Merge pull request #1819 from girder/openslide-background-color

Apply background color information from openslide sources

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Change Log
 
+## 1.31.2
+
+### Improvements
+
+- Apply background color information from openslide sources ([#1819](../../pull/1819))
+
 ## 1.31.1
 
 ### Improvements

sources/openslide/large_image_source_openslide/__init__.py

@@ -20,6 +20,7 @@
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
+import numpy as np
 import openslide
 import PIL
 import tifftools
@@ -186,6 +187,12 @@ def __init__(self, path, **kwargs):  # noqa
                 self._svslevels = self._svslevels[prevlevels - self.levels:]
         except Exception:
             pass
+        try:
+            self._background = tuple(int(
+                self._openslide.properties['openslide.background-color']
+                [i * 2:i * 2 + 2], 16) for i in range(3))
+        except Exception:
+            self._background = None
         self._populatedLevels = len({l['svslevel'] for l in self._svslevels})
 
     def _getTileSize(self):
@@ -356,6 +363,10 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
                     retries -= 1
                     if retries <= 0:
                         raise TileSourceError(msg)
+            if tile.mode == 'RGBA' and self._background:
+                tile = np.array(tile)
+                tile[tile[:, :, -1] == 0, :3] = self._background
+                tile = PIL.Image.fromarray(tile, 'RGBA')
             # Always scale to the svs level 0 tile size.
             if svslevel['scale'] != 1:
                 tile = tile.resize((self.tileWidth, self.tileHeight),