How to use the pyriemann.utils.distance.pairwise_distance function in pyriemann

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github alexandrebarachant / pyRiemann / tests / test_utils_distance.py View on Github external
def test_pairwise_distance_matrix():
    """Test pairwise distance"""
    A = np.array([2*np.eye(3), 3*np.eye(3)])
    B = np.array([2*np.eye(3), 3*np.eye(3)])
    pairwise_distance(A, B)
github alexandrebarachant / pyRiemann / pyriemann / stats.py View on Github external
def _score_ttest(self, X, y):
        """Get the score"""
        mdm = self.mdm.fit(X, y)
        covmeans = numpy.array(mdm.covmeans_)

        # estimates distances between means
        n_classes = len(covmeans)
        pairs = pairwise_distance(covmeans, metric=mdm.metric_dist)
        mean_dist = numpy.triu(pairs).sum()
        mean_dist /= (n_classes * (n_classes - 1)) / 2.0

        dist = 0
        for ix, classe in enumerate(mdm.classes_):
            di = (distance(
                X[y == classe], covmeans[ix], metric=mdm.metric_dist)
                  **2).mean()
            dist += (di / numpy.sum(y == classe))
        score = mean_dist / numpy.sqrt(dist)
        return score
github alexandrebarachant / pyRiemann / pyriemann / embedding.py View on Github external
def _get_affinity_matrix(self, X, eps):

        # make matrix with pairwise distances between points
        distmatrix = pairwise_distance(X, metric=self.metric)

        # determine which scale for the gaussian kernel
        if self.eps is None:
            eps = np.median(distmatrix)**2 / 2

        # make kernel matrix from the distance matrix
        kernel = np.exp(-distmatrix**2 / (4 * eps))

        # normalize the kernel matrix
        q = np.dot(kernel, np.ones(len(kernel)))
        kernel_n = np.divide(kernel, np.outer(q, q))

        return kernel_n
github alexandrebarachant / pyRiemann / pyriemann / stats.py View on Github external
def __init_transform(self, X):
        """Init tr"""
        self.mdm = MDM(metric=self.metric, n_jobs=self.n_jobs)
        if self.mode == 'ftest':
            self.global_mean = mean_covariance(X, metric=self.mdm.metric_mean)
        elif self.mode == 'pairwise':
            X = pairwise_distance(X, metric=self.mdm.metric_dist)**2
        return X