large-image-source-tiff 1.26.4.dev14__py3-none-any.whl → 1.27.1__py3-none-any.whl

large_image_source_tiff/__init__.py

@@ -645,7 +645,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 allowStyle = False
                 format = TILE_FORMAT_PIL
             else:
-                tile = dir.getTile(x, y)
+                tile = dir.getTile(x, y, asarray=numpyAllowed == 'always')
                 format = 'JPEG'
             if isinstance(tile, PIL.Image.Image):
                 format = TILE_FORMAT_PIL

large_image_source_tiff/tiff_reader.py

@@ -53,6 +53,21 @@ libtiff_ctypes.suppress_warnings()
 libtiff_ctypes.suppress_errors()
 
 
+_ctypesFormattbl = {
+    (8, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint8,
+    (8, libtiff_ctypes.SAMPLEFORMAT_INT): np.int8,
+    (16, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint16,
+    (16, libtiff_ctypes.SAMPLEFORMAT_INT): np.int16,
+    (16, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float16,
+    (32, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint32,
+    (32, libtiff_ctypes.SAMPLEFORMAT_INT): np.int32,
+    (32, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float32,
+    (64, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint64,
+    (64, libtiff_ctypes.SAMPLEFORMAT_INT): np.int64,
+    (64, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float64,
+}
+
+
 def patchLibtiff():
     libtiff_ctypes.libtiff.TIFFFieldWithTag.restype = \
         ctypes.POINTER(libtiff_ctypes.TIFFFieldInfo)
@@ -286,6 +301,7 @@ class TiledTiffDirectory:
         self._tileHeight = info.get('tilelength') or info.get('rowsperstrip')
         self._imageWidth = info.get('imagewidth')
         self._imageHeight = info.get('imagelength')
+        self._tilesAcross = (self._imageWidth + self._tileWidth - 1) // self._tileWidth
         if not info.get('tilelength'):
             self._stripsPerTile = int(max(1, math.ceil(256.0 / self._tileHeight)))
             self._stripHeight = self._tileHeight
@@ -404,12 +420,11 @@ class TiledTiffDirectory:
         #     raise InvalidOperationTiffError(
         #         'Tile x=%d, y=%d does not exist' % (x, y))
         if self._tiffInfo.get('istiled'):
-            tileNum = libtiff_ctypes.libtiff.TIFFComputeTile(
-                self._tiffFile, pixelX, pixelY, 0, 0).value
+            tileNum = pixelX // self._tileWidth + (pixelY // self._tileHeight) * self._tilesAcross
         else:
             # TIFFComputeStrip with sample=0 is just the row divided by the
             # strip height
-            tileNum = int(pixelY // self._stripHeight)
+            tileNum = pixelY // self._stripHeight
         return tileNum
 
     @methodcache(key=partial(strhash, '_getTileByteCountsType'))
@@ -569,34 +584,39 @@ class TiledTiffDirectory:
         :rtype: PIL.Image
         :raises: IOTiffError
         """
-        with self._tileLock:
-            if self._tiffInfo.get('istiled'):
-                tileSize = libtiff_ctypes.libtiff.TIFFTileSize(self._tiffFile).value
-            else:
+        if self._tiffInfo.get('istiled'):
+            if not hasattr(self, '_uncompressedTileSize'):
+                with self._tileLock:
+                    self._uncompressedTileSize = libtiff_ctypes.libtiff.TIFFTileSize(
+                        self._tiffFile).value
+            tileSize = self._uncompressedTileSize
+        else:
+            with self._tileLock:
                 stripSize = libtiff_ctypes.libtiff.TIFFStripSize(
                     self._tiffFile).value
-                stripsCount = min(self._stripsPerTile, self._stripCount - tileNum)
-                tileSize = stripSize * self._stripsPerTile
+            stripsCount = min(self._stripsPerTile, self._stripCount - tileNum)
+            tileSize = stripSize * self._stripsPerTile
         imageBuffer = ctypes.create_string_buffer(tileSize)
-        with self._tileLock:
-            if self._tiffInfo.get('istiled'):
+        if self._tiffInfo.get('istiled'):
+            with self._tileLock:
                 readSize = libtiff_ctypes.libtiff.TIFFReadEncodedTile(
                     self._tiffFile, tileNum, imageBuffer, tileSize)
-            else:
-                readSize = 0
-                for stripNum in range(stripsCount):
+        else:
+            readSize = 0
+            for stripNum in range(stripsCount):
+                with self._tileLock:
                     chunkSize = libtiff_ctypes.libtiff.TIFFReadEncodedStrip(
                         self._tiffFile,
                         tileNum + stripNum,
                         ctypes.byref(imageBuffer, stripSize * stripNum),
                         stripSize).value
-                    if chunkSize <= 0:
-                        msg = 'Read an unexpected number of bytes from an encoded strip'
-                        raise IOTiffError(msg)
-                    readSize += chunkSize
-                if readSize < tileSize:
-                    ctypes.memset(ctypes.byref(imageBuffer, readSize), 0, tileSize - readSize)
-                    readSize = tileSize
+                if chunkSize <= 0:
+                    msg = 'Read an unexpected number of bytes from an encoded strip'
+                    raise IOTiffError(msg)
+                readSize += chunkSize
+            if readSize < tileSize:
+                ctypes.memset(ctypes.byref(imageBuffer, readSize), 0, tileSize - readSize)
+                readSize = tileSize
         if readSize < tileSize:
             raise IOTiffError(
                 'Read an unexpected number of bytes from an encoded tile' if readSize >= 0 else
@@ -612,23 +632,10 @@ class TiledTiffDirectory:
             self._tiffInfo.get('bitspersample'),
             self._tiffInfo.get('sampleformat') if self._tiffInfo.get(
                 'sampleformat') is not None else libtiff_ctypes.SAMPLEFORMAT_UINT)
-        formattbl = {
-            (8, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint8,
-            (8, libtiff_ctypes.SAMPLEFORMAT_INT): np.int8,
-            (16, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint16,
-            (16, libtiff_ctypes.SAMPLEFORMAT_INT): np.int16,
-            (16, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float16,
-            (32, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint32,
-            (32, libtiff_ctypes.SAMPLEFORMAT_INT): np.int32,
-            (32, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float32,
-            (64, libtiff_ctypes.SAMPLEFORMAT_UINT): np.uint64,
-            (64, libtiff_ctypes.SAMPLEFORMAT_INT): np.int64,
-            (64, libtiff_ctypes.SAMPLEFORMAT_IEEEFP): np.float64,
-        }
         image = np.ctypeslib.as_array(ctypes.cast(
             imageBuffer, ctypes.POINTER(ctypes.c_uint8)), (tileSize, )).view(
-                formattbl[format]).reshape(
-                    (th, tw, self._tiffInfo.get('samplesperpixel')))
+                _ctypesFormattbl[format]).reshape(
+                    (th, tw, self._tiffInfo['samplesperpixel']))
         if (self._tiffInfo.get('samplesperpixel') == 3 and
                 self._tiffInfo.get('photometric') == libtiff_ctypes.PHOTOMETRIC_YCBCR):
             if self._tiffInfo.get('bitspersample') == 16:
@@ -754,7 +761,7 @@ class TiledTiffDirectory:
     def pixelInfo(self):
         return self._pixelInfo
 
-    def getTile(self, x, y):
+    def getTile(self, x, y, asarray=False):
         """
         Get the complete JPEG image from a tile.
 
@@ -762,6 +769,8 @@ class TiledTiffDirectory:
         :type x: int
         :param y: The row index of the desired tile.
         :type y: int
+        :param asarray: If True, read jpeg compressed images as arrays.
+        :type asarray: boolean
         :return: either a buffer with a JPEG or a PIL image.
         :rtype: bytes
         :raises: InvalidOperationTiffError or IOTiffError
@@ -774,11 +783,14 @@ class TiledTiffDirectory:
         tileNum = self._toTileNum(x, y)
 
         if (not self._tiffInfo.get('istiled') or
-                self._tiffInfo.get('compression') not in (
-                    libtiff_ctypes.COMPRESSION_JPEG, 33003, 33005, 34712) or
+                self._tiffInfo.get('compression') not in {
+                    libtiff_ctypes.COMPRESSION_JPEG, 33003, 33005, 34712} or
                 self._tiffInfo.get('bitspersample') != 8 or
                 self._tiffInfo.get('sampleformat') not in {
-                    None, libtiff_ctypes.SAMPLEFORMAT_UINT}):
+                    None, libtiff_ctypes.SAMPLEFORMAT_UINT} or
+                (asarray and self._tiffInfo.get('compression') not in {33003, 33005, 34712} and (
+                    self._tiffInfo.get('compression') != libtiff_ctypes.COMPRESSION_JPEG or
+                    self._tiffInfo.get('photometric') != libtiff_ctypes.PHOTOMETRIC_YCBCR))):
             return self._getUncompressedTile(tileNum)
 
         imageBuffer = io.BytesIO()

{large_image_source_tiff-1.26.4.dev14.dist-info → large_image_source_tiff-1.27.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.26.4.dev14
+Version: 1.27.1
 Summary: A TIFF tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,11 +17,11 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 License-File: LICENSE
-Requires-Dist: large-image >=1.26.4.dev14
+Requires-Dist: large-image >=1.27.1
 Requires-Dist: pylibtiff
 Requires-Dist: tifftools >=1.2.0
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.26.4.dev14 ; extra == 'girder'
+Requires-Dist: girder-large-image >=1.27.1 ; extra == 'girder'
 
 A TIFF tilesource for large_image.
 

large_image_source_tiff-1.27.1.dist-info/RECORD

@@ -0,0 +1,10 @@
+large_image_source_tiff/__init__.py,sha256=0XCpYfa6BDT4m22xtLYO6qlxJ7vCFrWopWQQQo37FGQ,33986
+large_image_source_tiff/exceptions.py,sha256=NgdwloaDCtbtUMe2BU2lXEU8IwQSYtaokIwGIFypCps,617
+large_image_source_tiff/girder_source.py,sha256=Dp2e3O4VTANYXZI_eybgzs5BcyuMcw2-MAzCUJ8zzPg,1031
+large_image_source_tiff/tiff_reader.py,sha256=hv9ux30nLh_A46MRJqgUJoEGUIoOuJAQfLh_5VrVyDk,38643
+large_image_source_tiff-1.27.1.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tiff-1.27.1.dist-info/METADATA,sha256=aTXwXf7KHZ4eMbMz7a6_6JvWvQOZSE9tmJe45xv07JA,1016
+large_image_source_tiff-1.27.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+large_image_source_tiff-1.27.1.dist-info/entry_points.txt,sha256=iZ43sIcj98SND7nDUC-_4qroBL6apyXN4iSbPXZ8LE4,166
+large_image_source_tiff-1.27.1.dist-info/top_level.txt,sha256=QRx_D2oeiOOz_5FlBOAoDPF-E4Q-aFmerUWlaeP14B8,24
+large_image_source_tiff-1.27.1.dist-info/RECORD,,

large_image_source_tiff-1.26.4.dev14.dist-info/RECORD

@@ -1,10 +0,0 @@
-large_image_source_tiff/__init__.py,sha256=mCcJqAbDqdaaCPqD5Zfu8saj-j8KZZoTqdMyy9RAlWw,33952
-large_image_source_tiff/exceptions.py,sha256=NgdwloaDCtbtUMe2BU2lXEU8IwQSYtaokIwGIFypCps,617
-large_image_source_tiff/girder_source.py,sha256=Dp2e3O4VTANYXZI_eybgzs5BcyuMcw2-MAzCUJ8zzPg,1031
-large_image_source_tiff/tiff_reader.py,sha256=i6HztBXfPWEIncUo_y3rWuhUNrv3CG8oAVKOUWCkn2A,38094
-large_image_source_tiff-1.26.4.dev14.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tiff-1.26.4.dev14.dist-info/METADATA,sha256=HdPgl7LxXryjQEjMuBCC18-chQteiScTLHTW-g2ut2k,1034
-large_image_source_tiff-1.26.4.dev14.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-large_image_source_tiff-1.26.4.dev14.dist-info/entry_points.txt,sha256=iZ43sIcj98SND7nDUC-_4qroBL6apyXN4iSbPXZ8LE4,166
-large_image_source_tiff-1.26.4.dev14.dist-info/top_level.txt,sha256=QRx_D2oeiOOz_5FlBOAoDPF-E4Q-aFmerUWlaeP14B8,24
-large_image_source_tiff-1.26.4.dev14.dist-info/RECORD,,