large-image-source-bioformats 1.27.5.dev6__py3-none-any.whl → 1.30.7.dev12__py3-none-any.whl

large_image_source_bioformats/__init__.py

@@ -23,6 +23,7 @@
 #   IFormatReader.html for interface details.
 
 import atexit
+import builtins
 import logging
 import math
 import os
@@ -61,8 +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|zarr(\.db|\.zip)))$'
+config.ConfigValues['source_bioformats_ignored_names'] = r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|geojson|fits|isyntax|mrxs|zip|zarr(\.db|\.zip)))$'  # noqa
 
 
 def _monitor_thread():
@@ -82,7 +82,7 @@ def _monitor_thread():
                     source._bioimage = None
                 except Exception:
                     pass
-        except AssertionError:
+        except Exception:
             pass
         finally:
             if javabridge.get_env():
@@ -106,7 +106,7 @@ def _reduceLogging():
             'org/slf4j/LoggerFactory', 'getLogger',
             '(Ljava/lang/String;)Lorg/slf4j/Logger;', rootLoggerName)
         logLevel = javabridge.get_static_field(
-            'ch/qos/logback/classic/Level', 'ERROR', 'Lch/qos/logback/classic/Level;')
+            'ch/qos/logback/classic/Level', 'OFF', 'Lch/qos/logback/classic/Level;')
         javabridge.call(rootLogger, 'setLevel', '(Lch/qos/logback/classic/Level;)V', logLevel)
     except Exception:
         pass
@@ -184,6 +184,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     extensions = {
         None: SourcePriority.FALLBACK,
         'czi': SourcePriority.PREFERRED,
+        'ets': SourcePriority.LOW,  # part of vsi
         'lif': SourcePriority.MEDIUM,
         'vsi': SourcePriority.PREFERRED,
     }
@@ -212,16 +213,42 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         largeImagePath = str(self._getLargeImagePath())
         config._ignoreSourceNames('bioformats', largeImagePath)
 
+        header = b''
+        if os.path.isfile(largeImagePath):
+            try:
+                header = builtins.open(largeImagePath, 'rb').read(5)
+            except Exception:
+                msg = 'File cannot be opened via Bioformats'
+                raise TileSourceError(msg)
+        # Never allow pdfs; they crash the JVM
+        if header[:5] == b'%PDF-':
+            msg = 'File cannot be opened via Bioformats'
+            raise TileSourceError(msg)
         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
@@ -294,8 +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([
@@ -343,6 +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
@@ -482,13 +517,15 @@ 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',
@@ -501,11 +538,11 @@ 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:
@@ -584,7 +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]
@@ -617,7 +654,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         height = min(height, sizeYAtScale - offsety)
 
         if scale >= 2 ** self._maxSkippedLevels:
-            tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+            tile, _format = self._getTileFromEmptyLevel(x, y, z, **kwargs)
             tile = large_image.tilesource.base._imageToNumpy(tile)[0]
             format = TILE_FORMAT_NUMPY
         else:
@@ -639,9 +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()
@@ -651,6 +693,8 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             fillValue = 0
             if tile.dtype == np.uint16:
                 fillValue = 65535
+            elif tile.dtype == np.int16:
+                fillValue = 32767
             elif tile.dtype == np.uint8:
                 fillValue = 255
             elif tile.dtype.kind == 'f':
@@ -681,7 +725,7 @@ 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:
@@ -699,6 +743,31 @@ 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
+            # 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-1.27.5.dev6.dist-info → large_image_source_bioformats-1.30.7.dev12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: large-image-source-bioformats
-Version: 1.27.5.dev6
+Version: 1.30.7.dev12
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,12 +15,26 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image >=1.27.5.dev6
-Requires-Dist: python-bioformats >=1.5.2
+Requires-Dist: large-image>=1.30.7.dev12
+Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.5.dev6 ; extra == 'girder'
+Requires-Dist: girder-large-image>=1.30.7.dev12; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 An bioformats tilesource for large_image.
 

large_image_source_bioformats-1.30.7.dev12.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.dev12.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_bioformats-1.30.7.dev12.dist-info/METADATA,sha256=F90J1NBmms4xP0N-aEmZaHxx652cARynfMm8mqgp0i4,1377
+large_image_source_bioformats-1.30.7.dev12.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_bioformats-1.30.7.dev12.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
+large_image_source_bioformats-1.30.7.dev12.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
+large_image_source_bioformats-1.30.7.dev12.dist-info/RECORD,,

{large_image_source_bioformats-1.27.5.dev6.dist-info → large_image_source_bioformats-1.30.7.dev12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_bioformats-1.27.5.dev6.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_bioformats/__init__.py,sha256=wqym0jzlyedMVBGrbNnTMmXq0Ju91HndNI0K_a44ZFo,30482
-large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
-large_image_source_bioformats-1.27.5.dev6.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_bioformats-1.27.5.dev6.dist-info/METADATA,sha256=N3ZJVc0Mf2nxn1TVRNyLx55ikT6ZSoHD7YYNxGSURnE,1034
-large_image_source_bioformats-1.27.5.dev6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_bioformats-1.27.5.dev6.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
-large_image_source_bioformats-1.27.5.dev6.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
-large_image_source_bioformats-1.27.5.dev6.dist-info/RECORD,,