Fixed multi-scale image/label handling (#131)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: timtreis

CHANGELOG.md

@@ -8,8 +8,20 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [Unreleased]
+## [0.0.3] - tbd
+
+### Fixed
+
+-   Multi-scale images/labels are now correctly substituted and the action is logged (#131).
+
+## [0.0.2] - 2023-06-25
+
+### Fixed
+
+-   Multiple bugfixes of which I didn't keep track of.
+
+## [0.0.1] - 2023-04-04
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+-   Initial release of `spatialdata-plot` with support for `images`, `labels`, `points` and `shapes`.

src/spatialdata_plot/pl/basic.py

@@ -41,7 +41,6 @@
     _get_extent,
     _maybe_set_colors,
     _mpl_ax_contains_elements,
-    _multiscale_to_image,
     _prepare_cmap_norm,
     _prepare_params_plot,
     _robust_transform,
@@ -544,9 +543,6 @@ def show(
             if not all(isinstance(t, str) for t in title):
                 raise TypeError("All titles must be strings.")
 
-        # Simplicstic solution: If the images are multiscale, just use the first
-        sdata = _multiscale_to_image(sdata)
-
         # get original axis extent for later comparison
         x_min_orig, x_max_orig = (np.inf, -np.inf)
         y_min_orig, y_max_orig = (np.inf, -np.inf)
@@ -608,19 +604,6 @@ 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.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(
             num_panels=len(coordinate_systems),

src/spatialdata_plot/pl/render.py

@@ -10,6 +10,7 @@
 import numpy as np
 import pandas as pd
 import scanpy as sc
+import spatial_image
 import spatialdata as sd
 from anndata import AnnData
 from geopandas import GeoDataFrame
@@ -19,6 +20,10 @@
 from matplotlib.patches import Circle, Polygon
 from pandas.api.types import is_categorical_dtype
 from scanpy._settings import settings as sc_settings
+from spatialdata.models import (
+    Image2DModel,
+    Labels2DModel,
+)
 
 from spatialdata_plot._logging import logger
 from spatialdata_plot.pl.utils import (
@@ -342,8 +347,11 @@ def _render_images(
         elements = list(sdata_filt.images.keys())
 
     images = [sdata.images[e] for e in elements]
+    for img, img_key in zip(images, elements):
+        if not isinstance(img, spatial_image.SpatialImage):
+            img = Image2DModel.parse(img["scale0"].ds.to_array().squeeze(axis=0))
+            logger.warning(f"Multi-scale images not yet supported, using scale0 of multi-scale image '{img_key}'.")
 
-    for img in images:
         if render_params.channel is None:
             channels = img.coords["c"].values
         else:
@@ -512,17 +520,21 @@ def _render_labels(
     if elements is None:
         elements = list(sdata_filt.labels.keys())
 
-    labels = [sdata.labels[e].values for e in elements]
+    labels = [sdata.labels[e] for e in elements]
+
+    for label, label_key in zip(labels, elements):
+        if not isinstance(label, spatial_image.SpatialImage):
+            label = Labels2DModel.parse(label["scale0"].ds.to_array().squeeze(axis=0))
+            logger.warning(f"Multi-scale labels not yet supported, using scale0 of multi-scale label '{label_key}'.")
 
-    for label, labels_key in zip(labels, elements):
         if sdata.table is None:
             instance_id = np.unique(label)
             table = AnnData(None, obs=pd.DataFrame(index=np.arange(len(instance_id))))
         else:
             instance_key = _get_instance_key(sdata)
             region_key = _get_region_key(sdata)
 
-            table = sdata.table[sdata.table.obs[region_key].isin([labels_key])]
+            table = sdata.table[sdata.table.obs[region_key].isin([label_key])]
 
             # get isntance id based on subsetted table
             instance_id = table.obs[instance_key].values
@@ -542,7 +554,7 @@ def _render_labels(
         if (render_params.fill_alpha != render_params.outline_alpha) and render_params.contour_px is not None:
             # First get the labels infill and plot them
             labels_infill = _map_color_seg(
-                seg=label,
+                seg=label.values,
                 cell_id=instance_id,
                 color_vector=color_vector,
                 color_source_vector=color_source_vector,
@@ -565,7 +577,7 @@ def _render_labels(
 
             # Then overlay the contour
             labels_contour = _map_color_seg(
-                seg=label,
+                seg=label.values,
                 cell_id=instance_id,
                 color_vector=color_vector,
                 color_source_vector=color_source_vector,

test_sandbox_data.ipynb

@@ -46,3 +46,19 @@ def test_plot_can_render_transformations_raccoon_mapaxis(self, sdata_raccoon: Sp
         set_transformation(sdata_raccoon.images["raccoon"], map_axis, to_coordinate_system="global")
 
         sdata_raccoon.pl.render_images().pl.render_labels().pl.render_shapes().pl.show()
+
+
+def test_plot_can_render_blobs_images(sdata_blobs: SpatialData):
+    sdata_blobs.pl.render_images().pl.show()
+
+
+def test_plot_can_render_blobs_points(sdata_blobs: SpatialData):
+    sdata_blobs.pl.render_points().pl.show()
+
+
+def test_plot_can_render_blobs_labels(sdata_blobs: SpatialData):
+    sdata_blobs.pl.render_labels().pl.show()
+
+
+def test_plot_can_render_blobs_shapes(sdata_blobs: SpatialData):
+    sdata_blobs.pl.render_shapes().pl.show()