def __getBackendResults(self):
"""
Private helper function to get the backend results.
"""
# Setup the histogram data in python.
self.__raw_histogram = stdVectorCoordinateToNumpy2DArray(self.__backend.histogramBuffer())
self.__bin_counters = self.__backend.histogramBinCounts()
self.__history_bin_counters = self.__backend.historyStepsHistogramBinCounts()
self.__hstep_counts = self.__backend.hstepCounts()
def testStdVectorCoordinateToNumpy2DArray(self):
""" Test the conversion from a std::vector<Coordinate> to a numpy array. """
# Get a reference.
ref_array = numpy.random.rand(6).reshape((2,3))
# Setup the data to convert.
cpp_vector = Backend.StdVectorCoordinate()
cpp_vector.push_back(Backend.Coordinate(ref_array[0,0], ref_array[0,1], ref_array[0,2]))
cpp_vector.push_back(Backend.Coordinate(ref_array[1,0], ref_array[1,1], ref_array[1,2]))
# Convert.
py_array = stdVectorCoordinateToNumpy2DArray(cpp_vector)
# Check.
diff = numpy.linalg.norm(ref_array - py_array)
self.assertAlmostEqual( diff, 0.0, 10 )
def testNumpy2DArrayToStdVectorCoordinate(self):
""" Test the conversion of a Nx3 2D numpy array to a std::vector<Coordinate> representation. """
nI = 12;
nJ = 3;
array = numpy.random.rand(nI,nJ)
# Convert to c++
cpp_vector = numpy2DArrayToStdVectorCoordinate(array)
# Check the size.
self.assertEqual(cpp_vector.size(), nI)
# Check the type.
self.assertTrue( isinstance(cpp_vector, Backend.StdVectorCoordinate) )
# Convert back and check values.
converted = stdVectorCoordinateToNumpy2DArray(cpp_vector)
self.assertAlmostEqual(numpy.linalg.norm(array-converted), 0.0, 10)
def testNumpy2DArrayToStdVectorCoordinate(self):
""" Test the conversion of a Nx3 2D numpy array to a std::vector<Coordinate> representation. """
nI = 12
nJ = 3
array = numpy.random.rand(nI, nJ)
# Convert to c++
cpp_vector = numpy2DArrayToStdVectorCoordinate(array)
# Check the size.
self.assertEqual(cpp_vector.size(), nI)
# Check the type.
self.assertTrue(isinstance(cpp_vector, Backend.StdVectorCoordinate))
# Convert back and check values.
converted = stdVectorCoordinateToNumpy2DArray(cpp_vector)
self.assertAlmostEqual(numpy.linalg.norm(array - converted), 0.0, 10)
def testStdVectorCoordinateToNumpy2DArray(self):
""" Test the conversion from a std::vector<Coordinate> to a numpy array. """
# Get a reference.
ref_array = numpy.random.rand(6).reshape((2, 3))
# Setup the data to convert.
cpp_vector = Backend.StdVectorCoordinate()
cpp_vector.push_back(
Backend.Coordinate(ref_array[0, 0], ref_array[0, 1], ref_array[0,
2]))
cpp_vector.push_back(
Backend.Coordinate(ref_array[1, 0], ref_array[1, 1], ref_array[1,
2]))
# Convert.
py_array = stdVectorCoordinateToNumpy2DArray(cpp_vector)
# Check.
diff = numpy.linalg.norm(ref_array - py_array)
self.assertAlmostEqual(diff, 0.0, 10)
def atomIDCoordinates(self):
"""
Query for the coordinates per atom id.
"""
return stdVectorCoordinateToNumpy2DArray(
self._backend().atomIDCoordinates())
def atomIDCoordinates(self):
"""
Query for the coordinates per atom id.
"""
return stdVectorCoordinateToNumpy2DArray(self._backend().atomIDCoordinates())
