def test_select_gmm_old_diag(verbose=0):
# Computing the BIC value for different configurations
# generate some data
dim = 2
x = np.concatenate((nr.randn(100, 2), 3 + 2 * nr.randn(100, 2)))
# estimate different GMMs of that data
k = 2
prec_type = "diag"
lgmm = gmm.GMM_old(k, dim, prec_type)
maxiter = 300
delta = 0.001
ninit = 5
kvals = np.arange(10) + 2
La, LL, bic = lgmm.optimize_with_bic(x, kvals, maxiter, delta, ninit, verbose)
if verbose:
# plot the result
xmin = 1.1 * x[:, 0].min() - 0.1 * x[:, 0].max()
xmax = 1.1 * x[:, 0].max() - 0.1 * x[:, 0].min()
ymin = 1.1 * x[:, 1].min() - 0.1 * x[:, 1].max()
ymax = 1.1 * x[:, 1].max() - 0.1 * x[:, 1].min()
gd = gmm.grid_descriptor(2)
gd.getinfo([xmin, xmax, ymin, ymax], [50, 50])
gmm.sample(gd, x, verbose=0)
assert_true(lgmm.k < 5)
def three_classes_GMM_fit(x, test=None, alpha=0.01, prior_strength=100,
verbose=0, fixed_scale=False, mpaxes=None, bias=0,
theta=0, return_estimator=False):
"""
Fit the data with a 3-classes Gaussian Mixture Model,
i.e. computing some probability that the voxels of a certain map
are in class disactivated, null or active
Parameters
----------
x array of shape (nvox,1): the map to be analysed
test=None array of shape(nbitems,1):
the test values for which the p-value needs to be computed
by default, test=x
alpha = 0.01 the prior weights of the positive and negative classes
prior_strength = 100 the confidence on the prior
(should be compared to size(x))
verbose=0 : verbosity mode
fixed_scale = False, boolean, variance parameterization
if True, the variance is locked to 1
otherwise, it is estimated from the data
mpaxes=None: axes handle used to plot the figure in verbose mode
if None, new axes are created
bias = 0: allows a recaling of the posterior probability
that takes into account the thershold theta. Not rigorous.
theta = 0 the threshold used to correct the posterior p-values
when bias=1; normally, it is such that test>theta
note that if theta = -np.infty, the method has a standard behaviour
return_estimator: boolean, optional
If return_estimator is true, the estimator object is
returned.
Results
-------
bfp : array of shape (nbitems,3):
the posterior probability of each test item belonging to each component
in the GMM (sum to 1 across the 3 classes)
if np.size(test)==0, i.e. nbitem==0, None is returned
estimator : nipy.neurospin.clustering.GMM object
The estimator object, returned only if return_estimator is true.
Note
----
Our convention is that
- class 1 represents the negative class
- class 2 represenst the null class
- class 3 represents the positsive class
"""
nvox = np.size(x)
x = np.reshape(x,(nvox,1))
if test==None:
test = x
if np.size(test)==0:
return None
from nipy.neurospin.clustering.bgmm import VBGMM
from nipy.neurospin.clustering.gmm import grid_descriptor
sx = np.sort(x,0)
nclasses=3
# set the priors from a reasonable model of the data (!)
# prior means
mb0 = np.mean(sx[:alpha*nvox])
mb2 = np.mean(sx[(1-alpha)*nvox:])
prior_means = np.reshape(np.array([mb0,0,mb2]),(nclasses,1))
if fixed_scale:
prior_scale = np.ones((nclasses,1,1)) * 1./(prior_strength)
else:
prior_scale = np.ones((nclasses,1,1)) * 1./(prior_strength*np.var(x))
prior_dof = np.ones(nclasses) * prior_strength
prior_weights = np.array([alpha,1-2*alpha,alpha]) * prior_strength
prior_shrinkage = np.ones(nclasses) * prior_strength
# instantiate the class and set the priors
BayesianGMM = VBGMM(nclasses,1,prior_means,prior_scale,
prior_weights, prior_shrinkage,prior_dof)
BayesianGMM.set_priors(prior_means, prior_weights, prior_scale,
prior_dof, prior_shrinkage)
# estimate the model
BayesianGMM.estimate(x,delta = 1.e-8,verbose=verbose)
# create a sampling grid
if (verbose or bias):
gd = grid_descriptor(1)
gd.getinfo([x.min(),x.max()],100)
gdm = gd.make_grid().squeeze()
lj = BayesianGMM.likelihood(gd.make_grid())
# estimate the prior weights
bfp = BayesianGMM.likelihood(test)
if bias:
lw = np.sum(lj[gdm>theta],0)
weights = BayesianGMM.weights/(BayesianGMM.weights.sum())
bfp = (lw/weights)*BayesianGMM.slikelihood(test)
if verbose>1:
BayesianGMM.show_components(x,gd,lj,mpaxes)
bfp = (bfp.T/bfp.sum(1)).T
if not return_estimator:
return bfp
else:
return bfp, BayesianGMM