def test_er_nifti_dataset_mapping():
"""Some mapping testing -- more tests is better
"""
# z,y,x
sample_size = (4, 3, 2)
# t,z,y,x
samples = np.arange(120).reshape((5, ) + sample_size)
dsmask = np.arange(24).reshape(sample_size) % 2
if externals.exists('nibabel'):
import nibabel
tds = fmri_dataset(nibabel.Nifti1Image(samples.T, None),
mask=nibabel.Nifti1Image(dsmask.T, None))
else:
import nifti
tds = fmri_dataset(nifti.NiftiImage(samples),
mask=nifti.NiftiImage(dsmask))
ds = eventrelated_dataset(tds,
events=[
Event(onset=0,
duration=2,
label=1,
chunk=1,
features=[1000, 1001]),
Event(onset=1,
duration=2,
label=2,
chunk=1,
features=[2000, 2001])
])
nfeatures = tds.nfeatures
mask = np.zeros(dsmask.shape, dtype='bool')
mask[0, 0, 0] = mask[1, 0, 1] = mask[0, 0, 1] = 1
fmask = ds.a.mapper.forward1(mask.T)
# select using mask in volume and all features in the other part
ds_sel = ds[:, fmask]
# now tests
assert_array_equal(mask.reshape(24).nonzero()[0], [0, 1, 7])
# two events, 2 orig features at 2 timepoints
assert_equal(ds_sel.samples.shape, (2, 4))
assert_array_equal(ds_sel.sa.features, [[1000, 1001], [2000, 2001]])
assert_array_equal(ds_sel.samples, [[1, 7, 25, 31], [25, 31, 49, 55]])
# reproducability
assert_array_equal(ds_sel.samples,
ds_sel.a.mapper.forward(np.rollaxis(samples.T, -1)))
# reverse-mapping
rmapped = ds_sel.a.mapper.reverse1(np.arange(10, 14))
assert_equal(np.rollaxis(rmapped, 0, 4).T.shape, (2, ) + sample_size)
expected = np.zeros((2, ) + sample_size, dtype='int')
expected[0, 0, 0, 1] = 10
expected[0, 1, 0, 1] = 11
expected[1, 0, 0, 1] = 12
expected[1, 1, 0, 1] = 13
assert_array_equal(np.rollaxis(rmapped, 0, 4).T, expected)
def test_er_nifti_dataset_mapping():
"""Some mapping testing -- more tests is better
"""
# z,y,x
sample_size = (4, 3, 2)
# t,z,y,x
samples = np.arange(120).reshape((5,) + sample_size)
dsmask = np.arange(24).reshape(sample_size) % 2
if externals.exists('nibabel'):
import nibabel
tds = fmri_dataset(nibabel.Nifti1Image(samples.T, None),
mask=nibabel.Nifti1Image(dsmask.T, None))
else:
import nifti
tds = fmri_dataset(nifti.NiftiImage(samples),
mask=nifti.NiftiImage(dsmask))
ds = eventrelated_dataset(
tds,
events=[Event(onset=0, duration=2, label=1,
chunk=1, features=[1000, 1001]),
Event(onset=1, duration=2, label=2,
chunk=1, features=[2000, 2001])])
nfeatures = tds.nfeatures
mask = np.zeros(dsmask.shape, dtype='bool')
mask[0, 0, 0] = mask[1, 0, 1] = mask[0, 0, 1] = 1
fmask = ds.a.mapper.forward1(mask.T)
# select using mask in volume and all features in the other part
ds_sel = ds[:, fmask]
# now tests
assert_array_equal(mask.reshape(24).nonzero()[0], [0, 1, 7])
# two events, 2 orig features at 2 timepoints
assert_equal(ds_sel.samples.shape, (2, 4))
assert_array_equal(ds_sel.sa.features,
[[1000, 1001], [2000, 2001]])
assert_array_equal(ds_sel.samples,
[[ 1, 7, 25, 31],
[ 25, 31, 49, 55]])
# reproducability
assert_array_equal(ds_sel.samples,
ds_sel.a.mapper.forward(np.rollaxis(samples.T, -1)))
# reverse-mapping
rmapped = ds_sel.a.mapper.reverse1(np.arange(10, 14))
assert_equal(np.rollaxis(rmapped, 0, 4).T.shape, (2,) + sample_size)
expected = np.zeros((2,)+sample_size, dtype='int')
expected[0,0,0,1] = 10
expected[0,1,0,1] = 11
expected[1,0,0,1] = 12
expected[1,1,0,1] = 13
assert_array_equal(np.rollaxis(rmapped, 0, 4).T, expected)
def test_er_nifti_dataset():
# setup data sources
tssrc = os.path.join(pymvpa_dataroot, 'bold.nii.gz')
evsrc = os.path.join(pymvpa_dataroot, 'fslev3.txt')
masrc = os.path.join(pymvpa_dataroot, 'mask.nii.gz')
evs = FslEV3(evsrc).to_events()
# load timeseries
ds_orig = fmri_dataset(tssrc)
# segment into events
ds = eventrelated_dataset(ds_orig, evs, time_attr='time_coords')
# we ask for boxcars of 9s length, and the tr in the file header says 2.5s
# hence we should get round(9.0/2.4) * np.prod((1,20,40) == 3200 features
assert_equal(ds.nfeatures, 3200)
assert_equal(len(ds), len(evs))
# the voxel indices are reflattened after boxcaring , but still 3D
assert_equal(ds.fa.voxel_indices.shape, (ds.nfeatures, 3))
# and they have been broadcasted through all boxcars
assert_array_equal(ds.fa.voxel_indices[:800], ds.fa.voxel_indices[800:1600])
# each feature got an event offset value
assert_array_equal(ds.fa.event_offsetidx, np.repeat([0,1,2,3], 800))
# check for all event attributes
assert_true('onset' in ds.sa)
assert_true('duration' in ds.sa)
assert_true('features' in ds.sa)
# check samples
origsamples = _load_anyimg(tssrc)[0]
for i, onset in \
enumerate([value2idx(e['onset'], ds_orig.sa.time_coords, 'floor')
for e in evs]):
assert_array_equal(ds.samples[i], origsamples[onset:onset+4].ravel())
assert_array_equal(ds.sa.time_indices[i], np.arange(onset, onset + 4))
assert_array_equal(ds.sa.time_coords[i],
np.arange(onset, onset + 4) * 2.5)
for evattr in [a for a in ds.sa
if a.count("event_attrs")
and not a.count('event_attrs_event')]:
assert_array_equal(evs[i]['_'.join(evattr.split('_')[2:])],
ds.sa[evattr].value[i])
# check offset: only the last one exactly matches the tr
assert_array_equal(ds.sa.orig_offset, [1, 1, 0])
# map back into voxel space, should ignore addtional features
nim = map2nifti(ds)
# origsamples has t,x,y,z
assert_equal(nim.get_shape(), origsamples.shape[1:] + (len(ds) * 4,))
# check shape of a single sample
nim = map2nifti(ds, ds.samples[0])
# pynifti image has [t,]z,y,x
assert_equal(nim.get_shape(), (40, 20, 1, 4))
# and now with masking
ds = fmri_dataset(tssrc, mask=masrc)
ds = eventrelated_dataset(ds, evs, time_attr='time_coords')
nnonzero = len(_load_anyimg(masrc)[0].nonzero()[0])
assert_equal(nnonzero, 530)
# we ask for boxcars of 9s length, and the tr in the file header says 2.5s
# hence we should get round(9.0/2.4) * np.prod((1,20,40) == 3200 features
assert_equal(ds.nfeatures, 4 * 530)
assert_equal(len(ds), len(evs))
# and they have been broadcasted through all boxcars
assert_array_equal(ds.fa.voxel_indices[:nnonzero],
ds.fa.voxel_indices[nnonzero:2*nnonzero])
def test_er_nifti_dataset():
# setup data sources
tssrc = os.path.join(pymvpa_dataroot, 'bold.nii.gz')
evsrc = os.path.join(pymvpa_dataroot, 'fslev3.txt')
masrc = os.path.join(pymvpa_dataroot, 'mask.nii.gz')
evs = FslEV3(evsrc).to_events()
# load timeseries
ds_orig = fmri_dataset(tssrc)
# segment into events
ds = eventrelated_dataset(ds_orig, evs, time_attr='time_coords')
# we ask for boxcars of 9s length, and the tr in the file header says 2.5s
# hence we should get round(9.0/2.4) * np.prod((1,20,40) == 3200 features
assert_equal(ds.nfeatures, 3200)
assert_equal(len(ds), len(evs))
# the voxel indices are reflattened after boxcaring , but still 3D
assert_equal(ds.fa.voxel_indices.shape, (ds.nfeatures, 3))
# and they have been broadcasted through all boxcars
assert_array_equal(ds.fa.voxel_indices[:800],
ds.fa.voxel_indices[800:1600])
# each feature got an event offset value
assert_array_equal(ds.fa.event_offsetidx, np.repeat([0, 1, 2, 3], 800))
# check for all event attributes
assert_true('onset' in ds.sa)
assert_true('duration' in ds.sa)
assert_true('features' in ds.sa)
# check samples
origsamples = _load_anyimg(tssrc)[0]
for i, onset in \
enumerate([value2idx(e['onset'], ds_orig.sa.time_coords, 'floor')
for e in evs]):
assert_array_equal(ds.samples[i], origsamples[onset:onset + 4].ravel())
assert_array_equal(ds.sa.time_indices[i], np.arange(onset, onset + 4))
assert_array_equal(ds.sa.time_coords[i],
np.arange(onset, onset + 4) * 2.5)
for evattr in [
a for a in ds.sa
if a.count("event_attrs") and not a.count('event_attrs_event')
]:
assert_array_equal(evs[i]['_'.join(evattr.split('_')[2:])],
ds.sa[evattr].value[i])
# check offset: only the last one exactly matches the tr
assert_array_equal(ds.sa.orig_offset, [1, 1, 0])
# map back into voxel space, should ignore addtional features
nim = map2nifti(ds)
if externals.exists('nibabel'):
# origsamples has t,x,y,z
assert_equal(nim.get_shape(), origsamples.shape[1:] + (len(ds) * 4, ))
# check shape of a single sample
nim = map2nifti(ds, ds.samples[0])
# pynifti image has [t,]z,y,x
assert_equal(nim.get_shape(), (40, 20, 1, 4))
else:
# origsamples has t,x,y,z but pynifti image has [t,]z,y,x
assert_equal(nim.data.T.shape, origsamples.shape[1:] + (len(ds) * 4, ))
# check shape of a single sample
nim = map2nifti(ds, ds.samples[0])
# pynifti image has [t,]z,y,x
assert_equal(nim.data.T.shape, (40, 20, 1, 4))
# and now with masking
ds = fmri_dataset(tssrc, mask=masrc)
ds = eventrelated_dataset(ds, evs, time_attr='time_coords')
nnonzero = len(_load_anyimg(masrc)[0].nonzero()[0])
assert_equal(nnonzero, 530)
# we ask for boxcars of 9s length, and the tr in the file header says 2.5s
# hence we should get round(9.0/2.4) * np.prod((1,20,40) == 3200 features
assert_equal(ds.nfeatures, 4 * 530)
assert_equal(len(ds), len(evs))
# and they have been broadcasted through all boxcars
assert_array_equal(ds.fa.voxel_indices[:nnonzero],
ds.fa.voxel_indices[nnonzero:2 * nnonzero])
def test_erdataset():
# 3 chunks, 5 targets, blocks of 5 samples each
nchunks = 3
ntargets = 5
blocklength = 5
nfeatures = 10
targets = np.tile(np.repeat(range(ntargets), blocklength), nchunks)
chunks = np.repeat(np.arange(nchunks), ntargets * blocklength)
samples = np.repeat(
np.arange(nchunks * ntargets * blocklength),
nfeatures).reshape(-1, nfeatures)
ds = dataset_wizard(samples, targets=targets, chunks=chunks)
# check if events are determined properly
evs = find_events(targets=ds.sa.targets, chunks=ds.sa.chunks)
for ev in evs:
assert_equal(ev['duration'], blocklength)
assert_equal(ntargets * nchunks, len(evs))
for t in range(ntargets):
assert_equal(len([ev for ev in evs if ev['targets'] == t]),
nchunks)
# now turn `ds` into an eventreleated dataset
erds = eventrelated_dataset(ds, evs)
# the only unprefixed sample attributes are
assert_equal(sorted([a for a in ds.sa if not a.startswith('event')]),
['chunks', 'targets'])
# samples as expected?
assert_array_equal(erds.samples[0],
np.repeat(np.arange(blocklength), nfeatures))
# that should also be the temporal feature offset
assert_array_equal(erds.samples[0], erds.fa.event_offsetidx)
assert_array_equal(erds.sa.event_onsetidx, np.arange(0,71,5))
# finally we should see two mappers
assert_equal(len(erds.a.mapper), 2)
assert_true(isinstance(erds.a.mapper[0], BoxcarMapper))
assert_true(isinstance(erds.a.mapper[1], FlattenMapper))
#
# now check the same dataset with event descretization
tr = 2.5
ds.sa['time'] = np.arange(nchunks * ntargets * blocklength) * tr
evs = [{'onset': 4.9, 'duration': 6.2}]
# doesn't work without conversion
assert_raises(ValueError, eventrelated_dataset, ds, evs)
erds = eventrelated_dataset(ds, evs, time_attr='time')
assert_equal(len(erds), 1)
assert_array_equal(erds.samples[0], np.repeat(np.arange(1,5), nfeatures))
assert_array_equal(erds.sa.orig_onset, [evs[0]['onset']])
assert_array_equal(erds.sa.orig_duration, [evs[0]['duration']])
assert_array_almost_equal(erds.sa.orig_offset, [2.4])
assert_array_equal(erds.sa.time, [np.arange(2.5, 11, 2.5)])
# now with closest match
erds = eventrelated_dataset(ds, evs, time_attr='time', match='closest')
expected_nsamples = 3
assert_equal(len(erds), 1)
assert_array_equal(erds.samples[0],
np.repeat(np.arange(2,2+expected_nsamples),
nfeatures))
assert_array_equal(erds.sa.orig_onset, [evs[0]['onset']])
assert_array_equal(erds.sa.orig_duration, [evs[0]['duration']])
assert_array_almost_equal(erds.sa.orig_offset, [-0.1])
assert_array_equal(erds.sa.time, [np.arange(5.0, 11, 2.5)])
# now test the way back
results = np.arange(erds.nfeatures)
assert_array_equal(erds.a.mapper.reverse1(results),
results.reshape(expected_nsamples, nfeatures))
# what about multiple results?
nresults = 5
results = dataset_wizard([results] * nresults)
# and let's have an attribute to make it more difficult
results.sa['myattr'] = np.arange(5)
rds = erds.a.mapper.reverse(results)
assert_array_equal(rds,
results.samples.reshape(nresults * expected_nsamples,
nfeatures))
assert_array_equal(rds.sa.myattr, np.repeat(results.sa.myattr,
expected_nsamples))