Merge pull request #1650 from girder/style-with-empty-levels

Fix styling images with empty tile layers
girder · Sep 25, 2024 · af9a8a7 · af9a8a7
2 parents 9911354 + d38b499
commit af9a8a7
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,10 @@
 - Better handle images without enough tile layers ([#1648](../../pull/1648))
 - Add users option to config files; have a default config file ([#1649](../../pull/1649))
 
+### Bug Fixes
+
+- Fix styling images with empty tile layers ([#1650](../../pull/1650))
+
 ## 1.29.11
 
 ### Changes

diff --git a/large_image/tilesource/base.py b/large_image/tilesource/base.py
@@ -1535,7 +1535,7 @@ def _getTileFromEmptyLevel(self, x: int, y: int, z: int, **kwargs) -> Tuple[
                             'Compositing tile from higher resolution tiles x=%d y=%d z=%d',
                             x * scale + newX, y * scale + newY, z)
                         lastlog = time.time()
-                    subtile = self.getTile(
+                    subtile = getattr(self, '_unstyledInstance', self).getTile(
                         x * scale + newX, y * scale + newY, z,
                         pilImageAllowed=False, numpyAllowed='always',
                         sparseFallback=True, edge=False, frame=kwargs.get('frame'))
@@ -1559,7 +1559,7 @@ def _getTileFromEmptyLevel(self, x: int, y: int, z: int, **kwargs) -> Tuple[
                         'Compositing tile from higher resolution tiles x=%d y=%d z=%d',
                         x * scale + newX, y * scale + newY, z)
                     lastlog = time.time()
-                subtile = self.getTile(
+                subtile = getattr(self, '_unstyledInstance', self).getTile(
                     x * scale + newX, y * scale + newY, z,
                     pilImageAllowed=True, numpyAllowed=False,
                     sparseFallback=True, edge=False, frame=kwargs.get('frame'))
@@ -1815,7 +1815,8 @@ def getRegion(self, format: Union[str, Tuple[str]] = (TILE_FORMAT_IMAGE, ), **kw
                 cast(Dict[str, Any], tiledimage), outWidth, outHeight, tileIter.info, **kwargs)
         if outWidth != regionWidth or outHeight != regionHeight:
             dtype = cast(np.ndarray, image).dtype
-            if dtype == np.uint8 or resample is not None:
+            if dtype == np.uint8 or (resample is not None and (
+                    dtype != np.uint16 or cast(np.ndarray, image).shape[-1] != 1)):
                 image = _imageToPIL(cast(np.ndarray, image), mode).resize(
                     (outWidth, outHeight),
                     getattr(PIL.Image, 'Resampling', PIL.Image).NEAREST
@@ -1828,7 +1829,7 @@ def getRegion(self, format: Union[str, Tuple[str]] = (TILE_FORMAT_IMAGE, ), **kw
             else:
                 cols = [int(idx * regionWidth / outWidth) for idx in range(outWidth)]
                 rows = [int(idx * regionHeight / outHeight) for idx in range(outHeight)]
-                image = np.take(np.take(image, rows, axis=0), cols, axis=1)
+                image = np.take(np.take(cast(np.ndarray, image), rows, axis=0), cols, axis=1)
         maxWidth = kwargs.get('output', {}).get('maxWidth')
         maxHeight = kwargs.get('output', {}).get('maxHeight')
         if kwargs.get('fill') and maxWidth and maxHeight:

diff --git a/sources/tiff/large_image_source_tiff/__init__.py b/sources/tiff/large_image_source_tiff/__init__.py
@@ -664,7 +664,6 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
         else:
             dir = self._tiffDirectories[z]
         try:
-            allowStyle = True
             if dir is None:
                 try:
                     if not kwargs.get('inSparseFallback'):
@@ -676,7 +675,6 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                         raise IOTiffError('Missing z level %d' % z)
                     else:
                         raise
-                allowStyle = False
             else:
                 tile = dir.getTile(x, y, asarray=numpyAllowed == 'always')
                 format = 'JPEG'
@@ -685,7 +683,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
             if isinstance(tile, np.ndarray):
                 format = TILE_FORMAT_NUMPY
             return self._outputTile(tile, format, x, y, z, pilImageAllowed,
-                                    numpyAllowed, applyStyle=allowStyle, **kwargs)
+                                    numpyAllowed, **kwargs)
         except InvalidOperationTiffError as e:
             raise TileSourceError(e.args[0])
         except IOTiffError as e:
@@ -734,7 +732,7 @@ def getTileIOTiffError(self, x, y, z, pilImageAllowed=False,
             else:
                 image = PIL.Image.new('RGBA', (self.tileWidth, self.tileHeight))
             return self._outputTile(image, TILE_FORMAT_PIL, x, y, z, pilImageAllowed,
-                                    numpyAllowed, applyStyle=False, **kwargs)
+                                    numpyAllowed, **kwargs)
         raise TileSourceError('Internal I/O failure: %s' % exception.args[0])
 
     def _nonemptyLevelsList(self, frame=0):