def test_em_gmm_largedim(verbose=0):
# testing the GMM model in larger dimensions
# generate some data
dim = 10
x = nr.randn(100, dim)
x[:30, :] += 1
# estimate different GMMs of that data
maxiter = 100
delta = 1.0e-4
for k in range(1, 3):
lgmm = GMM(k, dim)
lgmm.initialize(x)
bic = lgmm.estimate(x, maxiter, delta, verbose)
if verbose:
print "bic of the %d-classes model" % k, bic
z = lgmm.map_label(x)
# define the correct labelling
u = np.zeros(100)
u[:30] = 1
# check the correlation between the true labelling
# and the computed one
eta = np.absolute(np.dot(z - z.mean(), u - u.mean()) / (np.std(z) * np.std(u) * 100))
assert_true(eta > 0.3)
def test_model_selection_exact():
prng = np.random.RandomState(10)
data, XYZ, XYZvol, vardata, signal = make_data(n=30, dim=20, r=3,
amplitude=1, noise=0, jitter=0, prng=prng)
labels = (signal > 0).astype(int)
P1 = os.multivariate_stat(data, labels=labels)
P1.init_hidden_variables()
P1.evaluate(nsimu=100, burnin=10, verbose=verbose)
L1 = P1.compute_log_region_likelihood()
Prior1 = P1.compute_log_prior()
#v, m_mean, m_var = P1.v.copy(), P1.m_mean.copy(), P1.m_var.copy()
Post1 = P1.compute_log_posterior(nsimu=1e2, burnin=1e2, verbose=verbose)
M1 = L1 + Prior1[:-1] - Post1[:-1]
yield assert_almost_equal(M1.mean(),
P1.compute_marginal_likelihood().mean(), 0)
P0 = os.multivariate_stat(data, labels=labels)
P0.network *= 0
P0.init_hidden_variables()
P0.evaluate(nsimu=100, burnin=100, verbose=verbose)
L0 = P0.compute_log_region_likelihood()
Prior0 = P0.compute_log_prior()
Post0 = P0.compute_log_posterior(nsimu=1e2, burnin=1e2,
verbose=verbose)
M0 = L0 + Prior0[:-1] - Post0[:-1]
yield assert_almost_equal(M0.mean(),
P0.compute_marginal_likelihood().mean(), 0)
yield assert_true(M1[1] > M0[1])
yield assert_true(M1[0] < M0[0])
def test_series_from_mask():
""" Test the smoothing of the timeseries extraction
"""
# A delta in 3D
data = np.zeros((40, 40, 40, 2))
data[20, 20, 20] = 1
mask = np.ones((40, 40, 40), dtype=np.bool)
with InTemporaryDirectory():
for affine in (np.eye(4), np.diag((1, 1, -1, 1)),
np.diag((.5, 1, .5, 1))):
img = nib.Nifti1Image(data, affine)
nib.save(img, 'testing.nii')
series, header = series_from_mask('testing.nii', mask, smooth=9)
series = np.reshape(series[:, 0], (40, 40, 40))
vmax = series.max()
# We are expecting a full-width at half maximum of
# 9mm/voxel_size:
above_half_max = series > .5*vmax
for axis in (0, 1, 2):
proj = np.any(np.any(np.rollaxis(above_half_max,
axis=axis), axis=-1), axis=-1)
assert_equal(proj.sum(), 9/np.abs(affine[axis, axis]))
# Check that NaNs in the data do not propagate
data[10, 10, 10] = np.NaN
img = nib.Nifti1Image(data, affine)
nib.save(img, 'testing.nii')
series, header = series_from_mask('testing.nii', mask, smooth=9)
assert_true(np.all(np.isfinite(series)))
def test_em_gmm_multi(verbose=0):
# Playing with various initilizations on the same data
# generate some data
dim = 2
x = np.concatenate((nr.randn(1000, dim), 3 + 2 * nr.randn(100, dim)))
# estimate different GMMs of that data
maxiter = 100
delta = 1.0e-4
ninit = 5
k = 2
lgmm = GMM(k, dim)
bgmm = lgmm.initialize_and_estimate(x, maxiter, delta, ninit, verbose)
bic = bgmm.evidence(x)
if verbose:
print "bic of the best model", bic
if verbose:
# plot the result
from test_bgmm import plot2D
z = lgmm.map_label(x)
plot2D(x, lgmm, z, show=1, verbose=0)
assert_true(np.isfinite(bic))
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 test_em_gmm_cv(verbose=0):
# Comparison of different GMMs using cross-validation
# generate some data
dim = 2
xtrain = np.concatenate((nr.randn(100, dim), 3 + 2 * nr.randn(100, dim)))
xtest = np.concatenate((nr.randn(1000, dim), 3 + 2 * nr.randn(1000, dim)))
# estimate different GMMs for xtrain, and test it on xtest
prec_type = "full"
k = 2
maxiter = 300
delta = 1.0e-4
ll = []
# model 1
lgmm = GMM(k, dim, prec_type)
lgmm.initialize(xtrain)
bic = lgmm.estimate(xtrain, maxiter, delta)
ll.append(lgmm.test(xtest).mean())
prec_type = "diag"
# model 2
lgmm = GMM(k, dim, prec_type)
lgmm.initialize(xtrain)
bic = lgmm.estimate(xtrain, maxiter, delta)
ll.append(lgmm.test(xtest).mean())
for k in [1, 3, 10]:
lgmm = GMM(k, dim, prec_type)
lgmm.initialize(xtrain)
bic = lgmm.estimate(xtrain, maxiter, delta)
ll.append(lgmm.test(xtest).mean())
assert_true(ll[4] < ll[1])
def test_scaling_io_dtype():
# Does data dtype get set?
# Is scaling correctly applied?
rng = np.random.RandomState(19660520) # VBD
ulp1_f32 = np.finfo(np.float32).eps
types = (np.uint8, np.uint16, np.int16, np.int32, np.float32)
with InTemporaryDirectory():
for in_type in types:
for out_type in types:
data, _ = randimg_in2out(rng, in_type, out_type, 'img.nii')
img = load_image('img.nii')
# Check the output type is as expected
hdr = img.metadata['header']
assert_equal(hdr.get_data_dtype().type, out_type)
# Check the data is within reasonable bounds. The exact bounds
# are a little annoying to calculate - see
# nibabel/tests/test_round_trip for inspiration
data_back = img.get_data().copy() # copy to detach from file
del img
top = np.abs(data - data_back)
nzs = (top !=0) & (data !=0)
abs_err = top[nzs]
if abs_err.size != 0: # all exact, that's OK.
continue
rel_err = abs_err / data[nzs]
if np.dtype(out_type).kind in 'iu':
slope, inter = hdr.get_slope_inter()
abs_err_thresh = slope / 2.0
rel_err_thresh = ulp1_f32
elif np.dtype(out_type).kind == 'f':
abs_err_thresh = big_bad_ulp(data.astype(out_type))[nzs]
rel_err_thresh = ulp1_f32
assert_true(np.all(
(abs_err <= abs_err_thresh) |
(rel_err <= rel_err_thresh)))
def test_series_from_mask():
""" Test the smoothing of the timeseries extraction
"""
# A delta in 3D
data = np.zeros((40, 40, 40, 2))
data[20, 20, 20] = 1
mask = np.ones((40, 40, 40), dtype=np.bool)
with InTemporaryDirectory():
for affine in (np.eye(4), np.diag(
(1, 1, -1, 1)), np.diag((.5, 1, .5, 1))):
img = nib.Nifti1Image(data, affine)
nib.save(img, 'testing.nii')
series, header = series_from_mask('testing.nii', mask, smooth=9)
series = np.reshape(series[:, 0], (40, 40, 40))
vmax = series.max()
# We are expecting a full-width at half maximum of
# 9mm/voxel_size:
above_half_max = series > .5 * vmax
for axis in (0, 1, 2):
proj = np.any(np.any(np.rollaxis(above_half_max, axis=axis),
axis=-1),
axis=-1)
assert_equal(proj.sum(), 9 / np.abs(affine[axis, axis]))
# Check that NaNs in the data do not propagate
data[10, 10, 10] = np.NaN
img = nib.Nifti1Image(data, affine)
nib.save(img, 'testing.nii')
series, header = series_from_mask('testing.nii', mask, smooth=9)
assert_true(np.all(np.isfinite(series)))
def test_model_selection_mfx_spatial_rand_walk():
prng = np.random.RandomState(10)
data, XYZ, XYZvol, vardata, signal = make_data(n=20,
dim=np.array([1,20,20]),
r=3, amplitude=3, noise=1,
jitter=0.5, prng=prng)
labels = (signal > 0).astype(int)
P = os.multivariate_stat(data, vardata, XYZ, std=0.5, sigma=5, labels=labels)
P.network[:] = 0
P.init_hidden_variables()
P.evaluate(nsimu=100, burnin=100, verbose=verbose,
proposal='rand_walk', proposal_std=0.5)
L00 = P.compute_log_region_likelihood()
# Test simulated annealing procedure
P.estimate_displacements_SA(nsimu=100, c=0.99,
proposal_std=P.proposal_std, verbose=verbose)
L0 = P.compute_log_region_likelihood()
yield assert_true(L0.sum() > L00.sum())
#Prior0 = P.compute_log_prior()
#Post0 = P.compute_log_posterior(nsimu=1e2, burnin=1e2, verbose=verbose)
#M0 = L0 + Prior0[:-1] - Post0[:-1]
M0 = P.compute_marginal_likelihood(update_spatial=True)
#yield assert_almost_equal(M0.sum(), P.compute_marginal_likelihood(verbose=verbose).sum(), 0)
P.network[1] = 1
#P.init_hidden_variables(init_spatial=False)
P.init_hidden_variables(init_spatial=False)
P.evaluate(nsimu=100, burnin=100, verbose=verbose,
update_spatial=False, proposal_std=P.proposal_std)
#L1 = P.compute_log_region_likelihood()
#Prior1 = P.compute_log_prior()
#Post1 = P.compute_log_posterior(nsimu=1e2, burnin=1e2, verbose=verbose)
#M1 = L1 + Prior1[:-1] - Post1[:-1]
M1 = P.compute_marginal_likelihood(update_spatial=True)
#yield assert_almost_equal(0.1*M1.sum(), 0.1*P.compute_marginal_likelihood(verbose=verbose).sum(), 0)
yield assert_true(M1 > M0)
def test_em_gmm_diag(verbose=0):
# Computing the BIC value for GMMs with different number of classes,
# with diagonal covariance models The BIC should maximal for a
# number of classes of 1 or 2
# generate some data
dim = 2
x = np.concatenate((nr.randn(1000, dim), 3 + 2 * nr.randn(1000, dim)))
# estimate different GMMs of that data
maxiter = 100
delta = 1.0e-8
prec_type = "diag"
bic = np.zeros(5)
for k in range(1, 6):
lgmm = GMM(k, dim, prec_type)
lgmm.initialize(x)
bic[k - 1] = lgmm.estimate(x, maxiter, delta, verbose)
if verbose:
print "bic of the %d-classes model" % k, bic
z = lgmm.map_label(x)
assert_true((z.max() + 1 == lgmm.k) & (bic[4] < bic[1]))
def test_scaling_io_dtype():
# Does data dtype get set?
# Is scaling correctly applied?
rng = np.random.RandomState(19660520) # VBD
ulp1_f32 = np.finfo(np.float32).eps
types = (np.uint8, np.uint16, np.int16, np.int32, np.float32)
with InTemporaryDirectory():
for in_type in types:
for out_type in types:
data, _ = randimg_in2out(rng, in_type, out_type, 'img.nii')
img = load_image('img.nii')
# Check the output type is as expected
hdr = img.metadata['header']
assert_equal(hdr.get_data_dtype().type, out_type)
# Check the data is within reasonable bounds. The exact bounds
# are a little annoying to calculate - see
# nibabel/tests/test_round_trip for inspiration
data_back = img.get_data().copy() # copy to detach from file
del img
top = np.abs(data - data_back)
nzs = (top != 0) & (data != 0)
abs_err = top[nzs]
if abs_err.size != 0: # all exact, that's OK.
continue
rel_err = abs_err / data[nzs]
if np.dtype(out_type).kind in 'iu':
slope, inter = hdr.get_slope_inter()
abs_err_thresh = slope / 2.0
rel_err_thresh = ulp1_f32
elif np.dtype(out_type).kind == 'f':
abs_err_thresh = big_bad_ulp(data.astype(out_type))[nzs]
rel_err_thresh = ulp1_f32
assert_true(
np.all((abs_err <= abs_err_thresh)
| (rel_err <= rel_err_thresh)))
def test_as_image():
# test image creation / pass through function
img = as_image(funcfile) # string filename
img1 = as_image(six.text_type(funcfile)) # unicode
img2 = as_image(img)
assert_equal(img.affine, img1.affine)
assert_array_equal(img.get_data(), img1.get_data())
assert_true(img is img2)
def test_as_image():
# test image creation / pass through function
img = as_image(funcfile) # string filename
img1 = as_image(six.text_type(funcfile)) # unicode
img2 = as_image(img)
assert_equal(img.affine, img1.affine)
assert_array_equal(img.get_data(), img1.get_data())
assert_true(img is img2)
def test_agreement():
# The test: does Protocol manage to recreate the design of fMRIstat?
for design_type in ['event', 'block']:
dd = D[design_type]
for i in range(X[design_type].shape[1]):
_, cmax = matchcol(X[design_type][:,i], fmristat[design_type])
if not dd.dtype.names[i].startswith('ns'):
assert_true(np.greater(np.abs(cmax), 0.999))
def test_agreement():
# The test: does Protocol manage to recreate the design of fMRIstat?
X, c, D = create_protocols()
for design_type in ['event', 'block']:
dd = D[design_type]
for i in range(X[design_type].shape[1]):
_, cmax = matchcol(X[design_type][:, i], fmristat[design_type])
if not dd.dtype.names[i].startswith('ns'):
assert_true(np.greater(np.abs(cmax), 0.999))
def test_threshold_connect_components():
a = np.zeros((10, 10))
a[0, 0] = 1
a[3, 4] = 1
a = threshold_connect_components(a, 2)
assert_true(np.all(a == 0))
a[0, 0:3] = 1
b = threshold_connect_components(a, 2)
assert_true(np.all(a == b))
def test_threshold_connect_components():
a = np.zeros((10, 10))
a[0, 0] = 1
a[3, 4] = 1
a = threshold_connect_components(a, 2)
assert_true(np.all(a == 0))
a[0, 0:3] = 1
b = threshold_connect_components(a, 2)
assert_true(np.all(a == b))
def test_image_list():
img = load_image(funcfile)
exp_shape = (17, 21, 3, 20)
imglst = ImageList.from_image(img, axis=-1)
# Test empty ImageList
emplst = ImageList()
yield assert_equal(len(emplst.list), 0)
# Test non-image construction
a = np.arange(10)
yield assert_raises(ValueError, ImageList, a)
yield assert_raises(ValueError, ImageList.from_image, img, None)
# check all the axes
for i in range(4):
order = range(4)
order.remove(i)
order.insert(0,i)
img_re_i = img.reordered_reference(order).reordered_axes(order)
imglst_i = ImageList.from_image(img, axis=i)
yield assert_equal(imglst_i.list[0].shape, img_re_i.shape[1:])
# check the affine as well
yield assert_almost_equal(imglst_i.list[0].affine,
img_re_i.affine[1:,1:])
yield assert_equal(img.shape, exp_shape)
# length of image list should match number of frames
yield assert_equal(len(imglst.list), img.shape[3])
# check the affine
A = np.identity(4)
A[:3,:3] = img.affine[:3,:3]
A[:3,-1] = img.affine[:3,-1]
yield assert_almost_equal(imglst.list[0].affine, A)
# Slicing an ImageList should return an ImageList
sublist = imglst[2:5]
yield assert_true(isinstance(sublist, ImageList))
# Except when we're indexing one element
yield assert_true(isinstance(imglst[0], Image))
# Verify array interface
# test __array__
yield assert_true(isinstance(np.asarray(sublist), np.ndarray))
# Test __setitem__
sublist[2] = sublist[0]
yield assert_equal(np.asarray(sublist[0]).mean(),
np.asarray(sublist[2]).mean())
# Test iterator
for x in sublist:
yield assert_true(isinstance(x, Image))
yield assert_equal(x.shape, exp_shape[:3])
def test_same_basis():
arr4d = data['fmridata']
shp = arr4d.shape
arr2d = arr4d.reshape((np.prod(shp[:3]), shp[3]))
res = pca(arr2d, axis=-1)
p1b_0 = pos1basis(res)
for i in range(3):
res_again = pca(arr2d, axis=-1)
assert_true(np.all(pos1basis(res_again) ==
p1b_0))
def test_kernel():
# Verify that convolution with a delta function gives the correct
# answer.
tol = 0.9999
sdtol = 1.0e-8
for x in range(6):
shape = randint(30,60,(3,))
# pos of delta
ii, jj, kk = randint(11,17, (3,))
# random affine coordmap (diagonal and translations)
coordmap = AffineTransform.from_start_step('ijk', 'xyz',
randint(5,20,(3,))*0.25,
randint(5,10,(3,))*0.5)
# delta function in 3D array
signal = np.zeros(shape)
signal[ii,jj,kk] = 1.
signal = Image(signal, coordmap=coordmap)
# A filter with coordmap, shape matched to image
kernel = LinearFilter(coordmap, shape,
fwhm=randint(50,100)/10.)
# smoothed normalized 3D array
ssignal = kernel.smooth(signal).get_data()
ssignal[:] *= kernel.norms[kernel.normalization]
# 3 points * signal.size array
I = np.indices(ssignal.shape)
I.shape = (kernel.coordmap.ndims[0], np.product(shape))
# location of maximum in smoothed array
i, j, k = I[:, np.argmax(ssignal[:].flat)]
# same place as we put it before smoothing?
assert_equal((i,j,k), (ii,jj,kk))
# get physical points position relative to position of delta
Z = kernel.coordmap(I.T) - kernel.coordmap([i,j,k])
_k = kernel(Z)
_k.shape = ssignal.shape
assert_true((np.corrcoef(_k[:].flat, ssignal[:].flat)[0,1] > tol))
assert_true(((_k[:] - ssignal[:]).std() < sdtol))
def _indices(i,j,k,axis):
I = np.zeros((3,20))
I[0] += i
I[1] += j
I[2] += k
I[axis] += np.arange(-10,10)
return I.T
vx = ssignal[i,j,(k-10):(k+10)]
xformed_ijk = coordmap([i, j, k])
vvx = coordmap(_indices(i,j,k,2)) - xformed_ijk
assert_true((np.corrcoef(vx, kernel(vvx))[0,1] > tol))
vy = ssignal[i,(j-10):(j+10),k]
vvy = coordmap(_indices(i,j,k,1)) - xformed_ijk
assert_true((np.corrcoef(vy, kernel(vvy))[0,1] > tol))
vz = ssignal[(i-10):(i+10),j,k]
vvz = coordmap(_indices(i,j,k,0)) - xformed_ijk
assert_true((np.corrcoef(vz, kernel(vvz))[0,1] > tol))
def test_em_selection():
# test that the basic GMM-based model selection tool returns
# something sensible (i.e. the gmm used to represent the data has
# indeed one or two classes)
# generate some data
dim = 2
x = np.concatenate((nr.randn(100, dim), 3 + 2 * nr.randn(100, dim)))
krange = range(1, 10)
lgmm = gmm.best_fitting_GMM(x, krange, prec_type="full", niter=100, delta=1.0e-4, ninit=1, verbose=0)
assert_true(lgmm.k < 4)
def test_em_loglike1():
dim = 1
k = 3
n = 1000
x = nr.randn(n, dim)
lgmm = GMM(k, dim)
lgmm.initialize(x)
lgmm.estimate(x)
ll = lgmm.average_log_like(x)
ent = 0.5 * (1 + np.log(2 * np.pi))
print ll, ent
assert_true(np.absolute(ll + ent) < 3.0 / np.sqrt(n))
def test_is_image():
# tests for tests for image
img = load_image(anatfile)
yield assert_true(is_image(img))
class C(object): pass
yield assert_false(is_image(C()))
class C(object):
def __array__(self): pass
yield assert_false(is_image(C()))
class C(object):
coordmap = None
def __array__(self): pass
yield assert_true(is_image(img))
def test_em_loglike4():
dim = 5
k = 1
n = 1000
scale = 3.0
offset = 4.0
x = offset + scale * nr.randn(n, dim)
lgmm = GMM(k, dim)
lgmm.initialize(x)
lgmm.estimate(x)
ll = lgmm.average_log_like(x)
ent = dim * 0.5 * (1 + np.log(2 * np.pi * scale ** 2))
print ll, ent
assert_true(np.absolute(ll + ent) < dim * 3.0 / np.sqrt(n))
def test_as_image():
# test image creation / pass through function
img = as_image(funcfile) # string filename
img1 = as_image(unicode(funcfile))
img2 = as_image(img)
yield assert_equal(img.affine, img1.affine)
yield assert_array_equal(np.asarray(img), np.asarray(img1))
yield assert_true(img is img2)
def test_em_loglike6():
"""
"""
dim = 1
k = 1
n = 100
offset = 3.0
x = nr.randn(n, dim)
y = offset + nr.randn(n, dim)
lgmm = GMM(k, dim)
lgmm.initialize(x)
lgmm.estimate(x)
ll1 = lgmm.average_log_like(x)
ll2 = lgmm.average_log_like(y)
ent = 0.5 * (1 + np.log(2 * np.pi))
dkl = 0.5 * offset ** 2
print ll2, ll1, dkl
assert_true(ll2 < ll1)
def test_resid():
# Data is projected onto k=10 dimensional subspace then has its mean
# removed. Should still have rank 10.
k = 10
ncomp = 5
ntotal = k
X = np.random.standard_normal((data['nimages'], k))
p = pca(data['fmridata'], -1, ncomp=ncomp, design_resid=X)
assert_equal(p['basis_vectors'].shape, (data['nimages'], ntotal))
assert_equal(p['basis_projections'].shape, data['mask'].shape + (ncomp,))
assert_equal(p['pcnt_var'].shape, (ntotal,))
assert_almost_equal(p['pcnt_var'].sum(), 100.)
# if design_resid is None, we do not remove the mean, and we get
# full rank from our data
p = pca(data['fmridata'], -1, design_resid=None)
rank = p['basis_vectors'].shape[1]
assert_equal(rank, data['nimages'])
rarr = reconstruct(p['basis_vectors'], p['basis_projections'], -1)
# add back the sqrt MSE, because we standardized
rmse = root_mse(data['fmridata'], axis=-1)[...,None]
assert_true(np.allclose(rarr * rmse, data['fmridata']))
def test_mask():
mean_image = np.ones((9, 9))
mean_image[3:-3, 3:-3] = 10
mean_image[5, 5] = 100
mask1 = nnm.compute_mask(mean_image)
mask2 = nnm.compute_mask(mean_image, exclude_zeros=True)
# With an array with no zeros, exclude_zeros should not make
# any difference
assert_array_equal(mask1, mask2)
# Check that padding with zeros does not change the extracted mask
mean_image2 = np.zeros((30, 30))
mean_image2[:9, :9] = mean_image
mask3 = nnm.compute_mask(mean_image2, exclude_zeros=True)
assert_array_equal(mask1, mask3[:9, :9])
# However, without exclude_zeros, it does
mask3 = nnm.compute_mask(mean_image2)
assert_false(np.allclose(mask1, mask3[:9, :9]))
# check that opening is 2 by default
mask4 = nnm.compute_mask(mean_image, exclude_zeros=True, opening=2)
assert_array_equal(mask1, mask4)
# check that opening has an effect
mask5 = nnm.compute_mask(mean_image, exclude_zeros=True, opening=0)
assert_true(mask5.sum() > mask4.sum())
def test_mask():
mean_image = np.ones((9, 9))
mean_image[3:-3, 3:-3] = 10
mean_image[5, 5] = 100
mask1 = nnm.compute_mask(mean_image)
mask2 = nnm.compute_mask(mean_image, exclude_zeros=True)
# With an array with no zeros, exclude_zeros should not make
# any difference
assert_array_equal(mask1, mask2)
# Check that padding with zeros does not change the extracted mask
mean_image2 = np.zeros((30, 30))
mean_image2[:9, :9] = mean_image
mask3 = nnm.compute_mask(mean_image2, exclude_zeros=True)
assert_array_equal(mask1, mask3[:9, :9])
# However, without exclude_zeros, it does
mask3 = nnm.compute_mask(mean_image2)
assert_false(np.allclose(mask1, mask3[:9, :9]))
# check that opening is 2 by default
mask4 = nnm.compute_mask(mean_image, exclude_zeros=True, opening=2)
assert_array_equal(mask1, mask4)
# check that opening has an effect
mask5 = nnm.compute_mask(mean_image, exclude_zeros=True, opening=0)
assert_true(mask5.sum() > mask4.sum())
def test_em_gmm_full(verbose=0):
# Computing the BIC value for different configurations of a GMM with
# ful diagonal matrices The BIC should be maximal for a number of
# classes of 1 or 2
# generate some data
dim = 2
x = np.concatenate((nr.randn(100, dim), 3 + 2 * nr.randn(100, dim)))
# estimate different GMMs of that data
maxiter = 100
delta = 1.0e-4
bic = np.zeros(5)
for k in range(1, 6):
lgmm = GMM(k, dim)
lgmm.initialize(x)
bic[k - 1] = lgmm.estimate(x, maxiter, delta, verbose)
if verbose:
print "bic of the %d-classes model" % k, bic
z = lgmm.map_label(x)
assert_true(bic[4] < bic[1])
def test_2D():
# check that a standard 2D PCA works too
M = 100
N = 20
L = M-1 # rank after mean removal
data = np.random.uniform(size=(M, N))
p = pca(data)
ts = p['basis_vectors']
imgs = p['basis_projections']
assert_equal(ts.shape, (M, L))
assert_equal(imgs.shape, (L, N))
rimgs = reconstruct(ts, imgs)
# add back the sqrt MSE, because we standardized
data_mean = data.mean(0)[None,...]
demeaned = data - data_mean
rmse = root_mse(demeaned, axis=0)[None,...]
# also add back the mean
assert_array_almost_equal((rimgs * rmse) + data_mean, data)
# if standardize is set, or not, covariance is diagonal
assert_true(diagonal_covariance(imgs))
p = pca(data, standardize=False)
imgs = p['basis_projections']
assert_true(diagonal_covariance(imgs))
def test_2D():
# check that a standard 2D PCA works too
M = 100
N = 20
L = M-1 # rank after mean removal
data = np.random.uniform(size=(M, N))
p = pca(data)
ts = p['basis_vectors']
imgs = p['basis_projections']
yield assert_equal(ts.shape, (M, L))
yield assert_equal(imgs.shape, (L, N))
rimgs = reconstruct(ts, imgs)
# add back the sqrt MSE, because we standardized
data_mean = data.mean(0)[None,...]
demeaned = data - data_mean
rmse = root_mse(demeaned, axis=0)[None,...]
# also add back the mean
yield assert_array_almost_equal((rimgs * rmse) + data_mean, data)
# if standardize is set, or not, covariance is diagonal
yield assert_true(diagonal_covariance(imgs))
p = pca(data, standardize=False)
imgs = p['basis_projections']
yield assert_true(diagonal_covariance(imgs))
def test_call():
value = 10
yield assert_true(np.allclose(E.a(value), 2*value))
yield assert_true(np.allclose(E.b(value), 2*value))
# FIXME: this shape just below is not
# really expected for a CoordinateMap
yield assert_true(np.allclose(E.b([value]), 2*value))
yield assert_true(np.allclose(E.c(value), value/2))
yield assert_true(np.allclose(E.d(value), value/2))
value = np.array([1., 2., 3.])
yield assert_true(np.allclose(E.e(value), value))
# check that error raised for wrong shape
value = np.array([1., 2.,])
yield assert_raises(CoordinateSystemError, E.e, value)
def test_inverse2():
assert_true(np.allclose(E.e.affine, E.e.inverse().inverse().affine))
def test_compose_cmap():
value = np.array([1., 2., 3.])
b = compose(E.e, E.e)
assert_true(np.allclose(b(value), value))
def test_diagonality():
# basis_projections are diagonal, whether standarized or not
p = pca(data['fmridata'], -1) # standardized
assert_true(diagonal_covariance(p['basis_projections'], -1))
pns = pca(data['fmridata'], -1, standardize=False) # not
assert_true(diagonal_covariance(pns['basis_projections'], -1))
def test_diagonality():
# basis_projections are diagonal, whether standarized or not
p = pca(data['fmridata'], -1) # standardized
yield assert_true(diagonal_covariance(p['basis_projections'], -1))
pns = pca(data['fmridata'], -1, standardize=False) # not
yield assert_true(diagonal_covariance(pns['basis_projections'], -1))
def test_design_expression():
t1 = F.Term("x")
t2 = F.Term('y')
f = t1.formula + t2.formula
assert_true(str(f.design_expr) in ['[x, y]', '[y, x]'])