def _readOMETiffHeader(self, omeformat=True):
"""
get the right ImageReader directry from Java Class Wrapper
return ImageReader object just in case to do more work
"""
# https://github.com/CellProfiler/python-bioformats/issues/23
# also refer to bioformats.formatreader.py and metadatatools.py
clsOMEXMLService = javabridge.JClassWrapper(
'loci.formats.services.OMEXMLService')
serviceFactory = javabridge.JClassWrapper(
'loci.common.services.ServiceFactory')()
service = serviceFactory.getInstance(clsOMEXMLService.klass)
metadata = service.createOMEXMLMetadata()
level = bioformats.metadatatools.get_metadata_options(
bioformats.metadatatools.ALL)
if omeformat:
# for OME-Tiff only
self.is_ometiff = True
rdr = javabridge.JClassWrapper('loci.formats.in.OMETiffReader')()
rdr.setOriginalMetadataPopulated(True)
else:
# rather in general
rdr = bioformats.formatreader.make_image_reader_class()()
rdr.allowOpenToCheckType(True)
rdr.setMetadataStore(metadata)
rdr.setMetadataOptions(level)
rdr.setId(self.fn)
self.xml = service.getOMEXML(metadata)
return rdr
def save_figure(self, *args):
"""Save the current figure"""
default_filetype = self.canvas.get_default_filetype()
filetypes = self.canvas.get_supported_filetypes_grouped()
def compare(a, b):
aname, aextensions = a
bname, bextensions = b
if default_filetype in aextensions:
return 0 if default_filetype in bextensions else -1
elif default_filetype in bextensions:
return 1
else:
return cmp(aname, bname)
filetypes = list(filetypes.items())
filetypes.sort(cmp=compare)
chooser_cls = javabridge.JClassWrapper('javax.swing.JFileChooser')
chooser = chooser_cls()
chooser.setDialogTitle("Save figure")
filter_cls = javabridge.JClassWrapper(
'javax.swing.filechooser.FileNameExtensionFilter')
default_filter = None
for name, extensions in filetypes:
file_filter = filter_cls(name, *extensions)
chooser.addChoosableFileFilter(file_filter)
if default_filter is None:
default_filter = file_filter
chooser.setFileFilter(default_filter)
result = chooser.showSaveDialog(self.canvas.component)
if result == chooser_cls.APPROVE_OPTION:
path = chooser.getSelectedFile().getAbsolutePath()
exts = chooser.getFileFilter().getExtensions()
ext = javabridge.get_env().get_object_array_elements(exts.o)[0]
self.canvas.print_figure(path, format=javabridge.to_string(ext))
def __init__(self,
df,
penaltydiscount=4,
maxDegree=3,
faithfulnessAssumed=True,
numofthreads=2,
verbose=False,
priorKnowledge=None):
tetradData = pycausal.loadContinuousData(df)
score = javabridge.JClassWrapper('edu.cmu.tetrad.search.SemBicScore')(
tetradData)
score.setPenaltyDiscount(
penaltydiscount
) # set to 2 if variable# <= 50 otherwise set it to 4
fgs = javabridge.JClassWrapper('edu.cmu.tetrad.search.Fgs')(score)
fgs.setMaxDegree(maxDegree)
fgs.setNumPatternsToStore(0)
fgs.setFaithfulnessAssumed(faithfulnessAssumed)
fgs.setParallelism(numofthreads)
fgs.setVerbose(verbose)
if priorKnowledge is not None:
fgs.setKnowledge(priorKnowledge)
tetradGraph = fgs.search()
self.nodes = pycausal.extractTetradGraphNodes(tetradGraph)
self.edges = pycausal.extractTetradGraphEdges(tetradGraph)
self.graph = pycausal.generatePyDotGraph(self.nodes, self.edges)
def setup(self, arr):
# ome = bioformats.omexml
# bioformats/formatwriter.py
if arr.ndim == 3:
p = self.omexml.image(0).Pixels
p.SizeC = arr.shape[2]
p.Channel(0).SamplesPerPixel = pixels.shape[2]
self.omexml.structured_annotations.add_original_metadata(
ome.OM_SAMPLES_PER_PIXEL, str(pixels.shape[2]))
self.xml = self.omexml.to_xml()
self.xml = self.xml.replace('µ', '\xb5')
clsOMEXMLService = javabridge.JClassWrapper(
'loci.formats.services.OMEXMLService')
serviceFactory = javabridge.JClassWrapper(
'loci.common.services.ServiceFactory')()
service = serviceFactory.getInstance(clsOMEXMLService.klass)
metadata = service.createOMEXMLMetadata(self.xml)
if self.file.endswith(OMETIFF):
self.fp = javabridge.JClassWrapper(
'loci.formats.out.OMETiffWriter')()
else:
self.fp = javabridge.JClassWrapper('loci.formats.ImageWriter')()
self.fp.setMetadataRetrieve(metadata)
self.fp.setId(self.fn)
#if self.imgSequence in (0, 2, 3, 5):
# self.fp.setInterleaved(True)
#else:
self.fp.setInterleaved(False)
def __init__(self,
df,
continuous=True,
depth=3,
aggressivelyPreventCycles=False,
significance=0.05,
verbose=False,
priorKnowledge=None):
indTest = None
if (continuous):
tetradData = pycausal.loadContinuousData(df)
indTest = javabridge.JClassWrapper(
'edu.cmu.tetrad.search.IndTestFisherZ')(tetradData,
significance)
else:
tetradData = pycausal.loadDiscreteData(df)
indTest = javabridge.JClassWrapper(
'edu.cmu.tetrad.search.IndTestChiSquare')(tetradData,
significance)
cpcstable = javabridge.JClassWrapper(
'edu.cmu.tetrad.search.CpcStable')(indTest)
cpcstable.setDepth(depth)
cpcstable.setAggressivelyPreventCycles(aggressivelyPreventCycles)
cpcstable.setVerbose(verbose)
if priorKnowledge is not None:
cpcstable.setKnowledge(priorKnowledge)
tetradGraph = cpcstable.search()
self.nodes = pycausal.extractTetradGraphNodes(tetradGraph)
self.edges = pycausal.extractTetradGraphEdges(tetradGraph)
self.graph = pycausal.generatePyDotGraph(self.nodes, self.edges)
def __init__(self,
df,
continuous=True,
depth=3,
significance=0.05,
verbose=False,
priorKnowledge=None):
indTest = None
if (continuous):
tetradData = pycausal.loadContinuousData(df)
indTest = javabridge.JClassWrapper(
'edu.cmu.tetrad.search.IndTestFisherZ')(tetradData,
significance)
else:
tetradData = pycausal.loadDiscreteData(df)
indTest = javabridge.JClassWrapper(
'edu.cmu.tetrad.search.IndTestChiSquare')(tetradData,
significance)
ccd = javabridge.JClassWrapper('edu.cmu.tetrad.search.Ccd')(indTest)
ccd.setDepth(depth)
ccd.setVerbose(verbose)
if priorKnowledge is not None:
ccd.setKnowledge(priorKnowledge)
tetradGraph = ccd.search()
self.nodes = pycausal.extractTetradGraphNodes(tetradGraph)
self.edges = pycausal.extractTetradGraphEdges(tetradGraph)
def __init__(self,
df,
structurePrior=1.0,
samplePrior=1.0,
maxDegree=3,
faithfulnessAssumed=True,
numofthreads=2,
verbose=False,
priorKnowledge=None):
tetradData = pycausal.loadDiscreteData(df)
score = javabridge.JClassWrapper('edu.cmu.tetrad.search.BDeuScore')(
tetradData)
score.setStructurePrior(structurePrior)
score.setSamplePrior(samplePrior)
fgs = javabridge.JClassWrapper('edu.cmu.tetrad.search.Fgs')(score)
fgs.setMaxDegree(maxDegree)
fgs.setNumPatternsToStore(0)
fgs.setFaithfulnessAssumed(faithfulnessAssumed)
fgs.setParallelism(numofthreads)
fgs.setVerbose(verbose)
if priorKnowledge is not None:
fgs.setKnowledge(priorKnowledge)
tetradGraph = fgs.search()
self.nodes = pycausal.extractTetradGraphNodes(tetradGraph)
self.edges = pycausal.extractTetradGraphEdges(tetradGraph)
self.graph = pycausal.generatePyDotGraph(self.nodes, self.edges)
def __init__(self):
algorithmAnnotations = javabridge.JClassWrapper("edu.cmu.tetrad.annotation.AlgorithmAnnotations")
algoClasses = algorithmAnnotations.getInstance().getAnnotatedClasses()
for i in range(0,algoClasses.size()):
algo = algoClasses.get(i)
algoType = str(algo.getAnnotation().algoType())
if algoType != 'orient_pairwise':
self.algos[str(algo.getAnnotation().command())] = algo
testAnnotations = javabridge.JClassWrapper("edu.cmu.tetrad.annotation.TestOfIndependenceAnnotations")
testClasses = testAnnotations.getInstance().getAnnotatedClasses()
for i in range(0,testClasses.size()):
test = testClasses.get(i)
self.tests[str(test.getAnnotation().command())] = test
scoreAnnotations = javabridge.JClassWrapper("edu.cmu.tetrad.annotation.ScoreAnnotations")
scoreClasses = scoreAnnotations.getInstance().getAnnotatedClasses()
for i in range(0,scoreClasses.size()):
score = scoreClasses.get(i)
self.scores[str(score.getAnnotation().command())] = score
paramDescs = javabridge.JClassWrapper("edu.cmu.tetrad.util.ParamDescriptions")
self.paramDescs = paramDescs.getInstance()
self.algoFactory = javabridge.JClassWrapper("edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory")
def setUp(self):
self.no_seq = J.JClassWrapper('java.lang.Integer')(3)
self.a = J.JClassWrapper('java.util.ArrayList')()
self.assertEquals(len(self.a), 0)
self.ints = [0, 1, 2, 4, 8, 16]
self.assertEquals(len(self.ints), 6)
for i in self.ints:
self.a.add(i)
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 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,
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)
def __init__(self, num, figure):
self.frame = javabridge.JClassWrapper('javax.swing.JFrame')()
self.canvas = FigureCanvasSwing(figure)
dimension = javabridge.JClassWrapper('java.awt.Dimension')(
figure.bbox.width, figure.bbox.height)
border_layout_cls = javabridge.JClassWrapper('java.awt.BorderLayout')
self.canvas.component.setPreferredSize(dimension)
self.frame.add(self.canvas.component, border_layout_cls.CENTER)
self.toolbar = NavigationToolbar2Swing(self.canvas, self.frame)
self.frame.pack()
self.figmgr = FigureManagerSwing(self.canvas, num, self)
def read_metadata_with_bioformats(self):
# Using javabridge to parse and store all required metadata
# -------------------------------------------------
javabridge.start_vm(class_path=bioformats.JARS,
run_headless=True,
max_heap_size='2G')
bioformats_log4j.basic_config() # Configure logging for "WARN" level
rdr = javabridge.JClassWrapper('loci.formats.in.ZeissCZIReader')()
# ZeissCZIReader is the file format reader for Zeiss .czi files.
# rdr = javabridge.JClassWrapper('loci.formats.in.OMETiffReader')()
# OMETiffReader is the file format reader for OME-TIFF files
rdr.setOriginalMetadataPopulated(True)
# Specifies whether to save proprietary metadata in the MetadataStore.
clsOMEXMLService = javabridge.JClassWrapper(
'loci.formats.services.OMEXMLService')
# Classes in loci.formats.services that implement OMEXMLService
serviceFactory = javabridge.JClassWrapper(
'loci.common.services.ServiceFactory')()
# Constructor loading runtime initiation of services from the defult location
service = serviceFactory.getInstance(
clsOMEXMLService.klass
) # Retrieves an instance of a given service.
omemetadata = service.createOMEXMLMetadata()
# Creates OME-XML metadata object using reflection - avoids direct dependencies on loci.formats.ome package.
rdr.setMetadataStore(
omemetadata) # Sets the default metadata store for this reader.
rdr.setId(self.fname)
# Initializes a reader from the input file name.
# Calls initFile(String id) to initializes the input file
# Reads all of the metadata and sets the reader up for reading planes. This can take time here...
# rdr.saveOriginalMetadata = True
orgmetadata = service.getOriginalMetadata(omemetadata)
globalmetadata = rdr.getGlobalMetadata()
# Obtains the hashtable containing the metadata field/value pairs from the current file.
keys = globalmetadata.keySet().toString().split(',')
nkeys = globalmetadata.size()
metadatavalues = globalmetadata.values().toString().split(',')
metadatakeys = globalmetadata.keys()
# Get additional atrributes
self.dimOrder = copy.deepcopy(rdr.getDimensionOrder())
self.isChannelInterleaved = copy.deepcopy(rdr.isInterleaved())
self.isDimOrderCertain = copy.deepcopy(rdr.isOrderCertain())
for i in np.arange(0, nkeys):
key = metadatakeys.nextElement()
value = globalmetadata.get(key)
# print(key,value)
if key in zeiss_keymaps.linescan:
self.metadata[
zeiss_keymaps.linescan[key]] = comfun.string_convert(value)
# -----------------------------------
javabridge.kill_vm() # kill javabridge
print(self.metadata)
print('Metadata reading successful')
def loadDiscreteData(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.ix[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.lowercase) for i 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)
excludeVar = javabridge.JClassWrapper('java.util.HashSet')()
excludeVar.add("MULT")
# Read Data from File
f = javabridge.JClassWrapper('java.nio.file.Paths').get(temp_data_path)
dataReader = javabridge.JClassWrapper(
'edu.cmu.tetrad.io.VerticalTabularDiscreteDataReader')(f, '\t')
tetradData = dataReader.readInData(excludeVar)
os.remove(temp_data_path)
return tetradData
def test_02_05_constructor_varargs(self):
# Regression test of issue #41
#
args = ("foo", "bar")
f = J.JClassWrapper("javax.swing.filechooser.FileNameExtensionFilter")(
"baz", *args)
exts = J.get_env().get_object_array_elements(f.getExtensions().o)
self.assertEqual(args[0], J.to_string(exts[0]))
self.assertEqual(args[1], J.to_string(exts[1]))
# <AK> added
with self.assertRaisesRegex(TypeError,
"No matching constructor found"):
f = J.JClassWrapper(
"javax.swing.filechooser.FileNameExtensionFilter")()
def __init__(self, canvas, frame):
self._frame = frame
self._tools = {}
self._lastrect = None
NavigationToolbar2.__init__(self, canvas)
self._idle = True
clsCursor = javabridge.JClassWrapper('java.awt.Cursor')
self.cursor_map = {
cursors.MOVE: clsCursor(clsCursor.MOVE_CURSOR),
cursors.HAND: clsCursor(clsCursor.HAND_CURSOR),
cursors.POINTER: clsCursor(clsCursor.DEFAULT_CURSOR),
cursors.SELECT_REGION: clsCursor(clsCursor.CROSSHAIR_CURSOR)
}
self.white = javabridge.JClassWrapper('java.awt.Color').WHITE
def getAlgorithmDescription(self, algoId):
algo = self.algos.get(algoId)
algoClass = algo.getClazz()
algorithmDescriptions = javabridge.JClassWrapper("edu.cmu.tetrad.util.AlgorithmDescriptions")
algoDescs = algorithmDescriptions.getInstance()
print(algoDescs.get(algoId))
algorithmAnnotations = javabridge.JClassWrapper("edu.cmu.tetrad.annotation.AlgorithmAnnotations")
if algorithmAnnotations.getInstance().requireIndependenceTest(algoClass):
print("\nIt requires the independence test.")
if algorithmAnnotations.getInstance().requireScore(algoClass):
print("\nIt requires the score.")
if algorithmAnnotations.getInstance().acceptKnowledge(algoClass):
print("\nIt accepts the prior knowledge.")
def cp_stop_vm(kill=True):
'''Shut down the Java VM
Check for headlessness and the state of ImageJ and take
whatever action is needed to stop AWT and the JVM.
'''
from imagej.imagej2 import allow_quit, the_imagej_context
try:
ij1 = javabridge.JClassWrapper("ij.IJ").getInstance()
except javabridge.JavaException as e:
logger.debug("No available instance: %s" % str(e))
ij1 = None
if the_imagej_context is not None:
#
# Tell the app service that it's OK to quit without prompt
#
allow_quit()
javabridge.call(the_imagej_context.getContext(), "dispose", "()V")
if ij1 is not None:
#
# Yes, the proper way to get ImageJ to quit is
# to start it.
#
ij1.run()
if kill:
javabridge.kill_vm()
def patch_start_vm(*args, **kwargs):
jvm_args = list(args[0]) + [
"-Dloci.bioformats.loaded=true",
"-Djava.util.prefs.PreferencesFactory=" +
"org.cellprofiler.headlesspreferences" +
".HeadlessPreferencesFactory"
]
add_logback_xml_arg(jvm_args)
#
# Find the ij1patcher
#
if hasattr(sys, 'frozen') and sys.platform == 'win32':
root = os.path.dirname(sys.argv[0])
else:
root = os.path.dirname(__file__)
jardir = os.path.join(root, "imagej", "jars")
patchers = sorted([
x for x in os.listdir(jardir)
if x.startswith("ij1-patcher") and x.endswith(".jar")
])
if len(patchers) > 0:
jvm_args.append("-javaagent:%s=init" %
os.path.join(jardir, patchers[-1]))
result = start_vm(jvm_args, *args[1:], **kwargs)
if javabridge.get_env() is not None:
try:
event_service_cls = javabridge.JClassWrapper(
"org.bushe.swing.event.ThreadSafeEventService")
event_service_cls.CLEANUP_PERIOD_MS_DEFAULT = None
except:
pass
return result
def knowledge(forbiddirect=None, requiredirect=None, addtemporal=None):
prior = javabridge.JClassWrapper('edu.cmu.tetrad.data.Knowledge2')()
# forbidden directed edges
if forbiddirect is not None:
for i in range(0, len(forbiddirect)):
forbid = forbiddirect[i]
_from = forbid[0]
_to = forbid[1]
prior.setForbidden(_from, _to)
# required directed edges
if requiredirect is not None:
for i in range(0, len(requiredirect)):
require = requiredirect[i]
_from = require[0]
_to = require[1]
prior.setRequired(_from, _to)
# add temporal nodes' tiers
if addtemporal is not None:
for i in range(0, len(addtemporal)):
tier = i
temporal = addtemporal[i]
if isinstance(temporal, ForbiddenWithin):
prior.setTierForbiddenWithin(tier, True)
temporal = temporal.nodes
for j in range(0, len(temporal)):
node = temporal[j]
node = node.replace(' ', '.')
prior.addToTier(tier, node)
return prior
def test_02_02_set_field(self):
obj = J.JClassWrapper("org.cellprofiler.javabridge.test.RealRect")(1.5,
2.5,
3.5,
4.5)
obj.x = 2.5
self.assertEquals(obj.x, 2.5)
def test_01_03_globals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
self.cpython.execute(
"""
global javabridge
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", None, jglobals.o)
self.assertEqual(javabridge.to_string(jref.get(0)), "3")
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 popup_script_dlg(canvas):
joptionpane = javabridge.JClassWrapper("javax.swing.JOptionPane")
jresult = joptionpane.showInputDialog("Enter a script command")
if jresult is not None:
result = javabridge.to_string(jresult)
axes = canvas.figure.axes[0]
eval(result, globals(), locals())
canvas.draw()
def test_01_02_locals(self):
jlocals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jlocals.put("numerator", "6")
jlocals.put("denominator", "2")
code = """
global javabridge
import javabridge
def fn(numerator, denominator, answer):
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn(numerator, denominator, answer)
"""
jlocals.put("code", code)
jlocals.put("answer", jref.o)
self.cpython.execute(code, jlocals.o, None)
self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
def test_02_05_constructor_varargs(self):
# Regression test of issue #41
#
args = ("foo", "bar")
f = J.JClassWrapper("javax.swing.filechooser.FileNameExtensionFilter")(
"baz", *args)
exts = J.get_env().get_object_array_elements(f.getExtensions().o)
self.assertEqual(args[0], J.to_string(exts[0]))
self.assertEqual(args[1], J.to_string(exts[1]))
def test_02_04_static_call_varargs(self):
#
# Test calling a static function with a variable number of
# arguments.
#
c = J.JClassWrapper("java.lang.String")
self.assertEquals(c.format("Hello, %s.", "world"), "Hello, world.")
self.assertEquals(c.format("Goodbye %s %s.", "cruel", "world"),
"Goodbye cruel world.")
def test_01_04_globals_equals_locals(self):
jglobals = javabridge.JClassWrapper('java.util.HashMap')()
jref = javabridge.JClassWrapper('java.util.ArrayList')()
jglobals.put("numerator", "6")
jglobals.put("denominator", "2")
jglobals.put("answer", jref.o)
#
# The import will be added to "locals", but that will be the globals.
#
self.cpython.execute(
"""
import javabridge
def fn():
result = int(numerator) / int(denominator)
javabridge.call(answer, "add", "(Ljava/lang/Object;)Z", str(result))
fn()
""", jglobals.o, jglobals.o)
self.assertEqual(float(javabridge.to_string(jref.get(0))), 3)
def patch_start_vm(*args, **kwargs):
result = start_vm(*args, **kwargs)
if javabridge.get_env() is not None:
try:
event_service_cls = javabridge.JClassWrapper(
"org.bushe.swing.event.ThreadSafeEventService")
event_service_cls.CLEANUP_PERIOD_MS_DEFAULT = None
except:
pass
return result
