Closes issue 69 (#98)

Author: timtreis

src/spatialdata_plot/pl/basic.py

@@ -139,7 +139,7 @@ def _copy(
 
     def render_shapes(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         size: float = 1.0,
@@ -161,8 +161,8 @@ def render_shapes(
 
         Parameters
         ----------
-        element
-            The name of the shapes element to render. If `None`, the first
+        elements
+            The name of the shapes element(s) to render. If `None`, all
             shapes element in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
@@ -209,7 +209,7 @@ def render_shapes(
         )
         outline_params = _set_outline(size, outline, outline_width, outline_color)
         sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             outline_params=outline_params,
@@ -226,7 +226,7 @@ def render_shapes(
 
     def render_points(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         size: float = 1.0,
@@ -242,8 +242,8 @@ def render_points(
 
         Parameters
         ----------
-        element
-            The name of the points element to render. If `None`, the first
+        elements
+            The name of the points element(s) to render. If `None`, all
             shapes element in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
@@ -279,7 +279,7 @@ def render_points(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             cmap_params=cmap_params,
@@ -293,7 +293,7 @@ def render_points(
 
     def render_images(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         channel: list[str] | list[int] | int | str | None = None,
         cmap: Colormap | str | None = None,
         norm: Optional[Normalize] = None,
@@ -307,9 +307,9 @@ def render_images(
 
         Parameters
         ----------
-        element
-            The name of the image element to render. If `None`, the first
-            shapes element in the `SpatialData` object will be used.
+        elements
+            The name of the image element(s) to render. If `None`, all
+            shapes elements in the `SpatialData` object will be used.
         channel
             To select which channel to plot (all by default).
         cmap
@@ -338,7 +338,7 @@ def render_images(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
-            element=element,
+            elements=elements,
             channel=channel,
             cmap_params=cmap_params,
             palette=palette,
@@ -349,7 +349,7 @@ def render_images(
 
     def render_labels(
         self,
-        element: str | None = None,
+        elements: str | list[str] | None = None,
         color: str | None = None,
         groups: str | Sequence[str] | None = None,
         contour_px: int = 3,
@@ -369,9 +369,9 @@ def render_labels(
 
         Parameters
         ----------
-        element
-            The name of the labels element to render. If `None`, the first
-            labels element in the `SpatialData` object will be used.
+        elements
+            The name of the labels element(s) to render. If `None`, all
+            labels elements in the `SpatialData` object will be used.
         color
             Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
         groups
@@ -420,7 +420,7 @@ def render_labels(
             **kwargs,
         )
         sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
-            element=element,
+            elements=elements,
             color=color,
             groups=groups,
             contour_px=contour_px,
@@ -523,6 +523,15 @@ def show(
         # Simplicstic solution: If the images are multiscale, just use the first
         sdata = _multiscale_to_image(sdata)
 
+        # handle coordinate system
+        coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
+        if isinstance(coordinate_systems, str):
+            coordinate_systems = [coordinate_systems]
+
+        for cs in coordinate_systems:
+            if cs not in sdata.coordinate_systems:
+                raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
+
         extent = _get_extent(
             sdata=sdata,
             has_images="render_images" in render_cmds,
@@ -532,11 +541,6 @@ def show(
             coordinate_systems=coordinate_systems,
         )
 
-        # handle coordinate system
-        coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
-        if isinstance(coordinate_systems, str):
-            coordinate_systems = [coordinate_systems]
-
         # Use extent to filter out coordinate system without the relevant elements
         valid_cs = []
         for cs in coordinate_systems:
@@ -546,13 +550,18 @@ def show(
                 logg.info(f"Dropping coordinate system '{cs}' since it doesn't have relevant elements.")
         coordinate_systems = valid_cs
 
+        # print(coordinate_systems)
+        # cs_mapping = _get_coordinate_system_mapping(sdata)
+        # print(cs_mapping)
+
         # check that coordinate system and elements to be rendered match
-        for cmd, params in render_cmds.items():
-            if params.element is not None and len([params.element]) != len(coordinate_systems):
-                raise ValueError(
-                    f"Number of coordinate systems ({len(coordinate_systems)}) does not match number of elements "
-                    f"({len(params.element)}) in command {cmd}."
-                )
+        # for cmd, params in render_cmds.items():
+        #     if params.elements is not None and len([params.elements]) != len(coordinate_systems):
+        #         print(params.elements)
+        #         raise ValueError(
+        #             f"Number of coordinate systems ({len(coordinate_systems)}) does not match number of elements "
+        #             f"({len(params.elements)}) in command {cmd}."
+        #         )
 
         # set up canvas
         fig_params, scalebar_params = _prepare_params_plot(