large-image-source-bioformats 1.27.5.dev57__tar.gz → 1.27.5.dev63__tar.gz

{large-image-source-bioformats-1.27.5.dev57 → large-image-source-bioformats-1.27.5.dev63}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.27.5.dev57
+Version: 1.27.5.dev63
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-source-bioformats-1.27.5.dev57 → large-image-source-bioformats-1.27.5.dev63}/large_image_source_bioformats/__init__.py

@@ -61,8 +61,7 @@ _openImages = []
 
 
 # Default to ignoring files with no extension and some specific extensions.
-config.ConfigValues['source_bioformats_ignored_names'] = \
-    r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs|zarr(\.db|\.zip)))$'
+config.ConfigValues['source_bioformats_ignored_names'] = r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs|zip|zarr(\.db|\.zip)))$'  # noqa
 
 
 def _monitor_thread():
@@ -215,13 +214,28 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if not _startJavabridge(self.logger):
             msg = 'File cannot be opened by bioformats reader because javabridge failed to start'
             raise TileSourceError(msg)
+        self.addKnownExtensions()
 
         self._tileLock = threading.RLock()
 
         try:
             javabridge.attach()
             try:
-                self._bioimage = bioformats.ImageReader(largeImagePath)
+                self._bioimage = bioformats.ImageReader(largeImagePath, perform_init=False)
+                try:
+                    # So this as a separate step so, if it fails, we can ask to
+                    # open something that does not exist and bioformats will
+                    # release some file handles.
+                    self._bioimage.init_reader()
+                except Exception as exc:
+                    try:
+                        # Ask to open a file that should never exist
+                        self._bioimage.rdr.setId('__\0__')
+                    except Exception:
+                        pass
+                    self._bioimage.close()
+                    self._bioimage = None
+                    raise exc
             except (AttributeError, OSError) as exc:
                 if not os.path.isfile(largeImagePath):
                     raise TileSourceFileNotFoundError(largeImagePath) from None
@@ -699,6 +713,18 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     javabridge.detach()
         return large_image.tilesource.base._imageToPIL(image)
 
+    @classmethod
+    def addKnownExtensions(cls):
+        # This starts javabridge/bioformats if needed
+        _getBioformatsVersion()
+        if not hasattr(cls, '_addedExtensions'):
+            cls._addedExtensions = True
+            cls.extensions = cls.extensions.copy()
+            for dotext in bioformats.READABLE_FORMATS:
+                ext = dotext.strip('.')
+                if ext not in cls.extensions:
+                    cls.extensions[ext] = SourcePriority.IMPLICIT
+
 
 def open(*args, **kwargs):
     """

{large-image-source-bioformats-1.27.5.dev57 → large-image-source-bioformats-1.27.5.dev63}/large_image_source_bioformats.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.27.5.dev57
+Version: 1.27.5.dev63
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-source-bioformats-1.27.5.dev63/large_image_source_bioformats.egg-info/requires.txt

@@ -0,0 +1,5 @@
+large-image>=1.27.5.dev63
+python-bioformats>=1.5.2
+
+[girder]
+girder-large-image>=1.27.5.dev63

large-image-source-bioformats-1.27.5.dev57/large_image_source_bioformats.egg-info/requires.txt

@@ -1,5 +0,0 @@
-large-image>=1.27.5.dev57
-python-bioformats>=1.5.2
-
-[girder]
-girder-large-image>=1.27.5.dev57