large-image-source-bioformats 1.32.4__py3-none-any.whl → 1.32.4a124__py3-none-any.whl

large_image_source_bioformats/__init__.py

@@ -57,7 +57,6 @@ javabridge = None
 
 _javabridgeStarted = None
 _javabridgeStartLock = threading.Lock()
-_javabridgeAttachLock = threading.Lock()
 _bioformatsVersion = None
 _openImages = []
 
@@ -73,8 +72,7 @@ def _monitor_thread():
     main_thread.join()
     if len(_openImages):
         try:
-            with _javabridgeAttachLock:
-                javabridge.attach()
+            javabridge.attach()
             while len(_openImages):
                 source = _openImages.pop()
                 source = source()
@@ -89,9 +87,8 @@ def _monitor_thread():
         except Exception:
             pass
         finally:
-            with _javabridgeAttachLock:
-                if javabridge.get_env():
-                    javabridge.detach()
+            if javabridge.get_env():
+                javabridge.detach()
     _stopJavabridge()
 
 
@@ -237,8 +234,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._tileLock = threading.RLock()
 
         try:
-            with _javabridgeAttachLock:
-                javabridge.attach()
+            javabridge.attach()
             try:
                 self._bioimage = bioformats.ImageReader(largeImagePath, perform_init=False)
                 try:
@@ -317,9 +313,8 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             msg = 'The bioformats reader threw an unhandled exception.'
             raise TileSourceError(msg)
         finally:
-            with _javabridgeAttachLock:
-                if javabridge.get_env():
-                    javabridge.detach()
+            if javabridge.get_env():
+                javabridge.detach()
 
         if self.levels < 1:
             msg = 'Bioformats image must have at least one level.'
@@ -345,17 +340,15 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     def __del__(self):
         if getattr(self, '_bioimage', None) is not None:
             try:
-                with _javabridgeAttachLock:
-                    javabridge.attach()
+                javabridge.attach()
                 self._bioimage.close()
                 del self._bioimage
                 _openImages.remove(weakref.ref(self))
             except Exception:
                 pass
             finally:
-                with _javabridgeAttachLock:
-                    if javabridge.get_env():
-                        javabridge.detach()
+                if javabridge.get_env():
+                    javabridge.detach()
 
     def _metadataForCurrentSeries(self, rdr):
         self._metadata = getattr(self, '_metadata', {})
@@ -671,37 +664,33 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             tile = large_image.tilesource.base._imageToNumpy(tile)[0]
             format = TILE_FORMAT_NUMPY
         else:
-            with _javabridgeAttachLock:
-                javabridge.attach()
-            try:
-                if width > 0 and height > 0:
-                    with self._tileLock:
+            with self._tileLock:
+                try:
+                    javabridge.attach()
+                    if width > 0 and height > 0:
                         tile = self._bioimage.read(
-                            c=fc, z=fz, t=ft,
-                            series=fseries['series'][seriesLevel],
+                            c=fc, z=fz, t=ft, series=fseries['series'][seriesLevel],
                             rescale=False,  # return internal data types
                             XYWH=(offsetx, offsety, width, height))
-                else:
-                    # We need the same dtype, so read 1x1 at 0x0
-                    with self._tileLock:
+                    else:
+                        # We need the same dtype, so read 1x1 at 0x0
                         tile = self._bioimage.read(
                             c=fc, z=fz, t=ft, series=fseries['series'][seriesLevel],
                             rescale=False,  # return internal data types
                             XYWH=(0, 0, 1, 1))
-                    tile = np.zeros(tuple([0, 0] + list(tile.shape[2:])), dtype=tile.dtype)
-                format = TILE_FORMAT_NUMPY
-            except javabridge.JavaException as exc:
-                es = javabridge.to_string(exc.throwable)
-                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:
-                with _javabridgeAttachLock:
+                        tile = np.zeros(tuple([0, 0] + list(tile.shape[2:])), dtype=tile.dtype)
+                    format = TILE_FORMAT_NUMPY
+                except javabridge.JavaException as exc:
+                    es = javabridge.to_string(exc.throwable)
+                    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()
             if scale > 1:
@@ -744,20 +733,18 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if info is None:
             return None
         series = info['seriesNum']
-        with _javabridgeAttachLock:
-            javabridge.attach()
-        try:
-            with self._tileLock:
+        with self._tileLock:
+            try:
+                javabridge.attach()
                 image = self._bioimage.read(
                     series=series,
                     rescale=False,  # return internal data types
                     XYWH=(0, 0, info['sizeX'], info['sizeY']))
-        except javabridge.JavaException as exc:
-            es = javabridge.to_string(exc.throwable)
-            raise TileSourceError('Failed to get Bioformat series (%s, %r).' % (es, (
-                series, info['sizeX'], info['sizeY'])))
-        finally:
-            with _javabridgeAttachLock:
+            except javabridge.JavaException as exc:
+                es = javabridge.to_string(exc.throwable)
+                raise TileSourceError('Failed to get Bioformat series (%s, %r).' % (es, (
+                    series, info['sizeX'], info['sizeY'])))
+            finally:
                 if javabridge.get_env():
                     javabridge.detach()
         return large_image.tilesource.base._imageToPIL(image)

{large_image_source_bioformats-1.32.4.dist-info → large_image_source_bioformats-1.32.4a124.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: large-image-source-bioformats
-Version: 1.32.4
+Version: 1.32.4a124
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -18,10 +18,10 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.32.4
+Requires-Dist: large-image>=1.32.4.a124
 Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.32.4; extra == "girder"
+Requires-Dist: girder-large-image>=1.32.4.a124; extra == "girder"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

large_image_source_bioformats-1.32.4a124.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_bioformats/__init__.py,sha256=Mq4JqX1NF5rnYa125tG2uS519LlR6c2mmPs-AHOJcy8,34420
+large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
+large_image_source_bioformats-1.32.4a124.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_bioformats-1.32.4a124.dist-info/METADATA,sha256=PYLgA05faHT08ivRlH-lzG7W6hBsLhe6f547tm-gEAE,1315
+large_image_source_bioformats-1.32.4a124.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
+large_image_source_bioformats-1.32.4a124.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
+large_image_source_bioformats-1.32.4a124.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
+large_image_source_bioformats-1.32.4a124.dist-info/RECORD,,

large_image_source_bioformats-1.32.4.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_bioformats/__init__.py,sha256=mO0uF67YoJSjzdvmdnzlw259FU7M6g7s-Iuj9X2QNdA,34886
-large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
-large_image_source_bioformats-1.32.4.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_bioformats-1.32.4.dist-info/METADATA,sha256=x9Eh3xlY3P4iOOyO9nqADA2B_BmGeLSPXaBniGkWWkM,1301
-large_image_source_bioformats-1.32.4.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
-large_image_source_bioformats-1.32.4.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
-large_image_source_bioformats-1.32.4.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
-large_image_source_bioformats-1.32.4.dist-info/RECORD,,