Add tools for fMRI analysis

Author: hrayrhar

Diff for: experiments/fmri/fmri.py

@@ -0,0 +1,96 @@
+from __future__ import print_function
+from __future__ import division
+
+import nibabel as nib
+import numpy as np
+
+
+def compute_variance_of_cluster(clusters, cluster_index, coords):
+    filtered = coords[clusters == cluster_index]
+    return ((filtered - filtered.mean(axis=0)) ** 2).sum(axis=1).mean(axis=0)
+
+
+def plot_least_varying(plt, clusters, coords, left, right):
+    n_clusters = np.max(clusters) + 1
+    variances = [compute_variance_of_cluster(clusters, k, coords) for k in range(n_clusters)]
+    order = np.argsort(variances)
+    fig = plt.figure(figsize=(6, 6))
+    ax = fig.gca(projection='3d')
+    for k in range(left, right):
+        print(variances[order[k]])
+        index = (clusters == order[k])
+        filtered = coords[index]
+        ax.scatter(filtered[:, 0], filtered[:, 1], filtered[:, 2], s=5, alpha=0.1)
+
+
+def plot_most_important(plt, clusters, importance, coords, left, right, mode='absolute'):
+    a = np.array(importance).copy()
+    if mode == 'relative':
+        a = np.array(importance).copy()
+        n_clusters = np.max(clusters)
+        for j in range(n_clusters):
+            cnt = np.sum(clusters == j)
+            a[j] /= (cnt + 1e-4)
+
+    order = np.argsort(-a)
+    fig = plt.figure(figsize=(6, 6))
+    ax = fig.gca(projection='3d')
+    for k in range(left, right):
+        print(a[order[k]])
+        index = (clusters == order[k])
+        filtered = coords[index]
+        ax.scatter(filtered[:, 0], filtered[:, 1], filtered[:, 2], s=5, alpha=0.1)
+
+
+def plot_biggest(plt, clusters, coords, left, right):
+    n_clusters = np.max(clusters) + 1
+    cnt = [0] * n_clusters
+    for j in range(n_clusters):
+        cnt[j] = np.sum(clusters == j)
+    order = np.argsort(-np.array(cnt))
+    fig = plt.figure(figsize=(6, 6))
+    ax = fig.gca(projection='3d')
+    for k in range(left, right):
+        print(cnt[order[k]])
+        index = (clusters == order[k])
+        filtered = coords[index]
+        ax.scatter(filtered[:, 0], filtered[:, 1], filtered[:, 2], s=5, alpha=0.1)
+
+
+def plot_clusters_probabilistic(plotting, prob_clusters, coords, source_img):
+    """ Plot probabilistic atlas.
+    :param plotting: nilearn.plotting
+    :param prob_clusters: (n_clusters, n_voxels)
+    :param coords: (n_voxels, 3)
+    :return:
+    """
+    X, Y, Z, T = source_img.shape
+    a = np.zeros((X, Y, Z))
+    for j in range(prob_clusters.shape[0]):
+        for i in range(prob_clusters.shape[1]):
+            x = int(coords[i, 0])
+            y = int(coords[i, 1])
+            z = int(coords[i, 2])
+            a[x, y, z, j] = prob_clusters[j, i]
+    atlas = nib.Nifti1Image(a, affine=source_img.affine)
+    plotting.plot_prob_atlas(atlas, bg_img=False)
+
+
+def plot_clusters(plotting, clusters, coords, source_img, output_file=None, figure=None):
+    """ Plot probabilistic atlas.
+    :param plotting: nilearn.plotting
+    :param clusters: (n_voxels,)
+    :param coords: (n_voxels, 3)
+    :param output_file: if given the plot is saved here
+    :param figure: figure param to be passed to plotting.plot_roi function
+    :return:
+    """
+    X, Y, Z, T = source_img.shape
+    a = np.zeros((X, Y, Z))
+    for i in range(clusters.shape[0]):
+        x = int(coords[i, 0])
+        y = int(coords[i, 1])
+        z = int(coords[i, 2])
+        a[x, y, z] = clusters[i]
+    img = nib.Nifti1Image(a, affine=source_img.affine)
+    return plotting.plot_roi(img, output_file=output_file, figure=figure)

Diff for: experiments/utils.py

@@ -85,3 +85,116 @@ def plot_for_next_timestep(plt, data, covs, title="Negative log-likelihood of es
     plt.show()
     print("NLL for next time step = {}".format(np.mean(nll)))
     return np.mean(nll)
+
+
+""" Helper functions for working with large low-rank plus diagonal matrices
+"""
+
+
+def diag_from_left(A, d):
+    """ diag(d) A """
+    m, n = A.shape
+    X = np.zeros_like(A)
+    for i in range(m):
+        X[i, :] = A[i, :] * d[i]
+    return X
+
+
+def diag_from_right(A, d):
+    """ A diag(d) """
+    m, n = A.shape
+    X = np.zeros_like(A)
+    for i in range(n):
+        X[:, i] = A[:, i] * d[i]
+    return X
+
+
+def inverse(A, d):
+    """ Compute inverse of A^T A + diag(d) faster than n^2.
+        A - (m, n)
+        d - (n,)
+        Return: V, d_inv such that inverse = d_inv - V^T V
+    """
+    m, n = A.shape
+    d_inv = 1 / d
+    M = np.eye(m) + np.dot(diag_from_right(A, d_inv), A.T)  # m^2 * n
+    M_inv = np.linalg.inv(M)  # m^3
+    R = np.linalg.cholesky(M_inv)  # m^3
+    V = diag_from_left(np.dot(A.T, R), d_inv).T  # m^2 * n
+    return V, d_inv
+
+
+def compute_inverses(A):
+    """ Given the low-rank parts of correlation matrices, compute low-rank + diagonal representation
+    of inverse correlation matrices.
+    Returns: B, d_inv such that Sigma^{-1}_t = d_inv_t - B_t^T B_t
+    """
+    nt = len(A)
+    d = [None] * nt
+    d_inv = [None] * nt
+    B = [None] * nt
+    for t in range(nt):
+        d[t] = 1 - (A[t] ** 2).sum(axis=0)
+        d_inv[t] = 1.0 / d[t]
+
+    for t in range(nt):
+        B[t], d_inv[t] = inverse(A[t], d[t])
+
+    return B, d_inv
+
+
+def estimate_diff_norm(A_1, d_1, A_2, d_2, n_iters=300):
+    """ Estimates ||(d_1 - A_1^T A_1) - (d_2 - A_2^T A_2)|| using power method.
+    """
+    ret = 0
+    for iteration in range(n_iters):
+        if iteration == 0:
+            x = np.random.normal(size=(A_1.shape[1], 1))
+        else:
+            x = -np.dot(A_1.T, np.dot(A_1, x)) + np.dot(A_2.T, np.dot(A_2, x)) + (d_1 - d_2).reshape((-1, 1)) * x
+        s = np.linalg.norm(x, ord=2)
+        x = x / s
+        ret = s
+        # print("\tIteration: {}, ret: {}".format(iteration, ret), end='\r')
+    return ret
+
+
+def compute_diff_norms(A):
+    """ Given the low-rank parts of correlation matrices, compute spectral norm of differences of inverse
+    correlation matrices of neighboring time steps.
+    """
+    B, d_inv = compute_inverses(A)
+    nt = len(A)
+    diffs = [None] * (nt-1)
+    for t in range(nt - 1):
+        print("Estimating norm of difference at time step: {}".format(t))
+        diffs[t] = estimate_diff_norm(B[t], d_inv[t], B[t + 1], d_inv[t + 1])
+    return diffs
+
+
+def compute_diff_norm_fro(A, d_1, B, d_2):
+    """ Estimates ||(d_1 - A^T A) - (d_2 - B^T B)||_F analytically.
+    """
+    # First compute || B^T B - A^T A ||^2_F
+    _, sigma_a, _ = np.linalg.svd(A, full_matrices=False)
+    _, sigma_b, _ = np.linalg.svd(B, full_matrices=False)
+    low_rank_norm = np.sum(sigma_a ** 4) - 2 * np.trace(np.dot(np.dot(B, A.T), np.dot(A, B.T))) + np.sum(sigma_b ** 4)
+
+    # Let X = (B^T B - A^T A), D = diag(d_1 - d_2). Compute ||X + D||^2_F
+    d = d_1 - d_2
+    ret = low_rank_norm + (np.linalg.norm(d) ** 2) + 2 * np.inner(np.sum(B ** 2 - A ** 2, axis=0), d)
+    return np.sqrt(ret)
+
+
+def compute_diff_norms_fro(A):
+    """ Given the low-rank parts of correlation matrices, compute Frobenius norm of differences of inverse
+    correlation matrices of neighboring time steps.
+    """
+    B, d_inv = compute_inverses(A)
+    nt = len(A)
+    diffs = [None] * (nt-1)
+    for t in range(nt - 1):
+        print("Calculating Frobenius norm of difference at time step: {}".format(t))
+        diffs[t] = compute_diff_norm_fro(B[t], d_inv[t], B[t + 1], d_inv[t + 1])
+    return diffs
+