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
"""
class_path = []
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"])
pathname = os.path.dirname(prokaryote.__file__)
jar_files = [os.path.join(pathname, f) for f in os.listdir(pathname) if f.lower().endswith(".jar")]
class_path += javabridge.JARS + jar_files
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
"""
class_path = []
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"])
pathname = os.path.dirname(prokaryote.__file__)
jar_files = [
os.path.join(pathname, f) for f in os.listdir(pathname)
if f.lower().endswith(".jar")
]
class_path += javabridge.JARS + jar_files
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 run_maven(pom_path, goal="package",
quiet=False, run_tests=True, aggressive_update = True,
return_stdout = False, additional_args = []):
'''Run a Maven pom to install all of the needed jars
pom_path - the directory hosting the Maven POM
goal - the maven goal. "package" is the default which is pretty much
"do whatever the POM was built to do"
quiet - feed Maven the -q switch if true to make it run in quiet mode
run_tests - if False, set the "skip tests" maven flag. This is appropriate
if you're silently building a known-good downloaded source.
aggressive_update - if True, use the -U switch to make Maven go to the
internet and check for updates. If False, default behavior.
If None, use the -o switch to prevent Maven from any online
updates.
return_stdout - redirect stdout to capture a string and return it if True,
dump Maven output to console if False
additional_args - additional arguments for the command-line
Runs mvn package on the POM
'''
from javabridge.locate import find_jdk
maven_install_path = get_maven_install_path()
jdk_home = find_jdk()
env = os.environ.copy()
if jdk_home is not None:
env["JAVA_HOME"] = jdk_home
executeable_path = get_mvn_executable_path(maven_install_path)
args = [executeable_path]
if aggressive_update:
args.append("-U")
elif aggressive_update is None:
args.append("-o")
if quiet:
args.append("-q")
if not run_tests:
args.append("-Dmaven.test.skip=true")
args += additional_args
args.append(goal)
logging.debug("Running %s" % (" ".join(args)))
for key in list(env.keys()):
value = env[key]
if isinstance(key, unicode):
key = key.encode("utf-8")
if isinstance(value, unicode):
value = value.encode("utf-8")
env[key] = value
if return_stdout:
return check_output(args, cwd = pom_path, env=env)
else:
subprocess.check_call(args, cwd = pom_path, env=env)
def run_maven(pom_path, goal="package",
quiet=False, run_tests=True, aggressive_update = True,
return_stdout = False, additional_args = []):
'''Run a Maven pom to install all of the needed jars
pom_path - the directory hosting the Maven POM
goal - the maven goal. "package" is the default which is pretty much
"do whatever the POM was built to do"
quiet - feed Maven the -q switch if true to make it run in quiet mode
run_tests - if False, set the "skip tests" maven flag. This is appropriate
if you're silently building a known-good downloaded source.
aggressive_update - if True, use the -U switch to make Maven go to the
internet and check for updates. If False, default behavior.
If None, use the -o switch to prevent Maven from any online
updates.
return_stdout - redirect stdout to capture a string and return it if True,
dump Maven output to console if False
additional_args - additional arguments for the command-line
Runs mvn package on the POM
'''
from javabridge.locate import find_jdk
maven_install_path = get_maven_install_path()
jdk_home = find_jdk()
env = os.environ.copy()
if jdk_home is not None:
env["JAVA_HOME"] = jdk_home
executeable_path = get_mvn_executable_path(maven_install_path)
args = [executeable_path]
if aggressive_update:
args.append("-U")
elif aggressive_update is None:
args.append("-o")
if quiet:
args.append("-q")
if not run_tests:
args.append("-Dmaven.test.skip=true")
args += additional_args
args.append(goal)
logging.debug("Running %s" % (" ".join(args)))
for key in list(env.keys()):
value = env[key]
if isinstance(key, unicode):
key = key.encode("utf-8")
if isinstance(value, unicode):
value = value.encode("utf-8")
env[key] = value
if return_stdout:
return check_output(args, cwd = pom_path, env=env)
else:
subprocess.check_call(args, cwd = pom_path, env=env)
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
data_files += [('artwork', [
'artwork\\%s' % (x) for x in os.listdir('artwork')
if x.endswith(".png") or x.endswith(".psd") or x.endswith(".txt")
]),
('imagej\\jars',
['imagej\\jars\\%s' % x for x in os.listdir('imagej\\jars')])]
data_files += matplotlib.get_py2exe_datafiles()
################################
#
# Collect the JVM
#
################################
from javabridge.locate import find_jdk
jdk_dir = find_jdk()
temp_dir = tempfile.mkdtemp()
rofiles = []
def add_jre_files(path):
files = []
directories = []
local_path = os.path.join(jdk_dir, path)
for filename in os.listdir(local_path):
if filename.startswith("."):
continue
local_file = os.path.join(jdk_dir, path, filename)
relative_path = os.path.join(path, filename)
if not os.access(local_file, os.W_OK):
# distutils can't deal so well with read-only files
data_files += [('cellprofiler\\icons',
['cellprofiler\\icons\\%s'%(x)
for x in os.listdir('cellprofiler\\icons')
if x.endswith(".png")
or x.endswith(".psd") or x.endswith(".txt")]),
('imagej\\jars',
['imagej\\jars\\%s' % x for x in os.listdir('imagej\\jars')])]
data_files += matplotlib.get_py2exe_datafiles()
################################
#
# Collect the JVM
#
################################
from javabridge.locate import find_jdk
jdk_dir = find_jdk()
temp_dir = tempfile.mkdtemp()
rofiles = []
def add_jre_files(path):
files = []
directories = []
local_path = os.path.join(jdk_dir, path)
for filename in os.listdir(local_path):
if filename.startswith("."):
continue
local_file = os.path.join(jdk_dir, path, filename)
relative_path = os.path.join(path, filename)
if not os.access(local_file, os.W_OK):
# distutils can't deal so well with read-only files
old_local_file = local_file
temp_path = os.path.join(temp_dir, path)
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"
]
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")
