Example #1
0
    def test_apply_reduce_num_components(self):
        """
        Checks whether PCA performs dimensionality reduction
        """
        sut = PCA(self.num_components - 1, whiten=True)
        sut.apply(self.dataset, True)

        assert self.dataset.get_design_matrix().shape[1] ==\
            self.num_components - 1
    def test_apply_reduce_num_components(self):
        """
        Checks whether PCA performs dimensionality reduction
        """
        sut = PCA(self.num_components - 1, whiten=True)
        sut.apply(self.dataset, True)

        assert self.dataset.get_design_matrix().shape[1] ==\
            self.num_components - 1
Example #3
0
    def test_apply_whiten(self):
        """
        Confirms that PCA has decorrelated the input dataset and
        variance is the same along all principal components and equal to one
         """
        sut = PCA(self.num_components, whiten=True)
        sut.apply(self.dataset, True)
        cm = np.cov(self.dataset.get_design_matrix().T)  # covariance matrix

        # testing whether the covariance matrix is a diagonal one
        np.testing.assert_almost_equal(cm * (np.ones(cm.shape[0]) -
                                       np.eye(cm.shape[0])),
                                       np.zeros((cm.shape[0], cm.shape[0])))

        # testing whether the eigenvalues are all ones
        np.testing.assert_almost_equal(np.diag(cm), np.ones(cm.shape[0]))
    def test_apply_whiten(self):
        """
        Confirms that PCA has decorrelated the input dataset and
        variance is the same along all principal components and equal to one
         """
        sut = PCA(self.num_components, whiten=True)
        sut.apply(self.dataset, True)
        cm = np.cov(self.dataset.get_design_matrix().T)  # covariance matrix

        # testing whether the covariance matrix is a diagonal one
        np.testing.assert_almost_equal(
            cm * (np.ones(cm.shape[0]) - np.eye(cm.shape[0])),
            np.zeros((cm.shape[0], cm.shape[0])))

        # testing whether the eigenvalues are all ones
        np.testing.assert_almost_equal(np.diag(cm), np.ones(cm.shape[0]))
Example #5
0
    def test_apply_no_whiten(self):
        """
        Confirms that PCA has decorrelated the input dataset and
        principal components are arranged in decreasing order by variance
        """
        # sut is an abbreviation for System Under Test
        sut = PCA(self.num_components)
        sut.apply(self.dataset, True)
        cm = np.cov(self.dataset.get_design_matrix().T)  # covariance matrix

        # testing whether the covariance matrix is a diagonal one
        np.testing.assert_almost_equal(cm * (np.ones(cm.shape[0]) -
                                       np.eye(cm.shape[0])),
                                       np.zeros((cm.shape[0], cm.shape[0])))

        # testing whether the eigenvalues are in decreasing order
        assert (np.diag(cm)[:-1] > np.diag(cm)[1:]).all()
    def test_apply_no_whiten(self):
        """
        Confirms that PCA has decorrelated the input dataset and
        principal components are arranged in decreasing order by variance
        """
        # sut is an abbreviation for System Under Test
        sut = PCA(self.num_components)
        sut.apply(self.dataset, True)
        cm = np.cov(self.dataset.get_design_matrix().T)  # covariance matrix

        # testing whether the covariance matrix is a diagonal one
        np.testing.assert_almost_equal(
            cm * (np.ones(cm.shape[0]) - np.eye(cm.shape[0])),
            np.zeros((cm.shape[0], cm.shape[0])))

        # testing whether the eigenvalues are in decreasing order
        assert (np.diag(cm)[:-1] > np.diag(cm)[1:]).all()