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_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_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
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()
import cellprofiler.utilities.version
f = open("cellprofiler/frozen_version.py", "w")
f.write("# MACHINE_GENERATED\nversion_string = '%s'" %
cellprofiler.utilities.version.version_string)
f.close()
APPNAME = 'CellProfiler'
APP = ['CellProfiler.py']
icon_src_path = os.path.join('.', 'cellprofiler', 'icons')
DATA_FILES = [('cellprofiler/icons',
glob.glob(os.path.join(icon_src_path, '*.png')) +
[os.path.join(icon_src_path, "icon_copyrights.txt")])]
from javabridge import JARS
imagej_path = os.path.abspath(os.path.join(".", "imagej", "jars"))
jars = JARS + [
os.path.join(imagej_path, jar) for jar in get_cellprofiler_jars()
]
DATA_FILES.append(('imagej/jars', jars))
OPTIONS = {
'argv_emulation':
True,
'packages': ['cellprofiler', 'contrib', 'imagej', 'javabridge'],
'includes': [
'numpy', 'scipy', 'sklearn', 'sklearn.utils.sparsetools.*', 'wx',
'matplotlib', 'email.iterators', 'smtplib', 'zmq', 'javabridge',
'bioformats', 'sqlite3', 'libtiff', 'wx.lib.intctrl',
'libtiff.' + tiff_h_name, 'xml.dom.minidom', 'h5py', 'h5py.defs',
'h5py.utils', 'h5py._proxy', 'readline'
],
'excludes': ['pylab', 'Tkinter', 'Cython', 'scipy.weave', 'virtualenv'],
'resources': ['CellProfilerIcon.png'],
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 sys.platform == "darwin":
import cellprofiler.utilities.version
f = open("cellprofiler/frozen_version.py", "w")
f.write("# MACHINE_GENERATED\nversion_string = '%s'" % cellprofiler.utilities.version.version_string)
f.close()
APPNAME = 'CellProfiler'
APP = ['CellProfiler.py']
icon_src_path = os.path.join('.', 'cellprofiler', 'icons')
DATA_FILES = [('cellprofiler/icons',
glob.glob(os.path.join(icon_src_path, '*.png'))+
[os.path.join(icon_src_path, "icon_copyrights.txt")])]
from javabridge import JARS
imagej_path = os.path.abspath(os.path.join(".", "imagej", "jars"))
jars = JARS + [os.path.join(imagej_path, jar) for jar in get_cellprofiler_jars()]
jars.append(os.path.join(
imagej_path, "cellprofiler-java-dependencies-classpath.txt"))
DATA_FILES.append(('imagej/jars', jars))
OPTIONS = {'argv_emulation': True,
'packages': ['cellprofiler', 'contrib', 'imagej', 'javabridge'],
'includes': ['numpy', 'scipy', 'sklearn', 'sklearn.utils.sparsetools.*',
'wx', 'matplotlib','email.iterators', 'smtplib', 'zmq',
'javabridge', 'bioformats',
'sqlite3', 'libtiff', 'wx.lib.intctrl', 'libtiff.'+tiff_h_name,
'xml.dom.minidom', 'h5py', 'h5py.defs', 'h5py.utils', 'h5py._proxy', 'readline'],
'excludes': ['pylab', 'Tkinter', 'Cython', 'scipy.weave',
'virtualenv'],
'resources': ['CellProfilerIcon.png'],
'iconfile' : 'CellProfilerIcon.icns',
'frameworks' : [tiff_dylib, jpeg_dylib],
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")
