def get_jars():
'''Get the final list of JAR files passed to javabridge'''
imagej_path = get_path_to_jars()
if hasattr(sys, 'frozen'):
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = sorted(jar_files, cmp=sort_fn)
else:
jar_files = get_cellprofiler_jars()
jar_files = [os.path.join(imagej_path, f) for f in jar_files]
class_path = javabridge.JARS + jar_files
if os.environ.has_key("CLASSPATH"):
class_path += os.environ["CLASSPATH"].split(os.pathsep)
logging.debug("Adding Java class path from environment variable, "
"CLASSPATH"
"")
logging.debug(" CLASSPATH=" + os.environ["CLASSPATH"])
plugin_directory = cpprefs.get_ij_plugin_directory()
if (plugin_directory is not None and os.path.isdir(plugin_directory)):
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path.append(plugin_directory)
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path.append(jarpath)
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " +
plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from javabridge.locate 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.append(tools_jar)
else:
logger.warning("Failed to find tools.jar")
return class_path
def get_jars():
'''Get the final list of JAR files passed to javabridge'''
imagej_path = get_path_to_jars()
if hasattr(sys, 'frozen'):
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = sorted(jar_files, cmp = sort_fn)
else:
jar_files = get_cellprofiler_jars()
jar_files = [os.path.join(imagej_path, f) for f in jar_files]
class_path = javabridge.JARS + jar_files
if os.environ.has_key("CLASSPATH"):
class_path += os.environ["CLASSPATH"].split(os.pathsep)
logging.debug(
"Adding Java class path from environment variable, ""CLASSPATH""")
logging.debug(" CLASSPATH="+os.environ["CLASSPATH"])
plugin_directory = cpprefs.get_ij_plugin_directory()
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path.append(plugin_directory)
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path.append(jarpath)
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: "
+ plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from javabridge.locate 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.append(tools_jar)
else:
logger.warning("Failed to find tools.jar")
return class_path
def start_ij(self):
try:
self.client_socket.close()
self.server_socket.close()
except: pass
self.server_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
self.server_socket.bind(("", 0))
_, self.port = self.server_socket.getsockname()
self.server_socket.listen(5)
self.server_socket.listen(5)
print "ImageJ bridge TCPServer waiting for client on port", self.port
from cellprofiler.preferences import get_ij_plugin_directory
plugin_dir = get_ij_plugin_directory()
if plugin_dir is not None:
command = 'java -Xmx512m -Dplugins.dir=%s TCPClient %s' % (
plugin_dir, self.port)
else:
command = 'java -Xmx512m TCPClient %s' % self.port
self.ijproc = Popen(shlex.split(command),
stdin=None, stdout=None, stderr=None)
self.client_socket, address = self.server_socket.accept()
print "ImageJ bridge got a connection from", address
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej','jars')
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
jar_files = sorted(jar_files, cmp = sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej','jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " + plugin_directory)
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]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_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
if get_headless():
# We're running silently, so don't change the Java preferences
# The following definition uses a process-scope preferences factory
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
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 get_headless():
jutil.activate_awt()
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.analysis_worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP, CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
# sys.argv[0] points at
# CellProfiler.app/Contents/Resources/CellProfiler.py
# We want
# CellProfiler.app/Contents/MacOS/CellProfiler
#
contents_resources_dir = os.path.split(sys.argv[0])[0]
contents_dir = os.path.split(contents_resources_dir)[0]
cp_executable = os.path.join(contents_dir, "MacOS", "CellProfiler")
assert os.path.isfile(cp_executable), \
"Did not find CellProfiler in its expected place: %s" % cp_executable
assert os.access(cp_executable, os.EX_OK), \
"%s is not executable" % cp_executable
args = ["arch", "-x86_64", "-i386", cp_executable,
"--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
else:
aw_path = os.path.join(
os.path.split(
os.path.abspath(sys.argv[0]))[0],
"analysis_worker")
args = [aw_path,
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
worker = subprocess.Popen(args,
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source(),
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()],
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
def run_logger(workR, widx):
while(True):
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.analysis_worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP, CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
# sys.argv[0] points at
# CellProfiler.app/Contents/Resources/CellProfiler.py
# We want
# CellProfiler.app/Contents/MacOS/CellProfiler
#
contents_resources_dir = os.path.split(sys.argv[0])[0]
contents_dir = os.path.split(contents_resources_dir)[0]
cp_executable = os.path.join(contents_dir, "MacOS", "CellProfiler")
assert os.path.isfile(cp_executable), \
"Did not find CellProfiler in its expected place: %s" % cp_executable
assert os.access(cp_executable, os.EX_OK), \
"%s is not executable" % cp_executable
args = ["arch", "-x86_64", cp_executable,
"--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
else:
aw_path = os.path.join(
os.path.split(
os.path.abspath(sys.argv[0]))[0],
"analysis_worker")
args = [aw_path,
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
worker = subprocess.Popen(args,
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source(),
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()],
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
def run_logger(workR, widx):
while(True):
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej', 'jars')
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
jar_files = sorted(jar_files, cmp=sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej', 'jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
if (get_ij_plugin_directory() is not None
and os.path.isdir(get_ij_plugin_directory())):
plugin_directory = get_ij_plugin_directory()
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
#
# Add any .jar files in the directory
#
class_path += os.pathsep + os.pathsep.join([
os.path.join(plugin_directory, jarfile)
for jarfile in os.listdir(plugin_directory)
if jarfile.lower().endswith(".jar")
])
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
]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_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
if get_headless():
# We're running silently, so don't change the Java preferences
# The following definition uses a process-scope preferences factory
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
run_headless = (get_headless()
and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
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 get_headless():
jutil.activate_awt()
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej','jars')
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
jar_files = sorted(jar_files, cmp = sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej','jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " + plugin_directory)
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 = jutil.get_jvm_heap_size_arg()
if jvm_arg is None:
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]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_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
if plugin_directory is not None and os.path.isdir(plugin_directory):
# For IJ1 compatibility
args += [r"-Dplugins.dir=%s" % plugin_directory]
# In headless mode, we have to avoid changing the Java preferences.
#
# Aside from that, we need to prevent ImageJ from exiting and from
# displaying the updater dialog - at least temporarily, we do that
# through preferences. We use the HeadlessPreferencesFactory to
# limit the scope of the changes to this process - otherwise we'd
# turn off updating for the machine.
#
# TODO: ImageJ is implementing a pluggable mechanism to control the
# quit process. We can also contribute a pluggable mechanism
# that gives us more control over the updater.
#
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
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 get_headless():
jutil.activate_awt()
def cp_start_vm():
'''Start CellProfiler's JVM via Javabridge
JVM parameters are harvested from preferences and
the environment variables:
CP_JDWP_PORT - port # for debugging Java within the JVM
cpprefs.get_awt_headless() - controls java.awt.headless to prevent
awt from being invoked
'''
args = ["-Dloci.bioformats.loaded=true",
"-Dlogback.configurationFile=logback.xml",
"-Djava.util.prefs.PreferencesFactory="+
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
imagej_path = get_path_to_jars()
if hasattr(sys, 'frozen'):
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = sorted(jar_files, cmp = sort_fn)
else:
jar_files = get_cellprofiler_jars()
jar_files = [os.path.join(imagej_path, f) for f in jar_files]
class_path = javabridge.JARS + jar_files
if os.environ.has_key("CLASSPATH"):
class_path += os.environ["CLASSPATH"].split(os.pathsep)
logging.debug(
"Adding Java class path from environment variable, ""CLASSPATH""")
logging.debug(" CLASSPATH="+os.environ["CLASSPATH"])
plugin_directory = cpprefs.get_ij_plugin_directory()
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path.append(plugin_directory)
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path.append(jarpath)
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: "
+ plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from javabridge.locate 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.append(tools_jar)
else:
logger.warning("Failed to find tools.jar")
args += get_patcher_args(class_path)
awt_headless = cpprefs.get_awt_headless()
if awt_headless:
logger.debug("JVM will be started with AWT in headless mode")
args.append("-Djava.awt.headless=true")
heap_size = str(cpprefs.get_jvm_heap_mb())+"m"
if os.environ.has_key("CP_JDWP_PORT"):
args.append(
("-agentlib:jdwp=transport=dt_socket,address=127.0.0.1:%s"
",server=y,suspend=n") % os.environ["CP_JDWP_PORT"])
javabridge.start_vm(args=args,
class_path=class_path,
max_heap_size = heap_size)
#
# Enable Bio-Formats directory cacheing
#
try:
c_location = javabridge.JClassWrapper("loci.common.Location")
c_location.cacheDirectoryListings(True)
logger.debug("Enabled Bio-formats directory cacheing")
except:
logger.warning("Bioformats version does not support directory cacheing")
#
# Monkey-patch bioformats.formatreader.get_class_list to add
# the classes we added to loci.formats.in
#
import bioformats.formatreader
old_get_class_list = bioformats.formatreader.get_class_list
def get_class_list():
"Return a wrapped instance of loci.formats.ClassList"
env = javabridge.get_env()
class_list = old_get_class_list()
rais_classname = 'loci/common/RandomAccessInputStream'
#
# Move any class to the back that thinks it can read garbage
#
fd, path = tempfile.mkstemp(suffix=".garbage")
stream = None
try:
os.write(fd, "This is not an image file")
os.fsync(fd)
stream = javabridge.make_instance(
rais_classname, '(Ljava/lang/String;)V', path)
problem_classes = []
for klass in env.get_object_array_elements(class_list.get_classes()):
try:
instance = javabridge.call(
klass, "newInstance", "()Ljava/lang/Object;")
can_read_garbage = javabridge.call(
instance, "isThisType",
"(L%s;)Z" % rais_classname, stream)
if can_read_garbage:
problem_classes.append(klass)
class_list.remove_class(klass)
except:
logger.info("Caught exception in %s.isThisType",
javabridge.to_string(klass))
finally:
os.close(fd)
javabridge.call(stream, "close", "()V")
os.remove(path)
for classname in ("loci.formats.in.FlowSightReader",
"loci.formats.in.IM3Reader"):
klass = javabridge.class_for_name(classname)
class_list.add_class(klass)
for klass in problem_classes:
class_list.add_class(klass)
return class_list
bioformats.formatreader.get_class_list = get_class_list
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"-Djava.ext.dirs=%s"%__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
if ((get_headless() and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP
from cellprofiler.pipeline import CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
aw_args = ["--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
jvm_arg = "%dm" % cpprefs.get_jvm_heap_mb()
aw_args.append("--jvm-heap-size=%s" % jvm_arg)
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
executable = os.path.join(
os.path.dirname(sys.executable), "CellProfiler")
args = ([executable] + aw_args)
elif sys.platform.startswith('linux'):
aw_path = os.path.join(os.path.dirname(__file__),
"worker.py")
args = [sys.executable, aw_path] + aw_args
else:
args = [sys.executable] + aw_args
worker = subprocess.Popen(args,
env=find_worker_env(idx),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds=close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source()] + aw_args,
env=find_worker_env(idx),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds=close_fds)
def run_logger(workR, widx):
while True:
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej', 'jars')
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
jar_files = sorted(jar_files, cmp=sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej', 'jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " +
plugin_directory)
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 = jutil.get_jvm_heap_size_arg()
if jvm_arg is None:
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
]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_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
if plugin_directory is not None and os.path.isdir(plugin_directory):
# For IJ1 compatibility
args += [r"-Dplugins.dir=%s" % plugin_directory]
# In headless mode, we have to avoid changing the Java preferences.
#
# Aside from that, we need to prevent ImageJ from exiting and from
# displaying the updater dialog - at least temporarily, we do that
# through preferences. We use the HeadlessPreferencesFactory to
# limit the scope of the changes to this process - otherwise we'd
# turn off updating for the machine.
#
# TODO: ImageJ is implementing a pluggable mechanism to control the
# quit process. We can also contribute a pluggable mechanism
# that gives us more control over the updater.
#
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
run_headless = (get_headless()
and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
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 get_headless():
jutil.activate_awt()
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()
def cp_start_vm():
'''Start CellProfiler's JVM via Javabridge
JVM parameters are harvested from preferences and
the environment variables:
CP_JDWP_PORT - port # for debugging Java within the JVM
cpprefs.get_awt_headless() - controls java.awt.headless to prevent
awt from being invoked
'''
args = [
"-Dloci.bioformats.loaded=true",
"-Dlogback.configurationFile=logback.xml",
"-Djava.util.prefs.PreferencesFactory=" +
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
imagej_path = get_path_to_jars()
if hasattr(sys, 'frozen'):
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = sorted(jar_files, cmp=sort_fn)
else:
jar_files = get_cellprofiler_jars()
jar_files = [os.path.join(imagej_path, f) for f in jar_files]
class_path = javabridge.JARS + jar_files
if os.environ.has_key("CLASSPATH"):
class_path += os.environ["CLASSPATH"].split(os.pathsep)
logging.debug("Adding Java class path from environment variable, "
"CLASSPATH"
"")
logging.debug(" CLASSPATH=" + os.environ["CLASSPATH"])
plugin_directory = cpprefs.get_ij_plugin_directory()
if (plugin_directory is not None and os.path.isdir(plugin_directory)):
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path.append(plugin_directory)
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path.append(jarpath)
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " +
plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from javabridge.locate 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.append(tools_jar)
else:
logger.warning("Failed to find tools.jar")
args += get_patcher_args(class_path)
awt_headless = cpprefs.get_awt_headless()
if awt_headless:
logger.debug("JVM will be started with AWT in headless mode")
args.append("-Djava.awt.headless=true")
heap_size = str(cpprefs.get_jvm_heap_mb()) + "m"
if os.environ.has_key("CP_JDWP_PORT"):
args.append(("-agentlib:jdwp=transport=dt_socket,address=127.0.0.1:%s"
",server=y,suspend=n") % os.environ["CP_JDWP_PORT"])
javabridge.start_vm(args=args,
class_path=class_path,
max_heap_size=heap_size)
#
# Enable Bio-Formats directory cacheing
#
try:
c_location = javabridge.JClassWrapper("loci.common.Location")
c_location.cacheDirectoryListings(True)
logger.debug("Enabled Bio-formats directory cacheing")
except:
logger.warning(
"Bioformats version does not support directory cacheing")
def cp_start_vm():
'''Start CellProfiler's JVM via Javabridge
JVM parameters are harvested from preferences and
the environment variables:
CP_JDWP_PORT - port # for debugging Java within the JVM
cpprefs.get_awt_headless() - controls java.awt.headless to prevent
awt from being invoked
'''
args = ["-Dloci.bioformats.loaded=true",
"-Dlogback.configurationFile=logback.xml",
"-Djava.util.prefs.PreferencesFactory="+
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
imagej_path = get_path_to_jars()
if hasattr(sys, 'frozen'):
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = sorted(jar_files, cmp = sort_fn)
else:
jar_files = get_cellprofiler_jars()
jar_files = [os.path.join(imagej_path, f) for f in jar_files]
class_path = javabridge.JARS + jar_files
if os.environ.has_key("CLASSPATH"):
class_path += os.environ["CLASSPATH"].split(os.pathsep)
logging.debug(
"Adding Java class path from environment variable, ""CLASSPATH""")
logging.debug(" CLASSPATH="+os.environ["CLASSPATH"])
plugin_directory = cpprefs.get_ij_plugin_directory()
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path.append(plugin_directory)
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path.append(jarpath)
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: "
+ plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from javabridge.locate 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.append(tools_jar)
else:
logger.warning("Failed to find tools.jar")
args += get_patcher_args(class_path)
awt_headless = cpprefs.get_awt_headless()
if awt_headless:
logger.debug("JVM will be started with AWT in headless mode")
args.append("-Djava.awt.headless=true")
heap_size = str(cpprefs.get_jvm_heap_mb())+"m"
if os.environ.has_key("CP_JDWP_PORT"):
args.append(
("-agentlib:jdwp=transport=dt_socket,address=127.0.0.1:%s"
",server=y,suspend=n") % os.environ["CP_JDWP_PORT"])
javabridge.start_vm(args=args,
class_path=class_path,
max_heap_size = heap_size)
#
# Enable Bio-Formats directory cacheing
#
try:
c_location = javabridge.JClassWrapper("loci.common.Location")
c_location.cacheDirectoryListings(True)
logger.debug("Enabled Bio-formats directory cacheing")
except:
logger.warning("Bioformats version does not support directory cacheing")
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"-Djava.ext.dirs=%s"%__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
