Merge pull request #192 from scverse/bugfix/issue191-cannot-stack-multiple-render-commands-of-the-same-kind

Allow for stacking of render commands

Author: Sonja-Stockhaus

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning][].
 -   Multiscale image handling: user can specify a scale, else the best scale is selected automatically given the figure size and dpi (#164)
 -   Large images are automatically rasterized to speed up performance (#164)
 -   Added better error message for mismatch in cs and ax number (#185)
+-   Can now stack render commands (#190, #192)
 
 ### Fixed
 

src/spatialdata_plot/pl/basic.py

@@ -567,7 +567,7 @@ def show(
         ]
 
         # prepare rendering params
-        render_cmds = OrderedDict()
+        render_cmds = []
         for cmd, params in plotting_tree.items():
             # strip prefix from cmd and verify it's valid
             cmd = "_".join(cmd.split("_")[1:])
@@ -577,9 +577,9 @@ def show(
 
             if "render" in cmd:
                 # verify that rendering commands have been called before
-                render_cmds[cmd] = params
+                render_cmds.append((cmd, params))
 
-        if len(render_cmds.keys()) == 0:
+        if len(render_cmds) == 0:
             raise TypeError("Please specify what to plot using the 'render_*' functions before calling 'imshow()'.")
 
         if title is not None:
@@ -609,7 +609,7 @@ def show(
         # Check if user specified only certain elements to be plotted
         cs_contents = _get_cs_contents(sdata)
         elements_to_be_rendered = []
-        for cmd, params in render_cmds.items():
+        for cmd, params in render_cmds:
             if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]:  # noqa: SIM114
                 if params.elements is not None:
                     elements_to_be_rendered += (
@@ -632,13 +632,14 @@ def show(
                     )
 
         # filter out cs without relevant elements
+        cmds = [cmd for cmd, _ in render_cmds]
         coordinate_systems = _get_valid_cs(
             sdata=sdata,
             coordinate_systems=coordinate_systems,
-            render_images="render_images" in render_cmds,
-            render_labels="render_labels" in render_cmds,
-            render_points="render_points" in render_cmds,
-            render_shapes="render_shapes" in render_cmds,
+            render_images="render_images" in cmds,
+            render_labels="render_labels" in cmds,
+            render_points="render_points" in cmds,
+            render_shapes="render_shapes" in cmds,
             elements=elements_to_be_rendered,
         )
 
@@ -689,7 +690,7 @@ def show(
             wants_shapes = False
             wanted_elements = []
 
-            for cmd, params in render_cmds.items():
+            for cmd, params in render_cmds:
                 if cmd == "render_images" and has_images:
                     wants_images = True
                     wanted_images = params.elements if params.elements is not None else list(sdata.images.keys())

src/spatialdata_plot/pl/render.py

@@ -406,10 +406,13 @@ def _render_images(
             else:
                 cmap = _get_linear_colormap([render_params.palette], "k")[0]
 
+            # Overwrite alpha in cmap: https://stackoverflow.com/a/10127675
+            cmap._init()
+            cmap._lut[:, -1] = render_params.alpha
+
             im = ax.imshow(
-                layer,  # get rid of the channel dimension
+                layer,
                 cmap=cmap,
-                alpha=render_params.alpha,
             )
             im.set_transform(trans_data)
 
@@ -514,6 +517,12 @@ def _render_labels(
 ) -> None:
     elements = render_params.elements
 
+    if not isinstance(render_params.outline, bool):
+        raise TypeError("Parameter 'outline' must be a boolean.")
+
+    if not isinstance(render_params.contour_px, int):
+        raise TypeError("Parameter 'contour_px' must be an integer.")
+
     if render_params.groups is not None:
         if isinstance(render_params.groups, str):
             render_params.groups = [render_params.groups]

tests/_images/Images_can_stack_render_images.png

@@ -77,3 +77,10 @@ def test_plot_can_stop_rasterization_with_scale_full(self, sdata_blobs: SpatialD
         sdata_blobs["blobs_giant_image"] = img
 
         sdata_blobs.pl.render_images("blobs_giant_image", scale="full").pl.show()
+
+    def test_plot_can_stack_render_images(self, sdata_blobs: SpatialData):
+        (
+            sdata_blobs.pl.render_images(elements="blobs_image", channel=0, palette="red", alpha=0.5)
+            .pl.render_images(elements="blobs_image", channel=1, palette="blue", alpha=0.5)
+            .pl.show()
+        )

tests/_images/Labels_can_stack_render_labels.png

@@ -59,3 +59,14 @@ def test_plot_can_stop_rasterization_with_scale_full(self, sdata_blobs: SpatialD
         sdata_blobs.table.uns["spatialdata_attrs"]["region"] = "blobs_giant_labels"
 
         sdata_blobs.pl.render_labels("blobs_giant_labels", scale="full").pl.show()
+
+    def test_plot_can_stack_render_labels(self, sdata_blobs: SpatialData):
+        (
+            sdata_blobs.pl.render_labels(
+                elements="blobs_labels", na_color="red", fill_alpha=1, outline_alpha=0, outline=False
+            )
+            .pl.render_labels(
+                elements="blobs_labels", na_color="blue", fill_alpha=0, outline_alpha=1, outline=True, contour_px=10
+            )
+            .pl.show()
+        )

tests/_images/Points_can_stack_render_points.png

@@ -30,3 +30,10 @@ def test_plot_coloring_with_palette(self, sdata_blobs: SpatialData):
 
     def test_plot_coloring_with_cmap(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_points(color="genes", cmap="rainbow").pl.show()
+
+    def test_plot_can_stack_render_points(self, sdata_blobs: SpatialData):
+        (
+            sdata_blobs.pl.render_points(elements="blobs_points", na_color="red", size=30)
+            .pl.render_points(elements="blobs_points", na_color="blue", size=10)
+            .pl.show()
+        )

tests/_images/Shapes_can_stack_render_shapes.png

@@ -254,3 +254,10 @@ def test_plot_can_color_two_queried_shapes_elements_by_annotation(self, sdata_bl
         del sdata_cropped.labels["blobs_multiscale_labels"]
 
         sdata_cropped.pl.render_shapes(["blobs_circles", "blobs_polygons"], color="annotation").pl.show()
+
+    def test_plot_can_stack_render_shapes(self, sdata_blobs: SpatialData):
+        (
+            sdata_blobs.pl.render_shapes(elements="blobs_circles", na_color="red", fill_alpha=0.5)
+            .pl.render_shapes(elements="blobs_polygons", na_color="blue", fill_alpha=0.5)
+            .pl.show()
+        )