def init_reader(self):
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
self.rdr.setMetadataOptions(mdoptions)
self.rdr.setGroupFiles(False)
self.metadata = metadatatools.createOMEXMLMetadata()
self.rdr.setMetadataStore(self.metadata)
try:
self.rdr.setId(self.path)
except jutil.JavaException as e:
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
je = e.throwable
if has_omero_packages() and jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
# Handle at a higher level
raise
if jutil.is_instance_of(
je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause",
"()Ljava/lang/Throwable;")
if jutil.is_instance_of(
je, "java/io/FileNotFoundException"):
raise IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path,
path)
e2 = IOError(
errno.EINVAL, "Could not load the file as an image (see log for details)",
self.path.encode('utf-8'))
raise e2
def context_to_locals(context):
'''convert the local context as a Java map to a dictionary of locals'''
d = {"JWrapper": JWrapper, "importClass": importClass}
m = J.get_map_wrapper(context)
for k in m:
key = J.to_string(k)
o = m[k]
if isinstance(o, J.JB_Object):
if J.is_instance_of(o, "java/lang/String"):
d[key] = J.to_string(o)
continue
for class_name, method, signature in (("java/lang/Boolean",
"booleanValue", "()Z"),
("java/lang/Byte",
"byteValue", "()B"),
("java/lang/Integer",
"intValue", "()I"),
("java/lang/Long",
"longValue", "()L"),
("java/lang/Float",
"floatValue", "()F"),
("java/lang/Double",
"doubleValue", "()D")):
if J.is_instance_of(o, class_name):
d[key] = J.call(o, method, signature)
break
else:
d[key] = JWrapper(o)
else:
d[key] = o
return d
def init_reader(self):
mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
self.rdr.setMetadataOptions(mdoptions)
self.rdr.setGroupFiles(False)
self.metadata = metadatatools.createOMEXMLMetadata()
self.rdr.setMetadataStore(self.metadata)
try:
self.rdr.setId(self.path)
except jutil.JavaException as e:
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
je = e.throwable
if has_omero_packages() and jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
# Handle at a higher level
raise
if jutil.is_instance_of(je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause", "()Ljava/lang/Throwable;")
if jutil.is_instance_of(je, "java/io/FileNotFoundException"):
raise IOError(errno.ENOENT,
"The file, \"%s\", does not exist." % path, path)
e2 = IOError(
errno.EINVAL,
"Could not load the file as an image (see log for details)",
self.path.encode('utf-8'))
raise e2
def load_file(self, dfile, incremental=False):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:return: the full dataset or the header (if incremental)
:rtype: Instances
"""
self.enforce_type(self.jobject,
"weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V",
javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(
javabridge.call(self.jobject, "getStructure",
"()Lweka/core/Instances;"))
return self.structure
else:
return Instances(
javabridge.call(self.jobject, "getDataSet",
"()Lweka/core/Instances;"))
def load_file(self, dfile, incremental=False):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:return: the full dataset or the header (if incremental)
:rtype: Instances
:raises Exception: if the file does not exist
"""
self.enforce_type(self.jobject, "weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V", javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
# check whether file exists, otherwise previously set file gets loaded again
sfile = javabridge.to_string(dfile)
if not os.path.exists(sfile):
raise Exception("Dataset file does not exist: " + str(sfile))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(javabridge.call(self.jobject, "getStructure", "()Lweka/core/Instances;"))
return self.structure
else:
return Instances(javabridge.call(self.jobject, "getDataSet", "()Lweka/core/Instances;"))
def load_file(self, dfile, incremental=False):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:return: the full dataset or the header (if incremental)
:rtype: Instances
:raises Exception: if the file does not exist
"""
self.enforce_type(self.jobject,
"weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V",
javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
# check whether file exists, otherwise previously set file gets loaded again
sfile = javabridge.to_string(dfile)
if not os.path.exists(sfile):
raise Exception("Dataset file does not exist: " + str(sfile))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(
javabridge.call(self.jobject, "getStructure",
"()Lweka/core/Instances;"))
return self.structure
else:
return Instances(
javabridge.call(self.jobject, "getDataSet",
"()Lweka/core/Instances;"))
def test_haplotypeAllelePresenceForAllTaxa(self):
if debug: print "Testing haplotypeAllelePresenceForAllTaxa"
try:
bitset_major = self.data.haplotypeAllelePresenceForAllTaxa(0,True,WHICH_ALLELE.Major)
self.assertIsInstance(bitset_major,BitSet)
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['UnsupportedOperationException']))
def test_depthForAlleles(self):
if debug: print "Testing depthForAlleles"
try:
arr = self.data.depthForAlleles(0,0)
self.assertIsInstance(arr[0],metaInteger)
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['NullPointerException']))
def test_siteScores(self):
if debug: print "Testing siteScores"
try:
score = self.data.siteScores()
self.assertIsInstance(score,metaInteger)
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['IllegalStateException']))
def test_haplotypeAllelePresenceForSitesBlock(self):
if debug: print "Testing haplotypeAllelePresenceForSitesBlock"
try:
arr = self.data.haplotypeAllelePresenceForSitesBlock(0,True,WHICH_ALLELE.Major,
0,1)
self.assertIsInstance(arr,meta_long_array)
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['UnsupportedOperationException']))
def test_genomeVersion(self):
if debug: print "Testing genomeVersion"
try:
version = self.data.genomeVersion()
if version is not None:
self.assertIsInstance(version, metaString)
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['UnsupportedOperationException']))
def test_siteScoreType(self):
if debug: print "Testing siteScoreType"
try:
scoretype = self.data.siteScoreType()
self.assertTrue(any(map(lambda x: scoretype.equals(x),
self.data.SITE_SCORE_TYPE.__dict__.values())))
except JavaException as e:
self.assertTrue(is_instance_of(e.throwable, java_imports['NullPointerException']))
def test_01_11_02_isnt_instance_of(self):
klassByte = self.env.find_class("java/lang/Byte")
method_id = self.env.get_method_id(klassByte, '<init>',
'(Ljava/lang/String;)V')
jbyte = self.env.new_object(klassByte, method_id,
self.env.new_string_utf("55"))
klassString = self.env.find_class("java/lang/String")
self.assertFalse(self.env.is_instance_of(jbyte, klassString))
# <AK> added
self.assertFalse(javabridge.is_instance_of(None, "java/lang/String"))
def load_file(self, dfile, incremental=False, class_index=None):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:param class_index: the class index string to use ('first', 'second', 'third', 'last-2', 'last-1', 'last' or 1-based index)
:type class_index: str
:return: the full dataset or the header (if incremental)
:rtype: Instances
:raises Exception: if the file does not exist
"""
self.enforce_type(self.jobject,
"weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V",
javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
# check whether file exists, otherwise previously set file gets loaded again
sfile = javabridge.to_string(dfile)
if not os.path.exists(sfile):
raise Exception("Dataset file does not exist: " + str(sfile))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(
javabridge.call(self.jobject, "getStructure",
"()Lweka/core/Instances;"))
result = self.structure
else:
result = Instances(
javabridge.call(self.jobject, "getDataSet",
"()Lweka/core/Instances;"))
if class_index is not None:
if class_index == 'first':
result.class_index = 0
elif class_index == 'second':
result.class_index = 1
elif class_index == 'third':
result.class_index = 2
elif class_index == 'last-2':
result.class_index = result.num_attributes - 3
elif class_index == 'last-1':
result.class_index = result.num_attributes - 2
elif class_index == 'last':
result.class_index = result.num_attributes - 1
else:
result.class_index = int(class_index)
return result
def check_type(cls, jobject, intf_or_class, jni_intf_or_class=None):
"""
Returns whether the object implements the specified interface or is a subclass.
E.g.: self._check_type('weka.core.OptionHandler', 'Lweka/core/OptionHandler;')
or self._check_type('weka.core.converters.AbstractFileLoader')
:param jobject: the Java object to check
:type jobject: JB_Object
:param intf_or_class: the classname in Java notation (eg "weka.core.DenseInstance;")
:type jni_intf_or_class: str
:return: whether object implements interface or is subclass
:rtype: bool
"""
if jni_intf_or_class is None:
jni_intf_or_class = "L" + intf_or_class.replace(".", "/") + ";"
return javabridge.is_instance_of(jobject, jni_intf_or_class)
def save_file(self, data, dfile):
"""
Saves the Instances object in the specified file.
:param data: the data to save
:type data: Instances
:param dfile: the file to save the data to
:type dfile: str
"""
self.enforce_type(self.jobject, "weka.core.converters.FileSourcedConverter")
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V", javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
javabridge.call(self.jobject, "setInstances", "(Lweka/core/Instances;)V", data.jobject)
javabridge.call(self.jobject, "writeBatch", "()V")
def check_type(cls, jobject, intf_or_class, jni_intf_or_class=None):
"""
Returns whether the object implements the specified interface or is a subclass.
E.g.: self._check_type('weka.core.OptionHandler', 'Lweka/core/OptionHandler;')
or self._check_type('weka.core.converters.AbstractFileLoader')
:param jobject: the Java object to check
:type jobject: JB_Object
:param intf_or_class: the classname in Java notation (eg "weka.core.Instance")
:type intf_or_class: str
:param jni_intf_or_class: the classname in JNI notation (eg "Lweka/core/Instance;")
:type jni_intf_or_class: str
:return: whether object implements interface or is subclass
:rtype: bool
"""
if jni_intf_or_class is None:
jni_intf_or_class = "L" + intf_or_class.replace(".", "/") + ";"
return javabridge.is_instance_of(jobject, jni_intf_or_class)
def save_file(self, data, dfile):
"""
Saves the Instances object in the specified file.
:param data: the data to save
:type data: Instances
:param dfile: the file to save the data to
:type dfile: str
"""
self.enforce_type(self.jobject,
"weka.core.converters.FileSourcedConverter")
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V",
javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
javabridge.call(self.jobject, "setInstances",
"(Lweka/core/Instances;)V", data.jobject)
javabridge.call(self.jobject, "writeBatch", "()V")
def load_file(self, dfile, incremental=False):
"""
Loads the specified file and returns the Instances object.
In case of incremental loading, only the structure.
:param dfile: the file to load
:type dfile: str
:param incremental: whether to load the dataset incrementally
:type incremental: bool
:return: the full dataset or the header (if incremental)
:rtype: Instances
"""
self.enforce_type(self.jobject, "weka.core.converters.FileSourcedConverter")
self.incremental = incremental
if not javabridge.is_instance_of(dfile, "Ljava/io/File;"):
dfile = javabridge.make_instance(
"Ljava/io/File;", "(Ljava/lang/String;)V", javabridge.get_env().new_string_utf(str(dfile)))
javabridge.call(self.jobject, "reset", "()V")
javabridge.call(self.jobject, "setFile", "(Ljava/io/File;)V", dfile)
if incremental:
self.structure = Instances(javabridge.call(self.jobject, "getStructure", "()Lweka/core/Instances;"))
return self.structure
else:
return Instances(javabridge.call(self.jobject, "getDataSet", "()Lweka/core/Instances;"))
def __init__(self, path=None, url=None, perform_init=True):
self.stream = None
file_scheme = "file:"
self.using_temp_file = False
if url is not None:
url = str(url)
if url.lower().startswith(file_scheme):
url = url2pathname(url[len(file_scheme):])
path = url
self.path = path
if path is None:
if url.lower().startswith("omero:"):
while True:
#
# We keep trying to contact the OMERO server via the
# login dialog until the user gives up or we connect.
#
try:
self.rdr = get_omero_reader()
self.path = url
if perform_init:
self.init_reader()
return
except jutil.JavaException as e:
je = e.throwable
if jutil.is_instance_of(
je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause",
"()Ljava/lang/Throwable;")
if jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
omero_logout()
omero_login()
else:
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
if jutil.is_instance_of(
je, "java/io/FileNotFoundException"):
raise IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path,
path)
e2 = IOError(
errno.EINVAL, "Could not load the file as an image (see log for details)", path.encode('utf-8'))
raise e2
else:
#
# Other URLS, copy them to a tempfile location
#
ext = url[url.rfind("."):]
src = urlopen(url)
dest_fd, self.path = tempfile.mkstemp(suffix=ext)
try:
dest = os.fdopen(dest_fd, 'wb')
shutil.copyfileobj(src, dest)
except:
src.close()
dest.close()
os.remove(self.path)
self.using_temp_file = True
src.close()
dest.close()
urlpath = urlparse(url)[2]
filename = unquote(urlpath.split("/")[-1])
else:
if sys.platform.startswith("win"):
self.path = self.path.replace("/", os.path.sep)
filename = os.path.split(path)[1]
if not os.path.isfile(self.path):
raise IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path,
path)
self.stream = jutil.make_instance('loci/common/RandomAccessInputStream',
'(Ljava/lang/String;)V',
self.path)
self.rdr = None
class_list = get_class_list()
find_rdr_script = """
var classes = class_list.getClasses();
var rdr = null;
var lc_filename = java.lang.String(filename.toLowerCase());
for (pass=0; pass < 3; pass++) {
for (class_idx in classes) {
var maybe_rdr = classes[class_idx].newInstance();
if (pass == 0) {
if (maybe_rdr.isThisType(filename, false)) {
rdr = maybe_rdr;
break;
}
continue;
} else if (pass == 1) {
var suffixes = maybe_rdr.getSuffixes();
var suffix_found = false;
for (suffix_idx in suffixes) {
var suffix = java.lang.String(suffixes[suffix_idx]);
suffix = suffix.toLowerCase();
if (lc_filename.endsWith(suffix)) {
suffix_found = true;
break;
}
}
if (! suffix_found) continue;
}
if (maybe_rdr.isThisType(stream)) {
rdr = maybe_rdr;
break;
}
}
if (rdr) break;
}
rdr;
"""
IFormatReader = make_iformat_reader_class()
jrdr = jutil.run_script(find_rdr_script, dict(class_list = class_list,
filename = filename,
stream = self.stream))
if jrdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s", self.path)
self.rdr = IFormatReader()
self.rdr.o = jrdr
if perform_init:
self.init_reader()
def test_02_02_01_get_modules(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
self.assertTrue(J.is_instance_of(module_infos[0].o,
"org/scijava/module/ModuleInfo"))
def __iter__(self):
if not J.is_instance_of(self.o,'java/util/Collection'):
raise TypeError("%s is not a Collection and does not support __iter__" % self)
return self.Iterator(self)
def __setitem__(self, i, v):
if not J.is_instance_of(self.o,'java/util/Collection'):
raise TypeError("%s is not a Collection and does not support __setitem__" % self)
return self.set(i, v)
def test_02_02_01_get_modules(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
self.assertTrue(
J.is_instance_of(module_infos[0].o,
"org/scijava/module/ModuleInfo"))
def __init__(self, path=None, url=None, perform_init=True):
self.stream = None
file_scheme = "file:"
self.using_temp_file = False
if url is not None:
url = str(url)
if url.lower().startswith(file_scheme):
url = url2pathname(url[len(file_scheme):])
path = url
self.path = path
if path is None:
if url.lower().startswith("omero:"):
while True:
#
# We keep trying to contact the OMERO server via the
# login dialog until the user gives up or we connect.
#
try:
self.rdr = get_omero_reader()
self.path = url
if perform_init:
self.init_reader()
return
except jutil.JavaException as e:
je = e.throwable
if jutil.is_instance_of(
je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause",
"()Ljava/lang/Throwable;")
if jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
omero_logout()
omero_login()
else:
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
if jutil.is_instance_of(
je, "java/io/FileNotFoundException"):
raise IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path,
path)
e2 = IOError(
errno.EINVAL,
"Could not load the file as an image (see log for details)",
path.encode('utf-8'))
raise e2
else:
#
# Other URLS, copy them to a tempfile location
#
ext = url[url.rfind("."):]
src = urlopen(url)
dest_fd, self.path = tempfile.mkstemp(suffix=ext)
try:
dest = os.fdopen(dest_fd, 'wb')
shutil.copyfileobj(src, dest)
except:
src.close()
dest.close()
os.remove(self.path)
self.using_temp_file = True
src.close()
dest.close()
urlpath = urlparse(url)[2]
filename = unquote(urlpath.split("/")[-1])
else:
if sys.platform.startswith("win"):
self.path = self.path.replace("/", os.path.sep)
filename = os.path.split(path)[1]
if not os.path.isfile(self.path):
raise IOError(errno.ENOENT,
"The file, \"%s\", does not exist." % path, path)
self.stream = jutil.make_instance(
'loci/common/RandomAccessInputStream', '(Ljava/lang/String;)V',
self.path)
self.rdr = None
class_list = get_class_list()
find_rdr_script = """
var classes = class_list.getClasses();
var rdr = null;
var lc_filename = java.lang.String(filename.toLowerCase());
for (pass=0; pass < 3; pass++) {
for (class_idx in classes) {
var maybe_rdr = classes[class_idx].newInstance();
if (pass == 0) {
if (maybe_rdr.isThisType(filename, false)) {
rdr = maybe_rdr;
break;
}
continue;
} else if (pass == 1) {
var suffixes = maybe_rdr.getSuffixes();
var suffix_found = false;
for (suffix_idx in suffixes) {
var suffix = java.lang.String(suffixes[suffix_idx]);
suffix = suffix.toLowerCase();
if (lc_filename.endsWith(suffix)) {
suffix_found = true;
break;
}
}
if (! suffix_found) continue;
}
if (maybe_rdr.isThisType(stream)) {
rdr = maybe_rdr;
break;
}
}
if (rdr) break;
}
rdr;
"""
IFormatReader = make_iformat_reader_class()
jrdr = jutil.run_script(
find_rdr_script,
dict(class_list=class_list, filename=filename, stream=self.stream))
if jrdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s",
self.path)
self.rdr = IFormatReader()
self.rdr.o = jrdr
if perform_init:
self.init_reader()
def __setitem__(self, i, v):
if not J.is_instance_of(self.o, 'java/util/Collection'):
raise TypeError(
"%s is not a Collection and does not support __setitem__" %
self)
return self.set(i, v)
def __iter__(self):
if not J.is_instance_of(self.o, 'java/util/Collection'):
raise TypeError(
"%s is not a Collection and does not support __iter__" % self)
return self.Iterator(self)