def test_searchlight_errors_per_trial():
# To make sure that searchlight can return error/accuracy per trial
from mvpa2.clfs.gnb import GNB
from mvpa2.generators.partition import OddEvenPartitioner
from mvpa2.measures.base import CrossValidation
from mvpa2.measures.searchlight import sphere_searchlight
from mvpa2.measures.gnbsearchlight import sphere_gnbsearchlight
from mvpa2.testing.datasets import datasets
from mvpa2.misc.errorfx import prediction_target_matches
dataset = datasets['3dsmall'].copy()
# randomly permute samples so we break any random correspondence
# to strengthen tests below
sample_idx = np.arange(len(dataset))
dataset = dataset[np.random.permutation(sample_idx)]
dataset.sa.targets = ['L%d' % l for l in dataset.sa.targets]
dataset.fa['voxel_indices'] = dataset.fa.myspace
sample_clf = GNB() # fast and deterministic
part = OddEvenPartitioner()
# only do partial to save time
cv = CrossValidation(sample_clf, part, errorfx=None) #prediction_target_matches)
# Just to compare error
cv_error = CrossValidation(sample_clf, part)
# Large searchlight radius so we get entire ROI, 2 centers just to make sure
# that all stacking works correctly
sl = sphere_searchlight(cv, radius=10, center_ids=[0, 1])
results = sl(dataset)
sl_gnb = sphere_gnbsearchlight(sample_clf, part, radius=10, errorfx=None,
center_ids=[0, 1])
results_gnbsl = sl_gnb(dataset)
# inspect both results
# verify that partitioning was done correctly
partitions = list(part.generate(dataset))
for res in (results, results_gnbsl):
assert('targets' in res.sa.keys()) # should carry targets
assert('cvfolds' in res.sa.keys()) # should carry cvfolds
for ipart in xrange(len(partitions)):
assert_array_equal(dataset[partitions[ipart].sa.partitions == 2].targets,
res.sa.targets[res.sa.cvfolds == ipart])
assert_datasets_equal(results, results_gnbsl)
# one "accuracy" per each trial
assert_equal(results.shape, (len(dataset), 2))
# with accuracies the same in both searchlights since the same
# features were to be selected in both cases due too large radii
errors_dataset = cv(dataset)
assert_array_equal(errors_dataset.samples[:, 0], results.samples[:, 0])
assert_array_equal(errors_dataset.samples[:, 0], results.samples[:, 1])
# and error matching (up to precision) the one if we run with default error function
assert_array_almost_equal(np.mean(results.targets[:, None] != results.samples, axis=0)[0],
np.mean(cv_error(dataset)))
def test_partitionmapper():
ds = give_data()
oep = OddEvenPartitioner()
parts = list(oep.generate(ds))
assert_equal(len(parts), 2)
for i, p in enumerate(parts):
assert_array_equal(p.sa['partitions'].unique, [1, 2])
assert_equal(p.a.partitions_set, i)
assert_equal(len(p), len(ds))
def test_partitionmapper():
ds = give_data()
oep = OddEvenPartitioner()
parts = list(oep.generate(ds))
assert_equal(len(parts), 2)
for i, p in enumerate(parts):
assert_array_equal(p.sa['partitions'].unique, [1, 2])
assert_equal(p.a.partitions_set, i)
assert_equal(len(p), len(ds))
def generate_testing_datasets(specs):
# Lets permute upon each invocation of test, so we could possibly
# trigger some funny cases
nonbogus_pool = np.random.permutation([0, 1, 3, 5])
datasets = {}
# use a partitioner to flag odd/even samples as training and test
ttp = OddEvenPartitioner(space='train', count=1)
for kind, spec in specs.iteritems():
# set of univariate datasets
for nlabels in [2, 3, 4]:
basename = 'uni%d%s' % (nlabels, kind)
nonbogus_features = nonbogus_pool[:nlabels]
dataset = normal_feature_dataset(
nlabels=nlabels, nonbogus_features=nonbogus_features, **spec)
# full dataset
datasets[basename] = list(ttp.generate(dataset))[0]
# sample 3D
total = 2 * spec['perlabel']
nchunks = spec['nchunks']
data = np.random.standard_normal((total, 3, 6, 6))
labels = np.concatenate(
(np.repeat(0, spec['perlabel']), np.repeat(1, spec['perlabel'])))
data[:, 1, 0, 0] += 2 * labels # add some signal
chunks = np.asarray(range(nchunks) * (total // nchunks))
mask = np.ones((3, 6, 6), dtype='bool')
mask[0, 0, 0] = 0
mask[1, 3, 2] = 0
ds = Dataset.from_wizard(samples=data,
targets=labels,
chunks=chunks,
mask=mask,
space='myspace')
# and to stress tests on manipulating sa/fa possibly containing
# attributes of dtype object
ds.sa['test_object'] = [['a'], [1, 2]] * (ds.nsamples // 2)
datasets['3d%s' % kind] = ds
# some additional datasets
datasets['dumb2'] = dumb_feature_binary_dataset()
datasets['dumb'] = dumb_feature_dataset()
# dataset with few invariant features
_dsinv = dumb_feature_dataset()
_dsinv.samples = np.hstack((_dsinv.samples, np.zeros(
(_dsinv.nsamples, 1)), np.ones((_dsinv.nsamples, 1))))
datasets['dumbinv'] = _dsinv
# Datasets for regressions testing
datasets['sin_modulated'] = list(
ttp.generate(multiple_chunks(sin_modulated, 4, 30, 1)))[0]
# use the same full for training
datasets['sin_modulated_train'] = datasets['sin_modulated']
datasets['sin_modulated_test'] = sin_modulated(30, 1, flat=True)
# simple signal for linear regressors
datasets['chirp_linear'] = multiple_chunks(chirp_linear, 6, 50, 10, 2, 0.3,
0.1)
datasets['chirp_linear_test'] = chirp_linear(20, 5, 2, 0.4, 0.1)
datasets['wr1996'] = multiple_chunks(wr1996, 4, 50)
datasets['wr1996_test'] = wr1996(50)
datasets['hollow'] = Dataset(HollowSamples((40, 20)),
sa={'targets': np.tile(['one', 'two'], 20)})
return datasets
def generate_testing_datasets(specs):
# Lets permute upon each invocation of test, so we could possibly
# trigger some funny cases
nonbogus_pool = np.random.permutation([0, 1, 3, 5])
datasets = {}
# use a partitioner to flag odd/even samples as training and test
ttp = OddEvenPartitioner(space='train', count=1)
for kind, spec in specs.iteritems():
# set of univariate datasets
for nlabels in [ 2, 3, 4 ]:
basename = 'uni%d%s' % (nlabels, kind)
nonbogus_features = nonbogus_pool[:nlabels]
dataset = normal_feature_dataset(
nlabels=nlabels,
nonbogus_features=nonbogus_features,
**spec)
# full dataset
datasets[basename] = list(ttp.generate(dataset))[0]
# sample 3D
total = 2*spec['perlabel']
nchunks = spec['nchunks']
data = np.random.standard_normal(( total, 3, 6, 6 ))
labels = np.concatenate( ( np.repeat( 0, spec['perlabel'] ),
np.repeat( 1, spec['perlabel'] ) ) )
data[:, 1, 0, 0] += 2*labels # add some signal
chunks = np.asarray(range(nchunks)*(total/nchunks))
mask = np.ones((3, 6, 6), dtype='bool')
mask[0, 0, 0] = 0
mask[1, 3, 2] = 0
ds = Dataset.from_wizard(samples=data, targets=labels, chunks=chunks,
mask=mask, space='myspace')
# and to stress tests on manipulating sa/fa possibly containing
# attributes of dtype object
ds.sa['test_object'] = [['a'], [1, 2]] * (ds.nsamples/2)
datasets['3d%s' % kind] = ds
# some additional datasets
datasets['dumb2'] = dumb_feature_binary_dataset()
datasets['dumb'] = dumb_feature_dataset()
# dataset with few invariant features
_dsinv = dumb_feature_dataset()
_dsinv.samples = np.hstack((_dsinv.samples,
np.zeros((_dsinv.nsamples, 1)),
np.ones((_dsinv.nsamples, 1))))
datasets['dumbinv'] = _dsinv
# Datasets for regressions testing
datasets['sin_modulated'] = list(ttp.generate(multiple_chunks(sin_modulated, 4, 30, 1)))[0]
# use the same full for training
datasets['sin_modulated_train'] = datasets['sin_modulated']
datasets['sin_modulated_test'] = sin_modulated(30, 1, flat=True)
# simple signal for linear regressors
datasets['chirp_linear'] = multiple_chunks(chirp_linear, 6, 50, 10, 2, 0.3, 0.1)
datasets['chirp_linear_test'] = chirp_linear(20, 5, 2, 0.4, 0.1)
datasets['wr1996'] = multiple_chunks(wr1996, 4, 50)
datasets['wr1996_test'] = wr1996(50)
datasets['hollow'] = Dataset(HollowSamples((40,20)),
sa={'targets': np.tile(['one', 'two'], 20)})
return datasets