Merge branch 'main' into bugfix/issue172-add-tests-for-extent-of-plots

Author: timtreis

CHANGELOG.md

@@ -16,11 +16,13 @@ and this project adheres to [Semantic Versioning][].
 -   Large images are automatically rasterized to speed up performance (#164)
 -   Added better error message for mismatch in cs and ax number (#185)
 -   Beter test coverage for correct plotting of elements after transformation (#198)
+-   Can now stack render commands (#190, #192)
 
 ### Fixed
 
 -   Now dropping index when plotting shapes after spatial query (#177)
 -   Points are now being correctly rotated (#198)
+-   User can now pass Colormap objects to the cmap argument in render_images. When only one cmap is given for 3 channels, it is now applied to each channel (#188, #194)
 
 ## [0.0.6] - 2023-11-06
 

src/spatialdata_plot/pl/basic.py

@@ -362,9 +362,6 @@ def render_images(
         sdata = _verify_plotting_tree(sdata)
         n_steps = len(sdata.plotting_tree.keys())
 
-        if channel is None and cmap is None:
-            cmap = "brg"
-
         cmap_params: list[CmapParams] | CmapParams
         if isinstance(cmap, list):
             cmap_params = [
@@ -567,7 +564,7 @@ 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 +574,9 @@ 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 +606,7 @@ 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 +629,14 @@ 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 +687,7 @@ 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

@@ -403,10 +403,13 @@ 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)
 
@@ -431,10 +434,29 @@ def _render_images(
                     if render_params.cmap_params[i].norm is not None:
                         layers[c] = render_params.cmap_params[i].norm(layers[c])
 
-            # 2A) Image has 3 channels, no palette/cmap info -> use RGB
-            if n_channels == 3 and render_params.palette is None and not got_multiple_cmaps:
+            # 2A) Image has 3 channels, no palette info, and no/only one cmap was given
+            if n_channels == 3 and render_params.palette is None and not isinstance(render_params.cmap_params, list):
+                if render_params.cmap_params.is_default:  # -> use RGB
+                    stacked = np.stack([layers[c] for c in channels], axis=-1)
+                else:  # -> use given cmap for each channel
+                    channel_cmaps = [render_params.cmap_params.cmap] * n_channels
+                    # Apply cmaps to each channel, add up and normalize to [0, 1]
+                    stacked = (
+                        np.stack([channel_cmaps[i](layers[c]) for i, c in enumerate(channels)], 0).sum(0) / n_channels
+                    )
+                    # Remove alpha channel so we can overwrite it from render_params.alpha
+                    stacked = stacked[:, :, :3]
+                    logger.warning(
+                        "One cmap was given for multiple channels and is now used for each channel. "
+                        "You're blending multiple cmaps. "
+                        "If the plot doesn't look like you expect, it might be because your "
+                        "cmaps go from a given color to 'white', and not to 'transparent'. "
+                        "Therefore, the 'white' of higher layers will overlay the lower layers. "
+                        "Consider using 'palette' instead."
+                    )
+
                 im = ax.imshow(
-                    np.stack([layers[c] for c in channels], axis=-1),
+                    stacked,
                     alpha=render_params.alpha,
                 )
                 im.set_transform(trans_data)
@@ -511,6 +533,12 @@ 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]

src/spatialdata_plot/pl/utils.py

@@ -344,7 +344,13 @@ def _prepare_cmap_norm(
     **kwargs: Any,
 ) -> CmapParams:
     is_default = cmap is None
-    cmap = copy(matplotlib.colormaps[rcParams["image.cmap"] if cmap is None else cmap])
+    if cmap is None:
+        cmap = rcParams["image.cmap"]
+    if isinstance(cmap, str):
+        cmap = matplotlib.colormaps[cmap]
+
+    cmap = copy(cmap)
+
     cmap.set_bad("lightgray" if na_color is None else na_color)
 
     if isinstance(norm, Normalize) or not norm: