def _to_imglib_argb(source):
address = _get_address(source)
long_address = JLong(address)
long_arr_source = JArray(JLong)(source.shape[::-1])
if not (source.dtype == np.dtype('int32')
or source.dtype == np.dtype('uint32')):
raise NotImplementedError("source.dtype must be int32 or uint32")
if source.flags['CARRAY']:
return NumpyToImgLibConversions.toARGB(long_address, *long_arr_source)
else:
stride = np.array(source.strides[::-1]) / source.itemsize
long_arr_stride = JArray(JLong)(stride)
return NumpyToImgLibConversionsWithStride.toARGB(
long_address, long_arr_stride, long_arr_source)
def _to_imglib(source):
address = _get_address(source)
long_address = JLong(address)
long_arr_source = JArray(JLong)(source.shape[::-1])
if not source.dtype in numpy_dtype_to_conversion_method:
raise NotImplementedError(
"Cannot convert dtype to ImgLib2 type yet: {}".format(
source.dtype))
elif source.flags['CARRAY']:
return numpy_dtype_to_conversion_method[source.dtype](long_address,
*long_arr_source)
else:
stride = np.array(source.strides[::-1]) / source.itemsize
long_arr_stride = JArray(JLong)(stride)
return numpy_dtype_to_conversion_with_stride_method[source.dtype](
long_address, long_arr_stride, long_arr_source)
def testPrimitive(self):
test1 = self.__jp.Test1()
intexpectation = 'int' if not sys.version_info[
0] > 2 and sys.maxint == 2**31 - 1 else 'long'
self.assertEquals(intexpectation, test1.testPrimitive(5))
self.assertEquals('long', test1.testPrimitive(2**31))
self.assertEquals('byte', test1.testPrimitive(JByte(5)))
self.assertEquals('Byte', test1.testPrimitive(java.lang.Byte(5)))
self.assertEquals('short', test1.testPrimitive(JShort(5)))
self.assertEquals('Short', test1.testPrimitive(java.lang.Short(5)))
self.assertEquals('int', test1.testPrimitive(JInt(5)))
self.assertEquals('Integer', test1.testPrimitive(java.lang.Integer(5)))
self.assertEquals('long', test1.testPrimitive(JLong(5)))
self.assertEquals('Long', test1.testPrimitive(java.lang.Long(5)))
self.assertEquals('float', test1.testPrimitive(JFloat(5)))
self.assertEquals('Float', test1.testPrimitive(java.lang.Float(5.0)))
self.assertEquals('double', test1.testPrimitive(JDouble(5)))
self.assertEquals('Double', test1.testPrimitive(java.lang.Double(5.0)))
self.assertEquals('boolean', test1.testPrimitive(JBoolean(5)))
self.assertEquals('Boolean', test1.testPrimitive(java.lang.Boolean(5)))
self.assertEquals('char', test1.testPrimitive(JChar('5')))
self.assertEquals('Character',
test1.testPrimitive(java.lang.Character('5')))
def testPrimitive(self):
test1 = self.__jp.Test1()
intexpectation = 'long'
# FIXME it is not possible to determine if this is bool/char/byte currently
#self.assertEqual(intexpectation, test1.testPrimitive(5))
#self.assertEqual('long', test1.testPrimitive(2**31))
self.assertEqual('byte', test1.testPrimitive(JByte(5)))
self.assertEqual('Byte', test1.testPrimitive(java.lang.Byte(5)))
self.assertEqual('short', test1.testPrimitive(JShort(5)))
self.assertEqual('Short', test1.testPrimitive(java.lang.Short(5)))
self.assertEqual('int', test1.testPrimitive(JInt(5)))
self.assertEqual('Integer', test1.testPrimitive(java.lang.Integer(5)))
self.assertEqual('long', test1.testPrimitive(JLong(5)))
self.assertEqual('Long', test1.testPrimitive(java.lang.Long(5)))
self.assertEqual('float', test1.testPrimitive(JFloat(5)))
self.assertEqual('Float', test1.testPrimitive(java.lang.Float(5.0)))
self.assertEqual('double', test1.testPrimitive(JDouble(5)))
self.assertEqual('Double', test1.testPrimitive(java.lang.Double(5.0)))
self.assertEqual('boolean', test1.testPrimitive(JBoolean(5)))
self.assertEqual('Boolean', test1.testPrimitive(java.lang.Boolean(5)))
self.assertEqual('char', test1.testPrimitive(JChar('5')))
self.assertEqual('Character',
test1.testPrimitive(java.lang.Character('5')))
def execute(self, operation, params=None):
"""
Execute a sql statement with an optional set of parameters
:param operation: Sql text
:param params: a sequence or dictionary of parameters
Parameters can be positional templates ``%s`` or named templates ``:name``
:param operation:
:param params:
:return:
"""
if not self._connection_valid():
raise Error('the connection has been closed')
self._reset()
conn = self._connection.jdbc_connection()
# handle parameters
if params is not None:
operation, params = self._parse_params(operation, params)
# prepare the statement
self._statement = stmt = conn.prepareStatement(operation)
stmt.clearParameters()
for column, value in enumerate(params or [], start=1):
# note that in JDBC the first column index is 1
if isinstance(value, str):
jvalue = JString(value)
stmt.setString(column, jvalue)
elif isinstance(value, float):
jvalue = JDouble(value)
stmt.setDouble(column, jvalue)
elif isinstance(value, int):
try:
jvalue = JInt(value)
stmt.setInt(column, jvalue)
except Exception:
jvalue = JLong(value)
stmt.setLong(column, jvalue)
elif isinstance(value, bool):
jvalue = JBoolean(value)
stmt.setBoolean(column, jvalue)
elif isinstance(value, bytes):
ByteArray = JArray(JByte)
jvalue = ByteArray(value.decode('utf-8'))
stmt.setBytes(column, jvalue)
else:
stmt.setObject(column, value)
try:
has_resultset = stmt.execute()
except JClass('org.apache.hive.service.cli.HiveSQLException') as e:
raise ProgrammingError('Error executing statement:\n{}\n{}'.format(
operation, e)) from None
self._rowcount = -1
if has_resultset:
self._resultset = resultset = stmt.getResultSet()
self._metadata = resultset.getMetaData()
# get rowcount
if self._get_rowcounts:
try:
if self._resultset.last(
): # if the cursor can be moved to the last row.
self._rowcount = resultset.getRow()
resultset.beforeFirst()
except JClass('java.sql.SQLException'):
# ResultSet.last() is not supported
pass
else:
try:
self._rowcount = stmt.getUpdateCount()
except JClass('java.sql.SQLException'):
# not supported
pass
def rai_slice(rai, imin: Tuple, imax: Tuple, istep: Tuple):
"""Slice ImgLib2 images.
Slice ImgLib2 images using Python's slice notation to define the
desired slice range. Returned interval includes both imin and imax
:param rai: An ImgLib2 RandomAccessibleInterval
:param imin: Tuple of minimum interval range values.
:param imax: Tuple of maximum interval range values.
:return: Sliced ImgLib2 RandomAccisbleInterval.
"""
# HACK: Avoid importing JLong at global scope.
# Otherwise, building the sphinx docs in doc/rtd fails with:
#
# Warning, treated as error:
# autodoc: failed to determine imagej.stack.JLong (<java class 'JLong'>) to be documented, the following exception was raised:
# Java Virtual Machine is not running
#
# Which can be reproduced in a REPL like this:
#
# >>> from jpype import JLong
# >>> help(JLong)
#
# So while the import here is unfortunate, it avoids the issue.
from jpype import JArray, JLong
Views = sj.jimport("net.imglib2.view.Views")
shape = rai.shape
imin_fix = JArray(JLong)(len(shape))
imax_fix = JArray(JLong)(len(shape))
dim_itr = range(len(shape))
for py_dim, j_dim in zip(dim_itr, dim_itr):
# Set minimum
if imin[py_dim] == None:
index = 0
else:
index = imin[py_dim]
if index < 0:
index += shape[j_dim]
imin_fix[j_dim] = JLong(index)
# Set maximum
if imax[py_dim] == None:
index = shape[j_dim] - 1
else:
index = imax[py_dim]
if index < 0:
index += shape[j_dim]
imax_fix[j_dim] = JLong(index)
istep_fix = JArray(JLong)(istep)
if _index_within_range(imin_fix, shape) and _index_within_range(
imax_fix, shape):
intervaled = Views.interval(rai, imin_fix, imax_fix)
stepped = Views.subsample(intervaled, istep_fix)
# TODO: better mach NumPy squeeze behavior. See pyimagej/#1231
dimension_reduced = Views.dropSingletonDimensions(stepped)
return dimension_reduced