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)
def init_logger():
rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",
"ROOT_LOGGER_NAME", "Ljava/lang/String;")
rootLogger = javabridge.static_call("org/slf4j/LoggerFactory",
"getLogger", "(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",
"WARN", "Lch/qos/logback/classic/Level;")
javabridge.call(rootLogger, "setLevel", "(Lch/qos/logback/classic/Level;)V",
logLevel)
def init_logger():
rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",
"ROOT_LOGGER_NAME", "Ljava/lang/String;")
rootLogger = javabridge.static_call("org/slf4j/LoggerFactory",
"getLogger", "(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",
"WARN", "Lch/qos/logback/classic/Level;")
javabridge.call(rootLogger, "setLevel", "(Lch/qos/logback/classic/Level;)V",
logLevel)
def __init__(self,
tetradGraph,
dfs,
dataType='continuous',
numCategoriesToDiscretize=4,
rule='R1',
score='andersonDarling',
alpha=0.01,
epsilon=1.0,
zeta=0.0,
orientStrongerDirection=False,
r2Orient2Cycles=True,
edgeCorrected=False,
selfLoopStrength=1.0):
datasets = javabridge.JClassWrapper('java.util.ArrayList')()
pc = self.pc
for idx in range(len(dfs)):
df = dfs[idx]
tetradData = None
# Continuous
if dataType == 'continuous':
tetradData = pc.loadContinuousData(df, outputDataset=True)
# Discrete
elif dataType == 'discrete':
tetradData = pc.loadDiscreteData(df)
# Mixed
else:
tetradData = pc.loadMixedData(df, numCategoriesToDiscretize)
datasets.add(tetradData)
lofs2 = javabridge.JClassWrapper('edu.cmu.tetrad.search.Lofs2')(
tetradGraph, datasets)
rule = javabridge.get_static_field(
'edu/cmu/tetrad/search/Lofs2$Rule', rule,
'Ledu/cmu/tetrad/search/Lofs2$Rule;')
score = javabridge.get_static_field(
'edu/cmu/tetrad/search/Lofs$Score', score,
'Ledu/cmu/tetrad/search/Lofs$Score;')
lofs2.setRule(rule)
lofs2.setScore(score)
lofs2.setAlpha(alpha)
lofs2.setEpsilon(epsilon)
lofs2.setZeta(zeta)
lofs2.setOrientStrongerDirection(orientStrongerDirection)
lofs2.setR2Orient2Cycles(r2Orient2Cycles)
lofs2.setEdgeCorrected(edgeCorrected)
lofs2.setSelfLoopStrength(selfLoopStrength)
self.tetradGraph = lofs2.orient()
self.nodes = pc.extractTetradGraphNodes(self.tetradGraph)
self.edges = pc.extractTetradGraphEdges(self.tetradGraph)
class ModuleItem(object):
def __init__(self):
self.o = instance
IV_NORMAL = J.get_static_field("org/scijava/ItemVisibility",
"NORMAL",
"Lorg/scijava/ItemVisibility;")
IV_TRANSIENT = J.get_static_field("org/scijava/ItemVisibility",
"TRANSIENT",
"Lorg/scijava/ItemVisibility;")
IV_INVISIBLE = J.get_static_field("org/scijava/ItemVisibility",
"INVISIBLE",
"Lorg/scijava/ItemVisibility;")
IV_MESSAGE = J.get_static_field("org/scijava/ItemVisibility",
"MESSAGE",
"Lorg/scijava/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",
"(Lorg/scijava/module/Module;)Ljava/lang/Object;")
setValue = J.make_method(
"setValue", "(Lorg/scijava/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")
isRequired = J.make_method("isRequired", "()Z")
initialize = J.make_method("initialize", "(Lorg/scijava/module/Module;)V")
def __getattr__(self, name):
try:
jfield = self.klass.getField(name)
except:
raise AttributeError("Could not find field %s" % name)
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) != STATIC:
raise AttributeError("Field %s is not static" % name)
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_static_field(self.cname, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def __getattr__(self, name):
try:
jfield = self.klass.getField(name)
except:
raise AttributeError("Could not find field %s" % name)
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) != STATIC:
raise AttributeError("Field %s is not static" % name)
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_static_field(self.cname, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def init_vm():
javabridge.start_vm(class_path=bioformats.JARS)
#remove annoying logs
myloglevel = "ERROR" # user string argument for logLevel.
rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",
"ROOT_LOGGER_NAME",
"Ljava/lang/String;")
rootLogger = javabridge.static_call(
"org/slf4j/LoggerFactory", "getLogger",
"(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",
myloglevel,
"Lch/qos/logback/classic/Level;")
javabridge.call(rootLogger, "setLevel",
"(Lch/qos/logback/classic/Level;)V", logLevel)
def test_03_08_cw_get_field(self):
c = javabridge.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = javabridge.call(field, 'getModifiers', '()I')
static = javabridge.get_static_field('java/lang/reflect/Modifier',
'STATIC', 'I')
self.assertEqual((modifiers & static), static)
def __init__(self, o):
'''Initialize the JWrapper with a Java object
:param o: a Java object (class = JB_Object)
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
self.o = o
self.class_wrapper = J.get_class_wrapper(o)
env = J.get_env()
methods = env.get_object_array_elements(
self.class_wrapper.getMethods())
self.methods = {}
for jmethod in methods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) == STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in self.methods:
self.methods[name] = []
fn = lambda naame=name: lambda *args: self.__call(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ + "\n" + J.to_string(jmethod)
self.methods[name].append(method)
jfields = self.class_wrapper.getFields()
fields = env.get_object_array_elements(jfields)
def __init__(self, class_name):
'''Initialize to wrap a class name
:param class_name: name of class in dotted form, e.g. java.lang.Integer
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
self.cname = class_name.replace(".", "/")
self.klass = J.get_class_wrapper(J.class_for_name(class_name), True)
self.static_methods = {}
methods = env.get_object_array_elements(self.klass.getMethods())
self.methods = {}
for jmethod in methods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) != STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in self.methods:
self.methods[name] = []
fn = lambda naame=name: lambda *args: self.__call_static(
naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ + "\n" + J.to_string(jmethod)
self.methods[name].append(method)
def start_jvm():
javabridge.start_vm(class_path=bioformats.JARS)
log_level = 'ERROR'
# reduce log level
rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",
"ROOT_LOGGER_NAME",
"Ljava/lang/String;")
rootLogger = javabridge.static_call(
"org/slf4j/LoggerFactory", "getLogger",
"(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",
log_level,
"Lch/qos/logback/classic/Level;")
javabridge.call(rootLogger, "setLevel",
"(Lch/qos/logback/classic/Level;)V", logLevel)
def test_01_05_03_set_static_field(self):
class_name = "org/cellprofiler/javabridge/test/RealRect"
test_cases = (
("fs_boolean", "Z", True), # <AK> added
("fs_char", "C", "A"),
("fs_byte", "B", 3),
("fs_short", "S", 15),
("fs_int", "I", 392),
("fs_long", "J", -14),
("fs_float", "F", 1.03),
("fs_double", "D", -889.1),
("fs_object", "Ljava/lang/Object;",
javabridge.make_instance("java/lang/Integer", "(I)V", 15)),
("fs_object", "Ljava/lang/Object;", None))
for field_name, signature, value in test_cases:
javabridge.set_static_field(class_name, field_name, signature,
value)
v = javabridge.get_static_field(class_name, field_name, signature)
if isinstance(value, float):
self.assertAlmostEqual(v, value)
elif isinstance(value, javabridge.JB_Object):
self.assertTrue(
javabridge.call(value, "equals", "(Ljava/lang/Object;)Z",
v))
else:
self.assertEqual(v, value)
def __init__(self, class_name):
'''Initialize to wrap a class name
:param class_name: name of class in dotted form, e.g. java.lang.Integer
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
self.cname = class_name.replace(".", "/")
self.klass = J.get_class_wrapper(J.class_for_name(class_name), True)
self.static_methods = {}
env = J.get_env()
jmethods = env.get_object_array_elements(self.klass.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) != STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call_static(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ +"\n"+J.to_string(jmethod)
methods[name].append(method)
self.methods = methods
def loadDiscreteData(self, df):
tetradData = None
if (len(df.index) * df.columns.size <= 1500):
dataBox = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.VerticalIntDataBox')(len(df.index),
df.columns.size)
node_list = javabridge.JClassWrapper('java.util.ArrayList')()
col_no = 0
for col in df.columns:
cat_array = sorted(set(df[col]))
cat_list = javabridge.JClassWrapper('java.util.ArrayList')()
for cat in cat_array:
cat = str(cat)
cat_list.add(cat)
nodname = javabridge.JClassWrapper('java.lang.String')(col)
nodi = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.DiscreteVariable')(nodname, cat_list)
node_list.add(nodi)
for row in df.index:
value = javabridge.JClassWrapper('java.lang.Integer')(
cat_array.index(df.iloc[row, col_no]))
dataBox.set(row, col_no, value)
col_no = col_no + 1
tetradData = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.BoxDataSet')(dataBox, node_list)
else:
# Generate random name
temp_data_file = ''.join(
random.choice(string.ascii_lowercase + string.digits)
for _ in range(10)) + '.csv'
temp_data_path = os.path.join(tempfile.gettempdir(),
temp_data_file)
df.to_csv(temp_data_path, sep="\t", index=False)
# Read Data from File
f = javabridge.JClassWrapper('java.io.File')(temp_data_path)
delimiter = javabridge.get_static_field(
'edu/pitt/dbmi/data/Delimiter', 'TAB',
'Ledu/pitt/dbmi/data/Delimiter;')
dataReader = javabridge.JClassWrapper(
'edu.pitt.dbmi.data.reader.tabular.VerticalDiscreteTabularDataReader'
)(f, delimiter)
tetradData = dataReader.readInData()
tetradData = javabridge.static_call(
'edu/cmu/tetrad/util/DataConvertUtils', 'toDataModel',
'(Ledu/pitt/dbmi/data/Dataset;)Ledu/cmu/tetrad/data/DataModel;',
tetradData)
os.remove(temp_data_path)
return tetradData
def __init__(self, o):
'''Initialize the JWrapper with a Java object
:param o: a Java object (class = JB_Object)
'''
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
self.o = o
self.class_wrapper = J.get_class_wrapper(o)
env = J.get_env()
jmethods = env.get_object_array_elements(self.class_wrapper.getMethods())
methods = {}
for jmethod in jmethods:
if (J.call(jmethod, "getModifiers", "()I") & STATIC) == STATIC:
continue
method = J.get_method_wrapper(jmethod)
name = method.getName()
if name not in methods:
methods[name] = []
fn = lambda naame=name: lambda *args: self.__call(naame, *args)
fn = fn()
fn.__doc__ = J.to_string(jmethod)
setattr(self, name, fn)
else:
fn = getattr(self, name)
fn.__doc__ = fn.__doc__ +"\n"+J.to_string(jmethod)
methods[name].append(method)
self.methods = methods
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("net/imagej/updater/UpToDate", "setLatestNag", "(J)V", never)
def _init_logger():
"""This is so that Javabridge doesn't spill out a lot of DEBUG messages
during runtime.
From CellProfiler/python-bioformats.
"""
rootLoggerName = jb.get_static_field("org/slf4j/Logger",
"ROOT_LOGGER_NAME",
"Ljava/lang/String;")
rootLogger = jb.static_call("org/slf4j/LoggerFactory", "getLogger",
"(Ljava/lang/String;)Lorg/slf4j/Logger;",
rootLoggerName)
logLevel = jb.get_static_field("ch/qos/logback/classic/Level", "WARN",
"Lch/qos/logback/classic/Level;")
jb.call(rootLogger, "setLevel", "(Lch/qos/logback/classic/Level;)V",
logLevel)
def test_selectedtag(self):
"""
Tests the SelectedTag class.
"""
tags = classes.Tags(jobject=javabridge.get_static_field("Lweka/classifiers/functions/SMO;", "TAGS_FILTER", "[Lweka/core/Tag;"))
stag = classes.SelectedTag(tag_id=1, tags=tags)
self.assertEqual(1, stag.selected.ident, "ID differs")
stag = classes.SelectedTag(tag_text="2", tags=tags)
self.assertEqual(2, stag.selected.ident, "ID differs")
def loadContinuousData(self, df, outputDataset=False):
tetradData = None
if (len(df.index) * df.columns.size <= 1500):
dataBox = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.DoubleDataBox')(len(df.index),
df.columns.size)
node_list = javabridge.JClassWrapper('java.util.ArrayList')()
col_no = 0
for col in df.columns:
nodi = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.ContinuousVariable')(col)
node_list.add(nodi)
for row in df.index:
value = javabridge.JClassWrapper('java.lang.Double')(
df.iloc[row, col_no])
dataBox.set(row, col_no, value)
col_no = col_no + 1
tetradData = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.BoxDataSet')(dataBox, node_list)
else:
#Generate random name
temp_data_file = ''.join(
random.choice(string.ascii_lowercase + string.digits)
for _ in range(10)) + '.csv'
temp_data_path = os.path.join(tempfile.gettempdir(),
temp_data_file)
df.to_csv(temp_data_path, sep='\t', index=False)
# Read Data from File
f = javabridge.JClassWrapper('java.io.File')(temp_data_path)
path = f.toPath()
delimiter = javabridge.get_static_field(
'edu/pitt/dbmi/data/reader/Delimiter', 'TAB',
'Ledu/pitt/dbmi/data/reader/Delimiter;')
dataReader = javabridge.JClassWrapper(
'edu.pitt.dbmi.data.reader.tabular.ContinuousTabularDatasetFileReader'
)(path, delimiter)
tetradData = dataReader.readInData()
tetradData = javabridge.static_call(
'edu/cmu/tetrad/util/DataConvertUtils', 'toDataModel',
'(Ledu/pitt/dbmi/data/reader/Data;)Ledu/cmu/tetrad/data/DataModel;',
tetradData)
os.remove(temp_data_path)
if (not outputDataset):
tetradData = javabridge.JClassWrapper(
'edu.cmu.tetrad.data.CovarianceMatrixOnTheFly')(tetradData)
return tetradData
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_selectedtag(self):
"""
Tests the SelectedTag class.
"""
tags = classes.Tags(jobject=javabridge.get_static_field("Lweka/classifiers/functions/SMO;", "TAGS_FILTER", "[Lweka/core/Tag;"))
stag = classes.SelectedTag(tag_id=1, tags=tags)
self.assertEqual(1, stag.selected.ident, "ID differs")
stag = classes.SelectedTag(tag_text="2", tags=tags)
self.assertEqual(2, stag.selected.ident, "ID differs")
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("net/imagej/updater/UpToDate",
"setLatestNag", "(J)V", never)
def __init__(self, df, dataType = 'continuous', numCategoriesToDiscretize = 4, depth = 3, alpha = 0.05, priorKnowledge = None, numBootstrap = -1, ensembleMethod = 'Highest'):
tetradData = None
indTest = None
pc = self.pc
# Continuous
if dataType == 'continuous':
if numBootstrap < 1:
tetradData = pc.loadContinuousData(df)
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.search.IndTestFisherZ')(tetradData, alpha)
else:
tetradData = pc.loadContinuousData(df, outputDataset = True)
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.algcomparison.independence.FisherZ')()
# Discrete
elif dataType == 'discrete':
tetradData = pc.loadDiscreteData(df)
if numBootstrap < 1:
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.search.IndTestChiSquare')(tetradData, alpha)
else:
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.algcomparison.independence.ChiSquare')()
# Mixed
else:
tetradData = pc.loadMixedData(df, numCategoriesToDiscretize)
if numBootstrap < 1:
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.search.IndTestConditionalGaussianLRT')(tetradData, alpha, False)
else:
indTest = javabridge.JClassWrapper('edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT')()
ccd = None
if numBootstrap < 1:
ccd = javabridge.JClassWrapper('edu.cmu.tetrad.search.Ccd')(indTest)
ccd.setDepth(depth)
else:
algorithm = javabridge.JClassWrapper('edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Ccd')(indTest)
parameters = javabridge.JClassWrapper('edu.cmu.tetrad.util.Parameters')()
parameters.set('depth', depth)
parameters.set('alpha', alpha)
ccd = javabridge.JClassWrapper('edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest')(tetradData, algorithm, numBootstrap)
edgeEnsemble = javabridge.get_static_field('edu/pitt/dbmi/algo/bootstrap/BootstrapEdgeEnsemble',
ensembleMethod,
'Ledu/pitt/dbmi/algo/bootstrap/BootstrapEdgeEnsemble;')
ccd.setEdgeEnsemble(edgeEnsemble)
ccd.setParameters(parameters)
if priorKnowledge is not None:
ccd.setKnowledge(priorKnowledge)
self.tetradGraph = ccd.search()
self.nodes = pc.extractTetradGraphNodes(self.tetradGraph)
self.edges = pc.extractTetradGraphEdges(self.tetradGraph)
self.graph = pc.generatePyDotGraph(self.nodes,self.edges,self.tetradGraph)
def begin(self):
javabridge.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = javabridge.get_static_field("org/apache/log4j/Level","WARN",
"Lorg/apache/log4j/Level;")
javabridge.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
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 = javabridge.class_for_name('java.lang.String')
iclass = javabridge.get_static_field('java/lang/Integer', 'TYPE',
'Ljava/lang/Class;')
c = javabridge.get_class_wrapper('java.lang.String')
m = c.getMethod('charAt', [ iclass ])
self.assertEqual(javabridge.to_string(javabridge.call(m, 'getReturnType', '()Ljava/lang/Class;')), 'char')
m = c.getMethod('concat', [ sclass])
self.assertEqual(javabridge.to_string(javabridge.call(m, 'getReturnType', '()Ljava/lang/Class;')),
'class java.lang.String')
def begin(self):
javabridge.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = javabridge.get_static_field("org/apache/log4j/Level",
"WARN",
"Lorg/apache/log4j/Level;")
javabridge.call(log4j_logger, "setLevel",
"(Lorg/apache/log4j/Level;)V", warn_level)
def __setattr__(self, name, value):
try:
jfield = self.klass.getField(name)
except:
return object.__setattr__(self, name, value)
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) != STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.set_static_field(self.cname, name, sig(klass), value)
def __setattr__(self, name, value):
try:
jfield = self.klass.getField(name)
except:
return object.__setattr__(self, name, value)
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) != STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.set_static_field(self.cname, name, sig(klass), value)
def _start_lif_reader(self):
jv.start_vm(class_path=bf.JARS)
log_level = 'ERROR'
# reduce log level
rootLoggerName = jv.get_static_field("org/slf4j/Logger", "ROOT_LOGGER_NAME", "Ljava/lang/String;")
rootLogger = jv.static_call("org/slf4j/LoggerFactory", "getLogger", "(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
logLevel = jv.get_static_field("ch/qos/logback/classic/Level", log_level, "Lch/qos/logback/classic/Level;")
jv.call(rootLogger, "setLevel", "(Lch/qos/logback/classic/Level;)V", logLevel)
self.ir = bf.ImageReader(self.lif_file_path, perform_init=True)
mdroot = et.ElementTree.fromstring(bf.get_omexml_metadata(self.lif_file_path))
mds = list(map(lambda e: e.attrib, mdroot.iter('{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels')))
# lif can contain multiple images, select one that is likely to be the timeseries
self.metadata = None
self.lif_stack_idx = 0
for idx, md in enumerate(mds):
if int(md['SizeT']) > 1:
self.lif_stack_idx = idx
self.metadata = md
if not self.metadata: raise ValueError('lif does not contain an image with sizeT > 1')
def wrapped(*args, **kwargs):
try:
javabridge.start_vm(class_path=bioformats.JARS)
myloglevel = "ERROR" # user string argument for logLevel.
rootLoggerName = javabridge.get_static_field(
"org/slf4j/Logger", "ROOT_LOGGER_NAME", "Ljava/lang/String;")
rootLogger = javabridge.static_call(
"org/slf4j/LoggerFactory",
"getLogger",
"(Ljava/lang/String;)Lorg/slf4j/Logger;",
rootLoggerName,
)
logLevel = javabridge.get_static_field(
"ch/qos/logback/classic/Level",
myloglevel,
"Lch/qos/logback/classic/Level;",
)
javabridge.call(rootLogger, "setLevel",
"(Lch/qos/logback/classic/Level;)V", logLevel)
return func(*args, **kwargs)
finally:
javabridge.kill_vm()
def test_tags(self):
"""
Tests the Tags class.
"""
tag1 = classes.Tag(ident=1, ident_str="tag1", readable="blah 1")
tag2 = classes.Tag(ident=2, ident_str="tag2", readable="blah 2")
tag3 = classes.Tag(ident=3, ident_str="tag3", readable="blah 3")
tags = classes.Tags(tags=[tag1, tag2, tag3])
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("TAG1|TAG2|TAG3", str(tags), msg="String differs")
smo = classes.JavaObject(classes.JavaObject.new_instance(classname="weka.classifiers.functions.SMO"))
tags = classes.Tags(jobject=javabridge.get_static_field("Lweka/classifiers/functions/SMO;", "TAGS_FILTER", "[Lweka/core/Tag;"))
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("0|1|2", str(tags), msg="String differs")
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 __setattr__(self, name, value):
if name in ("o", "class_wrapper", "methods") or \
not hasattr(self, "methods"):
object.__setattr__(self, name, value)
return
try:
jfield = self.class_wrapper.getField(name)
except:
object.__setattr__(self, name, value)
return
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.set_field(self.o, name, sig(klass), value)
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 __setattr__(self, name, value):
if name in ("o", "class_wrapper", "methods", "field_names") or \
not hasattr(self, "methods"):
object.__setattr__(self, name, value)
return
try:
jfield = self.class_wrapper.getField(name)
except:
object.__setattr__(self, name, value)
return
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.set_field(self.o, name, sig(klass), value)
def loadDiscreteData(self, df):
tetradData = None
if(len(df.index)*df.columns.size <= 1500):
dataBox = javabridge.JClassWrapper('edu.cmu.tetrad.data.VerticalIntDataBox')(len(df.index),df.columns.size)
node_list = javabridge.JClassWrapper('java.util.ArrayList')()
col_no = 0
for col in df.columns:
cat_array = sorted(set(df[col]))
cat_list = javabridge.JClassWrapper('java.util.ArrayList')()
for cat in cat_array:
cat = str(cat)
cat_list.add(cat)
nodname = javabridge.JClassWrapper('java.lang.String')(col)
nodi = javabridge.JClassWrapper('edu.cmu.tetrad.data.DiscreteVariable')(nodname,cat_list)
node_list.add(nodi)
for row in df.index:
value = javabridge.JClassWrapper('java.lang.Integer')(cat_array.index(df.iloc[row,col_no]))
dataBox.set(row,col_no,value)
col_no = col_no + 1
tetradData = javabridge.JClassWrapper('edu.cmu.tetrad.data.BoxDataSet')(dataBox, node_list)
else:
# Generate random name
temp_data_file = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)) + '.csv'
temp_data_path = os.path.join(tempfile.gettempdir(), temp_data_file)
df.to_csv(temp_data_path, sep = "\t", index = False)
# Read Data from File
f = javabridge.JClassWrapper('java.io.File')(temp_data_path)
path = f.toPath()
delimiter = javabridge.get_static_field('edu/pitt/dbmi/data/reader/Delimiter','TAB','Ledu/pitt/dbmi/data/reader/Delimiter;')
dataReader = javabridge.JClassWrapper('edu.pitt.dbmi.data.reader.tabular.VerticalDiscreteTabularDatasetFileReader')(path,delimiter)
tetradData = dataReader.readInData()
tetradData = javabridge.static_call('edu/cmu/tetrad/util/DataConvertUtils','toDataModel','(Ledu/pitt/dbmi/data/reader/Data;)Ledu/cmu/tetrad/data/DataModel;', tetradData)
os.remove(temp_data_path)
return tetradData
def test_tags(self):
"""
Tests the Tags class.
"""
tag1 = classes.Tag(ident=1, ident_str="tag1", readable="blah 1")
tag2 = classes.Tag(ident=2, ident_str="tag2", readable="blah 2")
tag3 = classes.Tag(ident=3, ident_str="tag3", readable="blah 3")
tags = classes.Tags(tags=[tag1, tag2, tag3])
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("TAG1|TAG2|TAG3", str(tags), msg="String differs")
tags = classes.Tags(jobject=javabridge.get_static_field("Lweka/classifiers/functions/SMO;", "TAGS_FILTER", "[Lweka/core/Tag;"))
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("0|1|2", str(tags), msg="String differs")
tags = classes.Tags.get_tags("weka.classifiers.functions.SMO", "TAGS_FILTER")
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("0|1|2", str(tags), msg="String differs")
self.assertIsNotNone(tags.find("2"), msg="Should have found tag")
self.assertIsNone(tags.find("blah"), msg="Should not have found tag")
def test_tags(self):
"""
Tests the Tags class.
"""
tag1 = classes.Tag(ident=1, ident_str="tag1", readable="blah 1")
tag2 = classes.Tag(ident=2, ident_str="tag2", readable="blah 2")
tag3 = classes.Tag(ident=3, ident_str="tag3", readable="blah 3")
tags = classes.Tags(tags=[tag1, tag2, tag3])
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("TAG1|TAG2|TAG3", str(tags), msg="String differs")
tags = classes.Tags(jobject=javabridge.get_static_field("Lweka/classifiers/functions/SMO;", "TAGS_FILTER", "[Lweka/core/Tag;"))
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("0|1|2", str(tags), msg="String differs")
tags = classes.Tags.get_tags("weka.classifiers.functions.SMO", "TAGS_FILTER")
self.assertEqual(3, len(tags), "Number of tags differs!")
self.assertEqual("0|1|2", str(tags), msg="String differs")
self.assertIsNotNone(tags.find("2"), msg="Should have found tag")
self.assertIsNone(tags.find("blah"), msg="Should not have found tag")
def __getattr__(self, name):
if name in ("o", "class_wrapper", "methods"):
raise AttributeError()
if not hasattr(self, "methods"):
# not initialized
raise AttributeError()
try:
jfield = self.class_wrapper.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def __getattr__(self, name):
if name in ("o", "class_wrapper", "methods"):
raise AttributeError()
if not hasattr(self, "methods"):
# not initialized
raise AttributeError()
try:
jfield = self.class_wrapper.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def loadContinuousData(self, df, outputDataset = False):
tetradData = None
if(len(df.index)*df.columns.size <= 1500):
dataBox = javabridge.JClassWrapper('edu.cmu.tetrad.data.DoubleDataBox')(len(df.index),df.columns.size)
node_list = javabridge.JClassWrapper('java.util.ArrayList')()
col_no = 0
for col in df.columns:
nodi = javabridge.JClassWrapper('edu.cmu.tetrad.data.ContinuousVariable')(col)
node_list.add(nodi)
for row in df.index:
value = javabridge.JClassWrapper('java.lang.Double')(df.iloc[row,col_no])
dataBox.set(row,col_no,value)
col_no = col_no + 1
tetradData = javabridge.JClassWrapper('edu.cmu.tetrad.data.BoxDataSet')(dataBox, node_list)
else:
#Generate random name
temp_data_file = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(10)) + '.csv'
temp_data_path = os.path.join(tempfile.gettempdir(), temp_data_file)
df.to_csv(temp_data_path, sep = '\t', index = False)
# Read Data from File
f = javabridge.JClassWrapper('java.io.File')(temp_data_path)
path = f.toPath()
delimiter = javabridge.get_static_field('edu/pitt/dbmi/data/reader/Delimiter','TAB','Ledu/pitt/dbmi/data/reader/Delimiter;')
dataReader = javabridge.JClassWrapper('edu.pitt.dbmi.data.reader.tabular.ContinuousTabularDatasetFileReader')(path,delimiter)
tetradData = dataReader.readInData()
tetradData = javabridge.static_call('edu/cmu/tetrad/util/DataConvertUtils','toDataModel','(Ledu/pitt/dbmi/data/reader/Data;)Ledu/cmu/tetrad/data/DataModel;', tetradData)
os.remove(temp_data_path)
if(not outputDataset):
tetradData = javabridge.JClassWrapper('edu.cmu.tetrad.data.CovarianceMatrixOnTheFly')(tetradData)
return tetradData
def _init_toolbar(self):
self.toolbar = javabridge.JClassWrapper('javax.swing.JToolBar')()
self.toolbar.setFloatable(False)
self.radio_button_group = javabridge.JClassWrapper(
'javax.swing.ButtonGroup')()
for text, tooltip_text, image_file, callback in self.toolitems:
if text is None:
self.toolbar.addSeparator()
continue
callback = getattr(self, callback, None)
if callback is None:
continue
if text in ("Pan", "Zoom"):
self.add_radio_button(callback, image_file)
else:
self.add_button(callback, image_file)
north = javabridge.get_static_field('java/awt/BorderLayout', 'NORTH',
'Ljava/lang/String;')
javabridge.call(self._frame.o, "add",
"(Ljava/awt/Component;Ljava/lang/Object;)V",
self.toolbar.o, north)
def test_01_05_03_set_static_field(self):
class_name = "org/cellprofiler/javabridge/test/RealRect"
test_cases = (
("fs_char", "C", "A"),
("fs_byte", "B", 3),
("fs_short", "S", 15),
("fs_int", "I", 392),
("fs_long", "J", -14),
("fs_float", "F", 1.03),
("fs_double", "D", -889.1),
("fs_object", "Ljava/lang/Object;",
javabridge.make_instance("java/lang/Integer", "(I)V", 15)),
("fs_object", "Ljava/lang/Object;", None))
for field_name, signature, value in test_cases:
javabridge.set_static_field(class_name, field_name, signature, value)
v = javabridge.get_static_field(class_name, field_name, signature)
if isinstance(value, float):
self.assertAlmostEqual(v, value)
elif isinstance(value, javabridge.JB_Object):
self.assertTrue(javabridge.call(
value, "equals", "(Ljava/lang/Object;)Z", v))
else:
self.assertEqual(v, value)
def test_01_05_00_get_static_field(self):
klass = self.env.find_class("java/lang/Short")
self.assertEqual(javabridge.get_static_field(klass, "MAX_VALUE", "S"), 2**15 - 1)
def get_named_axis(self, axis_name):
return J.get_static_field("net/imglib2/meta/Axes", axis_name,
"Lnet/imglib2/meta/AxisType;")
def fn():
javabridge.get_static_field('java/lang/Object', "NoSuchField", "I")
def test_01_05_00_get_static_field(self):
klass = self.env.find_class("java/lang/Short")
self.assertEqual(javabridge.get_static_field(klass, "MAX_VALUE", "S"),
2**15 - 1)
def fn():
javabridge.get_static_field(
'no/such/class', "field", "I")
def fn():
javabridge.get_static_field(
'java/lang/Object', "NoSuchField", "I")
def test_03_08_cw_get_field(self):
c = javabridge.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = javabridge.call(field, 'getModifiers', '()I')
static = javabridge.get_static_field('java/lang/reflect/Modifier','STATIC','I')
self.assertEqual((modifiers & static), static)