def test_static_reverse_doesnt_work_after_feature_selection_tuneup_2():
from mvpa2.testing.tools import skip_if_no_external
skip_if_no_external('nibabel')
from mvpa2.datasets.mri import fmri_dataset
from mvpa2 import pymvpa_dataroot
from os.path import join as pathjoin
ds_orig = fmri_dataset(samples=pathjoin(pymvpa_dataroot, 'bold.nii.gz'),
mask=pathjoin(pymvpa_dataroot, 'mask.nii.gz'),
sprefix='voxel')
ds_orig_rev0 = ds_orig.a.mapper.reverse1(ds_orig.samples[0])
# would have gone all the way to 3d
assert_equal(ds_orig_rev0.ndim, 3)
bool_mask = np.ones((ds_orig.nfeatures,), dtype=bool)
bool_mask[0] = False
for idx in (bool_mask, [0, 2]):
ds = ds_orig[:, idx]
ds_rev0 = ds.a.mapper.reverse1(ds.samples[0])
# blow test fails since chain mapper thrown exception upon _oshape mismatch
# but chain mapper silently proceeded forward doing nothing
yield assert_equal, ds_rev0.ndim, 3
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Unit tests for cortical surface functionality"""
from mvpa2.testing.tools import skip_if_no_external
skip_if_no_external('matplotlib')
skip_if_no_external('griddata')
import matplotlib.pyplot as plt
import numpy as np
from numpy.testing.utils import assert_array_almost_equal
import random
from mvpa2.testing.tools import assert_almost_equal, assert_array_equal, \
assert_equal, assert_raises, assert_is_instance, unittest
from mvpa2.testing import sweepargs
from mvpa2.support.nibabel import surf
from mvpa2.support.nibabel.surf import vector_alignment_find_rotation, \
generate_plane, Surface
from mvpa2.misc.plot.flat_surf import flat_surface2xy, FlatSurfacePlotter
from mvpa2.base.dataset import AttrDataset
def test_group_clusterthreshold_simple(n_proc):
if n_proc > 1:
skip_if_no_external('joblib')
feature_thresh_prob = 0.005
nsubj = 10
# make a nice 1D blob and a speck
blob = np.array([0, 0, .5, 3, 5, 3, 3, 0, 2, 0])
blob = Dataset([blob])
# and some nice random permutations
nperms = 100 * nsubj
perm_samples = np.random.randn(nperms, blob.nfeatures)
perms = Dataset(perm_samples,
sa=dict(chunks=np.repeat(range(nsubj), len(perm_samples) / nsubj)),
fa=dict(fid=range(perm_samples.shape[1])))
# the algorithm instance
# scale number of bootstraps to match desired probability
# plus a safety margin to minimize bad luck in sampling
clthr = gct.GroupClusterThreshold(n_bootstrap=int(3. / feature_thresh_prob),
feature_thresh_prob=feature_thresh_prob,
fwe_rate=0.01, n_blocks=3, n_proc=n_proc)
clthr.train(perms)
# get the FE thresholds
thr = clthr._thrmap
# perms are normally distributed, hence the CDF should be close, std of the distribution
# will scale 1/sqrt(nsubj)
assert_true(np.abs(
feature_thresh_prob - (1 - norm.cdf(thr.mean(),
loc=0,
scale=1. / np.sqrt(nsubj)))) < 0.01)
clstr_sizes = clthr._null_cluster_sizes
# getting anything but a lonely one feature cluster is very unlikely
assert_true(max([c[0] for c in clstr_sizes.keys()]) <= 1)
# threshold orig map
res = clthr(blob)
#
# check output
#
# samples unchanged
assert_array_equal(blob.samples, res.samples)
# need to find the big cluster
assert_true(len(res.a.clusterstats) > 0)
assert_equal(len(res.a.clusterstats), res.fa.clusters_featurewise_thresh.max())
# probs need to decrease with size, clusters are sorted by size (decreasing)
assert_true(res.a.clusterstats['prob_raw'][0] <= res.a.clusterstats['prob_raw'][1])
# corrected probs for every uncorrected cluster
assert_true('prob_corrected' in res.a.clusterstats.dtype.names)
# fwe correction always increases the p-values (if anything)
assert_true(np.all(res.a.clusterstats['prob_raw'] <= res.a.clusterstats['prob_corrected']))
# check expected cluster sizes, ordered large -> small
assert_array_equal(res.a.clusterstats['size'], [4, 1])
# check max position
assert_array_equal(res.a.clusterlocations['max'], [[4], [8]])
# center of mass: eyeballed
assert_array_almost_equal(res.a.clusterlocations['center_of_mass'],
[[4.429], [8]],
3)
# other simple stats
#[0, 0, .5, 3, 5, 3, 3, 0, 2, 0]
assert_array_equal(res.a.clusterstats['mean'], [3.5, 2])
assert_array_equal(res.a.clusterstats['min'], [3, 2])
assert_array_equal(res.a.clusterstats['max'], [5, 2])
assert_array_equal(res.a.clusterstats['median'], [3, 2])
assert_array_almost_equal(res.a.clusterstats['std'], [0.866, 0], 3)
# fwe thresholding only ever removes clusters
assert_true(np.all(np.abs(res.fa.clusters_featurewise_thresh - res.fa.clusters_fwe_thresh) >= 0))
# FWE should kill the small one
assert_greater(res.fa.clusters_featurewise_thresh.max(),
res.fa.clusters_fwe_thresh.max())
# check that the cluster results aren't depending in the actual location of
# the clusters
shifted_blob = Dataset([[.5, 3, 5, 3, 3, 0, 0, 0, 2, 0]])
shifted_res = clthr(shifted_blob)
assert_array_equal(res.a.clusterstats, shifted_res.a.clusterstats)
# check that it averages multi-sample datasets
# also checks that scenarios work where all features are part of one big
# cluster
multisamp = Dataset(np.arange(30).reshape(3, 10) + 100)
avgres = clthr(multisamp)
assert_equal(len(avgres), 1)
assert_array_equal(avgres.samples[0], np.mean(multisamp.samples, axis=0))
# retrain, this time with data from only a single subject
perms = Dataset(perm_samples,
sa=dict(chunks=np.repeat(1, len(perm_samples))),
fa=dict(fid=range(perms.shape[1])))
clthr.train(perms)
# same blob -- 1st this should work without issues
sglres = clthr(blob)
# NULL estimation does no averaging
# -> more noise -> fewer clusters -> higher p
assert_greater_equal(len(res.a.clusterstats), len(sglres.a.clusterstats))
assert_greater_equal(np.round(sglres.a.clusterstats[0]['prob_raw'], 4),
np.round(res.a.clusterstats[0]['prob_raw'], 4))
# no again for real scientists: no FWE correction
superclthr = gct.GroupClusterThreshold(
n_bootstrap=int(3. / feature_thresh_prob),
feature_thresh_prob=feature_thresh_prob,
multicomp_correction=None, n_blocks=3,
n_proc=n_proc)
superclthr.train(perms)
superres = superclthr(blob)
assert_true('prob_corrected' in res.a.clusterstats.dtype.names)
assert_true('clusters_fwe_thresh' in res.fa)
assert_false('prob_corrected' in superres.a.clusterstats.dtype.names)
assert_false('clusters_fwe_thresh' in superres.fa)
# check validity test
assert_raises(ValueError, gct.GroupClusterThreshold,
n_bootstrap=10, feature_thresh_prob=.09, n_proc=n_proc)
# check mapped datasets
blob = np.array([[0, 0, .5, 3, 5, 3, 3, 0, 2, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
blob = dataset_wizard([blob])
# and some nice random permutations
nperms = 100 * nsubj
perm_samples = np.random.randn(*((nperms,) + blob.shape))
perms = dataset_wizard(
perm_samples, chunks=np.repeat(range(nsubj), len(perm_samples) / nsubj))
clthr.train(perms)
twodres = clthr(blob)
# finds two clusters of the same size
assert_array_equal(twodres.a.clusterstats['size'],
res.a.clusterstats['size'])
def test_cluster_count():
skip_if_no_external('scipy', min_version='0.10')
# we get a ZERO cluster count of one if there are no clusters at all
# this is needed to keept track of the number of bootstrap samples that yield
# no cluster at all (high treshold) in order to compute p-values when there is no
# actual cluster size histogram
assert_equal(gct._get_map_cluster_sizes([0, 0, 0, 0]), [0])
# if there is at least one cluster: no ZERO count
assert_equal(gct._get_map_cluster_sizes([0, 0, 1, 0]), [1])
for i in range(2): # rerun tests for bool type of test_M
test_M = np.array([[1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0],
[0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1],
[0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0],
[0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0],
[0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0],
[1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0]])
expected_result = [5, 4, 3, 3, 2, 0, 2] # 5 clusters of size 1,
# 4 clusters of size 2 ...
test_ds = Dataset([test_M])
if i == 1:
test_M = test_M.astype(bool)
test_M_3d = np.hstack((test_M.flatten(),
test_M.flatten())).reshape(2, 9, 16)
test_ds_3d = Dataset([test_M_3d])
# expected_result^2
expected_result_3d = np.array([0, 5, 0, 4, 0, 3, 0,
3, 0, 2, 0, 0, 0, 2])
size = 10000 # how many times bigger than test_M_3d
test_M_3d_big = np.hstack((test_M_3d.flatten(), np.zeros(144)))
test_M_3d_big = np.hstack((test_M_3d_big for i in range(size))
).reshape(3 * size, 9, 16)
test_ds_3d_big = Dataset([test_M_3d_big])
expected_result_3d_big = expected_result_3d * size
# check basic cluster size determination for plain arrays and datasets
# with a single sample
for t, e in ((test_M, expected_result),
(test_ds, expected_result),
(test_M_3d, expected_result_3d),
(test_ds_3d, expected_result_3d),
(test_M_3d_big, expected_result_3d_big),
(test_ds_3d_big, expected_result_3d_big)):
assert_array_equal(np.bincount(gct._get_map_cluster_sizes(t))[1:],
e)
# old
M = np.vstack([test_M_3d.flatten()] * 10)
# new
ds = dataset_wizard([test_M_3d] * 10)
assert_array_equal(M, ds)
expected_result = Counter(np.hstack([gct._get_map_cluster_sizes(test_M_3d)] * 10))
assert_array_equal(expected_result,
gct.get_cluster_sizes(ds))
# test the same with some arbitrary per-feature threshold
thr = 4
labels, num = measurements.label(test_M_3d)
area = measurements.sum(test_M_3d, labels,
index=np.arange(labels.max() + 1))
cluster_sizes_map = area[labels] # .astype(int)
thresholded_cluster_sizes_map = cluster_sizes_map > thr
# old
M = np.vstack([cluster_sizes_map.flatten()] * 10)
# new
ds = dataset_wizard([cluster_sizes_map] * 10)
assert_array_equal(M, ds)
expected_result = Counter(np.hstack(
[gct._get_map_cluster_sizes(thresholded_cluster_sizes_map)] * 10))
th_map = np.ones(cluster_sizes_map.flatten().shape) * thr
# threshold dataset by hand
ds.samples = ds.samples > th_map
assert_array_equal(expected_result,
gct.get_cluster_sizes(ds))
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Unit tests for Stelzer et al. cluster thresholding algorithm"""
from mvpa2.base import externals
from mvpa2.testing.tools import skip_if_no_external
# TODO a tiny bit also needs statsmodels
skip_if_no_external('statsmodels')
skip_if_no_external('scipy')
from collections import Counter
import numpy as np
import random
from mvpa2.testing import assert_array_equal, assert_raises, assert_equal, \
assert_array_almost_equal, assert_almost_equal, assert_true, assert_false
import mvpa2.algorithms.group_clusterthr as gct
from mvpa2.datasets import Dataset, dataset_wizard
from nose.tools import assert_greater_equal, assert_greater
from mvpa2.testing.sweep import sweepargs
from scipy.ndimage import measurements
from scipy.stats import norm
def test_cluster_count():
skip_if_no_external('scipy', min_version='0.10')
# we get a ZERO cluster count of one if there are no clusters at all
# this is needed to keept track of the number of bootstrap samples that yield
# no cluster at all (high treshold) in order to compute p-values when there is no
# actual cluster size histogram
assert_equal(gct._get_map_cluster_sizes([0, 0, 0, 0]), [0])
# if there is at least one cluster: no ZERO count
assert_equal(gct._get_map_cluster_sizes([0, 0, 1, 0]), [1])
for i in range(2): # rerun tests for bool type of test_M
test_M = np.array([[1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0],
[0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1],
[0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0],
[0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0],
[0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0],
[1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0]])
expected_result = [5, 4, 3, 3, 2, 0, 2] # 5 clusters of size 1,
# 4 clusters of size 2 ...
test_ds = Dataset([test_M])
if i == 1:
test_M = test_M.astype(bool)
test_M_3d = np.hstack(
(test_M.flatten(), test_M.flatten())).reshape(2, 9, 16)
test_ds_3d = Dataset([test_M_3d])
# expected_result^2
expected_result_3d = np.array(
[0, 5, 0, 4, 0, 3, 0, 3, 0, 2, 0, 0, 0, 2])
size = 10000 # how many times bigger than test_M_3d
test_M_3d_big = np.hstack((test_M_3d.flatten(), np.zeros(144)))
test_M_3d_big = np.hstack(
(test_M_3d_big for i in range(size))).reshape(3 * size, 9, 16)
test_ds_3d_big = Dataset([test_M_3d_big])
expected_result_3d_big = expected_result_3d * size
# check basic cluster size determination for plain arrays and datasets
# with a single sample
for t, e in ((test_M, expected_result), (test_ds, expected_result),
(test_M_3d, expected_result_3d), (test_ds_3d,
expected_result_3d),
(test_M_3d_big, expected_result_3d_big),
(test_ds_3d_big, expected_result_3d_big)):
assert_array_equal(
np.bincount(gct._get_map_cluster_sizes(t))[1:], e)
# old
M = np.vstack([test_M_3d.flatten()] * 10)
# new
ds = dataset_wizard([test_M_3d] * 10)
assert_array_equal(M, ds)
expected_result = Counter(
np.hstack([gct._get_map_cluster_sizes(test_M_3d)] * 10))
assert_array_equal(expected_result, gct.get_cluster_sizes(ds))
# test the same with some arbitrary per-feature threshold
thr = 4
labels, num = measurements.label(test_M_3d)
area = measurements.sum(test_M_3d,
labels,
index=np.arange(labels.max() + 1))
cluster_sizes_map = area[labels] # .astype(int)
thresholded_cluster_sizes_map = cluster_sizes_map > thr
# old
M = np.vstack([cluster_sizes_map.flatten()] * 10)
# new
ds = dataset_wizard([cluster_sizes_map] * 10)
assert_array_equal(M, ds)
expected_result = Counter(
np.hstack(
[gct._get_map_cluster_sizes(thresholded_cluster_sizes_map)] *
10))
th_map = np.ones(cluster_sizes_map.flatten().shape) * thr
# threshold dataset by hand
ds.samples = ds.samples > th_map
assert_array_equal(expected_result, gct.get_cluster_sizes(ds))
def test_group_clusterthreshold_simple(n_proc):
if n_proc > 1:
skip_if_no_external('joblib')
feature_thresh_prob = 0.005
nsubj = 10
# make a nice 1D blob and a speck
blob = np.array([0, 0, .5, 3, 5, 3, 3, 0, 2, 0])
blob = Dataset([blob])
# and some nice random permutations
nperms = 100 * nsubj
perm_samples = np.random.randn(nperms, blob.nfeatures)
perms = Dataset(perm_samples,
sa=dict(chunks=np.repeat(range(nsubj),
len(perm_samples) / nsubj)),
fa=dict(fid=range(perm_samples.shape[1])))
# the algorithm instance
# scale number of bootstraps to match desired probability
# plus a safety margin to mimimize bad luck in sampling
clthr = gct.GroupClusterThreshold(n_bootstrap=int(3. /
feature_thresh_prob),
feature_thresh_prob=feature_thresh_prob,
fwe_rate=0.01,
n_blocks=3,
n_proc=n_proc)
clthr.train(perms)
# get the FE thresholds
thr = clthr._thrmap
# perms are normally distributed, hence the CDF should be close, std of the distribution
# will scale 1/sqrt(nsubj)
assert_true(
np.abs(feature_thresh_prob -
(1 - norm.cdf(thr.mean(), loc=0, scale=1. / np.sqrt(nsubj)))) <
0.01)
clstr_sizes = clthr._null_cluster_sizes
# getting anything but a lonely one feature cluster is very unlikely
assert_true(max([c[0] for c in clstr_sizes.keys()]) <= 1)
# threshold orig map
res = clthr(blob)
#
# check output
#
# samples unchanged
assert_array_equal(blob.samples, res.samples)
# need to find the big cluster
assert_true(len(res.a.clusterstats) > 0)
assert_equal(len(res.a.clusterstats),
res.fa.clusters_featurewise_thresh.max())
# probs need to decrease with size, clusters are sorted by size (decreasing)
assert_true(
res.a.clusterstats['prob_raw'][0] <= res.a.clusterstats['prob_raw'][1])
# corrected probs for every uncorrected cluster
assert_true('prob_corrected' in res.a.clusterstats.dtype.names)
# fwe correction always increases the p-values (if anything)
assert_true(
np.all(res.a.clusterstats['prob_raw'] <=
res.a.clusterstats['prob_corrected']))
# check expected cluster sizes, ordered large -> small
assert_array_equal(res.a.clusterstats['size'], [4, 1])
# check max position
assert_array_equal(res.a.clusterlocations['max'], [[4], [8]])
# center of mass: eyeballed
assert_array_almost_equal(res.a.clusterlocations['center_of_mass'],
[[4.429], [8]], 3)
# other simple stats
#[0, 0, .5, 3, 5, 3, 3, 0, 2, 0]
assert_array_equal(res.a.clusterstats['mean'], [3.5, 2])
assert_array_equal(res.a.clusterstats['min'], [3, 2])
assert_array_equal(res.a.clusterstats['max'], [5, 2])
assert_array_equal(res.a.clusterstats['median'], [3, 2])
assert_array_almost_equal(res.a.clusterstats['std'], [0.866, 0], 3)
# fwe thresholding only ever removes clusters
assert_true(
np.all(
np.abs(res.fa.clusters_featurewise_thresh -
res.fa.clusters_fwe_thresh) >= 0))
# FWE should kill the small one
assert_greater(res.fa.clusters_featurewise_thresh.max(),
res.fa.clusters_fwe_thresh.max())
# check that the cluster results aren't depending in the actual location of
# the clusters
shifted_blob = Dataset([[.5, 3, 5, 3, 3, 0, 0, 0, 2, 0]])
shifted_res = clthr(shifted_blob)
assert_array_equal(res.a.clusterstats, shifted_res.a.clusterstats)
# check that it averages multi-sample datasets
# also checks that scenarios work where all features are part of one big
# cluster
multisamp = Dataset(np.arange(30).reshape(3, 10) + 100)
avgres = clthr(multisamp)
assert_equal(len(avgres), 1)
assert_array_equal(avgres.samples[0], np.mean(multisamp.samples, axis=0))
# retrain, this time with data from only a single subject
perms = Dataset(perm_samples,
sa=dict(chunks=np.repeat(1, len(perm_samples))),
fa=dict(fid=range(perms.shape[1])))
clthr.train(perms)
# same blob -- 1st this should work without issues
sglres = clthr(blob)
# NULL estimation does no averaging
# -> more noise -> fewer clusters -> higher p
assert_greater_equal(len(res.a.clusterstats), len(sglres.a.clusterstats))
assert_greater_equal(np.round(sglres.a.clusterstats[0]['prob_raw'], 4),
np.round(res.a.clusterstats[0]['prob_raw'], 4))
# no again for real scientists: no FWE correction
superclthr = gct.GroupClusterThreshold(
n_bootstrap=int(3. / feature_thresh_prob),
feature_thresh_prob=feature_thresh_prob,
multicomp_correction=None,
n_blocks=3,
n_proc=n_proc)
superclthr.train(perms)
superres = superclthr(blob)
assert_true('prob_corrected' in res.a.clusterstats.dtype.names)
assert_true('clusters_fwe_thresh' in res.fa)
assert_false('prob_corrected' in superres.a.clusterstats.dtype.names)
assert_false('clusters_fwe_thresh' in superres.fa)
# check validity test
assert_raises(ValueError,
gct.GroupClusterThreshold,
n_bootstrap=10,
feature_thresh_prob=.09,
n_proc=n_proc)
# check mapped datasets
blob = np.array([[0, 0, .5, 3, 5, 3, 3, 0, 2, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
blob = dataset_wizard([blob])
# and some nice random permutations
nperms = 100 * nsubj
perm_samples = np.random.randn(*((nperms, ) + blob.shape))
perms = dataset_wizard(perm_samples,
chunks=np.repeat(range(nsubj),
len(perm_samples) / nsubj))
clthr.train(perms)
twodres = clthr(blob)
# finds two clusters of the same size
assert_array_equal(twodres.a.clusterstats['size'],
res.a.clusterstats['size'])
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Unit tests for Stelzer et al. cluster thresholding algorithm"""
from mvpa2.base import externals
from mvpa2.testing.tools import skip_if_no_external
# TODO a tiny bit also needs statsmodels
skip_if_no_external('statsmodels')
skip_if_no_external('scipy')
from collections import Counter
import numpy as np
import random
from mvpa2.testing import assert_array_equal, assert_raises, assert_equal, \
assert_array_almost_equal, assert_almost_equal, assert_true, assert_false
import mvpa2.algorithms.group_clusterthr as gct
from mvpa2.datasets import Dataset, dataset_wizard
from nose.tools import assert_greater_equal, assert_greater
from mvpa2.testing.sweep import sweepargs
from scipy.ndimage import measurements
from scipy.stats import norm
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
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"""Unit tests for cortical surface functionality"""
from mvpa2.testing.tools import skip_if_no_external
skip_if_no_external('matplotlib')
skip_if_no_external('griddata')
import matplotlib.pyplot as plt
import numpy as np
from numpy.testing.utils import assert_array_almost_equal
import random
from mvpa2.testing.tools import assert_almost_equal, assert_array_equal, \
assert_equal, assert_raises, assert_is_instance, unittest
from mvpa2.testing import sweepargs
from mvpa2.support.nibabel import surf
from mvpa2.support.nibabel.surf import vector_alignment_find_rotation, \
generate_plane, Surface
from mvpa2.misc.plot.flat_surf import flat_surface2xy, FlatSurfacePlotter
from mvpa2.base.dataset import AttrDataset
