large-image-source-tifffile 1.27.5.dev6__py3-none-any.whl → 1.28.3.dev2__py3-none-any.whl

large_image_source_tifffile/__init__.py

@@ -109,6 +109,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._largeImagePath = str(self._getLargeImagePath())
 
         _lazyImport()
+        self.addKnownExtensions()
         try:
             self._tf = tifffile.TiffFile(self._largeImagePath)
         except Exception:
@@ -473,19 +474,12 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             sidx = frame // self._basis['P'][0]
         else:
             sidx = 0
-        series = self._tf.series[self._series[sidx]]
         nonempty = [None] * self.levels
         nonempty[self.levels - 1] = True
+        series = self._tf.series[self._series[sidx]]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
         for ll in range(1, len(series.levels)):
             scale = round(math.log(max(za[0].shape[xidx] / za[ll].shape[xidx],
                                        za[0].shape[yidx] / za[ll].shape[yidx])) / math.log(2))
@@ -496,6 +490,19 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._nonempty_levels_list[frame] = nonempty
         return nonempty
 
+    def _getZarrArray(self, series, sidx):
+        with self._zarrlock:
+            if sidx not in self._zarrcache:
+                if len(self._zarrcache) > 10:
+                    self._zarrcache = {}
+                za = zarr.open(series.aszarr(), mode='r')
+                hasgbs = hasattr(za[0], 'get_basic_selection')
+                if not hasgbs and math.prod(series.shape) < 256 * 1024 ** 2:
+                    za = series.asarray()
+                self._zarrcache[sidx] = (za, hasgbs)
+            za, hasgbs = self._zarrcache[sidx]
+        return za, hasgbs
+
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         frame = self._getFrame(**kwargs)
@@ -506,14 +513,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         else:
             sidx = 0
         series = self._tf.series[self._series[sidx]]
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
         if hasgbs:
@@ -558,6 +558,16 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
 
+    @classmethod
+    def addKnownExtensions(cls):
+        if not hasattr(cls, '_addedExtensions'):
+            _lazyImport()
+            cls._addedExtensions = True
+            cls.extensions = cls.extensions.copy()
+            for ext in tifffile.TIFF.FILE_EXTENSIONS:
+                if ext not in cls.extensions:
+                    cls.extensions[ext] = SourcePriority.IMPLICIT
+
 
 def open(*args, **kwargs):
     """

{large_image_source_tifffile-1.27.5.dev6.dist-info → large_image_source_tifffile-1.28.3.dev2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.27.5.dev6
+Version: 1.28.3.dev2
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,12 +17,12 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 License-File: LICENSE
-Requires-Dist: large-image >=1.27.5.dev6
+Requires-Dist: large-image >=1.28.3.dev2
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.5.dev6 ; extra == 'girder'
+Requires-Dist: girder-large-image >=1.28.3.dev2 ; extra == 'girder'
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.28.3.dev2.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_tifffile/__init__.py,sha256=7hREWGbhyYOcz94l_vxMAOTUSJKtJY37TEIZdkvamNw,25001
+large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
+large_image_source_tifffile-1.28.3.dev2.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tifffile-1.28.3.dev2.dist-info/METADATA,sha256=2XRfComEY1H1fO7m6luWIfzukgRCnPmPJw6RVkiDpZw,1061
+large_image_source_tifffile-1.28.3.dev2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+large_image_source_tifffile-1.28.3.dev2.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
+large_image_source_tifffile-1.28.3.dev2.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
+large_image_source_tifffile-1.28.3.dev2.dist-info/RECORD,,

large_image_source_tifffile-1.27.5.dev6.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_tifffile/__init__.py,sha256=7jHLRfFXszTDfTcD6aRylJthE03lK5FCHh4rKkHtHEw,24668
-large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
-large_image_source_tifffile-1.27.5.dev6.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tifffile-1.27.5.dev6.dist-info/METADATA,sha256=8nBvBa8UIknq6Y8vtuL_hKFRzWg9ne44VyqOsfA9M2U,1061
-large_image_source_tifffile-1.27.5.dev6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_tifffile-1.27.5.dev6.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
-large_image_source_tifffile-1.27.5.dev6.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
-large_image_source_tifffile-1.27.5.dev6.dist-info/RECORD,,