large-image-source-tiff 1.30.6.dev18__tar.gz → 1.30.6.dev22__tar.gz

{large_image_source_tiff-1.30.6.dev18 → large_image_source_tiff-1.30.6.dev22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.30.6.dev18
+Version: 1.30.6.dev22
 Summary: A TIFF tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,13 +19,13 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.6.dev18
+Requires-Dist: large-image>=1.30.6.dev22
 Requires-Dist: pylibtiff
 Requires-Dist: tifftools>=1.2.0
 Provides-Extra: all
 Requires-Dist: pylibjpeg-openjpeg; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.6.dev18; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6.dev22; extra == "girder"
 
 A TIFF tilesource for large_image.
 

{large_image_source_tiff-1.30.6.dev18 → large_image_source_tiff-1.30.6.dev22}/large_image_source_tiff/__init__.py

@@ -539,7 +539,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     associated._pixelInfo['width'] <= self._maxAssociatedImageSize and
                     associated._pixelInfo['height'] <= self._maxAssociatedImageSize and
                     id not in self._associatedImages):
-                image = associated._tiffFile.read_image()
+                image = associated.read_image()
                 # Optrascan scanners store xml image descriptions in a "tiled
                 # image".  Check if this is the case, and, if so, parse such
                 # data
@@ -794,9 +794,9 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         # _associatedImages.  There are some sample files where libtiff's
         # read_image fails to read the _associatedImage properly because of
         # separated jpeg information.  For the samples we currently have,
-        # preferring the _embeddedImages is sufficient, but if find other files
-        # with seemingly bad associated images, we may need to read them with a
-        # more complex process than read_image.
+        # preferring the _embeddedImages is sufficient, but if we find other
+        # files with seemingly bad associated images, we may need to read them
+        # with a more complex process than read_image.
         for td in self._tiffDirectories:
             if td is not None and td is not False and imageKey in td._embeddedImages:
                 return PIL.Image.open(io.BytesIO(base64.b64decode(td._embeddedImages[imageKey])))

{large_image_source_tiff-1.30.6.dev18 → large_image_source_tiff-1.30.6.dev22}/large_image_source_tiff/tiff_reader.py

@@ -896,3 +896,27 @@ class TiledTiffDirectory:
         except Exception:
             pass
         return True
+
+    def read_image(self):
+        """
+        Use the underlying _tiffFile to read an image.  But, if it is in a jp2k
+        encoding, read the raw data and convert it.
+        """
+        if self._tiffInfo.get('compression') not in {
+                libtiff_ctypes.COMPRESSION_JPEG, 33003, 33004, 33005, 34712}:
+            return self._tiffFile.read_image()
+        output = None
+        for yidx, y in enumerate(range(0, self.imageHeight, self.tileHeight)):
+            for xidx, x in enumerate(range(0, self.imageWidth, self.tileWidth)):
+                tile = self.getTile(xidx, yidx, asarray=True)
+                if len(tile.shape) == 2:
+                    tile = tile[:, :, np.newaxis]
+                if output is None:
+                    output = np.zeros(
+                        (self.imageHeight, self.imageWidth, tile.shape[2]), dtype=tile.dtype)
+                if tile.shape[0] > self.imageHeight - y:
+                    tile = tile[:self.imageHeight - y, :, :]
+                if tile.shape[1] > self.imageWidth - x:
+                    tile = tile[:, :self.imageWidth - x, :]
+                output[y:y + tile.shape[0], x:x + tile.shape[1], :] = tile
+        return output

{large_image_source_tiff-1.30.6.dev18 → large_image_source_tiff-1.30.6.dev22}/large_image_source_tiff.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.30.6.dev18
+Version: 1.30.6.dev22
 Summary: A TIFF tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,13 +19,13 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.6.dev18
+Requires-Dist: large-image>=1.30.6.dev22
 Requires-Dist: pylibtiff
 Requires-Dist: tifftools>=1.2.0
 Provides-Extra: all
 Requires-Dist: pylibjpeg-openjpeg; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.6.dev18; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6.dev22; extra == "girder"
 
 A TIFF tilesource for large_image.
 

{large_image_source_tiff-1.30.6.dev18 → large_image_source_tiff-1.30.6.dev22}/large_image_source_tiff.egg-info/requires.txt

@@ -1,4 +1,4 @@
-large-image>=1.30.6.dev18
+large-image>=1.30.6.dev22
 pylibtiff
 tifftools>=1.2.0
 
@@ -6,4 +6,4 @@ tifftools>=1.2.0
 pylibjpeg-openjpeg
 
 [girder]
-girder-large-image>=1.30.6.dev18
+girder-large-image>=1.30.6.dev22