Fix datashader fill_alpha applied twice

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

src/spatialdata_plot/pl/_datashader.py

@@ -268,16 +268,20 @@ def _render_ds_image(
  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."""
+ """Render a shaded datashader image onto matplotlib axes, with optional NaN overlay.
+
+ Alpha is NOT passed to ``ax.imshow`` because it is already encoded in
+ the RGBA channels produced by ``ds.tf.shade(min_alpha=...)``. Passing
+ it again would apply transparency twice (see #367).
+ """
  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)
+ _ax_show_and_transform(rgba_nan, trans_nan, ax, zorder=zorder, 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)
+ return _ax_show_and_transform(rgba_image, trans_data, ax, zorder=zorder, extent=extent)
 
 
 def _render_ds_outlines(
@@ -315,7 +319,7 @@ def _render_ds_outlines(
  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)
+ _ax_show_and_transform(rgba, trans, ax, zorder=render_params.zorder, extent=extent)
 
 
 def _build_ds_colorbar(

src/spatialdata_plot/pl/render.py

@@ -486,7 +486,6 @@ def _render_shapes(
  shaded,
  factor,
  render_params.zorder,
- render_params.fill_alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )
@@ -886,7 +885,6 @@ def _render_points(
  shaded,
  factor,
  render_params.zorder,
- render_params.alpha,
  x_ext + y_ext,
  nan_result=nan_shaded,
  )

tests/pl/test_render_points.py

@@ -701,3 +701,22 @@ def test_datashader_points_visible_with_nonuniform_scale(sdata_blobs: SpatialDat
  """
  _set_transformations(sdata_blobs["blobs_points"], {"global": Scale([1, 5], axes=("x", "y"))})
  sdata_blobs.pl.render_points("blobs_points", method="datashader", color="black").pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader alpha must not be applied twice (once in shade, once in imshow).
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_points(method="datashader", alpha=0.5, color="red").pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)

tests/pl/test_render_shapes.py

@@ -1093,3 +1093,28 @@ def test_datashader_outline_width_uses_points_units(sdata_blobs: SpatialData):
  sdata_blobs.pl.render_shapes(
  element="blobs_polygons", method="datashader", outline_alpha=1.0, outline_width=(8.0, 3.0)
  ).pl.show()
+
+
+def test_datashader_alpha_not_applied_twice(sdata_blobs: SpatialData):
+ """Datashader fill_alpha and outline_alpha must not be applied twice.
+
+ Regression test for https://github.com/scverse/spatialdata-plot/issues/367.
+ Before the fix, alpha was passed both to ds.tf.shade(min_alpha=...) and to
+ ax.imshow(alpha=...), resulting in effective transparency of alpha**2.
+ """
+ fig, ax = plt.subplots()
+ sdata_blobs.pl.render_shapes(
+ method="datashader",
+ fill_alpha=0.5,
+ color="red",
+ outline_alpha=0.5,
+ outline_color="blue",
+ ).pl.show(ax=ax)
+
+ axes_images = [c for c in ax.get_children() if isinstance(c, matplotlib.image.AxesImage)]
+ for img in axes_images:
+ assert img.get_alpha() is None, (
+ f"Datashader AxesImage has alpha={img.get_alpha()}, which would be applied "
+ "on top of the alpha already in the RGBA channels — causing double transparency."
+ )
+ plt.close(fig)