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 get_metadata_options(level):
'''Get an instance of the MetadataOptions interface
level - MINIMUM, NO_OVERLAYS or ALL to set the metadata retrieval level
The object returned can be used in setMetadataOptions in a format reader.
'''
jlevel = jutil.get_static_field('loci/formats/in/MetadataLevel', level,
'Lloci/formats/in/MetadataLevel;')
return jutil.make_instance('loci/formats/in/DefaultMetadataOptions',
'(Lloci/formats/in/MetadataLevel;)V', jlevel)
def get_metadata_options(level):
'''Get an instance of the MetadataOptions interface
level - MINIMUM, NO_OVERLAYS or ALL to set the metadata retrieval level
The object returned can be used in setMetadataOptions in a format reader.
'''
jlevel = jutil.get_static_field('loci/formats/in/MetadataLevel', level,
'Lloci/formats/in/MetadataLevel;')
return jutil.make_instance('loci/formats/in/DefaultMetadataOptions',
'(Lloci/formats/in/MetadataLevel;)V',
jlevel)
def get_tiled_reader(path):
"""
Read tiled czi image and get ZeissCZIReader without stitching
Parameters
---------
path : str
path to the czi file
Returns
-------
reader : ZeissCZIReader
tiled reader
"""
CZIAllowStitchKey = jutil.get_static_field(
"loci/formats/in/ZeissCZIReader",
"ALLOW_AUTOSTITCHING_KEY",
"Ljava/lang/String;",
)
CZIIncludeAttachmentKey = jutil.get_static_field(
"loci/formats/in/ZeissCZIReader",
"INCLUDE_ATTACHMENTS_KEY",
"Ljava/lang/String;",
)
jutil.set_static_field("loci/formats/in/ZeissCZIReader",
"ALLOW_AUTOSTITCHING_DEFAULT", "Z", False)
jutil.set_static_field("loci/formats/in/ZeissCZIReader",
"INCLUDE_ATTACHMENTS_DEFAULT", "Z", False)
rdr = bioformats.ImageReader(path, perform_init=False)
DynamicMetadataOptions = javabridge.JClassWrapper(
"loci.formats.in.DynamicMetadataOptions")
dynop = DynamicMetadataOptions()
dynop.set(CZIAllowStitchKey, "false")
dynop.set(CZIIncludeAttachmentKey, "false")
rdr.rdr.setMetadataOptions(dynop)
rdr.metadata = bioformats.metadatatools.createOMEXMLMetadata()
rdr.rdr.setMetadataStore(rdr.metadata)
rdr.rdr.setId(rdr.path)
return rdr
def test_01_05_get_static_field(self):
klass = self.env.find_class("java/lang/Short")
self.assertEqual(J.get_static_field(klass, "MAX_VALUE", "S"), 2**15 - 1)
def test_03_08_cw_get_field(self):
c = J.get_class_wrapper('java.lang.String')
field = c.getField('CASE_INSENSITIVE_ORDER')
modifiers = J.call(field, 'getModifiers', '()I')
static = J.get_static_field('java/lang/reflect/Modifier','STATIC','I')
self.assertEqual((modifiers & static), static)
def __init__(self):
klass = jutil.get_env().find_class('ome/xml/model/enums/PixelType')
self.INT8 = jutil.get_static_field(klass, 'INT8', 'Lome/xml/model/enums/PixelType;')
self.INT16 = jutil.get_static_field(klass, 'INT16', 'Lome/xml/model/enums/PixelType;')
self.INT32 = jutil.get_static_field(klass, 'INT32', 'Lome/xml/model/enums/PixelType;')
self.UINT8 = jutil.get_static_field(klass, 'UINT8', 'Lome/xml/model/enums/PixelType;')
self.UINT16 = jutil.get_static_field(klass, 'UINT16', 'Lome/xml/model/enums/PixelType;')
self.UINT32 = jutil.get_static_field(klass, 'UINT32', 'Lome/xml/model/enums/PixelType;')
self.FLOAT = jutil.get_static_field(klass, 'FLOAT', 'Lome/xml/model/enums/PixelType;')
self.BIT = jutil.get_static_field(klass, 'BIT', 'Lome/xml/model/enums/PixelType;')
self.DOUBLE = jutil.get_static_field(klass, 'DOUBLE', 'Lome/xml/model/enums/PixelType;')
self.COMPLEX = jutil.get_static_field(klass, 'COMPLEX', 'Lome/xml/model/enums/PixelType;')
self.DOUBLECOMPLEX = jutil.get_static_field(klass, 'DOUBLECOMPLEX', 'Lome/xml/model/enums/PixelType;')
def __init__(self):
klass = jutil.get_env().find_class(
'ome/xml/model/enums/PixelType')
self.INT8 = jutil.get_static_field(
klass, 'INT8', 'Lome/xml/model/enums/PixelType;')
self.INT16 = jutil.get_static_field(
klass, 'INT16', 'Lome/xml/model/enums/PixelType;')
self.INT32 = jutil.get_static_field(
klass, 'INT32', 'Lome/xml/model/enums/PixelType;')
self.UINT8 = jutil.get_static_field(
klass, 'UINT8', 'Lome/xml/model/enums/PixelType;')
self.UINT16 = jutil.get_static_field(
klass, 'UINT16', 'Lome/xml/model/enums/PixelType;')
self.UINT32 = jutil.get_static_field(
klass, 'UINT32', 'Lome/xml/model/enums/PixelType;')
self.FLOAT = jutil.get_static_field(
klass, 'FLOAT', 'Lome/xml/model/enums/PixelType;')
self.BIT = jutil.get_static_field(
klass, 'BIT', 'Lome/xml/model/enums/PixelType;')
self.DOUBLE = jutil.get_static_field(
klass, 'DOUBLE', 'Lome/xml/model/enums/PixelType;')
self.COMPLEX = jutil.get_static_field(
klass, 'COMPLEX', 'Lome/xml/model/enums/PixelType;')
self.DOUBLECOMPLEX = jutil.get_static_field(
klass, 'DOUBLECOMPLEX', 'Lome/xml/model/enums/PixelType;')
