def test_dimensionality_reduction_two_different_methods(self):
dims = [2, 3]
coordinates, details = \
encore.reduce_dimensionality(
[self.ens1, self.ens2],
method=[encore.StochasticProximityEmbeddingNative(dims[0]),
encore.PrincipalComponentAnalysis(dims[1])])
assert_equal(coordinates[1].shape[0], dims[1])
def test_dimensionality_reduction_different_method(self):
dimension = 3
coordinates, details = \
encore.reduce_dimensionality(
[self.ens1, self.ens2],
method=encore.PrincipalComponentAnalysis(dimension=dimension))
assert_equal(
coordinates.shape[0],
dimension,
err_msg="Unexpected result in dimensionality reduction: {0}".
format(coordinates))
def test_dimensionality_reduction_PCA_direct(self):
dimension = 2
method = encore.PrincipalComponentAnalysis(dimension=dimension)
coordinates = self.ens1.trajectory.timeseries(format='fac')
coordinates = np.reshape(coordinates, (coordinates.shape[0], -1))
coordinates, details = method(coordinates)
assert_equal(
coordinates.shape[0],
dimension,
err_msg="Unexpected result in dimensionality reduction: {0}".
format(coordinates))