large-image-source-bioformats 1.30.5.dev6__tar.gz → 1.30.6__tar.gz

{large_image_source_bioformats-1.30.5.dev6 → large_image_source_bioformats-1.30.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.30.5.dev6
+Version: 1.30.6
 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>=1.30.5.dev6
+Requires-Dist: large-image>=1.30.6
 Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.5.dev6; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6; extra == "girder"
 
 An bioformats tilesource for large_image.
 

{large_image_source_bioformats-1.30.5.dev6 → large_image_source_bioformats-1.30.6}/large_image_source_bioformats/__init__.py

@@ -62,7 +62,7 @@ _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|zip|zarr(\.db|\.zip)))$'  # noqa
+config.ConfigValues['source_bioformats_ignored_names'] = r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|geojson|fits|isyntax|mrxs|zip|zarr(\.db|\.zip)))$'  # noqa
 
 
 def _monitor_thread():
@@ -509,13 +509,15 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
 
     def _computeMagnification(self):
         self._magnification = {}
-        metadata = self._metadata['metadata']
+        metadata = self._metadata.get('seriesMetadata', {}).copy()
+        metadata.update(self._metadata['metadata'])
         valuekeys = {
             'x': [('Scaling|Distance|Value #1', 1e3)],
             'y': [('Scaling|Distance|Value #2', 1e3)],
         }
         tuplekeys = [
             ('Physical pixel size', 1e-3),
+            ('0028,0030 Pixel Spacing', 1),
         ]
         magkeys = [
             'Information|Instrument|Objective|NominalMagnification #1',
@@ -528,11 +530,11 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if 'mm_x' not in self._magnification and 'mm_y' not in self._magnification:
             for key, units in tuplekeys:
                 if metadata.get(key):
-                    found = re.match(r'^\D*(\d+(|\.\d+))\D+(\d+(|\.\d+))\D*$', metadata[key])
+                    found = re.match(r'^[^0-9.]*(\d*\.?\d+)[^0-9.]+(\d*\.?\d+)\D*$', metadata[key])
                     if found:
                         try:
                             self._magnification['mm_x'], self._magnification['mm_y'] = (
-                                float(found.groups()[0]) * units, float(found.groups()[2]) * units)
+                                float(found.groups()[0]) * units, float(found.groups()[1]) * units)
                         except Exception:
                             pass
         for key in magkeys:
@@ -710,7 +712,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         info = self._metadata['seriesAssociatedImages'].get(imageKey)
         if info is None:
-            return
+            return None
         series = info['seriesNum']
         with self._tileLock:
             try:
@@ -739,6 +741,19 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 ext = dotext.strip('.')
                 if ext not in cls.extensions:
                     cls.extensions[ext] = SourcePriority.IMPLICIT
+            # The python modules doesn't list all the extensions that can be
+            # read, so supplement from the jar
+            readerlist = zipfile.ZipFile(
+                pathlib.Path(bioformats.__file__).parent /
+                'jars/bioformats_package.jar',
+            ).open('loci/formats/readers.txt').read(100000).decode().split('\n')
+            pattern = re.compile(r'^loci\.formats\.in\..* # (?:.*?\b(\w{2,})\b(?:,|\s|$))')
+            for line in readerlist:
+                for ext in set(pattern.findall(line)) - {
+                        'pattern', 'urlreader', 'screen', 'zip', 'zarr', 'db',
+                        'fake', 'no'}:
+                    if ext not in cls.extensions:
+                        cls.extensions[ext] = SourcePriority.IMPLICIT
 
 
 def open(*args, **kwargs):

{large_image_source_bioformats-1.30.5.dev6 → large_image_source_bioformats-1.30.6}/large_image_source_bioformats.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.30.5.dev6
+Version: 1.30.6
 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>=1.30.5.dev6
+Requires-Dist: large-image>=1.30.6
 Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.5.dev6; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.6; extra == "girder"
 
 An bioformats tilesource for large_image.
 

large_image_source_bioformats-1.30.6/large_image_source_bioformats.egg-info/requires.txt

@@ -0,0 +1,5 @@
+large-image>=1.30.6
+python-bioformats>=1.5.2
+
+[girder]
+girder-large-image>=1.30.6

{large_image_source_bioformats-1.30.5.dev6 → large_image_source_bioformats-1.30.6}/setup.py

@@ -19,8 +19,7 @@ def prerelease_local_scheme(version):
 
     if os.getenv('CIRCLE_BRANCH') in ('master', ):
         return ''
-    else:
-        return get_local_node_and_date(version)
+    return get_local_node_and_date(version)
 
 
 try:

large_image_source_bioformats-1.30.5.dev6/large_image_source_bioformats.egg-info/requires.txt

@@ -1,5 +0,0 @@
-large-image>=1.30.5.dev6
-python-bioformats>=1.5.2
-
-[girder]
-girder-large-image>=1.30.5.dev6