large-image-source-bioformats 1.26.3.dev14__tar.gz → 1.26.3.dev24__tar.gz

{large-image-source-bioformats-1.26.3.dev14 → large-image-source-bioformats-1.26.3.dev24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.26.3.dev14
+Version: 1.26.3.dev24
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-source-bioformats-1.26.3.dev14 → large-image-source-bioformats-1.26.3.dev24}/large_image_source_bioformats/__init__.py

@@ -26,10 +26,12 @@ import atexit
 import logging
 import math
 import os
+import pathlib
 import re
 import threading
 import types
 import weakref
+import zipfile
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
@@ -53,6 +55,8 @@ bioformats = None
 javabridge = None
 
 _javabridgeStarted = None
+_javabridgeStartLock = threading.Lock()
+_bioformatsVersion = None
 _openImages = []
 
 
@@ -87,7 +91,7 @@ def _monitor_thread():
 
 
 def _reduceLogging():
-    # As of bioformat 4.0.0, org.apache.log4j isn't in the bundled
+    # As of python-bioformats 4.0.0, org.apache.log4j isn't in the bundled
     # jar file, so setting log levels just produces needless warnings.
     # bioformats.log4j.basic_config()
     # javabridge.JClassWrapper('loci.common.Log4jTools').setRootLevel(
@@ -110,30 +114,40 @@ def _reduceLogging():
 
 
 def _startJavabridge(logger):
-    global _javabridgeStarted
+    global _javabridgeStarted, _bioformatsVersion
+
+    with _javabridgeStartLock:
+        if _javabridgeStarted is None:
+            # Only import these when first asked.  They are slow to import.
+            global bioformats
+            global javabridge
+            if bioformats is None:
+                import bioformats
+                try:
+                    _bioformatsVersion = zipfile.ZipFile(
+                        pathlib.Path(bioformats.__file__).parent /
+                        'jars/bioformats_package.jar',
+                    ).open('META-INF/MANIFEST.MF').read(8192).split(
+                        b'Implementation-Version: ')[1].split()[0].decode()
+                    logger.info('Bioformats.jar version: %s', _bioformatsVersion)
+                except Exception:
+                    pass
+            if javabridge is None:
+                import javabridge
 
-    if _javabridgeStarted is None:
-        # Only import these when first asked.  They are slow to import.
-        global bioformats
-        global javabridge
-        if bioformats is None:
-            import bioformats
-        if javabridge is None:
-            import javabridge
-
-        # We need something to wake up at exit and shut things down
-        monitor = threading.Thread(target=_monitor_thread)
-        monitor.daemon = True
-        monitor.start()
-        try:
-            javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
-            _reduceLogging()
-            atexit.register(_stopJavabridge)
-            logger.info('Started JVM for Bioformats tile source.')
-            _javabridgeStarted = True
-        except RuntimeError:
-            logger.exception('Cannot start JVM for Bioformats tile source.')
-            _javabridgeStarted = False
+            # We need something to wake up at exit and shut things down
+            monitor = threading.Thread(target=_monitor_thread)
+            monitor.daemon = True
+            monitor.start()
+            try:
+                javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
+                _reduceLogging()
+                atexit.register(_stopJavabridge)
+                logger.info('Started JVM for Bioformats tile source.')
+                _javabridgeStarted = True
+            except RuntimeError:
+                logger.exception('Cannot start JVM for Bioformats tile source.')
+                _javabridgeStarted = False
     return _javabridgeStarted
 
 
@@ -145,6 +159,21 @@ def _stopJavabridge(*args, **kwargs):
     _javabridgeStarted = None
 
 
+def _getBioformatsVersion():
+    """
+    Get the version of the jar file.
+
+    :returns: the version string if it is in the expected format, None
+        otherwise.
+    """
+    if _bioformatsVersion is None:
+        from large_image import config
+
+        logger = config.getLogger()
+        _startJavabridge(logger)
+    return _bioformatsVersion
+
+
 class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     """
     Provides tile access to via Bioformats.

{large-image-source-bioformats-1.26.3.dev14 → large-image-source-bioformats-1.26.3.dev24}/large_image_source_bioformats.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-bioformats
-Version: 1.26.3.dev14
+Version: 1.26.3.dev24
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-source-bioformats-1.26.3.dev24/large_image_source_bioformats.egg-info/requires.txt

@@ -0,0 +1,5 @@
+large-image>=1.26.3.dev24
+python-bioformats>=1.5.2
+
+[girder]
+girder-large-image>=1.26.3.dev24

large-image-source-bioformats-1.26.3.dev14/large_image_source_bioformats.egg-info/requires.txt

@@ -1,5 +0,0 @@
-large-image>=1.26.3.dev14
-python-bioformats>=1.5.2
-
-[girder]
-girder-large-image>=1.26.3.dev14