def draw_surfs(self): from parsing_utils import demangle_hemi srf_scalar=self.ds.scalar_display_settings.surf_color if (self.ds.display_mode=='scalar' and srf_scalar): colors_lh=np.zeros((len(self.ds.srf.lh_verts)),) colors_rh=np.zeros((len(self.ds.srf.rh_verts)),) for i,l in enumerate(self.ds.labnam): #assumes that lh labels start with L and so on vertices=self.ds.labv[demangle_hemi(l)] if l[0]=='l': colors_lh[vertices]=self.ds.node_scalars[srf_scalar][i] elif l[0]=='r': colors_rh[vertices]=self.ds.node_scalars[srf_scalar][i] self.syrf_lh.mlab_source.scalars=colors_lh self.syrf_rh.mlab_source.scalars=colors_rh for syrf in (self.syrf_lh,self.syrf_rh): set_lut(syrf,self.ds.opts.scalar_map) syrf.actor.mapper.scalar_visibility=True else: for syrf in (self.syrf_lh,self.syrf_rh): syrf.actor.mapper.scalar_visibility=False
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 cracked_surfs_gen(self):
from parsing_utils import demangle_hemi
tri_inds_l, tri_inds_r = [], []
#all lh nodes are assumed to start with l
for l in self.ds.labnam:
if l[0] == 'l':
tris = self.ds.srf.lh_tris
tri_inds = tri_inds_l
elif l[0] == 'r':
tris = self.ds.srf.rh_tris
tri_inds = tri_inds_r
else:
self.error_dialog('Bad label name %s' % l)
return
#get the triangles entirely contained in this set of vertices
v_as_set = set(self.ds.labv[demangle_hemi(l)])
ts, = np.where([v_as_set.issuperset(tri) for tri in tris])
tri_inds.extend(ts)
self.syrf_lh = mlab.triangular_mesh(
self.ds.srf.lh_verts[:, 0],
self.ds.srf.lh_verts[:, 1],
self.ds.srf.lh_verts[:, 2],
self.ds.srf.lh_tris[tri_inds_l],
opacity=self.ds.opts.surface_visibility,
color=self.ds.default_glass_brain_color,
figure=self.scene.mayavi_scene)
self.syrf_rh = mlab.triangular_mesh(
self.ds.srf.rh_verts[:, 0],
self.ds.srf.rh_verts[:, 1],
self.ds.srf.rh_verts[:, 2],
self.ds.srf.rh_tris[tri_inds_r],
opacity=self.ds.opts.surface_visibility,
color=self.ds.default_glass_brain_color,
figure=self.scene.mayavi_scene)
self.surfs_cracked = True
for syrf in (self.syrf_lh, self.syrf_rh):
syrf.actor.actor.pickable = 0
set_lut(syrf, self.ds.opts.scalar_map)
self.ds.chg_lh_surfmask()
self.ds.chg_rh_surfmask()
def cracked_surfs_gen(self):
from parsing_utils import demangle_hemi
tri_inds_l,tri_inds_r=[],[]
#all lh nodes are assumed to start with l
for l in self.ds.labnam:
if l[0]=='l':
tris=self.ds.srf.lh_tris; tri_inds=tri_inds_l
elif l[0]=='r':
tris=self.ds.srf.rh_tris; tri_inds=tri_inds_r
else:
self.error_dialog('Bad label name %s'%l)
return
#get the triangles entirely contained in this set of vertices
v_as_set=set(self.ds.labv[demangle_hemi(l)])
ts,=np.where([v_as_set.issuperset(tri) for tri in tris])
tri_inds.extend(ts)
self.syrf_lh=mlab.triangular_mesh(
self.ds.srf.lh_verts[:,0],self.ds.srf.lh_verts[:,1],
self.ds.srf.lh_verts[:,2],self.ds.srf.lh_tris[tri_inds_l],
opacity=self.ds.opts.surface_visibility,
color=self.ds.default_glass_brain_color,
figure=self.scene.mayavi_scene)
self.syrf_rh=mlab.triangular_mesh(
self.ds.srf.rh_verts[:,0],self.ds.srf.rh_verts[:,1],
self.ds.srf.rh_verts[:,2],self.ds.srf.rh_tris[tri_inds_r],
opacity=self.ds.opts.surface_visibility,
color=self.ds.default_glass_brain_color,
figure=self.scene.mayavi_scene)
self.surfs_cracked=True
for syrf in (self.syrf_lh,self.syrf_rh):
syrf.actor.actor.pickable=0
set_lut(syrf,self.ds.opts.scalar_map)
self.ds.chg_lh_surfmask(); self.ds.chg_rh_surfmask()
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 draw_surfs(self):
from parsing_utils import demangle_hemi
srf_scalar = self.ds.scalar_display_settings.surf_color
nc = self.ds.scalar_display_settings.node_color
if (self.ds.display_mode == 'scalar' and srf_scalar):
scalars = self.ds.node_scalars[srf_scalar]
colors_lh = np.zeros((len(self.ds.srf.lh_verts)), )
colors_rh = np.zeros((len(self.ds.srf.rh_verts)), )
for i, l in enumerate(self.ds.labnam):
#assumes that lh labels start with L and so on
vertices = self.ds.labv[demangle_hemi(l)]
if l[0] == 'l':
colors_lh[vertices] = scalars[i]
elif l[0] == 'r':
colors_rh[vertices] = scalars[i]
self.syrf_lh.mlab_source.scalars = colors_lh
self.syrf_rh.mlab_source.scalars = colors_rh
for syrf in (self.syrf_lh, self.syrf_rh):
set_lut(syrf, self.ds.opts.scalar_map)
set_color_range(syrf, scalars)
syrf.actor.mapper.scalar_visibility = True
#we don't need to set the scalars properly, but lets set the scalar range
#of the surface properly so that a colorbar will capture it
elif (self.ds.display_mode == 'scalar' and nc):
scalars = self.ds.node_scalars[nc]
#the scalar colorbar refers to syrf_lh only
min_scale, max_scale = np.min(scalars), np.max(scalars)
colors = np.tile(min_scale, (len(self.ds.srf.lh_verts), ))
colors[0] = max_scale
self.syrf_lh.mlab_source.scalars = colors
for syrf in (self.syrf_lh, self.syrf_rh):
syrf.actor.mapper.scalar_visibility = False
elif (self.ds.display_mode == 'module_multi'
and self.ds.opts.modules_on_surface):
new_colors = np.array(self.ds.module_colors[:self.ds.nr_modules +
1])
for syrf, nodes, letter, verts in ((self.syrf_lh, self.ds.lhnodes,
'l', self.ds.srf.lh_verts),
(self.syrf_rh, self.ds.rhnodes,
'r', self.ds.srf.rh_verts)):
colors = np.zeros((len(verts)), )
manager = syrf.module_manager.scalar_lut_manager
#set the mayavi object to the dummy cmap
#so that when changed notifications will work correctly
manager.lut_mode = 'black-white'
#now adjust its LUT manually
manager.number_of_colors = self.ds.nr_modules
manager.lut.table = new_colors
import bct
ci = bct.ls2ci(self.ds.modules, zeroindexed=True)[nodes]
i = 0
for l in self.ds.labnam:
#assumes that lh labels start with L and so on
if not l[0] == letter:
continue
vertices = self.ds.labv[demangle_hemi(l)]
colors[vertices] = ci[i] + 1
i += 1
syrf.mlab_source.scalars = colors
set_color_range(syrf, (0., self.ds.nr_modules + 1))
syrf.actor.mapper.scalar_visibility = True
else:
for syrf in (self.syrf_lh, self.syrf_rh):
syrf.actor.mapper.scalar_visibility = False
def draw_surfs(self):
from parsing_utils import demangle_hemi
srf_scalar=self.ds.scalar_display_settings.surf_color
nc = self.ds.scalar_display_settings.node_color
if (self.ds.display_mode=='scalar' and srf_scalar):
scalars = self.ds.node_scalars[srf_scalar]
colors_lh=np.zeros((len(self.ds.srf.lh_verts)),)
colors_rh=np.zeros((len(self.ds.srf.rh_verts)),)
for i,l in enumerate(self.ds.labnam):
#assumes that lh labels start with L and so on
vertices=self.ds.labv[demangle_hemi(l)]
if l[0]=='l':
colors_lh[vertices] = scalars[i]
elif l[0]=='r':
colors_rh[vertices] = scalars[i]
self.syrf_lh.mlab_source.scalars=colors_lh
self.syrf_rh.mlab_source.scalars=colors_rh
for syrf in (self.syrf_lh,self.syrf_rh):
set_lut(syrf,self.ds.opts.scalar_map)
set_color_range(syrf, scalars)
syrf.actor.mapper.scalar_visibility=True
#we don't need to set the scalars properly, but lets set the scalar range
#of the surface properly so that a colorbar will capture it
elif (self.ds.display_mode=='scalar' and nc):
scalars = self.ds.node_scalars[nc]
#the scalar colorbar refers to syrf_lh only
min_scale, max_scale = np.min(scalars), np.max(scalars)
colors = np.tile(min_scale, (len(self.ds.srf.lh_verts),))
colors[0] = max_scale
self.syrf_lh.mlab_source.scalars = colors
for syrf in (self.syrf_lh,self.syrf_rh):
syrf.actor.mapper.scalar_visibility=False
elif (self.ds.display_mode=='module_multi' and
self.ds.opts.modules_on_surface):
new_colors=np.array(self.ds.module_colors[:self.ds.nr_modules+1])
for syrf,nodes,letter,verts in (
(self.syrf_lh,self.ds.lhnodes,'l',self.ds.srf.lh_verts),
(self.syrf_rh,self.ds.rhnodes,'r',self.ds.srf.rh_verts)):
colors=np.zeros((len(verts)),)
manager=syrf.module_manager.scalar_lut_manager
#set the mayavi object to the dummy cmap
#so that when changed notifications will work correctly
manager.lut_mode='black-white'
#now adjust its LUT manually
manager.number_of_colors=self.ds.nr_modules
manager.lut.table=new_colors
import bct
ci = bct.ls2ci(self.ds.modules,zeroindexed=True)[nodes]
i = 0
for l in self.ds.labnam:
#assumes that lh labels start with L and so on
if not l[0]==letter:
continue
vertices=self.ds.labv[demangle_hemi(l)]
colors[vertices] = ci[i]+1
i+=1
syrf.mlab_source.scalars = colors
set_color_range(syrf, (0., self.ds.nr_modules+1))
syrf.actor.mapper.scalar_visibility=True
else:
for syrf in (self.syrf_lh,self.syrf_rh):
syrf.actor.mapper.scalar_visibility=False
