def getColorModel(
color_space, has_alpha=False, is_alpha_premultiplied=False, transparency=OPAQUE, transfer_type=TYPE_BYTE
):
"""Return a java.awt.image.ColorModel color model
color_space - a java.awt.color.ColorSpace such as returned by
getGrayColorSpace or getRGBColorSpace
has_alpha - True if alpha channel is specified
is_alpha_premultiplied - True if other channel values have already
been reduced by the alpha multiplier, False if the channel values are
independent of the multiplier.
transparency - one of BITMASK, OPAQUE or TRANSPARENT.
transfer_type - one of TYPE_BYTE, TYPE_USHORT, TYPE_INT
"""
jtransparency = jutil.get_static_field("java/awt/Transparency", transparency, "I")
jtransfer_type = jutil.get_static_field("java/awt/image/DataBuffer", transfer_type, "I")
return jutil.make_instance(
"java/awt/image/ComponentColorModel",
"(Ljava/awt/color/ColorSpace;ZZII)V",
color_space,
has_alpha,
is_alpha_premultiplied,
jtransparency,
jtransfer_type,
)
def getColorModel(color_space,
has_alpha=False,
is_alpha_premultiplied = False,
transparency = OPAQUE,
transfer_type = TYPE_BYTE):
'''Return a java.awt.image.ColorModel color model
color_space - a java.awt.color.ColorSpace such as returned by
getGrayColorSpace or getRGBColorSpace
has_alpha - True if alpha channel is specified
is_alpha_premultiplied - True if other channel values have already
been reduced by the alpha multiplier, False if the channel values are
independent of the multiplier.
transparency - one of BITMASK, OPAQUE or TRANSPARENT.
transfer_type - one of TYPE_BYTE, TYPE_USHORT, TYPE_INT
'''
jtransparency = jutil.get_static_field('java/awt/Transparency',
transparency,
'I')
jtransfer_type = jutil.get_static_field('java/awt/image/DataBuffer',
transfer_type, 'I')
return jutil.make_instance('java/awt/image/ComponentColorModel',
'(Ljava/awt/color/ColorSpace;ZZII)V',
color_space, has_alpha, is_alpha_premultiplied,
jtransparency, jtransfer_type)
class ModuleItem(object):
def __init__(self):
self.o = instance
IV_NORMAL = J.get_static_field("imagej/module/ItemVisibility",
"NORMAL",
"Limagej/module/ItemVisibility;")
IV_TRANSIENT = J.get_static_field("imagej/module/ItemVisibility",
"TRANSIENT",
"Limagej/module/ItemVisibility;")
IV_INVISIBLE = J.get_static_field("imagej/module/ItemVisibility",
"INVISIBLE",
"Limagej/module/ItemVisibility;")
IV_MESSAGE = J.get_static_field("imagej/module/ItemVisibility",
"MESSAGE",
"Limagej/module/ItemVisibility;")
def getType(self):
jtype = J.call(self.o, "getType", "()Ljava/lang/Class;")
type_name = J.call(jtype, "getCanonicalName", "()Ljava/lang/String;")
if field_mapping.has_key(type_name):
return field_mapping[type_name]
for class_instance, result in field_class_mapping():
if J.call(class_instance, "isAssignableFrom",
"(Ljava/lang/Class;)Z", jtype):
return result
return None
getWidgetStyle = J.make_method("getWidgetStyle",
"()Ljava/lang/String;")
getMinimumValue = J.make_method("getMinimumValue",
"()Ljava/lang/Object;")
getMaximumValue = J.make_method("getMaximumValue",
"()Ljava/lang/Object;")
getStepSize = J.make_method("getStepSize",
"()Ljava/lang/Number;")
getColumnCount = J.make_method("getColumnCount", "()I")
getChoices = J.make_method("getChoices", "()Ljava/util/List;")
getValue = J.make_method("getValue",
"(Limagej/module/Module;)Ljava/lang/Object;")
setValue = J.make_method(
"setValue", "(Limagej/module/Module;Ljava/lang/Object;)V",
"Set the value associated with this item on the module")
getName = J.make_method("getName", "()Ljava/lang/String;")
getLabel = J.make_method("getLabel", "()Ljava/lang/String;")
getDescription = J.make_method("getDescription", "()Ljava/lang/String;")
loadValue = J.make_method("loadValue", "()Ljava/lang/Object;")
isInput = J.make_method("isInput", "()Z")
isOutput = J.make_method("isOutput", "()Z")
def test_03_08_cw_get_field(self):
c = J.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = J.call(field, 'getModifiers', '()I')
static = J.get_static_field('java/lang/reflect/Modifier', 'STATIC',
'I')
self.assertEqual((modifiers & static), static)
def getGrayColorSpace():
"""Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
"""
cs_gray = jutil.get_static_field("java/awt/color/ColorSpace", "CS_GRAY", "I")
return jutil.static_call("java/awt/color/ColorSpace", "getInstance", "(I)Ljava/awt/color/ColorSpace;", cs_gray)
class ModuleItem(object):
def __init__(self, instance):
self.o = instance
IV_NORMAL = J.get_static_field("imagej/ext/module/ItemVisibility",
"NORMAL",
"Limagej/ext/module/ItemVisibility;")
IV_TRANSIENT = J.get_static_field(
"imagej/ext/module/ItemVisibility", "TRANSIENT",
"Limagej/ext/module/ItemVisibility;")
IV_INVISIBLE = J.get_static_field(
"imagej/ext/module/ItemVisibility", "INVISIBLE",
"Limagej/ext/module/ItemVisibility;")
IV_MESSAGE = J.get_static_field("imagej/ext/module/ItemVisibility",
"MESSAGE",
"Limagej/ext/module/ItemVisibility;")
WS_DEFAULT = J.get_static_field("imagej/ext/module/ui/WidgetStyle",
"DEFAULT",
"Limagej/ext/module/ui/WidgetStyle;")
WS_NUMBER_SPINNER = J.get_static_field(
"imagej/ext/module/ui/WidgetStyle", "NUMBER_SPINNER",
"Limagej/ext/module/ui/WidgetStyle;")
WS_NUMBER_SLIDER = J.get_static_field(
"imagej/ext/module/ui/WidgetStyle", "NUMBER_SLIDER",
"Limagej/ext/module/ui/WidgetStyle;")
WS_NUMBER_SCROLL_BAR = J.get_static_field(
"imagej/ext/module/ui/WidgetStyle", "NUMBER_SCROLL_BAR",
"Limagej/ext/module/ui/WidgetStyle;")
def getType(self):
jtype = J.call(self.o, "getType", "()Ljava/lang/Class;")
type_name = J.call(jtype, "getCanonicalName",
"()Ljava/lang/String;")
if field_mapping.has_key(type_name):
return field_mapping[type_name]
for class_instance, result in field_class_mapping:
if J.call(class_instance, "isAssignableFrom",
"(Ljava/lang/Class;)Z", jtype):
return result
return None
getWidgetStyle = J.make_method("getWidgetStyle",
"()Limagej/ext/module/ui/WidgetStyle;")
getMinimumValue = J.make_method("getMinimumValue",
"()Ljava/lang/Object;")
getMaximumValue = J.make_method("getMaximumValue",
"()Ljava/lang/Object;")
getStepSize = J.make_method("getStepSize", "()Ljava/lang/Number;")
getColumnCount = J.make_method("getColumnCount", "()I")
getChoices = J.make_method("getChoices", "()Ljava/util/List;")
getValue = J.make_method(
"getValue", "(Limagej/ext/module/Module;)Ljava/lang/Object;")
getName = J.make_method("getName", "()Ljava/lang/String;")
getLabel = J.make_method("getLabel", "()Ljava/lang/String;")
getDescription = J.make_method("getDescription",
"()Ljava/lang/String;")
def update_never_remind():
"""Tell ImageJ never to remind us of updates
Not as harsh as it sounds - this is done with headless preferences
which go to /dev/null.
"""
never = J.get_static_field("java/lang/Long", "MAX_VALUE", "J")
J.static_call("imagej/updater/core/UpToDate", "setLatestNag", "(J)V", never)
def update_never_remind():
'''Tell ImageJ never to remind us of updates
Not as harsh as it sounds - this is done with headless preferences
which go to /dev/null.
'''
never = J.get_static_field("java/lang/Long", "MAX_VALUE", "J")
J.static_call("imagej/updater/core/UpToDate", "setLatestNag", "(J)V",
never)
def getGrayColorSpace():
'''Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
'''
cs_gray = jutil.get_static_field('java/awt/color/ColorSpace', 'CS_GRAY',
'I')
return jutil.static_call('java/awt/color/ColorSpace', 'getInstance',
'(I)Ljava/awt/color/ColorSpace;', cs_gray)
def test_03_09_cw_get_method(self):
sclass = J.class_for_name('java.lang.String')
iclass = J.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = J.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [ iclass ])
self.assertEqual(J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')), 'char')
m = c.getMethod('concat', [ sclass])
self.assertEqual(J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
def getGrayColorSpace():
'''Get a Java object that represents an RGB color space
See java.awt.color.ColorSpace: this returns the linear RGB color space
'''
cs_gray = jutil.get_static_field('java/awt/color/ColorSpace',
'CS_GRAY', 'I')
return jutil.static_call('java/awt/color/ColorSpace', 'getInstance',
'(I)Ljava/awt/color/ColorSpace;',
cs_gray)
def get_metadata_options(level):
'''Get an instance of the MetadataOptions interface
level - MINIMUM, NO_OVERLAYS or ALL to set the metadata retrieval level
The object returned can be used in setMetadataOptions in a format reader.
'''
jlevel = jutil.get_static_field('loci/formats/in/MetadataLevel', level,
'Lloci/formats/in/MetadataLevel;')
return jutil.make_instance('loci/formats/in/DefaultMetadataOptions',
'(Lloci/formats/in/MetadataLevel;)V', jlevel)
def get_metadata_options(level):
'''Get an instance of the MetadataOptions interface
level - MINIMUM, NO_OVERLAYS or ALL to set the metadata retrieval level
The object returned can be used in setMetadataOptions in a format reader.
'''
jlevel = jutil.get_static_field('loci/formats/in/MetadataLevel', level,
'Lloci/formats/in/MetadataLevel;')
return jutil.make_instance('loci/formats/in/DefaultMetadataOptions',
'(Lloci/formats/in/MetadataLevel;)V',
jlevel)
def create_img_plus(a, name):
'''Create an ImagePlus from a numpy array
a - numpy array. The values should be scaled to the range 0-255
name - a user-visible name for the image
returns an ImagePlus. The metadata axes will be Y, X and channel (if 3-d)
'''
x = J.get_static_field("net/imglib2/img/Axes", "X",
"Lnet/imglib2/img/Axes;")
y = J.get_static_field("net/imglib2/img/Axes", "Y",
"Lnet/imglib2/img/Axes;")
c = J.get_static_field("net/imglib2/img/Axes", "CHANNEL",
"Lnet/imglib2/img/Axes;")
img = create_planar_img(a)
img_plus = J.make_instance(
"net/imglib2/img/ImgPlus",
"(Lnet/imglib2/img/Img;Ljava/lang/String;[Lnet/imglib2/img/Axis;)V",
img, name, [y, x] if a.ndim == 2 else [y, x, c])
def create_img_plus(a, name):
'''Create an ImagePlus from a numpy array
a - numpy array. The values should be scaled to the range 0-255
name - a user-visible name for the image
returns an ImagePlus. The metadata axes will be Y, X and channel (if 3-d)
'''
x = J.get_static_field("net/imglib2/img/Axes", "X",
"Lnet/imglib2/img/Axes;")
y = J.get_static_field("net/imglib2/img/Axes", "Y",
"Lnet/imglib2/img/Axes;")
c = J.get_static_field("net/imglib2/img/Axes", "CHANNEL",
"Lnet/imglib2/img/Axes;")
img = create_planar_img(a)
img_plus = J.make_instance(
"net/imglib2/img/ImgPlus",
"(Lnet/imglib2/img/Img;Ljava/lang/String;[Lnet/imglib2/img/Axis;)V",
img, name, [y, x] if a.ndim == 2 else [y, x, c])
def test_03_09_cw_get_method(self):
sclass = J.class_for_name('java.lang.String')
iclass = J.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = J.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [iclass])
self.assertEqual(
J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'char')
m = c.getMethod('concat', [sclass])
self.assertEqual(
J.to_string(J.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
def test_10_04_engine_factory_wrapper(self):
svc = ij2.get_script_service(self.context)
factory = svc.getByName("ECMAScript")
factory.getEngineName()
factory.getEngineVersion()
factory.getExtensions()
factory.getMimeTypes()
factory.getNames()
factory.getLanguageName()
factory.getLanguageVersion()
factory.getParameter(J.get_static_field('javax/script/ScriptEngine',
'NAME', 'Ljava/lang/String;'))
factory.getMethodCallSyntax("myobject", "mymethod", ["param1", "param2"])
factory.getOutputStatement("Hello, world")
factory.getProgram(["I.do.this()", "I.do.that()"])
factory.getScriptEngine()
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()
class ScriptEngine(object):
def __init__(self, o=o):
self.o = o
ARGV = J.get_static_field(klass, "ARGV", "Ljava/lang/String;")
FILENAME = J.get_static_field(klass, "FILENAME", "Ljava/lang/String;")
ENGINE = J.get_static_field(klass, "ENGINE", "Ljava/lang/String;")
ENGINE_VERSION = J.get_static_field(klass, "ENGINE_VERSION",
"Ljava/lang/String;")
NAME = J.get_static_field(klass, "NAME", "Ljava/lang/String;")
LANGUAGE = J.get_static_field(klass, "LANGUAGE", "Ljava/lang/String;")
LANGUAGE_VERSION = J.get_static_field(klass, "LANGUAGE_VERSION",
"Ljava/lang/String;")
evalSSC = J.make_method(
"eval",
"(Ljava/lang/String;Ljavax/scriptScriptContext;)Ljava/lang/Object;",
doc="""Evaluate a script within a context
script - the script to run
script_context - The context describing the operational scope
during the evaluation.""")
evalRSC = J.make_method(
"eval",
"(Ljava/io/Reader;Ljavax/scriptScriptContext;)Ljava/lang/Object;",
doc="""Evaluate a script within a context
reader - read the script from this reader
script_context - The context describing the operational scope
during the evaluation.""")
evalS = J.make_method(
"eval",
"(Ljava/lang/String;)Ljava/lang/Object;",
doc="""Evaluate a script within the engine's default context
script - script to evaluate
""")
evalR = J.make_method(
"eval",
"(Ljava/io/Reader;)Ljava/lang/Object;",
doc="""Evaluate a script within the engine's default context
reader - read the script from here
""")
evalSB = J.make_method(
"eval",
"(Ljava/lang/String;Ljavax/script/Bindings;)Ljava/lang/Object;",
doc="""Evaluate the script using the bindings as the ENGINE_SCOPE
script - the script to be run
bindings - bindings of values to variables which are combined with
the non ENGINE_SCOPE bindings of the default context
to provide an execution scope.""")
evalRB = J.make_method(
"eval",
"(Ljava/io/Reader;Ljavax/script/Bindings;)Ljava/lang/Object;",
doc="""Evaluate the script using the bindings as the ENGINE_SCOPE
reader- read the script from here
bindings - bindings of values to variables which are combined with
the non ENGINE_SCOPE bindings of the default context
to provide an execution scope.""")
put = J.make_method("put",
"(Ljava/lang/String;Ljava/lang/Object;)V",
doc="""Set the value for some script engine key
For non-keywords, this generally adds a key/value binding to the default
ENGINE_SCOPE for the script engine.
key - name of the value to add
value - the value to be given to the key
""")
get = J.make_method("get",
"(Ljava/lang/String;)Ljava/lang/Object;",
doc="""Get a value set on the engine's state
key - the key to look up
""")
ENGINE_SCOPE = J.get_static_field("javax/script/ScriptContext",
"ENGINE_SCOPE", "I")
GLOBAL_SCOPE = J.get_static_field("javax/script/ScriptContext",
"GLOBAL_SCOPE", "I")
getBindings = J.make_method("getBindings",
"(I)Ljavax/script/Bindings;",
doc="""Returns a scope of named values.
scope - either ScriptContext.ENGINE_SCOPE to get the values set on
this engine or ScriptContext.GLOBAL_SCOPE to get the values
set by a ScriptEngineManager.
""")
setBindings = J.make_method(
"setBindings",
"(Ljavax/script/Bindings;I)V",
doc="""Sets the bindings to be used for the engine or global scope
bindings - the bindings to use
scope - ENGINE_SCOPE to set the script engine's bindings or
GLOBAL_SCOPE to set the scope at the manager level.
""")
createBindings = J.make_method(
"createBindings",
"()Ljavax/script/Bindings;",
doc="""Return a bindings instance appropriate for this engine""")
getContext = J.make_method(
"getContext",
"()Ljavax/script/ScriptContext;",
doc="""Return the default ScriptContext for this engine""")
setContext = J.make_method(
"setContext",
"(Ljavax/script/ScriptContext;)V",
doc="""Set the default ScriptContext for this engine""")
getFactory = J.make_method("getFactory",
"()Ljavax/script/ScriptEngineFactory;",
doc="Get this engine's factory")
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 get_named_axis(self, axis_name):
return J.get_static_field("net/imglib2/img/Axes", axis_name,
"Lnet/imglib2/img/Axes;")
def test_03_08_cw_get_field(self):
c = J.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = J.call(field, 'getModifiers', '()I')
static = J.get_static_field('java/lang/reflect/Modifier','STATIC','I')
self.assertEqual((modifiers & static), static)
class ScriptEngine(object):
def __init__(self, o=o):
self.o = o
ARGV = J.get_static_field(klass, "ARGV", "Ljava/lang/String;")
FILENAME = J.get_static_field(klass, "FILENAME", "Ljava/lang/String;")
ENGINE = J.get_static_field(klass, "ENGINE", "Ljava/lang/String;")
ENGINE_VERSION = J.get_static_field(klass, "ENGINE_VERSION",
"Ljava/lang/String;")
NAME = J.get_static_field(klass, "NAME", "Ljava/lang/String;")
LANGUAGE = J.get_static_field(klass, "LANGUAGE", "Ljava/lang/String;")
LANGUAGE_VERSION = J.get_static_field(klass, "LANGUAGE_VERSION",
"Ljava/lang/String;")
evalS = make_invoke_method(
"eval",
returns_value=True,
doc="""Evaluate a script within the engine's default context
script - script to evaluate
""")
put = J.make_method("put",
"(Ljava/lang/String;Ljava/lang/Object;)V",
doc="""Set the value for some script engine key
For non-keywords, this generally adds a key/value binding to the default
ENGINE_SCOPE for the script engine.
key - name of the value to add
value - the value to be given to the key
""")
get = J.make_method("get",
"(Ljava/lang/String;)Ljava/lang/Object;",
doc="""Get a value set on the engine's state
key - the key to look up
""")
ENGINE_SCOPE = J.get_static_field("javax/script/ScriptContext",
"ENGINE_SCOPE", "I")
GLOBAL_SCOPE = J.get_static_field("javax/script/ScriptContext",
"GLOBAL_SCOPE", "I")
getBindings = J.make_method("getBindings",
"(I)Ljavax/script/Bindings;",
doc="""Returns a scope of named values.
scope - either ScriptContext.ENGINE_SCOPE to get the values set on
this engine or ScriptContext.GLOBAL_SCOPE to get the values
set by a ScriptEngineManager.
""")
setBindings = J.make_method(
"setBindings",
"(Ljavax/script/Bindings;I)V",
doc="""Sets the bindings to be used for the engine or global scope
bindings - the bindings to use
scope - ENGINE_SCOPE to set the script engine's bindings or
GLOBAL_SCOPE to set the scope at the manager level.
""")
createBindings = J.make_method(
"createBindings",
"()Ljavax/script/Bindings;",
doc="""Return a bindings instance appropriate for this engine""")
getContext = J.make_method(
"getContext",
"()Ljavax/script/ScriptContext;",
doc="""Return the default ScriptContext for this engine""")
setContext = J.make_method(
"setContext",
"(Ljavax/script/ScriptContext;)V",
doc="""Set the default ScriptContext for this engine""")
getFactory = J.make_method("getFactory",
"()Ljavax/script/ScriptEngineFactory;",
doc="Get this engine's factory")
def test_01_05_get_static_field(self):
klass = self.env.find_class("java/lang/Short")
self.assertEqual(J.get_static_field(klass, "MAX_VALUE", "S"), 2**15 - 1)
def test_01_05_get_static_field(self):
klass = self.env.find_class("java/lang/Short")
self.assertEqual(J.get_static_field(klass, "MAX_VALUE", "S"),
2**15 - 1)
logger.warning("Bioformats version does not support directory cacheing")
finally:
jutil.detach()
# if get_headless() or sys.platform=="darwin":
# jutil.attach()
# jutil.static_call("java/lang/System", "setProperty", '(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;', "java.awt.headless", "true")
# jutil.detach()
#
# Start the log4j logger to avoid error messages.
#
if __init_logger:
jutil.attach()
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)
finally:
jutil.detach()
class PixelType(object):
'''Provide enums from ome.xml.model.enums.PixelType'''
klass = jutil.get_env().find_class('ome/xml/model/enums/PixelType')
INT8 = jutil.get_static_field(klass, 'INT8',
'Lome/xml/model/enums/PixelType;')
INT16 = jutil.get_static_field(klass, 'INT16',
'Lome/xml/model/enums/PixelType;')
INT32 = jutil.get_static_field(klass, 'INT32',
'Lome/xml/model/enums/PixelType;')
UINT8 = jutil.get_static_field(klass, 'UINT8',
'Lome/xml/model/enums/PixelType;')
UINT16 = jutil.get_static_field(klass, 'UINT16',
'Lome/xml/model/enums/PixelType;')
UINT32 = jutil.get_static_field(klass, 'UINT32',
'Lome/xml/model/enums/PixelType;')
FLOAT = jutil.get_static_field(klass, 'FLOAT',
'Lome/xml/model/enums/PixelType;')
BIT = jutil.get_static_field(klass, 'BIT',
'Lome/xml/model/enums/PixelType;')
DOUBLE = jutil.get_static_field(klass, 'DOUBLE',
'Lome/xml/model/enums/PixelType;')
COMPLEX = jutil.get_static_field(
klass, 'COMPLEX', 'Lome/xml/model/enums/PixelType;')
DOUBLECOMPLEX = jutil.get_static_field(
klass, 'DOUBLECOMPLEX', 'Lome/xml/model/enums/PixelType;')
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()
class FormatTools(object):
'''A wrapper for loci.formats.FormatTools
See http://hudson.openmicroscopy.org.uk/job/LOCI/javadoc/loci/formats/FormatTools.html
'''
env = jutil.get_env()
klass = env.find_class('loci/formats/FormatTools')
CAN_GROUP = jutil.get_static_field(klass, 'CAN_GROUP', 'I')
CANNOT_GROUP = jutil.get_static_field(klass, 'CANNOT_GROUP', 'I')
DOUBLE = jutil.get_static_field(klass, 'DOUBLE', 'I')
FLOAT = jutil.get_static_field(klass, 'FLOAT', 'I')
INT16 = jutil.get_static_field(klass, 'INT16', 'I')
INT32 = jutil.get_static_field(klass, 'INT32', 'I')
INT8 = jutil.get_static_field(klass, 'INT8', 'I')
MUST_GROUP = jutil.get_static_field(klass, 'MUST_GROUP', 'I')
UINT16 = jutil.get_static_field(klass, 'UINT16', 'I')
UINT32 = jutil.get_static_field(klass, 'UINT32', 'I')
UINT8 = jutil.get_static_field(klass, 'UINT8', 'I')
@classmethod
def getPixelTypeString(cls, pixel_type):
return jutil.static_call('loci/formats/FormatTools',
'getPixelTypeString',
'(I)Ljava/lang/String;', pixel_type)
def get_named_axis(self, axis_name):
return J.get_static_field("net/imglib2/meta/Axes", axis_name,
"Lnet/imglib2/meta/Axes;")
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 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()
jutil.detach()
# if get_headless() or sys.platform=="darwin":
# jutil.attach()
# jutil.static_call("java/lang/System", "setProperty", '(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;', "java.awt.headless", "true")
# jutil.detach()
#
# Start the log4j logger to avoid error messages.
#
if __init_logger:
jutil.attach()
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)
finally:
jutil.detach()
from formatreader import load_using_bioformats
