def apply_slhyper(queryengine,
dss=[ds0, ds1],
return_mappers=False,
**kw):
"""Helper for a common code to create/call slhyper"""
slhyper = SearchlightHyperalignment(queryengine=queryengine, **kw)
mappers = slhyper(dss)
proj = [m.proj.todense() for m in mappers]
return (proj, mappers) if return_mappers else proj
def __call__(self, datasets):
""" estimate mappers for each dataset.
Parameters
----------
datasets : list of datasets
Returns
-------
mappers_iter1: mappers from the first HA iteration
mappers_iter2: mappers from the second HA iteration
"""
debug.active += ['SHPAL', 'SLC']
mask_node_indices = np.concatenate(self.mask_node_indices)
qe = self.queryengine
nproc = self.nproc
dtype = self.dtype
nblocks = self.nblocks
ha_iter1 = SearchlightHyperalignment(queryengine=qe,
nproc=nproc,
nblocks=nblocks,
mask_node_ids=mask_node_indices,
dtype=dtype)
mappers_iter1 = ha_iter1(datasets)
aligned_iter1_datasets = self._apply_mappers(datasets, mappers_iter1)
h2a_input_data = self._prep_h2a_data(aligned_iter1_datasets, mask_node_indices)
ha_iter2 = SearchlightHyperalignment(queryengine=qe,
nproc=nproc,
nblocks=nblocks,
mask_node_ids=mask_node_indices,
dtype=dtype)
mappers_iter2 = ha_iter2(h2a_input_data)
# push the original data through the trained model
mappers_final = ha_iter2(datasets)
if self.get_all_mappers:
return mappers_iter1, mappers_iter2, mappers_final
return mappers_final
def run_hyperalignment(subjects_to_analyze, out_dir):
# Load subject data
ds_all = []
for subject_label in subjects_to_analyze:
ds_all.append(h5load('%s/sub-%s_data.hdf5' % (out_dir, subject_label)))
# Initialize searchlight hyperalignment
slhyper = SearchlightHyperalignment(radius=2,
nblocks=10,
sparse_radius=5,
dtype='float16')
hmappers = slhyper(ds_all)
return hmappers
def test_searchlight_hyperalignment_warnings_and_exceptions(self):
skip_if_no_external('scipy')
skip_if_no_external('hdf5') # needed for default results backend hdf5
ds_orig = datasets['3dsmall'][:, :1] # tiny dataset just to test exceptions
ds_orig.fa['voxel_indices'] = ds_orig.fa.myspace
slhyper = SearchlightHyperalignment()
self.assertRaises(ValueError, slhyper, [ds_orig]) # need more than 1
ds_orig.samples += 1.0 # not zscored for sure
# TODO: we need assert_warnings to also capture our own warnings,
# currently they are just suppressed :-/ So this is just a smoke test
mappers = slhyper([ds_orig, ds_orig.copy()])
def align_one_target(sources_train,
sources_test,
target_train,
target_test,
method,
masker,
pairwise_method,
clustering,
n_pieces,
n_jobs,
decoding_dir=None,
srm_atlas=None,
srm_components=40,
ha_radius=5,
ha_sparse_radius=3,
smoothing_fwhm=6,
surface=False):
overhead_time = 0
aligned_sources_test = []
if surface == "rh":
clustering = clustering.replace("lh", "rh")
# clustering = load_surf_data(
# "/storage/store2/tbazeill/schaeffer/FreeSurfer5.3/fsaverage/label/rh.Schaefer2018_700Parcels_17Networks_order.annot")
sources_train = np.asarray(
[t.replace("lh", "rh") for t in sources_train])
sources_test = np.asarray(
[t.replace("lh", "rh") for t in sources_test])
target_train.replace("lh", "rh")
target_test.replace("lh", "rh")
if surface in ["rh", "lh"]:
from nilearn.surface import load_surf_data
clustering = load_surf_data(clustering)
if method == "anat_inter_subject":
fit_start = time.process_time()
if surface in ["lh", "rh"]:
aligned_sources_test = load_clean(sources_test, masker)
aligned_target_test = load_clean(target_test, masker)
else:
aligned_sources_test = np.vstack(
[masker.transform(s) for s in sources_test])
aligned_target_test = masker.transform(target_test)
elif method == "smoothing":
fit_start = time.process_time()
smoothing_masker = NiftiMasker(mask_img=masker.mask_img_,
smoothing_fwhm=smoothing_fwhm).fit()
aligned_sources_test = np.vstack(
[smoothing_masker.transform(s) for s in sources_test])
aligned_target_test = smoothing_masker.transform(target_test)
elif method in ["pairwise", "intra_subject"]:
fit_start = time.process_time()
for source_train, source_test in zip(sources_train, sources_test):
if method == "pairwise":
if surface in ["lh", "rh"]:
source_align = SurfacePairwiseAlignment(
alignment_method=pairwise_method,
clustering=clustering,
n_jobs=n_jobs)
else:
source_align = PairwiseAlignment(
alignment_method=pairwise_method,
clustering=clustering,
n_pieces=n_pieces,
mask=masker,
n_jobs=n_jobs)
source_align.fit(source_train, target_train)
aligned_sources_test.append(
source_align.transform(source_test))
elif method == "intra_subject":
source_align = IntraSubjectAlignment(
alignment_method="ridge_cv",
clustering=clustering,
n_pieces=n_pieces,
mask=masker,
n_jobs=n_jobs)
source_align.fit(source_train, source_test)
aligned_sources_test.append(
source_align.transform(target_train))
if surface in ["lh", "rh"]:
aligned_sources_test = np.vstack(aligned_sources_test)
aligned_target_test = load_clean(target_test, masker)
else:
aligned_target_test = masker.transform(target_test)
aligned_sources_test = np.vstack(
[masker.transform(t) for t in aligned_sources_test])
elif method == "srm":
common_time = time.process_time()
fastsrm = FastSRM(atlas=srm_atlas,
n_components=srm_components,
n_iter=1000,
n_jobs=n_jobs,
aggregate="mean",
temp_dir=decoding_dir)
reduced_SR = fastsrm.fit_transform(
[masker.transform(t).T for t in sources_train])
overhead_time = time.process_time() - common_time
fit_start = time.process_time()
fastsrm.aggregate = None
fastsrm.add_subjects([masker.transform(t).T for t in [target_train]],
reduced_SR)
aligned_test = fastsrm.transform([
masker.transform(t).T
for t in np.hstack([sources_test, [target_test]])
])
aligned_sources_test = np.hstack(aligned_test[:-1]).T
aligned_target_test = aligned_test[-1].T
elif method == "HA":
overhead_time = 0
fit_start = time.process_time()
from mvpa2.algorithms.searchlight_hyperalignment import SearchlightHyperalignment
from mvpa2.datasets.base import Dataset
pymvpa_datasets = []
flat_mask = load_img(masker.mask_img_).get_fdata().flatten()
n_voxels = flat_mask.sum()
flat_coord_grid = make_coordinates_grid(
masker.mask_img_.shape).reshape((-1, 3))
masked_coord_grid = flat_coord_grid[flat_mask != 0]
for sub, sub_data in enumerate(
np.hstack([[target_train], sources_train])):
d = Dataset(masker.transform(sub_data))
d.fa['voxel_indices'] = masked_coord_grid
pymvpa_datasets.append(d)
ha = SearchlightHyperalignment(radius=ha_radius,
nproc=1,
sparse_radius=ha_sparse_radius)
ha.__call__(pymvpa_datasets)
aligned_sources_test = []
for j, source_test in enumerate(sources_test):
if surface in ["lh", "rh"]:
array_source = load_clean(source_test, masker)
else:
array_source = masker.transform(source_test)
aligned_sources_test.append(
array_source.dot(ha.projections[j + 1].proj.toarray()))
aligned_sources_test = np.vstack(aligned_sources_test)
aligned_target_test = masker.transform(target_test).dot(
ha.projections[0].proj.toarray())
fit_time = time.process_time() - fit_start
return aligned_sources_test, aligned_target_test, fit_time, overhead_time
# where to write out intermediate files
os.environ['TMPDIR'] = '/dartfs-hpc/scratch/f002d44/temp'
os.environ['TEMP'] = '/dartfs-hpc/scratch/f002d44/temp'
os.environ['TMP'] = '/dartfs-hpc/scratch/f002d44/temp'
t0 = time.time()
print('-------- beginning hyperalignment at {t0} --------'.format(t0=t0))
debug.active += ['SHPAL', 'SLC']
N_PROCS = 16
N_BLOCKS = 128
slhyper = SearchlightHyperalignment(
queryengine=qe, # pass it our surface query engine
nproc=N_PROCS, # the number of processes we want to use
nblocks=
N_BLOCKS, # the number of blocks we want to divide that into (the more you have the less memory it takes)
mask_node_ids=node_indices, # tell it which nodes you are masking
dtype='float64')
transformations = slhyper(dss)
elapsed = time.time() - t0
print('-------- time elapsed: {elapsed} --------'.format(elapsed=elapsed))
h5save(outdir + 'hyperalignment_mappers.hdf5.gz',
transformations,
compression=9)
# 7. You did it! Way to go. That saved a HDF5 file of each subject's transformation matrices into the common space.
# Now we save each individual's mapper as a npz.
from scipy.sparse import save_npz, load_npz
def __init__(self, **kwargs):
SearchlightHyperalignment.__init__(self, **kwargs)
ds.fa['voxel_indices'] = range(ds.shape[1])
#ds.sa['chunks'] = np.repeat(i,cnx_tx)
mv.zscore(ds, chunks_attr=None)
dss.append(ds)
print('Number of data sets in dss: ')
print(len(dss))
print('Size of data sets: ')
print(dss[0].shape)
# create SL hyperalignment instance
hyper = SearchlightHyperalignment(
queryengine=qe,
compute_recon=False, # We don't need to project back from common space to subject space
nproc=1,
nblocks=N_BLOCKS,
dtype ='float64'
)
# start timer
t0 = time.time()
# hyperalign dss
mappers = hyper(dss)
#save mappers
try:
h5save(toutdir, mappers)
print('saved hdf5 mappers')
except:
def test_custom_qas(self):
# Test if we could provide custom QEs per each of the datasets
skip_if_no_external('scipy')
skip_if_no_external('hdf5') # needed for default results backend hdf5
ns, nf = 10, 4 # # of samples/features -- a very BIG dataset ;)
ds0 = Dataset(np.random.normal(size=(ns, nf)))
zscore(ds0, chunks_attr=None)
ds1 = ds0[:, [3, 0, 1, 2]] # features circular shifted to the right
qe0 = FancyQE([[0], [1], [2], [3]]) # does nothing
qe1 = FancyQE([[1], [2], [3], [0]]) # knows to look into the right
def apply_slhyper(queryengine,
dss=[ds0, ds1],
return_mappers=False,
**kw):
"""Helper for a common code to create/call slhyper"""
slhyper = SearchlightHyperalignment(queryengine=queryengine, **kw)
mappers = slhyper(dss)
proj = [m.proj.todense() for m in mappers]
return (proj, mappers) if return_mappers else proj
# since this single qe resulted in trying to match non-matching time series
# projections should be non-identity, but no offdiagonal elements
assert_no_offdiag(apply_slhyper(qe0))
# both are provided
projs, mappers = apply_slhyper([qe0, qe1], return_mappers=True)
tprojs_shifted = [np.eye(nf), np.roll(np.eye(nf), 1, axis=0)]
assert_array_equal(
projs[0],
tprojs_shifted[0]) # must be identity since we made them so
assert_array_equal(
projs[1],
tprojs_shifted[1]) # pretty much incorporating that shift
# TODO -- not identity assert_array_equal(projs[0], np.eye(len(p))) # must be identity since we made them so
# and must restore data properly
assert_array_almost_equal(mappers[0].forward(ds0),
mappers[1].forward(ds1))
# give more then # of qes
assert_raises(ValueError,
SearchlightHyperalignment(queryengine=[qe0, qe1]),
[ds0, ds1, ds0])
# The one having no voxels for the "1st" id in "subj1"
qe1_ = FancyQE([[1], [], [3], [0]]) # knows to look into the right
projs = apply_slhyper(qe1_)
assert_no_offdiag(projs)
for proj in projs:
# assess that both have '2nd' one 0
# but not the others!
assert_array_equal(
np.diagonal(proj) != 0, [True, True, False, True])
# smoke test whenever combine is False
# In this case should work ok
apply_slhyper(qe0, combine_neighbormappers=False)
# this one ok as well since needs only matching ones in ref_ds
apply_slhyper([qe0, qe1], combine_neighbormappers=False)
# here since features do not match node_ids -- should raise ValueError
assert_raises(ValueError,
apply_slhyper,
qe1,
combine_neighbormappers=False)
assert_raises(ValueError,
apply_slhyper, [qe0, qe1],
ref_ds=1,
combine_neighbormappers=False)
# and now only one qe lacking for that id
projs = apply_slhyper([qe0, qe1_])
tproj0 = np.eye(nf)
tproj0[1, 1] = 0
tprojs_shifted_1st0 = [tproj0, np.roll(tproj0, 1, axis=0)]
for proj, tproj in zip(projs, tprojs_shifted_1st0):
# assess that both have '2nd' one 0
# but not the others!
assert_array_equal(proj, tproj)
# And now a test with varying number of selected fids, no shift
qe0 = FancyQE([[0], [1, 2], [1, 2, 3], [0, 1, 2, 3]])
projs = apply_slhyper(qe0)
# Test that in general we get larger coefficients for "correct" transformation
for p, tproj in zip(projs, tprojs_shifted):
assert (np.all(np.asarray(p)[tproj > 0] >= 1.0))
assert_array_lequal(np.mean(np.asarray(p)[tproj == 0]), 0.3)
qe1 = FancyQE([[0, 1, 2, 3], [1, 2, 3], [2, 3], [3]])
# Just a smoke test, for now TODO
projs = apply_slhyper([qe0, qe1])
def test_searchlight_hyperalignment(self):
skip_if_no_external('scipy')
skip_if_no_external('h5py')
ds_orig = datasets['3dsmall'].copy()[:, :15]
ds_orig.fa['voxel_indices'] = ds_orig.fa.myspace
space = 'voxel_indices'
# total number of datasets for the analysis
nds = 5
zscore(ds_orig, chunks_attr=None)
dss = [ds_orig]
# create a few distorted datasets to match the desired number of datasets
# not sure if this truly mimics the real data, but at least we can test
# implementation
while len(dss) < nds - 1:
sd = local_random_affine_transformations(
ds_orig,
scatter_neighborhoods(Sphere(1),
ds_orig.fa[space].value,
deterministic=True)[1],
Sphere(2),
space=space,
scale_fac=1.0,
shift_fac=0.0)
# sometimes above function returns dataset with nans, infs, we don't want that.
if np.sum(np.isnan(sd.samples)+np.isinf(sd.samples)) == 0 \
and np.all(sd.samples.std(0)):
dss.append(sd)
ds_orig_noisy = ds_orig.copy()
ds_orig_noisy.samples += 0.1 * np.random.random(
size=ds_orig_noisy.shape)
dss.append(ds_orig_noisy)
_ = [zscore(sd, chunks_attr=None) for sd in dss[1:]]
# we should have some distortion
for ds in dss[1:]:
assert_false(np.all(ds_orig.samples == ds.samples))
# testing checks
slhyp = SearchlightHyperalignment(ref_ds=1, exclude_from_model=[1])
self.assertRaises(ValueError, slhyp, dss[:3])
slhyp = SearchlightHyperalignment(ref_ds=3)
self.assertRaises(ValueError, slhyp, dss[:3])
# explicit test of exclude_from_model
slhyp = SearchlightHyperalignment(ref_ds=2,
exclude_from_model=[1],
featsel=0.7)
projs1 = slhyp(dss)
aligned1 = [proj.forward(ds) for proj, ds in zip(projs1, dss)]
samples = dss[1].samples.copy()
dss[1].samples += 0.1 * np.random.random(size=dss[1].shape)
projs2 = slhyp(dss)
aligned2 = [proj.forward(ds) for proj, ds in zip(projs1, dss)]
for i in [0, 2, 3, 4]:
assert_array_almost_equal(projs1[i].proj.todense(),
projs2[i].proj.todense())
assert_array_almost_equal(aligned1[i].samples, aligned2[i].samples)
assert_false(
np.all(projs1[1].proj.todense() == projs1[2].proj.todense()))
assert_false(np.all(aligned1[1].samples == aligned2[1].samples))
dss[1].samples = samples
# store projections for each mapper separately
projs = list()
# run the algorithm with all combinations of the two major parameters
# for projection calculation.
for kwargs in [{
'combine_neighbormappers': True,
'nproc': 1 + int(externals.exists('pprocess'))
}, {
'combine_neighbormappers': True,
'dtype': 'float64',
'compute_recon': True
}, {
'combine_neighbormappers': True,
'exclude_from_model': [2, 4]
}, {
'combine_neighbormappers': False
}, {
'combine_neighbormappers': False,
'mask_node_ids': np.arange(dss[0].nfeatures).tolist()
}, {
'combine_neighbormappers': True,
'sparse_radius': 1
}, {
'combine_neighbormappers': True,
'nblocks': 2
}]:
slhyp = SearchlightHyperalignment(radius=2, **kwargs)
mappers = slhyp(dss)
# one mapper per input ds
assert_equal(len(mappers), nds)
projs.append(mappers)
# some checks
for midx in range(nds):
# making sure mask_node_ids options works as expected
assert_array_almost_equal(projs[3][midx].proj.todense(),
projs[4][midx].proj.todense())
# recon check
assert_array_almost_equal(projs[0][midx].proj.todense(),
projs[1][midx].recon.T.todense(),
decimal=5)
assert_equal(projs[1][midx].proj.dtype, 'float64')
assert_equal(projs[0][midx].proj.dtype, 'float32')
# making sure the projections make sense
for proj in projs:
# no .max on sparse matrices on older scipy (e.g. on precise) so conver to array first
max_weight = proj[0].proj.toarray().max(1).squeeze()
diag_weight = proj[0].proj.diagonal()
# Check to make sure diagonal is the max weight, in almost all rows for reference subject
assert (np.sum(max_weight == diag_weight) / float(len(diag_weight))
>= 0.80)
# and not true for other subjects
for i in range(1, nds - 1):
assert (np.sum(proj[i].proj.toarray().max(1).squeeze() ==
proj[i].proj.diagonal()) /
float(proj[i].proj.shape[0]) < 0.80)
# Check to make sure projection weights match across duplicate datasets
max_weight = proj[-1].proj.toarray().max(1).squeeze()
diag_weight = proj[-1].proj.diagonal()
# Check to make sure diagonal is the max weight, in almost all rows for reference subject
assert (np.sum(max_weight == diag_weight) / float(len(diag_weight))
>= 0.80)
# project data
dss_hyper = [hm.forward(sd) for hm, sd in zip(projs[0], dss)]
_ = [zscore(sd, chunks_attr=None) for sd in dss_hyper]
ndcss = []
nf = ds_orig.nfeatures
for ds_hyper in dss_hyper:
ndcs = np.diag(np.corrcoef(ds_hyper.samples.T,
ds_orig.samples.T)[nf:, :nf],
k=0)
ndcss += [ndcs]
assert_true(np.median(ndcss[0]) > 0.9)
# noisy copy of original dataset should be similar to original after hyperalignment
assert_true(np.median(ndcss[-1]) > 0.9)
assert_true(np.all([np.median(ndcs) > 0.2 for ndcs in ndcss[1:-2]]))
for nst, split in enumerate(splits):
if nst == 0:
runs = [1, 2, 3]
elif nst == 1:
runs = [4, 5]
dss, node_indices = load_dss(lr, runs, subjects)
for ds in dss:
print(ds.shape)
debug.active += ['SHPAL', 'SLC']
ha = SearchlightHyperalignment(
queryengine=SurfaceQueryEngine(surf, radius),
nproc=N_JOBS,
nblocks=128,
compute_recon=False,
featsel=1.0,
mask_node_ids=node_indices,
dtype='float64',
)
Ts = ha(dss)
for T, subj in zip(Ts, subjects):
out_fn = '/out_fn/split_{split}/{subj}_{lr}h_{radius}_{runs}.hdf5.gz'\
''.format(split=split, subj=subj, lr=lr, radius=radius, runs='-'.join([str(_) for _ in runs]))
h5save(out_fn, T, compression=9)
for subj in subjects:
for lr in 'lr':
for nst, split in enumerate(splits):
if nst == 0:
def __init__(self, **kwargs):
SearchlightHyperalignment.__init__(self, **kwargs)
