def parcellate_voronoi_vol(mask, nb_parcels, seeds=None):
"""
Produce a parcellation from a Voronoi diagram built on random seeds.
The number of seeds is equal to the nb of parcels.
Seed are randomly placed within the mask, expect on edge positions
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
- seeds: TODO
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
-
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask !=0).sum()
for cc_mask in mg.split_mask_into_cc_iter(mask!=0):
# compute the required number of parcels within the current CC:
size_cc = cc_mask.sum()
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox*1.))), 1)
pyhrf.verbose(2, 'Treating a connected component (CC) of %d positions' \
%cc_mask.sum())
if cc_mask.sum() < 6:
continue
if seeds is None:
# perform voronoi on random seeds
eroded_mask = peelVolume3D(cc_mask)
eroded_mask_size = eroded_mask.sum()
if eroded_mask_size < nb_parcels: #do no erode, mask too small
eroded_mask_size = nvox
eroded_mask = mask.copy()
cc_seeds = np.random.randint(0,eroded_mask_size, cc_np)
mask_for_seed = np.zeros(eroded_mask_size, dtype=int)
mask_for_seed[cc_seeds] = 1
mask_for_seed = expand_array_in_mask(mask_for_seed, eroded_mask)
else:
mask_for_seed = seeds * cc_mask
pyhrf.verbose(2, 'Nb of seeds in current CC: %d' \
%mask_for_seed.sum())
cc_parcellation = voronoi(np.vstack(np.where(cc_mask)).T,
np.vstack(np.where(mask_for_seed)).T) + 1
pyhrf.verbose(3, 'CC parcellation labels: %s' \
%str(np.unique(cc_parcellation)))
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_parcellation + maxp, cc_mask)
pyhrf.verbose(3, 'Current parcellation labels: %s' \
%str(np.unique(parcellation)))
pyhrf.verbose(1, 'voronoi parcellation: %s, %s' \
%(str(parcellation.shape), str(parcellation.dtype)))
return parcellation
def parcellate_voronoi_vol(mask, nb_parcels, seeds=None):
"""
Produce a parcellation from a Voronoi diagram built on random seeds.
The number of seeds is equal to the nb of parcels.
Seed are randomly placed within the mask, expect on edge positions
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
- seeds: TODO
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
-
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask != 0).sum()
for cc_mask in mg.split_mask_into_cc_iter(mask != 0):
# compute the required number of parcels within the current CC:
size_cc = cc_mask.sum()
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox * 1.))), 1)
logger.info('Treating a connected component (CC) of %d positions',
cc_mask.sum())
if cc_mask.sum() < 6:
continue
if seeds is None:
# perform voronoi on random seeds
eroded_mask = peelVolume3D(cc_mask)
eroded_mask_size = eroded_mask.sum()
if eroded_mask_size < nb_parcels: # do no erode, mask too small
eroded_mask_size = nvox
eroded_mask = mask.copy()
cc_seeds = np.random.randint(0, eroded_mask_size, cc_np)
mask_for_seed = np.zeros(eroded_mask_size, dtype=int)
mask_for_seed[cc_seeds] = 1
mask_for_seed = expand_array_in_mask(mask_for_seed, eroded_mask)
else:
mask_for_seed = seeds * cc_mask
logger.info('Nb of seeds in current CC: %d', mask_for_seed.sum())
cc_parcellation = voronoi(
np.vstack(np.where(cc_mask)).T,
np.vstack(np.where(mask_for_seed)).T) + 1
logger.info('CC parcellation labels: %s',
str(np.unique(cc_parcellation)))
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_parcellation + maxp, cc_mask)
logger.info('Current parcellation labels: %s',
str(np.unique(parcellation)))
logger.info('voronoi parcellation: %s, %s', str(parcellation.shape),
str(parcellation.dtype))
return parcellation
def save(self, output_dir):
"""
Save paradigm to output_dir/paradigm.csv,
BOLD to output_dir/bold.nii, mask to output_dir/mask.nii
#TODO: handle multi-session
Return: tuple of file names in this order: (paradigm, bold, mask)
"""
from pyhrf.tools._io import write_volume, write_texture
paradigm_file = op.join(output_dir, 'paradigm.csv')
self.paradigm.save_csv(paradigm_file)
if self.data_type == 'volume':
# unflatten bold
bold_vol = expand_array_in_mask(self.bold, self.roiMask, 1)
bold_vol = np.rollaxis(bold_vol, 0, 4)
bold_file = op.join(output_dir, 'bold.nii')
write_volume(bold_vol, bold_file, self.meta_obj)
mask_file = op.join(output_dir, 'mask.nii')
write_volume(self.roiMask, mask_file, self.meta_obj)
elif self.data_type == 'surface': # TODO surface
bold_file = op.join(output_dir, 'bold.gii')
write_texture(self.bold_vol, bold_file, self.meta_obj)
pass
return paradigm_file, bold_file, mask_file
def save_time_series(k):
if simulation.has_key(k):
fn_stim_induced = add_prefix(op.join(output_dir, k + '.nii'),
prefix)
logger.info('%s flat shape %s', k, str(simulation[k].shape))
vol = expand_array_in_mask(simulation[k], mask_vol, flat_axis=1)
write_volume(np.rollaxis(vol, 0, 4), fn_stim_induced)
def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1,1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
# print 'labels:'
# print labels
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1+1, labels+1)[0]
self.assertEqual(dist, 0)
def save(self, output_dir):
"""
Save paradigm to output_dir/paradigm.csv,
BOLD to output_dir/bold.nii, mask to output_dir/mask.nii
#TODO: handle multi-session
Return: tuple of file names in this order: (paradigm, bold, mask)
"""
from pyhrf.tools._io import write_volume, write_texture
paradigm_file = op.join(output_dir, 'paradigm.csv')
self.paradigm.save_csv(paradigm_file)
if self.data_type == 'volume':
# unflatten bold
bold_vol = expand_array_in_mask(self.bold, self.roiMask, 1)
bold_vol = np.rollaxis(bold_vol, 0, 4)
bold_file = op.join(output_dir, 'bold.nii')
write_volume(bold_vol, bold_file, self.meta_obj)
mask_file = op.join(output_dir, 'mask.nii')
write_volume(self.roiMask, mask_file, self.meta_obj)
elif self.data_type == 'surface': # TODO surface
bold_file = op.join(output_dir, 'bold.gii')
write_texture(self.bold_vol, bold_file, self.meta_obj)
pass
return paradigm_file, bold_file, mask_file
def save_time_series(k):
if simulation.has_key(k):
fn_stim_induced = add_prefix(
op.join(output_dir, k + '.nii'), prefix)
logger.info('%s flat shape %s', k, str(simulation[k].shape))
vol = expand_array_in_mask(simulation[k], mask_vol, flat_axis=1)
write_volume(np.rollaxis(vol, 0, 4), fn_stim_induced)
def parcellation_dist(p1, p2, mask=None):
"""
Compute the distance between the two parcellation p1 and p2 as the minimum
number of positions to remove in order to obtain equal partitions.
"mask" may be a binary mask to limit the distance computation to some
specific positions.
Important convention: parcel label 0 is treated as background and
corresponding positions are discarded if no mask is provided.
Return:
(distance value, parcellation overlap)
"""
assert np.issubdtype(p1.dtype, np.int)
assert np.issubdtype(p2.dtype, np.int)
assert p1.shape == p2.shape
from munkres import Munkres
if mask is None:
mask = (p1 != 0)
m = np.where(mask)
pyhrf.verbose(6,'Nb pos inside mask: %d' %len(m[0]))
fp1 = p1[m].astype(np.int32)
fp2 = p2[m].astype(np.int32)
# allocate cost matrix, assume that region labels are contiguous
# ie all labels in [1, label_max] are represented
cost_matrix = np.zeros((fp1.max()+1, fp2.max()+1), dtype=np.int32)
pyhrf.verbose(6,'Cost matrix : %s' %str(cost_matrix.shape))
compute_intersection_matrix(fp1, fp2, cost_matrix)
# discard 0-labelled parcels (background)
cost_matrix = cost_matrix[1:,1:]
# solve the assignement problem:
indexes = np.array(Munkres().compute((cost_matrix*-1).tolist()))
if 0:
print 'assignement indexes:'
print indexes
print '->'
print (indexes[:,0], indexes[:,1])
print cost_matrix[(indexes[:,0], indexes[:,1])]
assignement = cost_matrix[(indexes[:,0], indexes[:,1])].sum()
to_keep = np.zeros_like(fp1)
for s1, s2 in indexes:
to_keep += np.bitwise_and(fp1==(s1+1), fp2==(s2+1))
return fp1.size - assignement, expand_array_in_mask(to_keep, mask)
def parcellation_dist(p1, p2, mask=None):
"""
Compute the distance between the two parcellation p1 and p2 as the minimum
number of positions to remove in order to obtain equal partitions.
"mask" may be a binary mask to limit the distance computation to some
specific positions.
Important convention: parcel label 0 is treated as background and
corresponding positions are discarded if no mask is provided.
Return:
(distance value, parcellation overlap)
"""
assert np.issubdtype(p1.dtype, np.int)
assert np.issubdtype(p2.dtype, np.int)
assert p1.shape == p2.shape
from munkres import Munkres
if mask is None:
mask = (p1 != 0)
m = np.where(mask)
logger.debug('Nb pos inside mask: %d', len(m[0]))
fp1 = p1[m].astype(np.int32)
fp2 = p2[m].astype(np.int32)
# allocate cost matrix, assume that region labels are contiguous
# ie all labels in [1, label_max] are represented
cost_matrix = np.zeros((fp1.max() + 1, fp2.max() + 1), dtype=np.int32)
logger.debug('Cost matrix : %s', str(cost_matrix.shape))
compute_intersection_matrix(fp1, fp2, cost_matrix)
# discard 0-labelled parcels (background)
cost_matrix = cost_matrix[1:, 1:]
# solve the assignement problem:
indexes = np.array(Munkres().compute((cost_matrix * -1).tolist()))
if 0:
print 'assignement indexes:'
print indexes
print '->'
print(indexes[:, 0], indexes[:, 1])
print cost_matrix[(indexes[:, 0], indexes[:, 1])]
assignement = cost_matrix[(indexes[:, 0], indexes[:, 1])].sum()
to_keep = np.zeros_like(fp1)
for s1, s2 in indexes:
to_keep += np.bitwise_and(fp1 == (s1 + 1), fp2 == (s2 + 1))
return fp1.size - assignement, expand_array_in_mask(to_keep, mask)
def parcellation_hemodynamics(fmri_data, feature_extraction_method,
parcellation_method, nb_clusters):
"""
Perform a hemodynamic-driven parcellation on masked fMRI data
Args:
- fmri_data (pyhrf.core.FmriData): input fMRI data
- feature_extraction_method (str): one of
'glm_hderiv', 'glm_hdisp' ...
- parcellation_method (str): one of
'spatial_ward', 'spatial_ward_uncertainty', ...
Return:
parcellation array (numpy array of integers) of the same shape
as fmri_data.roiMask
Examples
>>> fd = pyhrf.core.FmriData.from_simu_ui()
>>> parcellation_hemodynamics(fd, 'glm_hdisp', nb_clusters=2)
array([[[1], [1]], [[2], [2]]]) #dummy result #TOCHECK
"""
roi_ids = np.unique(fmri_data.roi_ids_in_mask)
if len(roi_ids) == 0:
# glm
#TODO
features, uncertainty = feature_extraction(fmri_data,
feature_extraction_method)
# parcellation process
if parcellation_method == 'spatial_ward':
parcellation = spatial_ward(features) #TODO
else:
parcellation = spatial_ward_with_uncertainty(features) #TODO
else: #parcellate each ROI separately
nb_voxels_all = fmri_data.nb_voxels_in_mask
parcellation = np.zeros(fmri_data.nb_voxels_all, dtype=int)
for rfd in fmri_data.roi_split():
# multiply nb_clusters by the fraction of the roi size
nb_clusters_roi = round(nb_clusters * rfd.nb_voxels_in_mask / \
nb_voxels_all)
p_roi = parcellation_hemodynamics(rfd, feature_extraction_method,
parcellation_method,
nb_clusters_roi)
parcellation += p_roi + parcellation.max()
return expand_array_in_mask(parcellation, fmri_data.roiMask)
def split_mask_into_cc_iter(mask, min_size=0, kerMask=None):
""" Return an iterator over all connected components (CC) within input mask. CC which are smaller than `min_size`
are discarded. `kerMask` defines the connectivity, e.g., kerMask3D_6n for 6-neighbours in 3D.
Examples
--------
.. code::
vol = np.array( [[1,1,0,1,1],
[1,1,0,1,1],
[0,0,0,0,0],
[1,0,1,1,0],
[0,0,1,1,0]], dtype=int )
for cc in split_mask_into_cc_iter(vol):
print cc
Should output:
.. code::
np.array( [[1,1,0,0,0],
[1,1,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0]]
np.array( [[0,0,0,1,1],
[0,0,0,1,1],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0]]
"""
assert isinstance(min_size, int)
flat_mask = mask[np.where(mask)]
# print 'flat_mask:', flat_mask.shape
g = graph_from_lattice(mask, kerMask)
for cc in connected_components_iter(g):
# print 'cc:'
# print cc
if len(cc) >= min_size:
flat_mask[:] = 0
flat_mask[cc] = 1
# print expand_array_in_mask(flat_mask, mask)
yield expand_array_in_mask(flat_mask, mask)
def split_mask_into_cc_iter(mask, min_size=0, kerMask=None):
""" Return an iterator over all connected components (CC) within input mask. CC which are smaller than `min_size`
are discarded. `kerMask` defines the connectivity, e.g., kerMask3D_6n for 6-neighbours in 3D.
Examples
--------
.. code::
vol = np.array( [[1,1,0,1,1],
[1,1,0,1,1],
[0,0,0,0,0],
[1,0,1,1,0],
[0,0,1,1,0]], dtype=int )
for cc in split_mask_into_cc_iter(vol):
print cc
Should output:
.. code::
np.array( [[1,1,0,0,0],
[1,1,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0]]
np.array( [[0,0,0,1,1],
[0,0,0,1,1],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0]]
"""
assert isinstance(min_size, int)
flat_mask = mask[np.where(mask)]
# print 'flat_mask:', flat_mask.shape
g = graph_from_lattice(mask, kerMask)
for cc in connected_components_iter(g):
# print 'cc:'
# print cc
if len(cc) >= min_size:
flat_mask[:] = 0
flat_mask[cc] = 1
# print expand_array_in_mask(flat_mask, mask)
yield expand_array_in_mask(flat_mask, mask)
def parcellate_balanced_vol(mask, nb_parcels):
"""
Performs a balanced partitioning on the input mask using a balloon patroling
algorithm [Eurol 2009]. Values with 0 are discarded position in the mask.
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask != 0).sum()
# Iterate over connected components in the input mask
for cc_mask in mg.split_mask_into_cc_iter(mask != 0):
logger.info('Treating a connected component (CC) of %d positions',
cc_mask.sum())
g = mg.graph_from_lattice(cc_mask)
size_cc = cc_mask.sum()
# compute the required number of parcels within the current CC:
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox * 1.))), 1)
logger.info('Split (CC) into %d parcels', cc_np)
cc_labels = np.ones(cc_mask.sum(), dtype=int)
if cc_np > 1:
split_parcel(cc_labels, {1: g},
1,
cc_np,
inplace=True,
verbosity=2,
balance_tolerance='draft')
else: # only one parcel expected, CC must be too small to be splited
cc_labels[:] = 1
logger.info('Split done!')
# accumulate parcellation result
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_labels + maxp, cc_mask > 0)
return parcellation
def test_ward_spatial_scikit_with_mask(self):
from pyhrf.parcellation import parcellation_dist, parcellation_ward_spatial
from pyhrf.graph import graph_from_lattice, kerMask2D_4n
from pyhrf.ndarray import expand_array_in_mask
if debug:
print 'data:'
print self.p1
print ''
mask = self.p1 != 0
graph = graph_from_lattice(mask, kerMask2D_4n)
X = self.p1[np.where(mask)].reshape(-1, 1)
labels = parcellation_ward_spatial(X, n_clusters=4, graph=graph)
labels = expand_array_in_mask(labels, mask)
#+1 because parcellation_dist sees 0 as background:
dist = parcellation_dist(self.p1 + 1, labels + 1)[0]
self.assertEqual(dist, 0)
def parcellate_balanced_vol(mask, nb_parcels):
"""
Performs a balanced partitioning on the input mask using a balloon patroling
algorithm [Eurol 2009]. Values with 0 are discarded position in the mask.
Args:
- mask (numpy.ndarray): binary 3D array of valid position to parcellate
- nb_parcels (int): the required number of parcels
Return:
- the parcellation (numpy.ndarray): a 3D array of integers
"""
parcellation = np.zeros(mask.shape, dtype=int)
nvox = (mask != 0).sum()
# Iterate over connected components in the input mask
for cc_mask in mg.split_mask_into_cc_iter(mask != 0):
pyhrf.verbose(2, 'Treating a connected component (CC) of %d positions' \
%cc_mask.sum())
g = mg.graph_from_lattice(cc_mask)
size_cc = cc_mask.sum()
# compute the required number of parcels within the current CC:
cc_np = max(int(np.round(nb_parcels * size_cc / (nvox*1.))), 1)
pyhrf.verbose(2, 'Split (CC) into %d parcels' %cc_np)
cc_labels = np.ones(cc_mask.sum(), dtype=int)
if cc_np > 1:
split_parcel(cc_labels, {1:g}, 1, cc_np, inplace=True,
verbosity=2, balance_tolerance='draft')
else: #only one parcel expected, CC must be too small to be splited
cc_labels[:] = 1
pyhrf.verbose(2, 'Split done!')
# accumulate parcellation result
maxp = parcellation.max()
parcellation += expand_array_in_mask(cc_labels + maxp, cc_mask>0)
return parcellation
def parcellation_for_jde(fmri_data, avg_parcel_size=250, output_dir=None,
method='gkm', glm_drift='Cosine', glm_hfcut=128):
"""
method: gkm, ward, ward_and_gkm
"""
if output_dir is None:
output_dir = tempfile.mkdtemp(prefix='pyhrf_JDE_parcellation_GLM',
dir=pyhrf.cfg['global']['tmp_path'])
glm_output_dir = op.join(output_dir, 'GLM_for_parcellation')
if not op.exists(glm_output_dir): os.makedirs(glm_output_dir)
pyhrf.verbose(1, 'GLM for parcellation')
# if fmri_data.data_type == 'volume':
# paradigm_file, bold_file, mask_file = fmri_data.save(glm_output_dir)
# beta_files = glm_nipy_from_files(bold_file, fmri_data.tr, paradigm_file,
# glm_output_dir, mask_file,
# drift_model=glm_drift, hfcut=glm_hfcut)
# elif fmri_data.data_type == 'surface':
# beta_files = glm_nipy(fmri_data, glm_output_dir,
# drift_model=glm_drift, hfcut=glm_hfcut)
g, dm, cons = glm_nipy(fmri_data, drift_model=glm_drift, hfcut=glm_hfcut)
pval_files = []
if cons is not None:
func_data = [('con_pval_%s' %cname, con.pvalue()) \
for cname, con in cons.iteritems()]
else:
reg_cst_drift = re.compile(".*constant.*|.*drift.*")
func_data = [('beta_%s' %reg_name, g.beta[ir]) \
for ir,reg_name in enumerate(dm.names) \
if not reg_cst_drift.match(reg_name)]
for name, data in func_data:
val_vol = expand_array_in_mask(data, fmri_data.roiMask>0)
val_fn = op.join(glm_output_dir, '%s.nii' %name)
write_volume(val_vol, val_fn, fmri_data.meta_obj)
pval_files.append(val_fn)
mask_file = op.join(glm_output_dir,'mask.nii')
write_volume(fmri_data.roiMask>0, mask_file, fmri_data.meta_obj)
nvox = fmri_data.get_nb_vox_in_mask()
nparcels = round_nb_parcels(nvox * 1. / avg_parcel_size)
pyhrf.verbose(1, 'Parcellation from GLM outputs, method: %s, ' \
'nb parcels: %d' %(method, nparcels))
if fmri_data.data_type == 'volume':
parcellation_file = op.join(output_dir, 'parcellation_%s_np%d.nii'
%(method, nparcels))
make_parcellation_from_files(pval_files, mask_file, parcellation_file,
nparcels, method)
parcellation,_ = read_volume(parcellation_file)
else:
mesh_file = fmri_data.data_files[-1]
parcellation_file = op.join(output_dir, 'parcellation_%s_np%d.gii'
%(method, nparcels))
make_parcellation_surf_from_files(pval_files, mesh_file,
parcellation_file, nparcels, method,
verbose=1)
parcellation,_ = read_texture(parcellation_file)
#print parcellation_file
pyhrf.verbose(1, parcellation_report(parcellation))
return parcellation, parcellation_file
def simulation_save_vol_outputs(
simulation, output_dir, bold_3D_vols_dir=None, simulation_graph_output=None, prefix=None, vol_meta=None
):
""" simulation_graph_output : None, 'simple', 'thumbnails' #TODO
"""
if simulation.has_key("paradigm"):
fn = add_prefix(op.join(output_dir, "paradigm.csv"), prefix)
simulation["paradigm"].save_csv(fn)
# Save all volumes in nifti format:
if simulation.has_key("labels_vol"):
mask_vol = np.ones_like(simulation["labels_vol"][0])
elif simulation.has_key("mask"):
mask_vol = simulation.get("mask", None)
elif simulation.has_key("labels"):
mask_vol = np.ones_like(simulation["labels"][0])
else:
raise Exception("Dunno where to get mask")
logger.info("Vol mask of shape %s", str(mask_vol.shape))
fn_mask = add_prefix(op.join(output_dir, "mask.nii"), prefix)
write_volume(mask_vol.astype(np.int32), fn_mask, vol_meta)
if simulation.has_key("hrf_territories"):
fn_h_territories = add_prefix(op.join(output_dir, "hrf_territories.nii"), prefix)
ht = expand_array_in_mask(simulation["hrf_territories"] + 1, mask_vol)
write_volume(ht, fn_h_territories, vol_meta)
if simulation.has_key("hrf"):
from pyhrf.ndarray import MRI3Daxes
fn_hrf = add_prefix(op.join(output_dir, "hrf.nii"), prefix)
logger.info("hrf flat shape %s", str(simulation["hrf"].shape))
if simulation["hrf"].ndim == 1:
hrf = np.ones(mask_vol.size) * simulation["hrf"][:, np.newaxis]
else:
hrf = simulation["hrf"]
hrfs_vol = expand_array_in_mask(hrf, mask_vol, flat_axis=1)
dt = simulation["dt"]
chrfs = xndarray(
hrfs_vol, axes_names=["time"] + MRI3Daxes, axes_domains={"time": np.arange(hrfs_vol.shape[0]) * dt}
)
chrfs.save(fn_hrf, vol_meta)
ttp_vol = hrfs_vol.argmax(0)
fn_ttp = add_prefix(op.join(output_dir, "ttp.nii"), prefix)
write_volume(ttp_vol, fn_ttp, vol_meta)
if simulation.has_key("brf"):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, "brf.nii"), prefix)
logger.info("brf flat shape %s", str(simulation["brf"].shape))
brfs_vol = expand_array_in_mask(simulation["brf"], mask_vol, flat_axis=1)
dt = simulation["dt"]
cbrfs = xndarray(
brfs_vol, axes_names=["time"] + MRI3Daxes, axes_domains={"time": np.arange(brfs_vol.shape[0]) * dt}
)
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key("prf"):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, "prf.nii"), prefix)
logger.info("prf flat shape %s", str(simulation["prf"].shape))
brfs_vol = expand_array_in_mask(simulation["prf"], mask_vol, flat_axis=1)
dt = simulation["dt"]
cbrfs = xndarray(
brfs_vol, axes_names=["time"] + MRI3Daxes, axes_domains={"time": np.arange(brfs_vol.shape[0]) * dt}
)
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key("drift"):
fn_drift = add_prefix(op.join(output_dir, "drift.nii"), prefix)
logger.info("drift flat shape %s", str(simulation["drift"].shape))
drift_vol = expand_array_in_mask(simulation["drift"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key("drift_coeffs"):
fn_drift = add_prefix(op.join(output_dir, "drift_coeffs.nii"), prefix)
logger.info("drift flat shape %s", str(simulation["drift_coeffs"].shape))
drift_vol = expand_array_in_mask(simulation["drift"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key("noise"):
fn_noise = add_prefix(op.join(output_dir, "noise.nii"), prefix)
logger.info("noise flat shape %s", str(simulation["noise"].shape))
noise_vol = expand_array_in_mask(simulation["noise"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(noise_vol, 0, 4), fn_noise, vol_meta)
fn_noise = add_prefix(op.join(output_dir, "noise_emp_var.nii"), prefix)
noise_vol = expand_array_in_mask(simulation["noise"].var(0), mask_vol)
write_volume(noise_vol, fn_noise, vol_meta)
if simulation.has_key("noise_var"):
fn_noise_var = add_prefix(op.join(output_dir, "noise_var.nii"), prefix)
logger.info("noise_var flat shape %s", str(simulation["noise_var"].shape))
noise_var_vol = expand_array_in_mask(simulation["noise_var"], mask_vol)
write_volume(noise_var_vol, fn_noise_var, vol_meta)
if simulation.has_key("stim_induced_signal"):
fn_stim_induced = add_prefix(op.join(output_dir, "stim_induced.nii"), prefix)
logger.info("stim_induced flat shape %s", str(simulation["stim_induced_signal"].shape))
stim_induced_vol = expand_array_in_mask(simulation["stim_induced_signal"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key("perf_stim_induced"):
fn_stim_induced = add_prefix(op.join(output_dir, "perf_stim_induced.nii"), prefix)
logger.info("asl_stim_induced flat shape %s", str(simulation["perf_stim_induced"].shape))
stim_induced_vol = expand_array_in_mask(simulation["perf_stim_induced"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
fn_stim_induced = add_prefix(op.join(output_dir, "perf_stim_induced_ct.nii"), prefix)
logger.info("asl_stim_induced flat shape %s", str(simulation["perf_stim_induced"].shape))
dsf = simulation["dsf"]
perf = np.dot(simulation["ctrl_tag_mat"], simulation["perf_stim_induced"][0:-1:dsf])
stim_induced_vol = expand_array_in_mask(perf, mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key("perf_baseline"):
fn = add_prefix(op.join(output_dir, "perf_baseline.nii"), prefix)
pb = np.zeros_like(simulation["bold"]) + simulation["perf_baseline"]
write_volume(expand_array_in_mask(pb[0], mask_vol), fn, vol_meta)
if simulation.has_key("bold_stim_induced"):
fn_stim_induced = add_prefix(op.join(output_dir, "bold_stim_induced.nii"), prefix)
logger.info("asl_stim_induced flat shape %s", str(simulation["bold_stim_induced"].shape))
stim_induced_vol = expand_array_in_mask(simulation["bold_stim_induced"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
m = np.where(mask_vol)
labels_and_mask = mask_vol.copy()[m]
for ic in xrange(simulation["labels"].shape[0]):
if simulation.has_key("condition_defs"):
c_name = simulation["condition_defs"][ic].name
else:
c_name = "cond%d" % ic
fn_labels = add_prefix(op.join(output_dir, "labels_%s.nii" % c_name), prefix)
if simulation.has_key("labels"):
labels_c = simulation["labels"][ic]
labels_and_mask[np.where(labels_c)] = ic + 2
write_volume(expand_array_in_mask(labels_c, mask_vol).astype(np.int32), fn_labels, vol_meta)
elif simulation.has_key("labels_vol"):
labels_c = simulation["labels_vol"][ic]
labels_and_mask[np.where(labels_c[m])] = ic + 2
write_volume(labels_c.astype(np.int32), fn_labels, vol_meta)
if simulation.has_key("nrls"):
nrls_c = simulation["nrls"][ic]
fn = add_prefix(op.join(output_dir, "nrls_%s.nii" % c_name), prefix)
write_volume(expand_array_in_mask(nrls_c, mask_vol), fn, vol_meta)
if simulation.has_key("nrls_session"):
nrls_session_c = simulation["nrls_session"][ic]
fn = add_prefix(op.join(output_dir, "nrls_session_%s.nii" % (c_name)), prefix)
write_volume(expand_array_in_mask(nrls_session_c, mask_vol), fn, vol_meta)
if simulation.has_key("brls"):
brls_c = simulation["brls"][ic]
fn = add_prefix(op.join(output_dir, "brls_%s.nii" % c_name), prefix)
write_volume(expand_array_in_mask(brls_c, mask_vol), fn, vol_meta)
if simulation.has_key("prls"):
prls_c = simulation["prls"][ic]
fn = add_prefix(op.join(output_dir, "prls_%s.nii" % c_name), prefix)
write_volume(expand_array_in_mask(prls_c, mask_vol), fn, vol_meta)
if simulation.has_key("neural_efficacies"):
ne_c = simulation["neural_efficacies"][ic]
fn = add_prefix(op.join(output_dir, "neural_efficacies_%s.nii" % c_name), prefix)
write_volume(expand_array_in_mask(ne_c, mask_vol), fn, vol_meta)
fn_labels_and_mask = add_prefix(op.join(output_dir, "mask_and_labels.nii"), prefix)
write_volume(expand_array_in_mask(labels_and_mask, mask_vol).astype(int), fn_labels_and_mask, vol_meta)
if simulation.has_key("bold_full_vol") or simulation.has_key("bold"):
fn = add_prefix(op.join(output_dir, "bold.nii"), prefix)
if simulation.has_key("bold_full_vol"):
bold4D = simulation["bold_full_vol"]
else:
bold = simulation["bold"]
bold4D = expand_array_in_mask(bold, mask_vol, flat_axis=1)
write_volume(np.rollaxis(bold4D, 0, 4), fn, vol_meta)
def save_time_series(k):
if simulation.has_key(k):
fn_stim_induced = add_prefix(op.join(output_dir, k + ".nii"), prefix)
logger.info("%s flat shape %s", k, str(simulation[k].shape))
vol = expand_array_in_mask(simulation[k], mask_vol, flat_axis=1)
write_volume(np.rollaxis(vol, 0, 4), fn_stim_induced)
save_time_series("flow_induction")
save_time_series("cbv")
save_time_series("hbr")
save_time_series("bold_stim_induced_rescaled")
if simulation.has_key("asl"):
fn = add_prefix(op.join(output_dir, "asl.nii"), prefix)
asl4D = expand_array_in_mask(simulation["asl"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(asl4D, 0, 4), fn, vol_meta)
if simulation.has_key("outliers"):
fn = add_prefix(op.join(output_dir, "outliers.nii"), prefix)
outliers = expand_array_in_mask(simulation["outliers"], mask_vol, flat_axis=1)
write_volume(np.rollaxis(outliers, 0, 4), fn, vol_meta)
if simulation.has_key("hrf_group"):
hrfgroup = simulation["hrf_group"]
nb_vox = mask_vol.size
fn_hrf = add_prefix(op.join(output_dir, "hrf_group.nii"), prefix)
logger.info("hrf group shape %s", str(simulation["hrf_group"].shape))
hrfGd = duplicate_hrf(nb_vox, hrfgroup)
hrfs_vol = expand_array_in_mask(hrfGd, mask_vol, flat_axis=1)
dt = simulation["dt"]
chrfs = xndarray(
hrfs_vol, axes_names=["time"] + MRI3Daxes, axes_domains={"time": np.arange(hrfs_vol.shape[0]) * dt}
)
chrfs.save(fn_hrf, vol_meta)
if bold_3D_vols_dir is not None:
assert op.exists(bold_3D_vols_dir)
for iscan, bscan in enumerate(bold4D):
fnout = add_prefix("bold_%06d.nii" % (iscan), prefix)
write_volume(bscan, op.join(bold_3D_vols_dir, fnout), vol_meta)
def simulation_save_vol_outputs(simulation, output_dir, bold_3D_vols_dir=None,
simulation_graph_output=None, prefix=None,
vol_meta=None):
""" simulation_graph_output : None, 'simple', 'thumbnails' #TODO
"""
if simulation.has_key('paradigm'):
fn = add_prefix(op.join(output_dir, 'paradigm.csv'), prefix)
simulation['paradigm'].save_csv(fn)
# Save all volumes in nifti format:
if simulation.has_key('labels_vol'):
mask_vol = np.ones_like(simulation['labels_vol'][0])
elif simulation.has_key('mask'):
mask_vol = simulation.get('mask', None)
elif simulation.has_key('labels'):
mask_vol = np.ones_like(simulation['labels'][0])
else:
raise Exception('Dunno where to get mask')
logger.info('Vol mask of shape %s', str(mask_vol.shape))
fn_mask = add_prefix(op.join(output_dir, 'mask.nii'), prefix)
write_volume(mask_vol.astype(np.int32), fn_mask, vol_meta)
if simulation.has_key('hrf_territories'):
fn_h_territories = add_prefix(op.join(output_dir, 'hrf_territories.nii'),
prefix)
ht = expand_array_in_mask(simulation['hrf_territories'] + 1, mask_vol)
write_volume(ht, fn_h_territories, vol_meta)
if simulation.has_key('hrf'):
from pyhrf.ndarray import MRI3Daxes
fn_hrf = add_prefix(op.join(output_dir, 'hrf.nii'), prefix)
logger.info('hrf flat shape %s', str(simulation['hrf'].shape))
if simulation['hrf'].ndim == 1:
hrf = (np.ones(mask_vol.size) * simulation['hrf'][:, np.newaxis])
else:
hrf = simulation['hrf']
hrfs_vol = expand_array_in_mask(hrf, mask_vol, flat_axis=1)
dt = simulation['dt']
chrfs = xndarray(hrfs_vol, axes_names=['time', ] + MRI3Daxes,
axes_domains={'time': np.arange(hrfs_vol.shape[0]) * dt})
chrfs.save(fn_hrf, vol_meta)
ttp_vol = hrfs_vol.argmax(0)
fn_ttp = add_prefix(op.join(output_dir, 'ttp.nii'), prefix)
write_volume(ttp_vol, fn_ttp, vol_meta)
if simulation.has_key('brf'):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, 'brf.nii'), prefix)
logger.info('brf flat shape %s', str(simulation['brf'].shape))
brfs_vol = expand_array_in_mask(
simulation['brf'], mask_vol, flat_axis=1)
dt = simulation['dt']
cbrfs = xndarray(brfs_vol, axes_names=['time', ] + MRI3Daxes,
axes_domains={'time': np.arange(brfs_vol.shape[0]) * dt})
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key('prf'):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, 'prf.nii'), prefix)
logger.info('prf flat shape %s', str(simulation['prf'].shape))
brfs_vol = expand_array_in_mask(
simulation['prf'], mask_vol, flat_axis=1)
dt = simulation['dt']
cbrfs = xndarray(brfs_vol, axes_names=['time', ] + MRI3Daxes,
axes_domains={'time': np.arange(brfs_vol.shape[0]) * dt})
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key('drift'):
fn_drift = add_prefix(op.join(output_dir, 'drift.nii'), prefix)
logger.info('drift flat shape %s', str(simulation['drift'].shape))
drift_vol = expand_array_in_mask(simulation['drift'], mask_vol,
flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key('drift_coeffs'):
fn_drift = add_prefix(op.join(output_dir, 'drift_coeffs.nii'), prefix)
logger.info(
'drift flat shape %s', str(simulation['drift_coeffs'].shape))
drift_vol = expand_array_in_mask(simulation['drift'], mask_vol,
flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key('noise'):
fn_noise = add_prefix(op.join(output_dir, 'noise.nii'), prefix)
logger.info('noise flat shape %s', str(simulation['noise'].shape))
noise_vol = expand_array_in_mask(simulation['noise'], mask_vol,
flat_axis=1)
write_volume(np.rollaxis(noise_vol, 0, 4), fn_noise, vol_meta)
fn_noise = add_prefix(op.join(output_dir, 'noise_emp_var.nii'), prefix)
noise_vol = expand_array_in_mask(simulation['noise'].var(0), mask_vol)
write_volume(noise_vol, fn_noise, vol_meta)
if simulation.has_key('noise_var'):
fn_noise_var = add_prefix(op.join(output_dir, 'noise_var.nii'), prefix)
logger.info(
'noise_var flat shape %s', str(simulation['noise_var'].shape))
noise_var_vol = expand_array_in_mask(simulation['noise_var'], mask_vol)
write_volume(noise_var_vol, fn_noise_var, vol_meta)
if simulation.has_key('stim_induced_signal'):
fn_stim_induced = add_prefix(op.join(output_dir, 'stim_induced.nii'),
prefix)
logger.info('stim_induced flat shape %s',
str(simulation['stim_induced_signal'].shape))
stim_induced_vol = expand_array_in_mask(simulation['stim_induced_signal'],
mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key('perf_stim_induced'):
fn_stim_induced = add_prefix(op.join(output_dir, 'perf_stim_induced.nii'),
prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['perf_stim_induced'].shape))
stim_induced_vol = expand_array_in_mask(simulation['perf_stim_induced'],
mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
fn_stim_induced = add_prefix(op.join(output_dir,
'perf_stim_induced_ct.nii'),
prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['perf_stim_induced'].shape))
dsf = simulation['dsf']
perf = np.dot(simulation['ctrl_tag_mat'],
simulation['perf_stim_induced'][0:-1:dsf])
stim_induced_vol = expand_array_in_mask(perf, mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key('perf_baseline'):
fn = add_prefix(op.join(output_dir, 'perf_baseline.nii'), prefix)
pb = np.zeros_like(simulation['bold']) + simulation['perf_baseline']
write_volume(expand_array_in_mask(pb[0], mask_vol), fn, vol_meta)
if simulation.has_key('bold_stim_induced'):
fn_stim_induced = add_prefix(op.join(output_dir, 'bold_stim_induced.nii'),
prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['bold_stim_induced'].shape))
stim_induced_vol = expand_array_in_mask(simulation['bold_stim_induced'],
mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
m = np.where(mask_vol)
labels_and_mask = mask_vol.copy()[m]
for ic in xrange(simulation['labels'].shape[0]):
if simulation.has_key('condition_defs'):
c_name = simulation['condition_defs'][ic].name
else:
c_name = 'cond%d' % ic
fn_labels = add_prefix(op.join(output_dir, 'labels_%s.nii' % c_name),
prefix)
if simulation.has_key('labels'):
labels_c = simulation['labels'][ic]
labels_and_mask[np.where(labels_c)] = ic + 2
write_volume(expand_array_in_mask(labels_c, mask_vol).astype(np.int32),
fn_labels, vol_meta)
elif simulation.has_key('labels_vol'):
labels_c = simulation['labels_vol'][ic]
labels_and_mask[np.where(labels_c[m])] = ic + 2
write_volume(labels_c.astype(np.int32), fn_labels, vol_meta)
if simulation.has_key('nrls'):
nrls_c = simulation['nrls'][ic]
fn = add_prefix(
op.join(output_dir, 'nrls_%s.nii' % c_name), prefix)
write_volume(expand_array_in_mask(nrls_c, mask_vol), fn, vol_meta)
if simulation.has_key('nrls_session'):
nrls_session_c = simulation['nrls_session'][ic]
fn = add_prefix(op.join(output_dir, 'nrls_session_%s.nii'
% (c_name)), prefix)
write_volume(expand_array_in_mask(nrls_session_c, mask_vol),
fn, vol_meta)
if simulation.has_key('brls'):
brls_c = simulation['brls'][ic]
fn = add_prefix(
op.join(output_dir, 'brls_%s.nii' % c_name), prefix)
write_volume(expand_array_in_mask(brls_c, mask_vol), fn, vol_meta)
if simulation.has_key('prls'):
prls_c = simulation['prls'][ic]
fn = add_prefix(
op.join(output_dir, 'prls_%s.nii' % c_name), prefix)
write_volume(expand_array_in_mask(prls_c, mask_vol), fn, vol_meta)
if simulation.has_key('neural_efficacies'):
ne_c = simulation['neural_efficacies'][ic]
fn = add_prefix(op.join(output_dir, 'neural_efficacies_%s.nii'
% c_name), prefix)
write_volume(expand_array_in_mask(ne_c, mask_vol), fn, vol_meta)
fn_labels_and_mask = add_prefix(op.join(output_dir, 'mask_and_labels.nii'),
prefix)
write_volume(expand_array_in_mask(labels_and_mask, mask_vol).astype(int),
fn_labels_and_mask, vol_meta)
if simulation.has_key('bold_full_vol') or simulation.has_key('bold'):
fn = add_prefix(op.join(output_dir, 'bold.nii'), prefix)
if simulation.has_key('bold_full_vol'):
bold4D = simulation['bold_full_vol']
else:
bold = simulation['bold']
bold4D = expand_array_in_mask(bold, mask_vol, flat_axis=1)
write_volume(np.rollaxis(bold4D, 0, 4), fn, vol_meta)
def save_time_series(k):
if simulation.has_key(k):
fn_stim_induced = add_prefix(
op.join(output_dir, k + '.nii'), prefix)
logger.info('%s flat shape %s', k, str(simulation[k].shape))
vol = expand_array_in_mask(simulation[k], mask_vol, flat_axis=1)
write_volume(np.rollaxis(vol, 0, 4), fn_stim_induced)
save_time_series('flow_induction')
save_time_series('cbv')
save_time_series('hbr')
save_time_series('bold_stim_induced_rescaled')
if simulation.has_key('asl'):
fn = add_prefix(op.join(output_dir, 'asl.nii'), prefix)
asl4D = expand_array_in_mask(simulation['asl'], mask_vol, flat_axis=1)
write_volume(np.rollaxis(asl4D, 0, 4), fn, vol_meta)
if simulation.has_key('outliers'):
fn = add_prefix(op.join(output_dir, 'outliers.nii'), prefix)
outliers = expand_array_in_mask(simulation['outliers'], mask_vol,
flat_axis=1)
write_volume(np.rollaxis(outliers, 0, 4), fn, vol_meta)
if simulation.has_key('hrf_group'):
hrfgroup = simulation['hrf_group']
nb_vox = mask_vol.size
fn_hrf = add_prefix(op.join(output_dir, 'hrf_group.nii'), prefix)
logger.info('hrf group shape %s', str(simulation['hrf_group'].shape))
hrfGd = duplicate_hrf(nb_vox, hrfgroup)
hrfs_vol = expand_array_in_mask(hrfGd, mask_vol, flat_axis=1)
dt = simulation['dt']
chrfs = xndarray(hrfs_vol, axes_names=['time', ] + MRI3Daxes,
axes_domains={'time': np.arange(hrfs_vol.shape[0]) * dt})
chrfs.save(fn_hrf, vol_meta)
if bold_3D_vols_dir is not None:
assert op.exists(bold_3D_vols_dir)
for iscan, bscan in enumerate(bold4D):
fnout = add_prefix('bold_%06d.nii' % (iscan), prefix)
write_volume(bscan, op.join(bold_3D_vols_dir, fnout), vol_meta)
def simulation_save_vol_outputs(simulation,
output_dir,
bold_3D_vols_dir=None,
simulation_graph_output=None,
prefix=None,
vol_meta=None):
""" simulation_graph_output : None, 'simple', 'thumbnails' #TODO
"""
if simulation.has_key('paradigm'):
fn = add_prefix(op.join(output_dir, 'paradigm.csv'), prefix)
simulation['paradigm'].save_csv(fn)
# Save all volumes in nifti format:
if simulation.has_key('labels_vol'):
mask_vol = np.ones_like(simulation['labels_vol'][0])
elif simulation.has_key('mask'):
mask_vol = simulation.get('mask', None)
elif simulation.has_key('labels'):
mask_vol = np.ones_like(simulation['labels'][0])
else:
raise Exception('Dunno where to get mask')
logger.info('Vol mask of shape %s', str(mask_vol.shape))
fn_mask = add_prefix(op.join(output_dir, 'mask.nii'), prefix)
write_volume(mask_vol.astype(np.int32), fn_mask, vol_meta)
if simulation.has_key('hrf_territories'):
fn_h_territories = add_prefix(
op.join(output_dir, 'hrf_territories.nii'), prefix)
ht = expand_array_in_mask(simulation['hrf_territories'] + 1, mask_vol)
write_volume(ht, fn_h_territories, vol_meta)
if simulation.has_key('hrf'):
from pyhrf.ndarray import MRI3Daxes
fn_hrf = add_prefix(op.join(output_dir, 'hrf.nii'), prefix)
logger.info('hrf flat shape %s', str(simulation['hrf'].shape))
if simulation['hrf'].ndim == 1:
hrf = (np.ones(mask_vol.size) * simulation['hrf'][:, np.newaxis])
else:
hrf = simulation['hrf']
hrfs_vol = expand_array_in_mask(hrf, mask_vol, flat_axis=1)
dt = simulation['dt']
chrfs = xndarray(
hrfs_vol,
axes_names=[
'time',
] + MRI3Daxes,
axes_domains={'time': np.arange(hrfs_vol.shape[0]) * dt})
chrfs.save(fn_hrf, vol_meta)
ttp_vol = hrfs_vol.argmax(0)
fn_ttp = add_prefix(op.join(output_dir, 'ttp.nii'), prefix)
write_volume(ttp_vol, fn_ttp, vol_meta)
if simulation.has_key('brf'):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, 'brf.nii'), prefix)
logger.info('brf flat shape %s', str(simulation['brf'].shape))
brfs_vol = expand_array_in_mask(simulation['brf'],
mask_vol,
flat_axis=1)
dt = simulation['dt']
cbrfs = xndarray(
brfs_vol,
axes_names=[
'time',
] + MRI3Daxes,
axes_domains={'time': np.arange(brfs_vol.shape[0]) * dt})
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key('prf'):
from pyhrf.ndarray import MRI3Daxes
fn_brf = add_prefix(op.join(output_dir, 'prf.nii'), prefix)
logger.info('prf flat shape %s', str(simulation['prf'].shape))
brfs_vol = expand_array_in_mask(simulation['prf'],
mask_vol,
flat_axis=1)
dt = simulation['dt']
cbrfs = xndarray(
brfs_vol,
axes_names=[
'time',
] + MRI3Daxes,
axes_domains={'time': np.arange(brfs_vol.shape[0]) * dt})
cbrfs.save(fn_brf, vol_meta)
if simulation.has_key('drift'):
fn_drift = add_prefix(op.join(output_dir, 'drift.nii'), prefix)
logger.info('drift flat shape %s', str(simulation['drift'].shape))
drift_vol = expand_array_in_mask(simulation['drift'],
mask_vol,
flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key('drift_coeffs'):
fn_drift = add_prefix(op.join(output_dir, 'drift_coeffs.nii'), prefix)
logger.info('drift flat shape %s',
str(simulation['drift_coeffs'].shape))
drift_vol = expand_array_in_mask(simulation['drift'],
mask_vol,
flat_axis=1)
write_volume(np.rollaxis(drift_vol, 0, 4), fn_drift)
if simulation.has_key('noise'):
fn_noise = add_prefix(op.join(output_dir, 'noise.nii'), prefix)
logger.info('noise flat shape %s', str(simulation['noise'].shape))
noise_vol = expand_array_in_mask(simulation['noise'],
mask_vol,
flat_axis=1)
write_volume(np.rollaxis(noise_vol, 0, 4), fn_noise, vol_meta)
fn_noise = add_prefix(op.join(output_dir, 'noise_emp_var.nii'), prefix)
noise_vol = expand_array_in_mask(simulation['noise'].var(0), mask_vol)
write_volume(noise_vol, fn_noise, vol_meta)
if simulation.has_key('noise_var'):
fn_noise_var = add_prefix(op.join(output_dir, 'noise_var.nii'), prefix)
logger.info('noise_var flat shape %s',
str(simulation['noise_var'].shape))
noise_var_vol = expand_array_in_mask(simulation['noise_var'], mask_vol)
write_volume(noise_var_vol, fn_noise_var, vol_meta)
if simulation.has_key('stim_induced_signal'):
fn_stim_induced = add_prefix(op.join(output_dir, 'stim_induced.nii'),
prefix)
logger.info('stim_induced flat shape %s',
str(simulation['stim_induced_signal'].shape))
stim_induced_vol = expand_array_in_mask(
simulation['stim_induced_signal'], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key('perf_stim_induced'):
fn_stim_induced = add_prefix(
op.join(output_dir, 'perf_stim_induced.nii'), prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['perf_stim_induced'].shape))
stim_induced_vol = expand_array_in_mask(
simulation['perf_stim_induced'], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
fn_stim_induced = add_prefix(
op.join(output_dir, 'perf_stim_induced_ct.nii'), prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['perf_stim_induced'].shape))
dsf = simulation['dsf']
perf = np.dot(simulation['ctrl_tag_mat'],
simulation['perf_stim_induced'][0:-1:dsf])
stim_induced_vol = expand_array_in_mask(perf, mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
if simulation.has_key('perf_baseline'):
fn = add_prefix(op.join(output_dir, 'perf_baseline.nii'), prefix)
pb = np.zeros_like(simulation['bold']) + simulation['perf_baseline']
write_volume(expand_array_in_mask(pb[0], mask_vol), fn, vol_meta)
if simulation.has_key('bold_stim_induced'):
fn_stim_induced = add_prefix(
op.join(output_dir, 'bold_stim_induced.nii'), prefix)
logger.info('asl_stim_induced flat shape %s',
str(simulation['bold_stim_induced'].shape))
stim_induced_vol = expand_array_in_mask(
simulation['bold_stim_induced'], mask_vol, flat_axis=1)
write_volume(np.rollaxis(stim_induced_vol, 0, 4), fn_stim_induced)
m = np.where(mask_vol)
labels_and_mask = mask_vol.copy()[m]
for ic in xrange(simulation['labels'].shape[0]):
if simulation.has_key('condition_defs'):
c_name = simulation['condition_defs'][ic].name
else:
c_name = 'cond%d' % ic
fn_labels = add_prefix(op.join(output_dir, 'labels_%s.nii' % c_name),
prefix)
if simulation.has_key('labels'):
labels_c = simulation['labels'][ic]
labels_and_mask[np.where(labels_c)] = ic + 2
write_volume(
expand_array_in_mask(labels_c, mask_vol).astype(np.int32),
fn_labels, vol_meta)
elif simulation.has_key('labels_vol'):
labels_c = simulation['labels_vol'][ic]
labels_and_mask[np.where(labels_c[m])] = ic + 2
write_volume(labels_c.astype(np.int32), fn_labels, vol_meta)
if simulation.has_key('nrls'):
nrls_c = simulation['nrls'][ic]
fn = add_prefix(op.join(output_dir, 'nrls_%s.nii' % c_name),
prefix)
write_volume(expand_array_in_mask(nrls_c, mask_vol), fn, vol_meta)
if simulation.has_key('nrls_session'):
nrls_session_c = simulation['nrls_session'][ic]
fn = add_prefix(
op.join(output_dir, 'nrls_session_%s.nii' % (c_name)), prefix)
write_volume(expand_array_in_mask(nrls_session_c, mask_vol), fn,
vol_meta)
if simulation.has_key('brls'):
brls_c = simulation['brls'][ic]
fn = add_prefix(op.join(output_dir, 'brls_%s.nii' % c_name),
prefix)
write_volume(expand_array_in_mask(brls_c, mask_vol), fn, vol_meta)
if simulation.has_key('prls'):
prls_c = simulation['prls'][ic]
fn = add_prefix(op.join(output_dir, 'prls_%s.nii' % c_name),
prefix)
write_volume(expand_array_in_mask(prls_c, mask_vol), fn, vol_meta)
if simulation.has_key('neural_efficacies'):
ne_c = simulation['neural_efficacies'][ic]
fn = add_prefix(
op.join(output_dir, 'neural_efficacies_%s.nii' % c_name),
prefix)
write_volume(expand_array_in_mask(ne_c, mask_vol), fn, vol_meta)
fn_labels_and_mask = add_prefix(op.join(output_dir, 'mask_and_labels.nii'),
prefix)
write_volume(
expand_array_in_mask(labels_and_mask, mask_vol).astype(int),
fn_labels_and_mask, vol_meta)
if simulation.has_key('bold_full_vol') or simulation.has_key('bold'):
fn = add_prefix(op.join(output_dir, 'bold.nii'), prefix)
if simulation.has_key('bold_full_vol'):
bold4D = simulation['bold_full_vol']
else:
bold = simulation['bold']
bold4D = expand_array_in_mask(bold, mask_vol, flat_axis=1)
write_volume(np.rollaxis(bold4D, 0, 4), fn, vol_meta)
def save_time_series(k):
if simulation.has_key(k):
fn_stim_induced = add_prefix(op.join(output_dir, k + '.nii'),
prefix)
logger.info('%s flat shape %s', k, str(simulation[k].shape))
vol = expand_array_in_mask(simulation[k], mask_vol, flat_axis=1)
write_volume(np.rollaxis(vol, 0, 4), fn_stim_induced)
save_time_series('flow_induction')
save_time_series('cbv')
save_time_series('hbr')
save_time_series('bold_stim_induced_rescaled')
if simulation.has_key('asl'):
fn = add_prefix(op.join(output_dir, 'asl.nii'), prefix)
asl4D = expand_array_in_mask(simulation['asl'], mask_vol, flat_axis=1)
write_volume(np.rollaxis(asl4D, 0, 4), fn, vol_meta)
if simulation.has_key('outliers'):
fn = add_prefix(op.join(output_dir, 'outliers.nii'), prefix)
outliers = expand_array_in_mask(simulation['outliers'],
mask_vol,
flat_axis=1)
write_volume(np.rollaxis(outliers, 0, 4), fn, vol_meta)
if simulation.has_key('hrf_group'):
hrfgroup = simulation['hrf_group']
nb_vox = mask_vol.size
fn_hrf = add_prefix(op.join(output_dir, 'hrf_group.nii'), prefix)
logger.info('hrf group shape %s', str(simulation['hrf_group'].shape))
hrfGd = duplicate_hrf(nb_vox, hrfgroup)
hrfs_vol = expand_array_in_mask(hrfGd, mask_vol, flat_axis=1)
dt = simulation['dt']
chrfs = xndarray(
hrfs_vol,
axes_names=[
'time',
] + MRI3Daxes,
axes_domains={'time': np.arange(hrfs_vol.shape[0]) * dt})
chrfs.save(fn_hrf, vol_meta)
if bold_3D_vols_dir is not None:
assert op.exists(bold_3D_vols_dir)
for iscan, bscan in enumerate(bold4D):
fnout = add_prefix('bold_%06d.nii' % (iscan), prefix)
write_volume(bscan, op.join(bold_3D_vols_dir, fnout), vol_meta)
def glm_nipy_from_files(bold_file, tr, paradigm_csv_file, output_dir,
mask_file, session=0, contrasts=None,
con_test_baseline=0.0,
hrf_model='Canonical',
drift_model='Cosine', hfcut=128,
residuals_model='spherical', fit_method='ols',
fir_delays=[0]):
"""
#TODO: handle surface data
hrf_model : Canonical | Canonical with Derivative | FIR
"""
fdata = FmriData.from_vol_files(mask_file, paradigm_csv_file,
[bold_file], tr)
g, dm, cons = glm_nipy(fdata, contrasts=contrasts, hrf_model=hrf_model,
hfcut=hfcut, drift_model=drift_model,
residuals_model=residuals_model,
fit_method=fit_method, fir_delays=fir_delays)
ns, nr = dm.matrix.shape
cdesign_matrix = xndarray(dm.matrix, axes_names=['time','regressor'],
axes_domains={'time':np.arange(ns)*tr,
'regressor':dm.names})
cdesign_matrix.save(op.join(output_dir, 'design_matrix.nii'))
beta_files = []
beta_values = dict.fromkeys(dm.names)
beta_vars = dict.fromkeys(dm.names)
beta_vars_voxels = dict.fromkeys(dm.names)
for ib, bname in enumerate(dm.names):
#beta values
beta_vol = expand_array_in_mask(g.beta[ib], fdata.roiMask>0)
beta_fn = op.join(output_dir, 'beta_%s.nii' %bname)
write_volume(beta_vol, beta_fn, fdata.meta_obj)
beta_files.append(beta_fn)
beta_values[bname] = beta_vol
#normalized variance of betas
beta_vars[bname] = sp.diag(g.nvbeta)[ib] #variance: diag of cov matrix
#sig2 = g.s2 #ResMS
var_cond = sp.diag(g.nvbeta)[ib]*g.s2 #variance for all voxels, condition ib
beta_vars_voxels[bname] = var_cond
#beta_var_fn = op.join(output_dir, 'var_beta_%s.nii' %bname)
#write_volume(beta_var, beta_var_fn, fdata.meta_obj)
#beta_var_files.append(beta_var_fn)
if cons is not None:
con_files = []
pval_files = []
for cname, con in cons.iteritems():
con_vol = expand_array_in_mask(con.effect, fdata.roiMask>0)
con_fn = op.join(output_dir, 'con_effect_%s.nii' %cname)
write_volume(con_vol, con_fn, fdata.meta_obj)
con_files.append(con_fn)
pval_vol = expand_array_in_mask(con.pvalue(con_test_baseline),
fdata.roiMask>0)
pval_fn = op.join(output_dir, 'con_pvalue_%s.nii' %cname)
write_volume(pval_vol, pval_fn, fdata.meta_obj)
pval_files.append(pval_fn)
else:
con_files = None
pval_files = None
dof = g.dof
#if do_ppm:
#for
#TODO: FIR stuffs
return beta_files, beta_values, beta_vars_voxels, dof#, con_files, pval_files
# ax.set_title('Design matrix')
# plt.savefig(op.join(output_dir, 'design_matrix.png'))
# design_matrix.save(...)
# GLM fit
my_glm = nipy.labs.glm.glm()
pyhrf.verbose(1, 'Fit GLM - method: %s, residual model: %s' \
%(fit_method,residuals_model))
glm = my_glm.fit(Y.T, design_matrix.matrix, method=fit_method,
model=residuals_model)
# Beta outputs
beta_files = []
affine = fmri_image.get_affine()
for ib, bname in enumerate(design_matrix.names):
beta_vol = expand_array_in_mask(my_glm.beta[ib], mask_array)
beta_image = Nifti1Image(beta_vol, affine)
beta_file = op.join(output_dir, 'beta_%s.nii' %bname)
save(beta_image, beta_file)
beta_files.append(beta_file)
from nipy.modalities.fmri.hemodynamic_models import _regressor_names
from pyhrf.ndarray import MRI3Daxes
if hrf_model == 'FIR':
drnames = design_matrix.names
nvox = mask_array.sum()
print 'nvox:', nvox
for cn in set(paradigm.con_id):
fir_rnames = _regressor_names(cn, 'FIR', fir_delays)
#lfir = len(fir_rnames)
def parcellation_for_jde(fmri_data,
avg_parcel_size=250,
output_dir=None,
method='gkm',
glm_drift='Cosine',
glm_hfcut=128):
"""
method: gkm, ward, ward_and_gkm
"""
if output_dir is None:
output_dir = tempfile.mkdtemp(prefix='pyhrf_JDE_parcellation_GLM',
dir=pyhrf.cfg['global']['tmp_path'])
glm_output_dir = op.join(output_dir, 'GLM_for_parcellation')
if not op.exists(glm_output_dir):
os.makedirs(glm_output_dir)
logger.info('GLM for parcellation')
g, dm, cons = glm_nipy(fmri_data, drift_model=glm_drift, hfcut=glm_hfcut)
pval_files = []
if cons is not None:
func_data = [('con_pval_%s' % cname, con.pvalue())
for cname, con in cons.iteritems()]
else:
reg_cst_drift = re.compile(".*constant.*|.*drift.*")
func_data = [('beta_%s' % reg_name, g.beta[ir])
for ir, reg_name in enumerate(dm.names)
if not reg_cst_drift.match(reg_name)]
for name, data in func_data:
val_vol = expand_array_in_mask(data, fmri_data.roiMask > 0)
val_fn = op.join(glm_output_dir, '%s.nii' % name)
write_volume(val_vol, val_fn, fmri_data.meta_obj)
pval_files.append(val_fn)
mask_file = op.join(glm_output_dir, 'mask.nii')
write_volume(fmri_data.roiMask > 0, mask_file, fmri_data.meta_obj)
nvox = fmri_data.get_nb_vox_in_mask()
nparcels = round_nb_parcels(nvox * 1. / avg_parcel_size)
logger.info('Parcellation from GLM outputs, method: %s, nb parcels: %d',
method, nparcels)
if fmri_data.data_type == 'volume':
parcellation_file = op.join(
output_dir, 'parcellation_%s_np%d.nii' % (method, nparcels))
make_parcellation_from_files(pval_files, mask_file, parcellation_file,
nparcels, method)
parcellation, _ = read_volume(parcellation_file)
else:
mesh_file = fmri_data.data_files[-1]
parcellation_file = op.join(
output_dir, 'parcellation_%s_np%d.gii' % (method, nparcels))
make_parcellation_surf_from_files(pval_files,
mesh_file,
parcellation_file,
nparcels,
method,
verbose=1)
parcellation, _ = read_texture(parcellation_file)
logger.info(parcellation_report(parcellation))
return parcellation, parcellation_file
def glm_nipy_from_files(bold_file,
tr,
paradigm_csv_file,
output_dir,
mask_file,
session=0,
contrasts=None,
con_test_baseline=0.0,
hrf_model='Canonical',
drift_model='Cosine',
hfcut=128,
residuals_model='spherical',
fit_method='ols',
fir_delays=[0]):
"""
#TODO: handle surface data
hrf_model : Canonical | Canonical with Derivative | FIR
"""
fdata = FmriData.from_vol_files(mask_file, paradigm_csv_file, [bold_file],
tr)
g, dm, cons = glm_nipy(fdata,
contrasts=contrasts,
hrf_model=hrf_model,
hfcut=hfcut,
drift_model=drift_model,
residuals_model=residuals_model,
fit_method=fit_method,
fir_delays=fir_delays)
ns, nr = dm.matrix.shape
cdesign_matrix = xndarray(dm.matrix,
axes_names=['time', 'regressor'],
axes_domains={
'time': np.arange(ns) * tr,
'regressor': dm.names
})
cdesign_matrix.save(op.join(output_dir, 'design_matrix.nii'))
beta_files = []
beta_values = dict.fromkeys(dm.names)
beta_vars = dict.fromkeys(dm.names)
beta_vars_voxels = dict.fromkeys(dm.names)
for ib, bname in enumerate(dm.names):
# beta values
beta_vol = expand_array_in_mask(g.beta[ib], fdata.roiMask > 0)
beta_fn = op.join(output_dir, 'beta_%s.nii' % bname)
write_volume(beta_vol, beta_fn, fdata.meta_obj)
beta_files.append(beta_fn)
beta_values[bname] = beta_vol
# normalized variance of betas
# variance: diag of cov matrix
beta_vars[bname] = sp.diag(g.nvbeta)[ib]
# sig2 = g.s2 #ResMS
# variance for all voxels, condition ib
var_cond = sp.diag(g.nvbeta)[ib] * g.s2
beta_vars_voxels[bname] = var_cond
#beta_var_fn = op.join(output_dir, 'var_beta_%s.nii' %bname)
#write_volume(beta_var, beta_var_fn, fdata.meta_obj)
# beta_var_files.append(beta_var_fn)
if cons is not None:
con_files = []
pval_files = []
for cname, con in cons.iteritems():
con_vol = expand_array_in_mask(con.effect, fdata.roiMask > 0)
con_fn = op.join(output_dir, 'con_effect_%s.nii' % cname)
write_volume(con_vol, con_fn, fdata.meta_obj)
con_files.append(con_fn)
pval_vol = expand_array_in_mask(con.pvalue(con_test_baseline),
fdata.roiMask > 0)
pval_fn = op.join(output_dir, 'con_pvalue_%s.nii' % cname)
write_volume(pval_vol, pval_fn, fdata.meta_obj)
pval_files.append(pval_fn)
else:
con_files = None
pval_files = None
dof = g.dof
# if do_ppm:
# for
# TODO: FIR stuffs
# , con_files, pval_files
return beta_files, beta_values, beta_vars_voxels, dof
