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",
"-Djava.util.prefs.PreferencesFactory="+
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
add_logback_xml_arg(args)
class_path = get_jars()
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",
dir=cpprefs.get_temporary_directory())
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"):
try:
klass = javabridge.class_for_name(classname)
class_list.add_class(klass)
except:
logger.warn("Could not find Bio-formats reader %s" % classname,
exc_info=1)
for klass in problem_classes:
class_list.add_class(klass)
return class_list
bioformats.formatreader.get_class_list = get_class_list
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 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
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"
]
class_path = get_jars()
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
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 = "%dm" % get_jvm_heap_mb()
args = [r"-Djava.class.path="+class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Dlogback.configurationFile=logback.xml",
r"-Xmx%s" % jvm_arg]
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")
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")
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 = "%dm" % get_jvm_heap_mb()
args = [
r"-Djava.class.path=" + class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Dlogback.configurationFile=logback.xml",
r"-Xmx%s" % jvm_arg
]
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_awt_headless()
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")
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")