def setPixelsSizeY(self, y, imageIndex, binDataIndex):
try:
jutil.call(self.o, 'setPixelsSizeY',
'(Lome/xml/model/primitives/PositiveInteger;I)V',
PositiveInteger(y), imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsSizeY',
'(Ljava/lang/Integer;II)V', y, imageIndex, binDataIndex)
def setPixelsSizeY(self, y, imageIndex, binDataIndex):
try:
jutil.call(self.o, 'setPixelsSizeY',
'(Lome/xml/model/primitives/PositiveInteger;I)V',
PositiveInteger(y), imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsSizeY', '(Ljava/lang/Integer;II)V', y,
imageIndex, binDataIndex)
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 setLogicalChannelSamplesPerPixel(self, samplesPerPixel, imageIndex, channelIndex):
'For a particular LogicalChannel, sets number of channel components in the logical channel.'
try:
jutil.call(self.o, 'setChannelSamplesPerPixel',
'(Lome/xml/model/primitives/PositiveInteger;II)V',
PositiveInteger(samplesPerPixel),
imageIndex, channelIndex)
except jutil.JavaException:
jutil.call(self.o, 'setLogicalChannelSamplesPerPixel',
'(Ljava/lang/Integer;II)V', samplesPerPixel,
imageIndex, channelIndex)
def setLogicalChannelSamplesPerPixel(self, samplesPerPixel, imageIndex,
channelIndex):
'For a particular LogicalChannel, sets number of channel components in the logical channel.'
try:
jutil.call(self.o, 'setChannelSamplesPerPixel',
'(Lome/xml/model/primitives/PositiveInteger;II)V',
PositiveInteger(samplesPerPixel), imageIndex,
channelIndex)
except jutil.JavaException:
jutil.call(self.o, 'setLogicalChannelSamplesPerPixel',
'(Ljava/lang/Integer;II)V', samplesPerPixel, imageIndex,
channelIndex)
def setPixelsDimensionOrder(self, dimension_order, imageIndex, binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V',
dimension_order, imageIndex, binDataIndex)
def setPixelsBigEndian(self, bigEndian, imageIndex, binDataIndex):
'''Set the endianness for a particular image
bigEndian - True for big-endian, False for little-endian
imageIndex - index of the image in question from IFormatReader.get_index?
binDataIndex - ???
'''
# Post loci_tools 4.2
try:
jutil.call(self.o, 'setPixelsBinDataBigEndian',
'(Ljava/lang/Boolean;II)V',
bigEndian, imageIndex, binDataIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsBigEndian', '(Ljava/lang/Boolean;II)V',
bigEndian, imageIndex, binDataIndex)
def setPixelsBigEndian(self, bigEndian, imageIndex, binDataIndex):
'''Set the endianness for a particular image
bigEndian - True for big-endian, False for little-endian
imageIndex - index of the image in question from IFormatReader.get_index?
binDataIndex - ???
'''
# Post loci_tools 4.2
try:
jutil.call(self.o, 'setPixelsBinDataBigEndian',
'(Ljava/lang/Boolean;II)V', bigEndian, imageIndex,
binDataIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsBigEndian',
'(Ljava/lang/Boolean;II)V', bigEndian, imageIndex,
binDataIndex)
def setPixelsDimensionOrder(self, dimension_order, imageIndex,
binDataIndex):
'''Set the dimension order for a series'''
# Post loci_tools 4.2 - use ome.xml.model.DimensionOrder
try:
jdimension_order = jutil.static_call(
'ome/xml/model/enums/DimensionOrder', 'fromString',
'(Ljava/lang/String;)Lome/xml/model/enums/DimensionOrder;',
dimension_order)
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Lome/xml/model/enums/DimensionOrder;I)V',
jdimension_order, imageIndex)
except jutil.JavaException:
jutil.call(self.o, 'setPixelsDimensionOrder',
'(Ljava/lang/String;II)V', dimension_order, imageIndex,
binDataIndex)
def test_03_07_cw_get_fields(self):
c = J.get_class_wrapper('java.lang.String')
fields = c.getFields()
fields = J.get_env().get_object_array_elements(fields)
self.assertEqual(len(fields), 1)
self.assertEqual(J.call(fields[0], 'getName', '()Ljava/lang/String;'),
"CASE_INSENSITIVE_ORDER")
def test_01_06_get_enumeration_wrapper(self):
properties = J.static_call("java/lang/System", "getProperties",
"()Ljava/util/Properties;")
keys = J.call(properties, "keys", "()Ljava/util/Enumeration;")
enum = J.get_enumeration_wrapper(keys)
has_java_vm_name = False
while(enum.hasMoreElements()):
key = J.to_string(enum.nextElement())
if key == "java.vm.name":
has_java_vm_name = True
self.assertTrue(has_java_vm_name)
def test_02_03_death_and_resurrection(self):
'''Put an object into another in Java, delete it in Python and recover it'''
np.random.seed(24)
my_value = np.random.randint(0, 1000)
jobj = J.make_instance("java/lang/Integer", "(I)V", my_value)
integer_klass = self.env.find_class("java/lang/Integer")
jcontainer = self.env.make_object_array(1, integer_klass)
self.env.set_object_array_element(jcontainer, 0, jobj)
del jobj
gc.collect()
jobjs = self.env.get_object_array_elements(jcontainer)
jobj = jobjs[0]
self.assertEqual(J.call(jobj, "intValue", "()I"), my_value)
def test_01_11_class_for_name(self):
c = J.class_for_name('java.lang.String')
name = J.call(c, 'getCanonicalName', '()Ljava/lang/String;')
self.assertEqual(name, 'java.lang.String')
def test_01_03_call(self):
jstring = self.env.new_string_utf("Hello, world")
self.assertEqual(J.call(jstring, "charAt", "(I)C", 0), "H")
def test_03_11_cw_get_constructor(self):
c = J.get_class_wrapper('java.lang.String')
sclass = J.class_for_name('java.lang.String')
constructor = c.getConstructor([sclass])
self.assertEqual(J.call(constructor, 'getName', '()Ljava/lang/String;'),
'java.lang.String')
def test_03_10_cw_get_methods(self):
c = J.get_class_wrapper('java.lang.String')
mmm = J.get_env().get_object_array_elements(c.getMethods())
self.assertTrue(any([J.call(m, 'getName', '()Ljava/lang/String;') == 'concat'
for m in mmm]))
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)