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#!/usr/bin/env python3
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
__doc__ = """
Example of a script that performs histogram analysis of an activation
image, to estimate activation Z-score with various heuristics:
* Gamma-Gaussian model
* Gaussian mixture model
* Empirical normal null
This example is based on a (simplistic) simulated image.
Needs matplotlib
"""
# Author : Bertrand Thirion, Gael Varoquaux 2008-2009
print(__doc__)
import numpy as np
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
import nipy.algorithms.statistics.empirical_pvalue as en
import nipy.labs.utils.simul_multisubject_fmri_dataset as simul
###############################################################################
# simulate the data
shape = (60, 60)
pos = 2 * np.array([[6, 7], [10, 10], [15, 10]])
ampli = np.array([3, 4, 4])
dataset = simul.surrogate_2d_dataset(n_subj=1, shape=shape, pos=pos,
ampli=ampli, width=10.0).squeeze()
fig = plt.figure(figsize=(12, 10))
plt.subplot(3, 3, 1)
plt.imshow(dataset, cmap=plt.cm.hot)
plt.colorbar()
plt.title('Raw data')
Beta = dataset.ravel().squeeze()
###############################################################################
# fit Beta's histogram with a Gamma-Gaussian mixture
gam_gaus_pp = en.gamma_gaussian_fit(Beta, Beta)
gam_gaus_pp = np.reshape(gam_gaus_pp, (shape[0], shape[1], 3))
plt.figure(fig.number)
plt.subplot(3, 3, 4)
plt.imshow(gam_gaus_pp[..., 0], cmap=plt.cm.hot)
plt.title('Gamma-Gaussian mixture,\n first component posterior proba.')
plt.colorbar()
plt.subplot(3, 3, 5)
plt.imshow(gam_gaus_pp[..., 1], cmap=plt.cm.hot)
plt.title('Gamma-Gaussian mixture,\n second component posterior proba.')
plt.colorbar()
plt.subplot(3, 3, 6)
plt.imshow(gam_gaus_pp[..., 2], cmap=plt.cm.hot)
plt.title('Gamma-Gaussian mixture,\n third component posterior proba.')
plt.colorbar()
###############################################################################
# fit Beta's histogram with a mixture of Gaussians
alpha = 0.01
gaus_mix_pp = en.three_classes_GMM_fit(Beta, None, alpha, prior_strength=100)
gaus_mix_pp = np.reshape(gaus_mix_pp, (shape[0], shape[1], 3))
plt.figure(fig.number)
plt.subplot(3, 3, 7)
plt.imshow(gaus_mix_pp[..., 0], cmap=plt.cm.hot)
plt.title('Gaussian mixture,\n first component posterior proba.')
plt.colorbar()
plt.subplot(3, 3, 8)
plt.imshow(gaus_mix_pp[..., 1], cmap=plt.cm.hot)
plt.title('Gaussian mixture,\n second component posterior proba.')
plt.colorbar()
plt.subplot(3, 3, 9)
plt.imshow(gaus_mix_pp[..., 2], cmap=plt.cm.hot)
plt.title('Gamma-Gaussian mixture,\n third component posterior proba.')
plt.colorbar()
###############################################################################
# Fit the null mode of Beta with an empirical normal null
efdr = en.NormalEmpiricalNull(Beta)
emp_null_fdr = efdr.fdr(Beta)
emp_null_fdr = emp_null_fdr.reshape(shape)
plt.subplot(3, 3, 3)
plt.imshow(1 - emp_null_fdr, cmap=plt.cm.hot)
plt.colorbar()
plt.title('Empirical FDR\n ')
plt.show()
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