def test_readwritedata():
img = gi.read(DATA_FILE2)
with InTemporaryDirectory():
gi.write(img, "test.gii")
img2 = gi.read("test.gii")
assert_equal(img.numDA, img2.numDA)
assert_array_almost_equal(img.darrays[0].data, img2.darrays[0].data)
def load_texture(path):
"""Return an array from texture data stored in a gifti file
Parameters
----------
path string or list of strings
path of the texture files
Returns
-------
data array of shape (nnode) or (nnode, len(path))
the corresponding data
"""
from nibabel.gifti import read
# use alternative libraries than nibabel if necessary
if hasattr(path, '__iter__'):
tex_data = []
for f in path:
ftex = read(f).getArraysFromIntent('NIFTI_INTENT_TIME_SERIES')
tex = np.array([f.data for f in ftex])
tex_data.append(tex)
tex_data = np.array(tex_data)
if len(tex_data.shape) > 2:
tex_data = np.squeeze(tex_data)
else:
tex_ = read(path)
tex_data = np.array([darray.data for darray in tex_.darrays])
return tex_data
def check_surf_mesh(self, index):
from nilearn._utils.compat import _basestring
import nibabel
# if input is a filename, try to load it
surf_mesh = self.meshes[index]
if isinstance(surf_mesh, _basestring):
if (surf_mesh.endswith('orig') or surf_mesh.endswith('pial') or
surf_mesh.endswith('white') or surf_mesh.endswith('sphere') or
surf_mesh.endswith('inflated')):
coords, faces = nibabel.freesurfer.io.read_geometry(surf_mesh)
elif surf_mesh.endswith('gii'):
coords, faces = gifti.read(surf_mesh).darrays[0].data, \
gifti.read(surf_mesh).darrays[1].data
else:
raise ValueError('Format of mesh file not recognized.')
# if a dictionary is given, check it contains entries for coords and faces
elif isinstance(surf_mesh, dict):
if ('faces' in surf_mesh and 'coords' in surf_mesh):
coords, faces = surf_mesh['coords'], surf_mesh['faces']
else:
raise ValueError('If surf_mesh is given as a dictionary it must '
'contain items with keys "coords" and "faces"')
else:
raise ValueError('surf_mesh must be a either filename or a dictionary '
'containing items with keys "coords" and "faces"')
return coords, faces
def load_conte_mesh(conte_atlas, inflation):
""" Load conte69 mesh: load midthickness nomatter what and then other """
l_atlas = os.path.join(conte_atlas, 'Conte69.L.{}.32k_fs_LR.surf.gii')
r_atlas = l_atlas.replace('Conte69.L.', 'Conte69.R.')
l_surf = gifti.read(l_atlas.format('midthickness'))
verts_L_data, faces_L_data = l_surf.darrays[0].data, l_surf.darrays[1].data
r_surf = gifti.read(r_atlas.format('midthickness'))
verts_R_data, faces_R_data = r_surf.darrays[0].data, r_surf.darrays[1].data
if inflation != 'low':
if inflation == 'medium':
inf = 'inflated'
elif inflation == 'high':
inf = 'very_inflated'
l_surf2 = gifti.read(l_atlas.format(inf))
verts_L_display = l_surf2.darrays[0].data
faces_L_display = l_surf2.darrays[1].data
r_surf2 = gifti.read(r_atlas.format(inf))
verts_R_display = r_surf2.darrays[0].data
faces_R_display = r_surf2.darrays[1].data
else:
verts_L_display = verts_L_data.copy()
verts_R_display = verts_R_data.copy()
faces_L_display = faces_L_data.copy()
faces_R_display = faces_R_data.copy()
return (verts_L_data, faces_L_data, verts_R_data, faces_R_data,
verts_L_display, verts_R_display, faces_L_display, faces_R_display)
def check_surf_mesh(self, index):
from nilearn._utils.compat import _basestring
import nibabel
# if input is a filename, try to load it
surf_mesh = self.meshes[index]
if isinstance(surf_mesh, _basestring):
if (surf_mesh.endswith('orig') or surf_mesh.endswith('pial')
or surf_mesh.endswith('white')
or surf_mesh.endswith('sphere')
or surf_mesh.endswith('inflated')):
coords, faces = nibabel.freesurfer.io.read_geometry(surf_mesh)
elif surf_mesh.endswith('gii'):
coords, faces = gifti.read(surf_mesh).darrays[0].data, \
gifti.read(surf_mesh).darrays[1].data
else:
raise ValueError('Format of mesh file not recognized.')
# if a dictionary is given, check it contains entries for coords and faces
elif isinstance(surf_mesh, dict):
if ('faces' in surf_mesh and 'coords' in surf_mesh):
coords, faces = surf_mesh['coords'], surf_mesh['faces']
else:
raise ValueError(
'If surf_mesh is given as a dictionary it must '
'contain items with keys "coords" and "faces"')
else:
raise ValueError(
'surf_mesh must be a either filename or a dictionary '
'containing items with keys "coords" and "faces"')
return coords, faces
def test_readwritedata():
img = gi.read(DATA_FILE2)
newp = pjoin(tempfile.gettempdir(), 'test.gii')
gi.write(img, newp)
img2 = gi.read(newp)
assert_equal(img.numDA, img2.numDA)
assert_array_almost_equal(img.darrays[0].data, img2.darrays[0].data)
def test_readwritedata():
img = gi.read(DATA_FILE2)
newp = pjoin(tempfile.gettempdir(), "test.gii")
gi.write(img, newp)
img2 = gi.read(newp)
assert_equal(img.numDA, img2.numDA)
assert_array_almost_equal(img.darrays[0].data, img2.darrays[0].data)
def test_read_ordering():
# DATA_FILE1 has an expected darray[0].data shape of (3,3). However if we
# read another image first (DATA_FILE2) then the shape is wrong
# Read an image
img2 = gi.read(DATA_FILE2)
assert_equal(img2.darrays[0].data.shape, (143479, 1))
# Read image for which we know output shape
img = gi.read(DATA_FILE1)
assert_equal(img.darrays[0].data.shape, (3, 3))
def test_read_ordering():
# DATA_FILE1 has an expected darray[0].data shape of (3,3). However if we
# read another image first (DATA_FILE2) then the shape is wrong
# Read an image
img2 = gi.read(DATA_FILE2)
assert_equal(img2.darrays[0].data.shape, (143479, 1))
# Read image for which we know output shape
img = gi.read(DATA_FILE1)
assert_equal(img.darrays[0].data.shape, (3, 3))
def test_constraint_structure():
''' Tests if we recover the right structure from a gifti surface '''
l_surf = gifti.read('./logpar/cli/tests/data/L.white.surf.gii')
r_surf = gifti.read('./logpar/cli/tests/data/R.pial.surf.gii')
l_struct = cifti_utils.principal_structure(l_surf)
r_struct = cifti_utils.principal_structure(r_surf)
assert (l_struct == 'CIFTI_STRUCTURE_CORTEX_LEFT')
assert (r_struct == 'CIFTI_STRUCTURE_CORTEX_RIGHT')
def loadsurf_gifti(fname, surftype, quiet=True):
from nibabel import gifti
from dataset import SurfData
fname = '%s.%sgii' % (fname, '%s')
fname = match_gifti_intent(fname, 'surface')
surf_lh = gifti.read(parse.hemineutral(fname) % 'lh')
surf_rh = gifti.read(parse.hemineutral(fname) % 'rh')
sverts_lh, sfaces_lh = surf_lh.darrays[0].data, surf_lh.darrays[1].data
sverts_rh, sfaces_rh = surf_rh.darrays[0].data, surf_rh.darrays[1].data
return SurfData(sverts_lh, sfaces_lh, sverts_rh, sfaces_rh, surftype)
def loadsurf_gifti(fname,surftype,quiet=True):
from nibabel import gifti
from dataset import SurfData
fname = '%s.%sgii'%(fname,'%s')
fname = match_gifti_intent(fname, 'surface')
surf_lh = gifti.read(parse.hemineutral(fname)%'lh')
surf_rh = gifti.read(parse.hemineutral(fname)%'rh')
sverts_lh,sfaces_lh = surf_lh.darrays[0].data, surf_lh.darrays[1].data
sverts_rh,sfaces_rh = surf_rh.darrays[0].data, surf_rh.darrays[1].data
return SurfData(sverts_lh,sfaces_lh,sverts_rh,sfaces_rh,surftype)
def GetMesh(g):
# read a gifti (.gii) surface file
#g = '/mesh/cortex_20484.surf.gii'
v, f = gifti.read(g).getArraysFromIntent(1008)[0].data, \
gifti.read(g).getArraysFromIntent(1009)[0].data
Centre = spherefit(v)
v[0] = v[0] - Centre[0]
v[1] = v[1] - Centre[1]
v[2] = v[2] - Centre[2]
#v = fixboundary(v)
return v, f
def check_surf_data(self, index, gii_darray=0):
from nilearn._utils.compat import _basestring
import nibabel
surf_data = self.backgrounds[index]
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz') or
surf_data.endswith('mgz')):
data = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc') or
surf_data.endswith('thickness')):
data = nibabel.freesurfer.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data = nibabel.freesurfer.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data = nibabel.freesurfer.io.read_label(surf_data)
elif surf_data.endswith('gii'):
data = gifti.read(surf_data).darrays[gii_darray].data
else:
raise ValueError('Format of data file not recognized.')
# if the input is an array, it should have a single dimension
elif isinstance(surf_data, np.ndarray):
data = np.squeeze(surf_data)
if len(data.shape) is not 1:
raise ValueError('Data array cannot have more than one dimension.')
return data
def get_surface(fname, subject, hemi, trans=None):
""" Get surface whith a file
Parameters
----------
fname : str
Filename of the surface
subject : str
Name of the subject
hemi : 'lh' | 'rh'
Hemisphere of interest
trans : str | array | None
The matrix transformation or the filename to get this
Returns
-------
surface : instance of mne.SourceSpace ?
Surface source space
"""
try:
coords, triangles = mne.read_surface(fname)
except Exception:
try:
giftiImage = gifti.read(fname)
coords = giftiImage.darrays[0].data
triangles = giftiImage.darrays[1].data
except Exception:
raise Exception('surface file must be in FreeSurfer or BrainVisa format')
# Apply trans to coords
coords = compute_trans(coords, trans) ######################
# coords = tranform(coords, trans)
# Locations in meters
coords = coords * 1e-3
inuse = np.ones(len(coords), dtype=int)
remains = len(coords)
vertno = np.where(inuse == 1)[0]
if hemi == 'lh':
Id = 101
elif hemi == 'rh':
Id = 102
# Creating surface dict
surface = {'rr': coords, 'coord_frame': np.array((FIFF.FIFFV_COORD_MRI), np.int32), 'tris': triangles,
'ntri': len(triangles), 'use_tris': None, 'np': len(coords), 'inuse': inuse, 'nuse_tris': 0,
'nuse': remains, 'vertno': vertno, 'subject_his_id': subject, 'type': 'surf', 'id': Id,
'nearest': None, 'dist': None}
surface = mne.surface.complete_surface_info(surface)
# Invert normals since BrainVISA surfaces give in-ward pointing dipoles
surface['nn'] *= -1.
return surface
def display(fun_dir, fs_dir, contrast):
mlab.figure(bgcolor=(1, 1, 1))
left_mesh = freesurfer.read_geometry(os.path.join(fs_dir, 'lh.inflated'))
right_mesh = freesurfer.read_geometry(os.path.join(fs_dir, 'rh.inflated'))
left_curv = os.path.join(fs_dir, 'lh.curv')
right_curv = os.path.join(fs_dir, 'rh.curv')
meshes = [left_mesh, right_mesh]
curves = [left_curv, right_curv]
for hemisphere, mesh_file, curv_file in zip(['lh', 'rh'], meshes, curves):
fun_file = os.path.join(fun_dir, '%s_z_map_%s.gii' % (
contrast, hemisphere))
coords, triangles = mesh_file
x, y, z = coords.T
if hemisphere == 'lh':
x -= 50
else:
x += 50
curv = freesurfer.read_morph_data(curv_file).astype(np.float)
tex = np.array([darrays.data for darrays in
read(fun_file).darrays]).ravel()
print fun_file, tex.min(), tex.max()
name = ''
cmin = -1
cmax = 1
mlab.triangular_mesh(x, y, z, triangles, transparent=True, opacity=1.,
name=name, scalars=curv, colormap="bone",
vmin=cmin, vmax=cmax)
func_mesh = mlab.pipeline.triangular_mesh_source(
x, y, z, triangles, scalars=tex)
thresh = mlab.pipeline.threshold(func_mesh, low=THRESHOLD)
mlab.pipeline.surface(thresh, colormap="hot", vmin=THRESHOLD, vmax=7)
def check_surf_data(self, index, gii_darray=0):
from nilearn._utils.compat import _basestring
import nibabel
import numpy as np
surf_data = self.backgrounds[index]
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz')
or surf_data.endswith('mgz')):
data = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc')
or surf_data.endswith('thickness')):
data = nibabel.freesurfer.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data = nibabel.freesurfer.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data = nibabel.freesurfer.io.read_label(surf_data)
elif surf_data.endswith('gii'):
data = gifti.read(surf_data).darrays[gii_darray].data
else:
raise ValueError('Format of data file not recognized.')
# if the input is an array, it should have a single dimension
elif isinstance(surf_data, np.ndarray):
data = np.squeeze(surf_data)
if len(data.shape) is not 1:
raise ValueError(
'Data array cannot have more than one dimension.')
return data
def run_surface_glm(dmtx, contrasts, fmri_path, subject_session_output_dir):
""" """
from nibabel.gifti import read, write, GiftiDataArray, GiftiImage
from nilearn.glm.first_level import run_glm as run_glm_nl
from nilearn.glm import compute_contrast
Y = np.array([darrays.data for darrays in read(fmri_path).darrays])
labels, res = run_glm_nl(Y, dmtx.values)
# Estimate the contrasts
print('Computing contrasts...')
side = fmri_path[-6:-4]
for index, contrast_id in enumerate(contrasts):
print(' Contrast % i out of %i: %s' %
(index + 1, len(contrasts), contrast_id))
# compute contrasts
con_ = contrasts[contrast_id]
contrast_ = compute_contrast(labels, res, con_)
stats = [
contrast_.z_score(), contrast_.stat_, contrast_.effect,
contrast_.variance
]
for map_type, out_map in zip(['z', 't', 'effects', 'variance'], stats):
map_dir = os.path.join(subject_session_output_dir,
'%s_surf' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(map_dir, '%s_%s.gii' % (contrast_id, side))
print("\t\tWriting %s ..." % map_path)
tex = GiftiImage(darrays=[
GiftiDataArray().from_array(out_map, intent='t test')
])
write(tex, map_path)
def read_surface(filename):
# load gifti image
surface = gifti.read(filename)
# get point set
points = surface.get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0]
# get triangle set
trig = surface.get_arrays_from_intent('NIFTI_INTENT_TRIANGLE')[0]
# create output dict
output_dict = {}
output_dict['vertices'] = []
output_dict['faces'] = []
# store data in dict
for item in points.data:
dataset = [float(element) for element in item]
output_dict['vertices'].append(dataset)
for item in trig.data:
dataset = [int(element) for element in item]
output_dict['faces'].append(dataset)
# return dict
return output_dict
def run_from_args(args):
if args.thickness is not None and args.algorithm != 'line':
raise ValueError("Optional thickness output only available for the 'line algorithm, not for %s" % args.algorithm)
white = CorticalMesh.read(args.white)
pial = CorticalMesh.read(args.pial)
if args.sulcal_depth is None:
sd = np.zeros(white.nvertices)
else:
sd = gifti.read(args.sulcal_depth).darrays[0].data
img_mask = nibabel.load(args.mask)
mask = img_mask.get_data()
if mask.ndim != 3:
raise ValueError("Input mask should be 3-dimenasional")
wo = WeightedOrientation(white, pial, sd, 1., img_mask.affine)
wo._flip_inpr = args.flip_inpr
rough = wo.closest_vertex_grid(mask, zval=args.zval, outside_pial=args.outside_pial)
if args.algorithm == 'closest':
field = rough
elif args.algorithm == 'line':
field, thickness = wo.average_line_grid(mask, norient=args.norient, power_dist=args.power_dist, zval=args.zval)
# line algorithm might fail for voxels on the edge
replace = ~np.isfinite(thickness[..., 0])
field[replace] = rough[replace]
if args.thickness is not None:
nibabel.Nifti1Image(thickness, affine=img_mask.affine).to_filename(args.thickness)
elif args.algorithm == 'interp':
field = wo.average_point_grid(mask, power_dist=args.power_dist, zval=args.zval, outside_pial=args.outside_pial)
flipped = align_vector_field(field, rough)
coords = make_perpendicular(flipped[..., 0], flipped[..., 1])
nibabel.Nifti1Image(coords, affine=img_mask.affine).to_filename(args.output)
def get_surface(fname, subject='S4', hemi='lh', trans=None):
"""get surface whith a file
Parameters
----------
fname : float
Filename of the surface
subject : float
Name of the subject
hemi : 'lh' | 'rh'
Hemisphere of interest
trans : str | array | None
The matrix transformation or the filename to get this
Returns
-------
surface : instance of Surface
-------
Author : Alexandre Fabre
"""
try:
coords, triangles = mne.read_surface(fname)
except Exception:
try:
giftiImage = gifti.read(fname)
coords = giftiImage.darrays[0].data
triangles = giftiImage.darrays[1].data
except Exception:
raise Exception('surface file must be in FreeSurfer or BrainVisa format')
surface = Surface(coords, triangles, subject=subject, hemi=hemi, trans=trans)
return surface
def domain_from_mesh(mesh):
"""Instantiate a StructuredDomain from a gifti mesh
Parameters
----------
mesh: nibabel gifti mesh instance, or path to such a mesh
"""
if isinstance(mesh, basestring):
from nibabel.gifti import read
mesh_ = read(mesh)
else:
mesh_ = mesh
if len(mesh_.darrays) == 2:
cor, tri = mesh_.darrays
elif len(mesh_.darrays) == 3:
cor, nor, tri = mesh_.darrays
else:
raise Exception("%d arrays in gifti file (case not handled)" \
% len(mesh_.darrays))
mesh_dom = MeshDomain(cor.data, tri.data)
vol = mesh_dom.area()
topology = mesh_dom.topology()
dim = 2
return StructuredDomain(dim, mesh_dom.coord, vol, topology)
def read_mesh(filename):
if has_ext_gzsafe(filename, 'gii'):
mesh_gii = gifti.read(filename)
cor,tri = (mesh_gii.darrays[0].data, mesh_gii.darrays[1].data)
return cor,tri,mesh_gii.darrays[0].coordsys
else:
raise Exception('Unsupported file format (%s)' %filename)
def domain_from_mesh(mesh):
"""Instantiate a StructuredDomain from a gifti mesh
Parameters
----------
mesh: nibabel gifti mesh instance, or path to such a mesh
"""
if isinstance(mesh, basestring):
from nibabel.gifti import read
mesh_ = read(mesh)
else:
mesh_ = mesh
if len(mesh_.darrays) == 2:
cor, tri = mesh_.darrays
elif len(mesh_.darrays) == 3:
cor, nor, tri = mesh_.darrays
else:
raise Exception("%d arrays in gifti file (case not handled)" \
% len(mesh_.darrays))
mesh_dom = MeshDomain(cor.data, tri.data)
vol = mesh_dom.area()
topology = mesh_dom.topology()
dim = 2
return StructuredDomain(dim, mesh_dom.coord, vol, topology)
def read_mesh(filename):
if has_ext_gzsafe(filename, 'gii'):
mesh_gii = gifti.read(filename)
cor, tri = (mesh_gii.darrays[0].data, mesh_gii.darrays[1].data)
return cor, tri, mesh_gii.darrays[0].coordsys
else:
raise Exception('Unsupported file format (%s)' % filename)
def loadannot_gifti(parcname,
subject,
subjects_dir,
labnam=None,
surf_type='pial',
surf_struct=None,
quiet=False):
import numpy as np
from nibabel import gifti
fname = os.path.join(subjects_dir, subject, 'label',
'lh.%s.%sgii' % (parcname, '%s'))
fname = match_gifti_intent(fname, 'label')
annot_lh = gifti.read(parse.hemineutral(fname) % 'lh')
annot_rh = gifti.read(parse.hemineutral(fname) % 'rh')
#unpack the annotation data
labdict_lh = parse.appendhemis(annot_lh.labeltable.get_labels_as_dict(),
"lh_")
labv_lh = map(labdict_lh.get, annot_lh.darrays[0].data)
labdict_rh = parse.appendhemis(annot_rh.labeltable.get_labels_as_dict(),
"rh_")
labv_rh = map(labdict_rh.get, annot_rh.darrays[0].data)
labv = labv_lh + labv_rh
#return labv
#The objective is now to create MNE label files for these on the fly
vertices = np.vstack((surf_struct.lh_verts, surf_struct.rh_verts))
mne_labels = []
for lab in labnam:
cur_lab_verts = np.flatnonzero(np.array(labv) == lab)
cur_lab_pos = vertices[cur_lab_verts]
cur_lab = mne.Label(cur_lab_verts,
pos=cur_lab_pos / 1000,
hemi=lab[:2],
name=parse.demangle_hemi(lab))
mne_labels.append(cur_lab)
return mne_labels
def load_gii(img_path):
"""Load Gifti."""
try:
img = gifti.read(img_path)
except:
raise NPDLError('Image file ({}) could not be loaded'.format(img))
img = np.array(map(lambda d: d.data, img.darrays))
return img
def test_getbyintent():
img = gi.read(DATA_FILE1)
da = img.getArraysFromIntent("NIFTI_INTENT_POINTSET")
assert_equal(len(da), 1)
da = img.getArraysFromIntent("NIFTI_INTENT_TRIANGLE")
assert_equal(len(da), 1)
da = img.getArraysFromIntent("NIFTI_INTENT_CORREL")
assert_equal(len(da), 0)
assert_equal(da, [])
def test_getbyintent():
img = gi.read(DATA_FILE1)
da = img.getArraysFromIntent("NIFTI_INTENT_POINTSET")
assert_equal(len(da), 1)
da = img.getArraysFromIntent("NIFTI_INTENT_TRIANGLE")
assert_equal(len(da), 1)
da = img.getArraysFromIntent("NIFTI_INTENT_CORREL")
assert_equal(len(da), 0)
assert_equal(da, [])
def test_metadata():
for i, dat in enumerate(datafiles):
img = gi.read(dat)
me = img.get_metadata()
medat = me.get_metadata()
assert_equal(numda[i], img.numDA)
assert_equal(img.version, '1.0')
def test_metadata():
for i, dat in enumerate(datafiles):
img = gi.read(dat)
me = img.get_metadata()
medat = me.get_metadata()
assert_equal(numda[i], img.numDA)
assert_equal(img.version, "1.0")
def texture_gradient(mesh, texture, mask=None):
""" Compute the gradient of a given texture at each point of the mesh
Parameters
---------
mesh: string, a path to a mesh file
texture: string, a path to a texture file
mask: string, optional, a path to mask texture for that mesh/subject,
so that only part of the vertices are conssidered.
Returns
-------
gradient: array of shape (mesh.n_vertices, 3)
the gradient vector at each mesh node.
fixme
-----
Put in mesh_processing
Note
----
the gradient is expressedn in 3D space, note on surface coordinates
"""
# get coordinates and triangles
coord, triangles = mesh_arrays(mesh)
if mask == None:
mask = np.ones(coord.shape[0]).astype(np.bool)
else:
mask = read(mask).darrays[0].data.astype(np.bool)
# compute the neighborhood system
neighb = mesh_to_graph(mesh).to_coo_matrix().tolil().rows
# read the texture
y = read(texture).darrays[0].data
# compute the gradient
gradient = []
for i in np.where(mask)[0]:
yi = y[neighb[i]]
yi[mask[neighb[i]] == False] = y[i]
grad = np.linalg.lstsq(coord[neighb[i]], yi)[0]
gradient.append(grad)
return np.array(gradient)
def texture_gradient(mesh, texture, mask=None):
""" Compute the gradient of a given texture at each point of the mesh
Parameters
---------
mesh: string, a path to a mesh file
texture: string, a path to a texture file
mask: string, optional, a path to mask texture for that mesh/subject,
so that only part of the vertices are conssidered.
Returns
-------
gradient: array of shape (mesh.n_vertices, 3)
the gradient vector at each mesh node.
fixme
-----
Put in mesh_processing
Note
----
the gradient is expressedn in 3D space, note on surface coordinates
"""
# get coordinates and triangles
coord, triangles = mesh_arrays(mesh)
if mask is None:
mask = np.ones(coord.shape[0]).astype(np.bool)
else:
mask = gifti.read(mask).darrays[0].data.astype(np.bool)
# compute the neighborhood system
neighb = mesh_to_graph(mesh).to_coo_matrix().tolil().rows
# read the texture
y = gifti.read(texture).darrays[0].data
# compute the gradient
gradient = []
for i in np.where(mask)[0]:
yi = y[neighb[i]]
yi[mask[neighb[i]] is False] = y[i]
grad = np.linalg.lstsq(coord[neighb[i]], yi)[0]
gradient.append(grad)
return np.array(gradient)
def extract_ts_from_mesh(mesh_file, num_ts=1200):
mesh = gi.read(mesh_file)
data = []
if (num_ts != len(mesh.darrays)):
print(len(mesh.darrays))
assert (num_ts == len(mesh.darrays))
for i in range(num_ts):
data.append(mesh.darrays[i].data)
data = np.asarray(data).T
return data
def load_surf_data(surf_data):
"""Loading data to be represented on a surface mesh.
Parameters
----------
surf_data : str or numpy.ndarray
Either a file containing surface data (valid format are .gii,
.gii.gz, .mgz, .nii, .nii.gz, or Freesurfer specific files such as
.thickness, .curv, .sulc, .annot, .label) or
a Numpy array containing surface data.
Returns
-------
data : numpy.ndarray
An array containing surface data
"""
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz')
or surf_data.endswith('mgz')):
data = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc')
or surf_data.endswith('thickness')):
data = nibabel.freesurfer.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data = nibabel.freesurfer.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data = nibabel.freesurfer.io.read_label(surf_data)
elif surf_data.endswith('gii'):
if LooseVersion(nibabel.__version__) >= LooseVersion('2.1.0'):
gii = nibabel.load(surf_data)
else:
gii = gifti.read(surf_data)
data = _gifti_img_to_data(gii)
elif surf_data.endswith('gii.gz'):
gii = _load_surf_files_gifti_gzip(surf_data)
data = _gifti_img_to_data(gii)
else:
raise ValueError(('The input type is not recognized. %r was given '
'while valid inputs are a Numpy array or one of '
'the following file formats: .gii, .gii.gz, '
'.mgz, .nii, .nii.gz, Freesurfer specific files '
'such as .curv, .sulc, .thickness, .annot, '
'.label') % surf_data)
# if the input is a numpy array
elif isinstance(surf_data, np.ndarray):
data = np.squeeze(surf_data)
else:
raise ValueError('The input type is not recognized. '
'Valid inputs are a Numpy array or one of the '
'following file formats: .gii, .gii.gz, .mgz, .nii, '
'.nii.gz, Freesurfer specific files such as .curv, '
'.sulc, .thickness, .annot, .label')
return data
def load_surf_data(surf_data):
"""Loading data to be represented on a surface mesh.
Parameters
----------
surf_data : str or numpy.ndarray
Either a file containing surface data (valid format are .gii,
.gii.gz, .mgz, .nii, .nii.gz, or Freesurfer specific files such as
.thickness, .curv, .sulc, .annot, .label) or
a Numpy array containing surface data.
Returns
-------
data : numpy.ndarray
An array containing surface data
"""
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz') or
surf_data.endswith('mgz')):
data = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc') or
surf_data.endswith('thickness')):
data = nibabel.freesurfer.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data = nibabel.freesurfer.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data = nibabel.freesurfer.io.read_label(surf_data)
elif surf_data.endswith('gii'):
if LooseVersion(nibabel.__version__) >= LooseVersion('2.1.0'):
gii = nibabel.load(surf_data)
else:
gii = gifti.read(surf_data)
data = _gifti_img_to_data(gii)
elif surf_data.endswith('gii.gz'):
gii = _load_surf_files_gifti_gzip(surf_data)
data = _gifti_img_to_data(gii)
else:
raise ValueError(('The input type is not recognized. %r was given '
'while valid inputs are a Numpy array or one of '
'the following file formats: .gii, .gii.gz, '
'.mgz, .nii, .nii.gz, Freesurfer specific files '
'such as .curv, .sulc, .thickness, .annot, '
'.label') % surf_data)
# if the input is a numpy array
elif isinstance(surf_data, np.ndarray):
data = np.squeeze(surf_data)
else:
raise ValueError('The input type is not recognized. '
'Valid inputs are a Numpy array or one of the '
'following file formats: .gii, .gii.gz, .mgz, .nii, '
'.nii.gz, Freesurfer specific files such as .curv, '
'.sulc, .thickness, .annot, .label')
return data
def test_labeltable():
img = gi.read(DATA_FILE6)
assert_array_almost_equal(img.darrays[0].data[:3], DATA_FILE6_darr1)
assert_equal(len(img.labeltable.labels), 36)
labeldict = img.labeltable.get_labels_as_dict()
assert_true(labeldict.has_key(660700))
assert_equal(labeldict[660700], u"entorhinal")
assert_equal(img.labeltable.labels[1].key, 2647065)
assert_equal(img.labeltable.labels[1].red, 0.0980392)
assert_equal(img.labeltable.labels[1].green, 0.392157)
assert_equal(img.labeltable.labels[1].blue, 0.156863)
assert_equal(img.labeltable.labels[1].alpha, 1)
def smooth_data_as_texture(data, subject, hemi):
"""To smooth the data, save them as texture,
surfs2surf and extract the data """
from nibabel.gifti import read, write, GiftiImage, GiftiDataArray as gda
file_raw = '/tmp/data.gii'
file_smooth = '/tmp/smooth_data.gii'
write(GiftiImage(darrays=[gda(data=data.astype('float32'))]), file_raw)
os.system('$FREESURFER_HOME/bin/mri_surf2surf' +
' --srcsubject %s' % subject + ' --srcsurfval %s' % file_raw +
' --trgsurfval %s' % file_smooth + ' --trgsubject %s' % subject +
' --hemi %s' % hemi + ' --nsmooth-out 2')
return read(file_smooth).darrays[0].data
def load_surf_data(surf_data):
"""Loading data to be represented on a surface mesh.
Parameters
----------
surf_data : str or numpy.ndarray
Either a file containing surface data (valid format are .gii,
.mgz, .nii, .nii.gz, or Freesurfer specific files such as
.thickness, .curv, .sulc, .annot, .label) or
a Numpy array containing surface data.
Returns
-------
data : numpy.ndarray
An array containing surface data
"""
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz')
or surf_data.endswith('mgz')):
data = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc')
or surf_data.endswith('thickness')):
data = nibabel.freesurfer.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data = nibabel.freesurfer.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data = nibabel.freesurfer.io.read_label(surf_data)
elif surf_data.endswith('gii'):
gii = gifti.read(surf_data)
try:
data = np.zeros((len(gii.darrays[0].data), len(gii.darrays)))
for arr in range(len(gii.darrays)):
data[:, arr] = gii.darrays[arr].data
data = np.squeeze(data)
except IndexError:
raise ValueError('Gifti must contain at least one data array')
else:
raise ValueError(('The input type is not recognized. %r was given '
'while valid inputs are a Numpy array or one of '
'the following file formats: .gii, .mgz, .nii, '
'.nii.gz, Freesurfer specific files such as '
'.curv, .sulc, .thickness, .annot, '
'.label') % surf_data)
# if the input is a numpy array
elif isinstance(surf_data, np.ndarray):
data = np.squeeze(surf_data)
else:
raise ValueError('The input type is not recognized. '
'Valid inputs are a Numpy array or one of the '
'following file formats: .gii, .mgz, .nii, .nii.gz, '
'Freesurfer specific files such as .curv, .sulc, '
'.thickness, .annot, .label')
return data
def test_correctly_configured_32bit():
''' Tests the clustering with many different parameters using 32bit
TODO: Improve this '''
cifti_test = './logpar/cli/tests/data/test.dconn.nii'
l_surf = './logpar/cli/tests/data/L.white.surf.gii'
r_surf = './logpar/cli/tests/data/R.pial.surf.gii'
cifti = nibabel.load(cifti_test)
header = cifti.header
data = cifti.get_data()[0, 0, 0, 0].astype(numpy.float32)
output = NamedTemporaryFile(mode='w', delete=True, suffix='.csv').name
for direction in ["ROW", "COLUMN"]:
for constraint in [None, l_surf, r_surf]:
for to_logodds in [True, False]:
# Result from cifti_parcellate CLI
cifti_parcellate.cifti_parcellate(cifti_test,
output,
direction=direction,
constraint=constraint,
to_logodds=to_logodds)
dendro1 = numpy.loadtxt(output, delimiter=',')
# Result from clustering function
test_data = data.copy()
if direction == 'COLUMN':
test_data = test_data.T
ady_matrix = None
if constraint is not None:
surf = gifti.read(constraint)
struc = cifti_utils.principal_structure(surf)
off, ind = cifti_utils.surface_attributes(
header, struc, direction)
test_data = test_data[off:off + len(ind)]
ady_matrix = cifti_utils.constraint_from_surface(surf, ind)
if to_logodds:
test_data = transform.to_logodds(test_data, True)
dendro2 = our_hie.clustering(test_data, constraints=ady_matrix)
# They should be the same
try:
numpy.testing.assert_almost_equal(dendro1, dendro2)
except AssertionError:
print direction, constraint, to_logodds, ady_matrix
raise
def mesh_arrays(mesh, nibabel=True):
""" Returns the arrays associated with a mesh
if len(output)==2, the arrays are coordiantes and triangle lists
if len(output)==3, the arrays are coordiantes, triangle lists
and outer normal
fixme: use intent !
"""
if isinstance(mesh, str):
mesh_ = gifti.read(mesh)
else:
mesh_ = mesh
cor = mesh_.getArraysFromIntent("NIFTI_INTENT_POINTSET")[0].data
tri = mesh_.getArraysFromIntent("NIFTI_INTENT_TRIANGLE")[0].data
return cor, tri
def mesh_arrays(mesh, nibabel=True):
""" Returns the arrays associated with a mesh
if len(output)==2, the arrays are coordiantes and triangle lists
if len(output)==3, the arrays are coordiantes, triangle lists
and outer normal
fixme: use intent !
"""
if isinstance(mesh, basestring):
mesh_ = read(mesh)
else:
mesh_ = mesh
cor = mesh_.getArraysFromIntent("NIFTI_INTENT_POINTSET")[0].data
tri = mesh_.getArraysFromIntent("NIFTI_INTENT_TRIANGLE")[0].data
return cor, tri
def test_dataarray1():
img = gi.read(DATA_FILE1)
assert_array_almost_equal(img.darrays[0].data, DATA_FILE1_darr1)
assert_array_almost_equal(img.darrays[1].data, DATA_FILE1_darr2)
me = img.darrays[0].meta.get_metadata()
assert_true("AnatomicalStructurePrimary" in me)
assert_true("AnatomicalStructureSecondary" in me)
assert_equal(me["AnatomicalStructurePrimary"], "CortexLeft")
assert_array_almost_equal(img.darrays[0].coordsys.xform, np.eye(4, 4))
assert_equal(gi.xform_codes.niistring[img.darrays[0].coordsys.dataspace], "NIFTI_XFORM_TALAIRACH")
assert_equal(gi.xform_codes.niistring[img.darrays[0].coordsys.xformspace], "NIFTI_XFORM_TALAIRACH")
def loadannot_gifti(parcname, subject, subjects_dir, labnam=None, surf_type='pial',
surf_struct=None, quiet=False):
import numpy as np
from nibabel import gifti
fname = os.path.join(subjects_dir, subject, 'label', 'lh.%s.%sgii'%(parcname,'%s'))
fname = match_gifti_intent(fname, 'label')
annot_lh = gifti.read(parse.hemineutral(fname)%'lh')
annot_rh = gifti.read(parse.hemineutral(fname)%'rh')
#unpack the annotation data
labdict_lh=parse.appendhemis(annot_lh.labeltable.get_labels_as_dict(),"lh_")
labv_lh=map(labdict_lh.get,annot_lh.darrays[0].data)
labdict_rh=parse.appendhemis(annot_rh.labeltable.get_labels_as_dict(),"rh_")
labv_rh=map(labdict_rh.get,annot_rh.darrays[0].data)
labv=labv_lh+labv_rh
#return labv
#The objective is now to create MNE label files for these on the fly
vertices = np.vstack((surf_struct.lh_verts, surf_struct.rh_verts))
mne_labels = []
for lab in labnam:
cur_lab_verts = np.flatnonzero(np.array(labv)==lab)
cur_lab_pos = vertices[cur_lab_verts]
cur_lab = mne.Label(cur_lab_verts, pos=cur_lab_pos/1000, hemi=lab[:2],
name = parse.demangle_hemi(lab))
mne_labels.append(cur_lab)
return mne_labels
def __init__(self, surf_path, max_neighbors=50):
self.surf_path = surf_path
try:
surf = gifti.read(surf_path)
except:
raise NPDLError(('Surface: {} does not exist ' +
'or is not a valid Gifti file.').format(surf))
self.coords, self.faces = [surf.darrays[i].data for i in 0, 1]
self.coords = self.coords.astype(np.float64)
self.faces = self.faces.astype(np.int32)
self.num_verts = self.coords.shape[0]
self.neighbors = self.construct_neighbors(max_neighbors)
return
def test_dataarray1():
img = gi.read(DATA_FILE1)
assert_array_almost_equal(img.darrays[0].data, DATA_FILE1_darr1)
assert_array_almost_equal(img.darrays[1].data, DATA_FILE1_darr2)
me = img.darrays[0].meta.get_metadata()
assert_true('AnatomicalStructurePrimary' in me)
assert_true('AnatomicalStructureSecondary' in me)
assert_equal(me['AnatomicalStructurePrimary'], 'CortexLeft')
assert_array_almost_equal(img.darrays[0].coordsys.xform, np.eye(4, 4))
assert_equal(gi.xform_codes.niistring[img.darrays[0].coordsys.dataspace],
'NIFTI_XFORM_TALAIRACH')
assert_equal(gi.xform_codes.niistring[img.darrays[0].coordsys.xformspace],
'NIFTI_XFORM_TALAIRACH')
def gii_convert_to_texture(gii_f, out_gii_f=None, meta=None, verbose=0):
""" Change intent of first data array and create a new Gifti """
# TODO: verify the that description is good and function is general
orig_gii = ng.read(gii_f)
data = orig_gii.darrays[len(orig_gii.darrays) - 1].data[0]
darray = ng.GiftiDataArray(data=data, intent='NIFTI_INTENT_ESTIMATE')
gii = ng.GiftiImage(darrays=[darray])
if meta:
gii.meta = ng.GiftiMetaData().from_dict(meta)
out_f = out_gii_f if out_gii_f else gii_f
ng.write(gii, out_f)
if verbose > 0:
print("Texture saved at: {}".format(out_f))
def read_texture(tex):
if has_ext_gzsafe(tex, 'gii'):
#from gifti import loadImage
#texture = loadImage(tex).arrays[0].data
tex_gii = gifti.read(tex)
if len(tex_gii.darrays) > 1: #2D texture ... #TODO: check
texture = np.vstack([a.data for a in tex_gii.darrays])
else:
texture = tex_gii.darrays[0].data
return texture, tex_gii
elif has_ext_gzsafe(tex, 'tex'):
from pyhrf.tools.io.tio import Texture
texture = Texture.read(tex).data
return texture, None
else:
raise NotImplementedError('Unsupported %s extension' \
%op.splitext(tex)[1])
def read_texture(tex):
if has_ext_gzsafe(tex, 'gii'):
#from gifti import loadImage
#texture = loadImage(tex).arrays[0].data
tex_gii = gifti.read(tex)
if len(tex_gii.darrays) > 1: # 2D texture ... #TODO: check
texture = np.vstack([a.data for a in tex_gii.darrays])
else:
texture = tex_gii.darrays[0].data
return texture, tex_gii
elif has_ext_gzsafe(tex, 'tex'):
from pyhrf.tools._io.tio import Texture
texture = Texture.read(tex).data
return texture, None
else:
raise NotImplementedError('Unsupported %s extension'
% op.splitext(tex)[1])
def test_constraint_matrix():
''' Test that the constraint matrix is correctly generated '''
surf_left = gifti.read('./logpar/cli/tests/data/L.white.surf.gii')
triangles = surf_left.darrays[1].data
N = len(surf_left.darrays[0].data)
ady_matrix = numpy.zeros((N, N), dtype=numpy.int8)
for (edg1, edg2, edg3) in triangles:
ady_matrix[edg1, edg2] = ady_matrix[edg2, edg1] = 1
ady_matrix[edg1, edg3] = ady_matrix[edg3, edg1] = 1
ady_matrix[edg2, edg3] = ady_matrix[edg3, edg2] = 1
vertices = numpy.arange(0, N, 2)
sub_ady_matrix = cifti_utils.constraint_from_surface(surf_left, vertices)
base = squareform(ady_matrix[vertices[:, None], vertices])
numpy.testing.assert_equal(sub_ady_matrix, base)
def compute_normal_vertex(mesh, mask=None):
""" Compute the normal vector at each vertex of the mesh
Parameters
---------
mesh: string, a path to a mesh file
Returns
-------
normals: array of shape (mesh.n_vertices, 3)
the normal vector at each mesh node
mask: string, optional, a path to mask texture for that mesh/subject,
so that only part of the vertices are conssidered.
fixme
-----
Put in mesh_processing
"""
# get coordinates and triangles
coord, triangles = mesh_arrays(mesh)
if mask == None:
mask = np.ones(coord.shape[0]).astype(np.bool)
else:
mask = read(mask).darrays[0].data.astype(np.bool)
# compute the normal for each triangle
norms = np.zeros((mask.size, 3))
for triangle in triangles:
if mask[triangle].any():
sa, sb, sc = triangle
a = coord[sb] - coord[sa]
b = coord[sc] - coord[sa]
norm = vectp(a, b)
norms[sa] += norm
norms[sb] += norm
norms[sc] += norm
# normalize the normal at each vertex
eps = 1.e-15
norms = (norms.T / np.sqrt(eps + np.sum(norms ** 2, 1))).T
return norms[mask]
def isomap_patch(mesh, mask, show=False):
"""return low-dimensional coordinates for the the patch
Parameters
==========
mesh: string or nibabel mesh,
the input mesh to be cherted
mask: string or array of shape (n_vertices)
a mask for the region of interest on the mesh
show: boolean, optional,
if yes, make an image of the coordinates
"""
from sklearn.manifold.isomap import Isomap
# Read the data
coord, tri = mesh_arrays(mesh)
if isinstance(mask, basestring):
mask = read(mask).darrays[0].data > 0
else:
mask = mask.astype(np.bool)
coord, tri = coord[mask], tri[mask[tri].all(1)]
tri = np.hstack((0, np.cumsum(mask)[:-1]))[tri]
# perform the dimension reduction
xy = Isomap().fit_transform(coord)
# try to make the sign invariant and repect the orientations
xy *= np.sign((xy ** 3).sum(0))
a, b, c = tri[0]
xy[:, 1] *= np.sign(np.linalg.det(np.vstack((xy[b] - xy[a], xy[c] -xy[a]))))
if show:
import matplotlib.pyplot as plt
plt.figure()
plt.tripcolor(xy.T[0], xy.T[1], tri, (xy ** 2).sum(1),
shading='faceted')
plt.show()
return xy
design_matrix = make_dmtx(
frametimes, add_regs=reg_matrix, add_reg_names=reg,
drift_model=drift_model, hfcut=hfcut)
# plot the design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
pylab.savefig(os.path.join(write_dir, 'design_matrix_%s.png') %\
session)
# get the data
if side == False:
Y, _ = data_scaling(load(fmri_data).get_data()[mask_array].T)
affine = load(fmri_data).get_affine()
else:
Y = np.array([x.data for x in read(fmri_data).darrays])
Y, _ = data_scaling(Y)
if sess == 0: # do not redefine the mask later !
mask_array = np.var(Y, 0) > 0
Y = Y[:, mask_array]
# fit the glm
print 'Fitting a GLM'
result = GeneralLinearModel(design_matrix.matrix)
result.fit(Y, model='ar1', steps=100)
for contrast_id, contrast_val in contrasts.iteritems():
if (contrast_val[session] == 0).all():
continue
contrast_obj[contrast_id] =\
result.contrast(contrast_val[session])
def load_surf_mesh(surf_mesh):
"""Loading a surface mesh geometry
Parameters
----------
surf_mesh : str or numpy.ndarray
Either a file containing surface mesh geometry (valid formats
are .gii .gii.gz or Freesurfer specific files such as .orig, .pial,
.sphere, .white, .inflated) or a list or tuple of two Numpy arrays,
the first containing the x-y-z coordinates of the mesh
vertices, the second containing the indices (into coords)
of the mesh faces.
Returns
--------
[coords, faces] : List of two numpy.ndarray
The first containing the x-y-z coordinates of the mesh vertices,
the second containing the indices (into coords) of the mesh faces.
"""
# if input is a filename, try to load it
if isinstance(surf_mesh, _basestring):
# resolve globbing
file_list = _resolve_globbing(surf_mesh)
if len(file_list) == 1:
surf_mesh = file_list[0]
elif len(file_list) > 1:
# empty list is handled inside _resolve_globbing function
raise ValueError(("More than one file matching path: %s \n"
"load_surf_mesh can only load one file at a time")
% surf_mesh)
if (surf_mesh.endswith('orig') or surf_mesh.endswith('pial') or
surf_mesh.endswith('white') or surf_mesh.endswith('sphere') or
surf_mesh.endswith('inflated')):
coords, faces = fs.io.read_geometry(surf_mesh)
elif surf_mesh.endswith('gii'):
if LooseVersion(nibabel.__version__) >= LooseVersion('2.1.0'):
gifti_img = nibabel.load(surf_mesh)
else:
gifti_img = gifti.read(surf_mesh)
coords, faces = _gifti_img_to_mesh(gifti_img)
elif surf_mesh.endswith('.gii.gz'):
gifti_img = _load_surf_files_gifti_gzip(surf_mesh)
coords, faces = _gifti_img_to_mesh(gifti_img)
else:
raise ValueError(('The input type is not recognized. %r was given '
'while valid inputs are one of the following '
'file formats: .gii, .gii.gz, Freesurfer '
'specific files such as .orig, .pial, .sphere, '
'.white, .inflated or a list containing two '
'Numpy arrays [vertex coordinates, face indices]'
) % surf_mesh)
elif isinstance(surf_mesh, (list, tuple)):
try:
coords, faces = surf_mesh
except Exception:
raise ValueError(('If a list or tuple is given as input, '
'it must have two elements, the first is '
'a Numpy array containing the x-y-z coordinates '
'of the mesh vertices, the second is a Numpy '
'array containing the indices (into coords) of '
'the mesh faces. The input was a list with '
'%r elements.') % len(surf_mesh))
else:
raise ValueError('The input type is not recognized. '
'Valid inputs are one of the following file '
'formats: .gii, .gii.gz, Freesurfer specific files '
'such as .orig, .pial, .sphere, .white, .inflated '
'or a list containing two Numpy arrays '
'[vertex coordinates, face indices]')
return [coords, faces]
def load_surf_data(surf_data):
"""Loading data to be represented on a surface mesh.
Parameters
----------
surf_data : str or numpy.ndarray
Either a file containing surface data (valid format are .gii,
.gii.gz, .mgz, .nii, .nii.gz, or Freesurfer specific files such as
.thickness, .curv, .sulc, .annot, .label), lists of 1D data files are
returned as 2D arrays, or
a Numpy array containing surface data.
Returns
-------
data : numpy.ndarray
An array containing surface data
"""
# if the input is a filename, load it
if isinstance(surf_data, _basestring):
# resolve globbing
file_list = _resolve_globbing(surf_data)
# _resolve_globbing handles empty lists
for f in range(len(file_list)):
surf_data = file_list[f]
if (surf_data.endswith('nii') or surf_data.endswith('nii.gz') or
surf_data.endswith('mgz')):
data_part = np.squeeze(nibabel.load(surf_data).get_data())
elif (surf_data.endswith('curv') or surf_data.endswith('sulc') or
surf_data.endswith('thickness')):
data_part = fs.io.read_morph_data(surf_data)
elif surf_data.endswith('annot'):
data_part = fs.io.read_annot(surf_data)[0]
elif surf_data.endswith('label'):
data_part = fs.io.read_label(surf_data)
elif surf_data.endswith('gii'):
if LooseVersion(nibabel.__version__) >= LooseVersion('2.1.0'):
gii = nibabel.load(surf_data)
else:
gii = gifti.read(surf_data)
data_part = _gifti_img_to_data(gii)
elif surf_data.endswith('gii.gz'):
gii = _load_surf_files_gifti_gzip(surf_data)
data_part = _gifti_img_to_data(gii)
else:
raise ValueError(('The input type is not recognized. %r was '
'given while valid inputs are a Numpy array '
'or one of the following file formats: .gii,'
' .gii.gz, .mgz, .nii, .nii.gz, Freesurfer '
'specific files such as .curv, .sulc, '
'.thickness, .annot, .label') % surf_data)
if len(data_part.shape) == 1:
data_part = data_part[:, np.newaxis]
if f == 0:
data = data_part
elif f > 0:
try:
data = np.concatenate((data, data_part), axis=1)
except ValueError:
raise ValueError('When more than one file is input, all '
'files must contain data with the same '
'shape in axis=0')
# if the input is a numpy array
elif isinstance(surf_data, np.ndarray):
data = surf_data
else:
raise ValueError('The input type is not recognized. '
'Valid inputs are a Numpy array or one of the '
'following file formats: .gii, .gii.gz, .mgz, .nii, '
'.nii.gz, Freesurfer specific files such as .curv, '
'.sulc, .thickness, .annot, .label')
return np.squeeze(data)
def test_dataarray2():
img2 = gi.read(DATA_FILE2)
assert_array_almost_equal(img2.darrays[0].data[:10], DATA_FILE2_darr1)
def test_dataarray5():
img3 = gi.read(DATA_FILE5)
assert_array_almost_equal(img3.darrays[0].data, DATA_FILE5_darr1)
assert_array_almost_equal(img3.darrays[1].data, DATA_FILE5_darr2)
def test_dataarray4():
img4 = gi.read(DATA_FILE4)
assert_array_almost_equal(img4.darrays[0].data[:10], DATA_FILE4_darr1)
def test_dataarray3():
img3 = gi.read(DATA_FILE3)
assert_array_almost_equal(img3.darrays[0].data[30:50], DATA_FILE3_darr1)
