large-image-source-tiff 1.30.5.dev8__tar.gz → 1.30.6__tar.gz

{large_image_source_tiff-1.30.5.dev8 → large_image_source_tiff-1.30.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.30.5.dev8
+Version: 1.30.6
 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>=1.30.5.dev8
+Requires-Dist: large-image>=1.30.6
 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>=1.30.5.dev8; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6; extra == "girder"
 
 A TIFF tilesource for large_image.
 

{large_image_source_tiff-1.30.5.dev8 → large_image_source_tiff-1.30.6}/large_image_source_tiff/__init__.py

@@ -141,7 +141,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 continue
             # If a layer is a multiple of the tile size, the number of tiles
             # should be a power of two rounded up from the primary.
-            if (not (td.imageWidth % td.tileWidth) and not (td.imageHeight % td.tileHeight)):
+            if not (td.imageWidth % td.tileWidth) and not (td.imageHeight % td.tileHeight):
                 htw = highest.imageWidth // td.tileWidth
                 hth = highest.imageHeight // td.tileHeight
                 ttw = td.imageWidth // td.tileWidth
@@ -327,12 +327,19 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._info = info
         frames = []
         associated = []  # for now, a list of directories
+        used_subifd = False
         for idx, ifd in enumerate(info['ifds']):
             # if not tiles, add to associated images
             if tifftools.Tag.tileWidth.value not in ifd['tags']:
-                associated.append(idx)
+                associated.append((idx, False))
                 continue
-            level = self._levelFromIfd(ifd, info['ifds'][0])
+            try:
+                level = self._levelFromIfd(ifd, info['ifds'][0])
+            except TileSourceError:
+                if idx and used_subifd:
+                    associated.append((idx, True))
+                    continue
+                raise
             # if the same resolution as the main image, add a frame
             if level == self.levels - 1:
                 frames.append({'dirs': [None] * self.levels})
@@ -371,9 +378,13 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                             tifftools.Tag.TileOffsets.value not in subifds[0]['tags']):
                         msg = 'Subifd has no strip or tile offsets.'
                         raise TileSourceMalformedError(msg)
-                    level = self._levelFromIfd(subifds[0], info['ifds'][0])
+                    try:
+                        level = self._levelFromIfd(subifds[0], info['ifds'][0])
+                    except Exception:
+                        break
                     if level < self.levels - 1 and frames[-1]['dirs'][level] is None:
                         frames[-1]['dirs'][level] = (idx, subidx + 1)
+                        used_subifd = True
                     else:
                         msg = 'Tile layers are in a surprising order'
                         raise TileSourceError(msg)
@@ -407,8 +418,8 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 self._iccprofiles.append(ifd['tags'][
                     tifftools.Tag.ICCProfile.value]['data'])
         self._associatedImages = {}
-        for dirNum in associated:
-            self._addAssociatedImage(dirNum)
+        for dirNum, isTiled in associated:
+            self._addAssociatedImage(dirNum, isTiled)
         self._frames = frames
         self._tiffDirectories = [
             self.getTiffDir(
@@ -490,7 +501,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 frame.setdefault('frame', {})
                 frame['frame']['IndexC'] = idx
 
-    def _addAssociatedImage(self, directoryNum, mustBeTiled=False, topImage=None):
+    def _addAssociatedImage(self, directoryNum, mustBeTiled=False, topImage=None, imageId=None):
         """
         Check if the specified TIFF directory contains an image with a sensible
         image description that can be used as an ID.  If so, and if the image
@@ -501,6 +512,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
            untiled images.
         :param topImage: if specified, add image-embedded metadata to this
            image.
+        :param imageId: if specified, use this as the image name.
         """
         try:
             associated = self.getTiffDir(directoryNum, mustBeTiled)
@@ -514,6 +526,8 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 id = 'dir%d' % directoryNum
                 if not len(self._associatedImages):
                     id = 'macro'
+            if imageId:
+                id = imageId
             if not id and not mustBeTiled:
                 id = {1: 'label', 9: 'macro'}.get(associated._tiffInfo.get('subfiletype'))
             if not isinstance(id, str):
@@ -525,7 +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
@@ -681,8 +695,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 except Exception:
                     if sparseFallback:
                         raise IOTiffError('Missing z level %d' % z)
-                    else:
-                        raise
+                    raise
             else:
                 tile = dir.getTile(x, y, asarray=numpyAllowed == 'always')
                 format = 'JPEG'
@@ -765,7 +778,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         imageList = set(self._associatedImages)
         for td in self._tiffDirectories:
-            if td is not None:
+            if td is not None and td is not False:
                 imageList |= set(td._embeddedImages)
         return sorted(imageList)
 
@@ -780,11 +793,11 @@ 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 imageKey in td._embeddedImages:
+            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])))
         if imageKey in self._associatedImages:
             return PIL.Image.fromarray(self._associatedImages[imageKey])

{large_image_source_tiff-1.30.5.dev8 → large_image_source_tiff-1.30.6}/large_image_source_tiff/tiff_reader.py

@@ -447,12 +447,11 @@ class TiledTiffDirectory:
 
         if tileByteCountsLibtiffType == libtiff_ctypes.TIFFDataType.TIFF_LONG8:
             return ctypes.c_uint64
-        elif tileByteCountsLibtiffType == \
+        if tileByteCountsLibtiffType == \
                 libtiff_ctypes.TIFFDataType.TIFF_SHORT:
             return ctypes.c_uint16
-        else:
-            raise IOTiffError(
-                'Invalid type for TIFFTAG_TILEBYTECOUNTS: %s' % tileByteCountsLibtiffType)
+        raise IOTiffError(
+            'Invalid type for TIFFTAG_TILEBYTECOUNTS: %s' % tileByteCountsLibtiffType)
 
     def _getJpegFrameSize(self, tileNum):
         """
@@ -529,10 +528,10 @@ class TiledTiffDirectory:
         if bytesRead == -1:
             msg = 'Failed to read raw tile'
             raise IOTiffError(msg)
-        elif bytesRead < rawTileSize:
+        if bytesRead < rawTileSize:
             msg = 'Buffer underflow when reading tile'
             raise IOTiffError(msg)
-        elif bytesRead > rawTileSize:
+        if bytesRead > rawTileSize:
             # It's unlikely that this will ever occur, but incomplete reads will
             # be checked for by looking for the JPEG end marker
             msg = 'Buffer overflow when reading tile'
@@ -788,11 +787,13 @@ class TiledTiffDirectory:
 
         if (not self._tiffInfo.get('istiled') or
                 self._tiffInfo.get('compression') not in {
-                    libtiff_ctypes.COMPRESSION_JPEG, 33003, 33005, 34712} or
+                    libtiff_ctypes.COMPRESSION_JPEG, 33003, 33004, 33005, 34712} or
                 self._tiffInfo.get('bitspersample') != 8 or
                 self._tiffInfo.get('sampleformat') not in {
                     None, libtiff_ctypes.SAMPLEFORMAT_UINT} or
-                (asarray and self._tiffInfo.get('compression') not in {33003, 33005, 34712} and (
+                (asarray and self._tiffInfo.get('compression') not in {
+                    33003, 33004, 33005, 34712,
+                } and (
                     self._tiffInfo.get('compression') != libtiff_ctypes.COMPRESSION_JPEG or
                     self._tiffInfo.get('photometric') != libtiff_ctypes.PHOTOMETRIC_YCBCR))):
             return self._getUncompressedTile(tileNum)
@@ -811,7 +812,7 @@ class TiledTiffDirectory:
         # Get the whole frame, which is in a JPEG or JPEG 2000 format
         frame = self._getJpegFrame(tileNum, True)
         # For JP2K, see if we can convert it faster than PIL
-        if self._tiffInfo.get('compression') in {33003, 33005}:
+        if self._tiffInfo.get('compression') in {33003, 33004, 33005, 34712}:
             try:
                 import openjpeg
 
@@ -836,7 +837,7 @@ class TiledTiffDirectory:
         self._embeddedImages = {}
 
         if not meta:
-            return
+            return None
         if not isinstance(meta, str):
             meta = meta.decode(errors='ignore')
         try:
@@ -858,7 +859,7 @@ class TiledTiffDirectory:
                         meta.split('|MPP = ', 1)[1].split('|')[0].strip()) * 0.001
                 except Exception:
                     pass
-            return
+            return None
         try:
             image = xml.find(
                 ".//DataObject[@ObjectType='DPScannedImage']")
@@ -894,3 +895,26 @@ 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 {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-1.30.5.dev8 → large_image_source_tiff-1.30.6}/large_image_source_tiff.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.30.5.dev8
+Version: 1.30.6
 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>=1.30.5.dev8
+Requires-Dist: large-image>=1.30.6
 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>=1.30.5.dev8; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6; extra == "girder"
 
 A TIFF tilesource for large_image.
 

{large_image_source_tiff-1.30.5.dev8 → large_image_source_tiff-1.30.6}/large_image_source_tiff.egg-info/requires.txt

@@ -1,4 +1,4 @@
-large-image>=1.30.5.dev8
+large-image>=1.30.6
 pylibtiff
 tifftools>=1.2.0
 
@@ -6,4 +6,4 @@ tifftools>=1.2.0
 pylibjpeg-openjpeg
 
 [girder]
-girder-large-image>=1.30.5.dev8
+girder-large-image>=1.30.6

{large_image_source_tiff-1.30.5.dev8 → large_image_source_tiff-1.30.6}/setup.py

@@ -19,8 +19,7 @@ def prerelease_local_scheme(version):
 
     if os.getenv('CIRCLE_BRANCH') in ('master', ):
         return ''
-    else:
-        return get_local_node_and_date(version)
+    return get_local_node_and_date(version)
 
 
 try: