Merge pull request #1318 from girder/refactor-associated-image

Refactor fetching extra associated images from openslide

CHANGELOG.md

@@ -11,6 +11,7 @@
 
 ### Changes
 - Remove a needless guard around getting an icc profile ([#1316](../../pull/1316))
+- Refactor fetching extra associated images from openslide ([#1318](../../pull/1318))
 
 ### Bug Fixes
 - Guard against potential bad event stream timestamp ([#1306](../../pull/1306))

sources/openslide/large_image_source_openslide/__init__.py

@@ -14,6 +14,7 @@
 #  limitations under the License.
 ##############################################################################
 
+import io
 import math
 import os
 
@@ -26,12 +27,6 @@
 from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource, nearPowerOfTwo
 
-try:
-    from libtiff import libtiff_ctypes
-except ImportError:
-    libtiff_ctypes = False
-
-
 try:
     from importlib.metadata import PackageNotFoundError
     from importlib.metadata import version as _importlib_version
@@ -376,13 +371,9 @@ def _getAssociatedImage(self, imageKey):
                 # Reopen handle after a lowlevel error
                 self._openslide = openslide.OpenSlide(self._largeImagePath)
                 return None
-        bytePath = self._largeImagePath
-        if not isinstance(bytePath, bytes):
-            bytePath = bytePath.encode()
-        _tiffFile = libtiff_ctypes.TIFF.open(bytePath)
-        _tiffFile.SetDirectory(images[imageKey])
-        img = _tiffFile.read_image()
-        return PIL.Image.fromarray(img)
+        tiff_buffer = io.BytesIO()
+        tifftools.write_tiff(self._tiffinfo['ifds'][images[imageKey]], tiff_buffer)
+        return PIL.Image.open(tiff_buffer)
 
 
 def open(*args, **kwargs):