large-image-source-bioformats 1.30.7.dev10__py3-none-any.whl → 1.30.7.dev18__py3-none-any.whl

large_image_source_bioformats/__init__.py

@@ -321,8 +321,15 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if self.sizeX <= 0 or self.sizeY <= 0:
             msg = 'Bioformats tile size is invalid.'
             raise TileSourceError(msg)
+        if ('JPEG' in self._metadata['readerClassName'] and
+                (self._metadata['optimalTileWidth'] > 16384 or
+                 self._metadata['optimalTileHeight'] > 16384)):
+            msg = 'Bioformats will be too inefficient to read this file.'
+            raise TileSourceError(msg)
         try:
+            self._lastGetTileException = 'raise'
             self.getTile(0, 0, self.levels - 1)
+            delattr(self, '_lastGetTileException')
         except Exception as exc:
             raise TileSourceError('Bioformats cannot read a tile: %r' % exc)
         self._populatedLevels = len([
@@ -370,6 +377,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             'optimalTileWidth': rdr.getOptimalTileWidth(),
             'optimalTileHeight': rdr.getOptimalTileHeight(),
             'resolutionCount': rdr.getResolutionCount(),
+            'readerClassName': rdr.get_class_name(),
         })
 
     def _getSeriesStarts(self, rdr):  # noqa
@@ -613,7 +621,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         return self._metadata
 
     @methodcache()
-    def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
+    def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):  # noqa
         self._xyzInRange(x, y, z)
         ft = fc = fz = 0
         fseries = self._metadata['frameSeries'][0]
@@ -668,9 +676,14 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     format = TILE_FORMAT_NUMPY
                 except javabridge.JavaException as exc:
                     es = javabridge.to_string(exc.throwable)
-                    raise TileSourceError('Failed to get Bioformat region (%s, %r).' % (es, (
-                        fc, fz, ft, fseries, self.sizeX, self.sizeY, offsetx,
-                        offsety, width, height)))
+                    self.logger.exception('Failed to getTile (%r)', es)
+                    if getattr(self, '_lastGetTileException', None) == 'raise':
+                        raise TileSourceError('Failed to get Bioformat region (%s, %r).' % (es, (
+                            fc, fz, ft, fseries, self.sizeX, self.sizeY, offsetx,
+                            offsety, width, height)))
+                    self._lastGetTileException = repr(es)
+                    tile = np.zeros((1, 1))
+                    format = TILE_FORMAT_NUMPY
                 finally:
                     if javabridge.get_env():
                         javabridge.detach()

{large_image_source_bioformats-1.30.7.dev10.dist-info → large_image_source_bioformats-1.30.7.dev18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: large-image-source-bioformats
-Version: 1.30.7.dev10
+Version: 1.30.7.dev18
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,10 +19,10 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.7.dev10
+Requires-Dist: large-image>=1.30.7.dev18
 Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.7.dev10; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.7.dev18; extra == "girder"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

large_image_source_bioformats-1.30.7.dev18.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_bioformats/__init__.py,sha256=KGs5DY7YZrmaEhkvSYeQOdz3Wt-DDnHaIi4vfHAe07Q,33975
+large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
+large_image_source_bioformats-1.30.7.dev18.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_bioformats-1.30.7.dev18.dist-info/METADATA,sha256=ChTGGM4U9Eg88FlhIO_pIKI9EZxc-LFCzG11vfGl_Bw,1377
+large_image_source_bioformats-1.30.7.dev18.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_bioformats-1.30.7.dev18.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
+large_image_source_bioformats-1.30.7.dev18.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
+large_image_source_bioformats-1.30.7.dev18.dist-info/RECORD,,

large_image_source_bioformats-1.30.7.dev10.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_bioformats/__init__.py,sha256=lJawSrn3ScKHffmtl7Rut_tgmVKJru3xbbmMn47c1p0,33201
-large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
-large_image_source_bioformats-1.30.7.dev10.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_bioformats-1.30.7.dev10.dist-info/METADATA,sha256=P3z_lom_tPQYEMFbs_btzvJnzpT2ayoOUjYcuvZriPk,1377
-large_image_source_bioformats-1.30.7.dev10.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-large_image_source_bioformats-1.30.7.dev10.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
-large_image_source_bioformats-1.30.7.dev10.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
-large_image_source_bioformats-1.30.7.dev10.dist-info/RECORD,,