Use the class_path keyword argument to start_vm.

See CellProfiler/python-javabridge@0977f26

Author: ljosa

bioformats/__init__.py

@@ -20,8 +20,11 @@
 from . import formatwriter as _formatwriter
 
 _jars_dir = os.path.join(os.path.dirname(__file__), 'jars')
+
 JARS = javabridge.JARS + [os.path.realpath(os.path.join(_jars_dir, name + '.jar'))
                           for name in ['loci_tools']]
+"""List of directories, jar files, and zip files that should be added
+to the Java virtual machine's class path."""
 
 # See http://www.loci.wisc.edu/software/bio-formats
 READABLE_FORMATS = ('al3d', 'am', 'amiramesh', 'apl', 'arf', 'avi', 'bmp', 

demo/demo.py

@@ -5,15 +5,14 @@
 import bioformats
 from bioformats import log4j
 
-class_path = os.pathsep.join(bioformats.JARS + javabridge.JARS)
-javabridge.start_vm(['-Djava.class.path=' + class_path], 
+javabridge.start_vm(class_path=bioformats.JARS,
                     run_headless=True)
 try:
     log4j.basic_config()
     image_path = os.path.join(os.path.dirname(bioformats.__file__), 'tests', 
                               'Channel1-01-A-01.tif')
-    image, scale = bioformats.load_using_bioformats(image_path, rescale=False,
-                                                    wants_max_intensity=True)
+    image, scale = bioformats.load_image(image_path, rescale=False,
+                                         wants_max_intensity=True)
     print image.shape
 finally:
     javabridge.kill_vm()

docs/conf.py

@@ -249,4 +249,4 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {'javabridge': ('http://pythonhosted.org/javabridge/', None)}

docs/index.rst

@@ -37,6 +37,21 @@ Running the unit tests requires Nose.
     python setup.py nosetests
 
 
+Starting the JVM
+================
+
+When starting the Java virtual machine with python-javabridge's
+:py:func:`javabridge.start_vm`, you must add the contents of
+:py:data:`bioformats.JARS` to the class path. Example:
+
+>>> import javabridge
+>>> import bioformats
+>>> javabridge.start_vm(class_path=bioformats.JARS)
+
+.. autodata:: bioformats.JARS
+   :annotation: list of strings
+
+
 Reading images
 ==============
 

setup.py

@@ -13,6 +13,7 @@
     it. Python-bioformats was developed for and is used by the cell
     image analysis software CellProfiler (cellprofiler.org).''',
     url="http://github.com/CellProfiler/python-bioformats/",
+    bugtrack_url="http://github.com/CellProfiler/python-bioformats/issues",
     packages=['bioformats'],
     classifiers=['Development Status :: 5 - Production/Stable',
                  'License :: OSI Approved :: BSD License',
@@ -22,7 +23,7 @@
              ],
     license='BSD License',
     package_data={'bioformats': ['jars/*.jar']},
-
+    install_requires=['javabridge>=1.0'],
     tests_require='nose',
     entry_points={'nose.plugins.0.10': [
             'javabridge = javabridge.noseplugin:JavabridgePlugin',