'mov', 'ome', 'ome.tiff', 'png', 'ps', 'tif', 'tiff')
if hasattr(sys, 'frozen') and sys.platform != 'darwin':
__root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
else:
__root_path = os.path.abspath(os.path.split(__file__)[0])
__root_path = os.path.split(__root_path)[0]
__path = os.path.join(__root_path, 'bioformats')
__imagej_path = os.path.join(__root_path, 'imagej')
__loci_jar = os.path.join(__path, "loci_tools.jar")
__ij2_jar = os.path.join(__imagej_path, "imagej-2.0-SNAPSHOT-all.jar")
__ij_jar = os.path.join(__imagej_path, "ij.jar")
__imglib_jar = os.path.join(__imagej_path, "imglib.jar")
__javacl_jar = os.path.join(__imagej_path, "javacl-1.0-beta-4-shaded.jar")
__precompiled_headless_jar = os.path.join(__imagej_path, "precompiled_headless.jar")
USE_IJ2 = get_ij_version() == IJ_2
if os.path.exists(__ij2_jar) and USE_IJ2:
__class_path = os.pathsep.join((__loci_jar, __ij2_jar))
USE_IJ2 = True
else:
USE_IJ2 = False
__class_path = os.pathsep.join((__loci_jar, __ij_jar, __imglib_jar,
__javacl_jar))
if sys.platform == "darwin":
# Start ImageJ headless
# precompiled_headless.jar contains substitute classes for running
# headless.
#
__class_path = os.pathsep.join((__precompiled_headless_jar, __class_path))
if os.environ.has_key("CLASSPATH"):
__class_path += os.pathsep + os.environ["CLASSPATH"]
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global USE_IJ2
global logger
if hasattr(sys, 'frozen') and sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
else:
root_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(root_path)[0]
path = os.path.join(root_path, 'bioformats')
imagej_path = os.path.join(root_path, 'imagej')
loci_jar = os.path.join(path, "loci_tools.jar")
ij2_jar = os.path.join(imagej_path, "imagej-2.0-SNAPSHOT-all.jar")
ij_jar = os.path.join(imagej_path, "ij.jar")
imglib_jar = os.path.join(imagej_path, "imglib.jar")
javacl_jar = os.path.join(imagej_path, "javacl-1.0-beta-4-shaded.jar")
USE_IJ2 = get_ij_version() == IJ_2
if os.path.exists(ij2_jar) and USE_IJ2:
class_path = os.pathsep.join((loci_jar, ij2_jar))
USE_IJ2 = True
else:
USE_IJ2 = False
class_path = os.pathsep.join((loci_jar, ij_jar, imglib_jar,
javacl_jar))
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib","tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = [x.groups()[0] for x in [
re.match('--jvm-heap-size=([0-9]+[gGkKmM])', y) for y in sys.argv]
if x is not None]
if len(jvm_arg) > 0:
jvm_arg = jvm_arg[0]
else:
jvm_arg = "512m"
args = [r"-Djava.class.path="+class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg]
if get_ij_plugin_directory() is not None:
args.append("-Dplugins.dir="+get_ij_plugin_directory())
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/"+log4j_properties.replace(os.path.sep, "/")
args += [r"-Dlog4j.configuration="+log4j_properties]
init_logger = False
else:
init_logger = True
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location",
"cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning("Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level","WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not run_headless:
jutil.activate_awt()
if hasattr(sys, 'frozen') and sys.platform != 'darwin':
__root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
else:
__root_path = os.path.abspath(os.path.split(__file__)[0])
__root_path = os.path.split(__root_path)[0]
__path = os.path.join(__root_path, 'bioformats')
__imagej_path = os.path.join(__root_path, 'imagej')
__loci_jar = os.path.join(__path, "loci_tools.jar")
__ij2_jar = os.path.join(__imagej_path, "imagej-2.0-SNAPSHOT-all.jar")
__ij_jar = os.path.join(__imagej_path, "ij.jar")
__imglib_jar = os.path.join(__imagej_path, "imglib.jar")
__javacl_jar = os.path.join(__imagej_path, "javacl-1.0-beta-4-shaded.jar")
__precompiled_headless_jar = os.path.join(__imagej_path,
"precompiled_headless.jar")
USE_IJ2 = get_ij_version() == IJ_2
if os.path.exists(__ij2_jar) and USE_IJ2:
__class_path = os.pathsep.join((__loci_jar, __ij2_jar))
USE_IJ2 = True
else:
USE_IJ2 = False
__class_path = os.pathsep.join(
(__loci_jar, __ij_jar, __imglib_jar, __javacl_jar))
if sys.platform == "darwin":
# Start ImageJ headless
# precompiled_headless.jar contains substitute classes for running
# headless.
#
__class_path = os.pathsep.join(
(__precompiled_headless_jar, __class_path))
if os.environ.has_key("CLASSPATH"):
