shapes"],
+) -> tuple[Any, tuple[Any, Any] | None, Any | None]:
+    """Aggregate spatial elements with datashader.
+
+    Dispatches between categorical (ds.by), continuous (reduction function),
+    and no-color (ds.count) aggregation modes.
+
+    Returns (agg, reduction_bounds, nan_agg).
+    """
+    reduction_bounds = None
+    nan_agg = None
+
+    def _agg_call(element: Any, agg_func: Any) -> Any:
+        if geom_type == "shapes":
+            return cvs.polygons(element, geometry="geometry", agg=agg_func)
+        return cvs.points(element, "x", "y", agg=agg_func)
+
+    if col_for_color is not None:
+        if color_by_categorical:
+            transformed_element[col_for_color] = _inject_ds_nan_sentinel(transformed_element[col_for_color])
+            agg = _agg_call(transformed_element, ds.by(col_for_color, ds.count()))
+        else:
+            reduction_name = ds_reduction if ds_reduction is not None else default_reduction
+            logger.info(
+                f'Using the datashader reduction "{reduction_name}". "max" will give an output '
+                "very close to the matplotlib result."
+            )
+            agg = _datashader_aggregate_with_function(ds_reduction, cvs, transformed_element, col_for_color, geom_type)
+            reduction_bounds = (agg.min(), agg.max())
+
+            nan_elements = transformed_element[transformed_element[col_for_color].isnull()]
+            if len(nan_elements) > 0:
+                nan_agg = _datashader_aggregate_with_function("any", cvs, nan_elements, None, geom_type)
+    else:
+        agg = _agg_call(transformed_element, ds.count())
+
+    return agg, reduction_bounds, nan_agg
+
+
+def _apply_ds_norm(
+    agg: Any,
+    norm: Normalize,
+) -> tuple[Any, list[float] | None]:
+    """Apply norm vmin/vmax to a datashader aggregate.
+
+    When vmin == vmax, maps the value to 0.5 using an artificial [0, 1] span.
+    Returns (agg, color_span) where color_span is None if no norm was set.
+    """
+    if norm.vmin is None and norm.vmax is None:
+        return agg, None
+    norm.vmin = np.min(agg) if norm.vmin is None else norm.vmin
+    norm.vmax = np.max(agg) if norm.vmax is None else norm.vmax
+    color_span: list[float] = [norm.vmin, norm.vmax]
+    if norm.vmin == norm.vmax:
+        color_span = [0, 1]
+        if norm.clip:
+            agg = (agg - agg) + 0.5
+        else:
+            agg = agg.where((agg >= norm.vmin) | (np.isnan(agg)), other=-1)
+            agg = agg.where((agg <= norm.vmin) | (np.isnan(agg)), other=2)
+            agg = agg.where((agg != norm.vmin) | (np.isnan(agg)), other=0.5)
+    return agg, color_span
+
+
+def _build_color_key(
+    transformed_element: Any,
+    col_for_color: str | None,
+    color_by_categorical: bool,
+    color_vector: Any,
+    na_color_hex: str,
+) -> dict[str, str] | None:
+    """Build a datashader color key mapping categories to hex colors.
+
+    Returns None when not coloring by a categorical column.
+    """
+    if not color_by_categorical or col_for_color is None:
+        return None
+    cat_series = _coerce_categorical_source(transformed_element[col_for_color])
+    return _build_datashader_color_key(cat_series, color_vector, na_color_hex)
+
+
+def _ds_shade_continuous(
+    agg: Any,
+    color_span: list[float] | None,
+    norm: Normalize,
+    cmap: Any,
+    alpha: float,
+    reduction_bounds: tuple[Any, Any] | None,
+    nan_agg: Any | None,
+    na_color_hex: str,
+    spread_px: int | None = None,
+    ds_reduction: _DsReduction | None = None,
+) -> tuple[Any, Any | None, tuple[Any, Any] | None]:
+    """Shade a continuous datashader aggregate, optionally applying spread and NaN coloring.
+
+    Returns (shaded, nan_shaded, reduction_bounds).
+    """
+    if spread_px is not None:
+        spread_how = _datshader_get_how_kw_for_spread(ds_reduction)
+        agg = ds.tf.spread(agg, px=spread_px, how=spread_how)
+        reduction_bounds = (agg.min(), agg.max())
+
+    ds_cmap = cmap
+    if (
+        reduction_bounds is not None
+        and reduction_bounds[0] == reduction_bounds[1]
+        and (color_span is None or color_span != [0, 1])
+    ):
+        ds_cmap = matplotlib.colors.to_hex(cmap(0.0), keep_alpha=False)
+        reduction_bounds = (
+            reduction_bounds[0],
+            reduction_bounds[0] + 1,
+        )
+
+    shaded = _datashader_map_aggregate_to_color(
+        agg,
+        cmap=ds_cmap,
+        min_alpha=_convert_alpha_to_datashader_range(alpha),
+        span=color_span,
+        clip=norm.clip,
+    )
+
+    nan_shaded = None
+    if nan_agg is not None:
+        shade_kwargs: dict[str, Any] = {"cmap": na_color_hex, "how": "linear"}
+        if spread_px is not None:
+            nan_agg = ds.tf.spread(nan_agg, px=spread_px, how="max")
+        else:
+            # only shapes (no spread) pass min_alpha for NaN shading
+            shade_kwargs["min_alpha"] = _convert_alpha_to_datashader_range(alpha)
+        nan_shaded = ds.tf.shade(nan_agg, **shade_kwargs)
+
+    return shaded, nan_shaded, reduction_bounds
+
+
+def _ds_shade_categorical(
+    agg: Any,
+    color_key: dict[str, str] | None,
+    color_vector: Any,
+    alpha: float,
+    spread_px: int | None = None,
+) -> Any:
+    """Shade a categorical or no-color datashader aggregate."""
+    ds_cmap = None
+    if color_vector is not None:
+        ds_cmap = color_vector[0]
+        if isinstance(ds_cmap, str) and ds_cmap[0] == "#":
+            ds_cmap = _hex_no_alpha(ds_cmap)
+
+    agg_to_shade = ds.tf.spread(agg, px=spread_px) if spread_px is not None else agg
+    return _datashader_map_aggregate_to_color(
+        agg_to_shade,
+        cmap=ds_cmap,
+        color_key=color_key,
+        min_alpha=_convert_alpha_to_datashader_range(alpha),
+    )
+
+
+# ---------------------------------------------------------------------------
+# Image rendering
+# ---------------------------------------------------------------------------
+
+
+def _render_ds_image(
+    ax: matplotlib.axes.SubplotBase,
+    shaded: Any,
+    factor: float,
+    zorder: int,
+    alpha: float,
+    extent: list[float] | None,
+    nan_result: Any | None = None,
+) -> Any:
+    """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay."""
+    if nan_result is not None:
+        rgba_nan, trans_nan = _create_image_from_datashader_result(nan_result, factor, ax)
+        _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, alpha=alpha, extent=extent)
+    rgba_image, trans_data = _create_image_from_datashader_result(shaded, factor, ax)
+    return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, alpha=alpha, extent=extent)
+
+
+def _render_ds_outlines(
+    cvs: Any,
+    transformed_element: Any,
+    render_params: ShapesRenderParams,
+    fig_params: FigParams,
+    ax: matplotlib.axes.SubplotBase,
+    factor: float,
+    extent: list[float],
+) -> None:
+    """Aggregate, shade, and render shape outlines (outer and inner) with datashader."""
+    ds_lw_factor = fig_params.fig.dpi / 72
+    assert len(render_params.outline_alpha) == 2  # noqa: S101
+
+    for idx, (outline_color_obj, linewidth) in enumerate(
+        [
+            (render_params.outline_params.outer_outline_color, render_params.outline_params.outer_outline_linewidth),
+            (render_params.outline_params.inner_outline_color, render_params.outline_params.inner_outline_linewidth),
+        ]
+    ):
+        alpha = render_params.outline_alpha[idx]
+        if alpha <= 0:
+            continue
+        agg_outline = cvs.line(
+            transformed_element,
+            geometry="geometry",
+            line_width=linewidth * ds_lw_factor,
+        )
+        if isinstance(outline_color_obj, Color):
+            shaded = ds.tf.shade(
+                agg_outline,
+                cmap=outline_color_obj.get_hex(),
+                min_alpha=_convert_alpha_to_datashader_range(alpha),
+                how="linear",
+            )
+            rgba, trans = _create_image_from_datashader_result(shaded, factor, ax)
+            _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, alpha=alpha, extent=extent)
+
+
+def _build_ds_colorbar(
+    reduction_bounds: tuple[Any, Any] | None,
+    norm: Normalize,
+    cmap: Any,
+) -> ScalarMappable | None:
+    """Create a ScalarMappable for the colorbar from datashader reduction bounds.
+
+    Returns None if there is no continuous reduction.
+    """
+    if reduction_bounds is None:
+        return None
+    vmin = reduction_bounds[0].values if norm.vmin is None else norm.vmin
+    vmax = reduction_bounds[1].values if norm.vmax is None else norm.vmax
+    if (norm.vmin is not None or norm.vmax is not None) and norm.vmin == norm.vmax:
+        assert norm.vmin is not None
+        assert norm.vmax is not None
+        vmin = norm.vmin - 0.5
+        vmax = norm.vmin + 0.5
+    return ScalarMappable(
+        norm=matplotlib.colors.Normalize(vmin=vmin, vmax=vmax),
+        cmap=cmap,
+    )