def set_node_colors(self):
#set node_colors
if self.display_mode == 'normal':
self.node_colors = list(self.node_colors_default)
elif self.display_mode == 'scalar':
#node colors are not used here, instead the scalar value is set directly
self.node_colors = list(self.node_colors_default)
elif self.display_mode == 'module_single':
new_colors = np.tile(.3, self.nr_labels)
new_colors[self.get_module()] = .8
self.node_colors = list(self.opts.default_map._pl(new_colors))
elif self.display_mode == 'module_multi':
while self.nr_modules > len(self.module_colors):
i, j = np.random.randint(18, size=(2, ))
col = (np.array(self.module_colors[i]) +
self.module_colors[j]) / 2
col = np.array(col, dtype=int)
self.module_colors.append(col.tolist())
#perm=np.random.permutation(len(self.module_colors))
#mayavi scalars depend on saving the module colors
#self.module_colors=np.array(self.module_colors)[perm].tolist()
cols = self.module_colors[:self.nr_modules]
import bct
ci = bct.ls2ci(self.modules, zeroindexed=True)
self.node_colors = ((np.array(self.module_colors)[ci]) /
255).tolist()
def draw_nodes(self): nc=self.ds.scalar_display_settings.node_color ns=self.ds.scalar_display_settings.node_size lhn=self.nodes_lh; lhn_ix=self.ds.lhnodes rhn=self.nodes_rh; rhn_ix=self.ds.rhnodes for nodes,ixes in ((lhn,lhn_ix),(rhn,rhn_ix)): nr=len(ixes) #set node size if self.ds.display_mode=='scalar' and ns: nodes.glyph.scale_mode='scale_by_vector' nodes.glyph.glyph.scale_factor=8 nodes.mlab_source.dataset.point_data.vectors=( np.tile(self.ds.node_scalars[ns][ixes],(3,1)).T) else: nodes.glyph.scale_mode='data_scaling_off' nodes.glyph.glyph.scale_factor=3 #set node color -- we dont care about ds.node_colors for mayavi if (self.ds.display_mode=='normal' or (self.ds.display_mode=='scalar' and not nc)): set_lut(nodes,self.ds.opts.default_map) nodes.mlab_source.dataset.point_data.scalars=np.tile(.3,nr) elif self.ds.display_mode=='scalar': #and nc must be true set_lut(nodes,self.ds.opts.scalar_map) nodes.mlab_source.dataset.point_data.scalars=( self.ds.node_scalars[nc][ixes]) elif self.ds.display_mode=='module_single': set_lut(nodes,self.ds.opts.default_map) new_colors=np.tile(.3,self.ds.nr_labels) new_colors[self.ds.get_module()]=.8 nodes.mlab_source.dataset.point_data.scalars=new_colors[ixes] elif self.ds.display_mode=='module_multi': new_colors=np.array(self.ds.module_colors[:self.ds.nr_modules]) manager=nodes.module_manager.scalar_lut_manager #set the mayavi object to the dummy cmap that we hide from user #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 #set the mayavi scalars to be fractions between 0 and 1 import bct nodes.mlab_source.dataset.point_data.scalars=(bct.ls2ci( self.ds.modules,zeroindexed=True)/self.ds.nr_modules)[ixes] mlab.draw()
def calculate_graph_stats(self,thres):
import graph,bct
thres_adj = self.adj.copy()
thres_adj[thres_adj < thres] = 0
self.verbose_msg('Threshold for graph calculations: %s'%str(thres))
try:
self.graph_stats=graph.do_summary(thres_adj,bct.ls2ci(self.modules),
self.opts.intermediate_graphopts_list)
for name,arr in self.graph_stats.iteritems():
self.save_scalar(name,arr,passive=True)
except CVUError:
self.error_dialog("Community structure required for some of "
"the calculations specified. Try calculating modules first.")
def calculate_graph_stats(self, thres):
import graph, bct
thres_adj = self.adj.copy()
thres_adj[thres_adj < thres] = 0
self.verbose_msg('Threshold for graph calculations: %s' % str(thres))
try:
self.graph_stats = graph.do_summary(
thres_adj, bct.ls2ci(self.modules),
self.opts.intermediate_graphopts_list)
for name, arr in self.graph_stats.iteritems():
self.save_scalar(name, arr, passive=True)
except CVUError:
self.error_dialog(
"Community structure required for some of "
"the calculations specified. Try calculating modules first.")
def set_node_colors(self): #set node_colors if self.display_mode=='normal': self.node_colors=list(self.node_colors_default) elif self.display_mode=='scalar': #node colors are not used here, instead the scalar value is set directly self.node_colors=list(self.node_colors_default) elif self.display_mode=='module_single': new_colors=np.tile(.3,self.nr_labels) new_colors[self.get_module()]=.8 self.node_colors=list(self.opts.default_map._pl(new_colors)) elif self.display_mode=='module_multi': while self.nr_modules > len(self.module_colors): i,j=np.random.randint(18,size=(2,)) col=(np.array(self.module_colors[i])+self.module_colors[j])/2 col=np.array(col,dtype=int) self.module_colors.append(col.tolist()) perm=np.random.permutation(len(self.module_colors)) #mayavi scalars depend on saving the module colors self.module_colors=np.array(self.module_colors)[perm].tolist() cols=self.module_colors[:self.nr_modules] import bct ci=bct.ls2ci(self.modules,zeroindexed=True) self.node_colors=((np.array(self.module_colors)[ci])/255).tolist()
def draw_nodes(self):
nc = self.ds.scalar_display_settings.node_color
ns = self.ds.scalar_display_settings.node_size
lhn = self.nodes_lh
lhn_ix = self.ds.lhnodes
rhn = self.nodes_rh
rhn_ix = self.ds.rhnodes
for nodes, ixes in ((lhn, lhn_ix), (rhn, rhn_ix)):
nr = len(ixes)
#set node size
if self.ds.display_mode == 'scalar' and ns:
scalars = self.ds.node_scalars[ns]
#for node size, the scalars need to be scaled to 0-1
scalars = (scalars - np.min(scalars)) / (np.max(scalars) -
np.min(scalars))
#logarithmic scaling does a better job of differentiating large nodes
scalars = (np.exp(scalars * np.log(2)) - 1) / (np.e - 1)
#scalars=(4**(scalars*np.log(3)/np.log(4))-1)/3
#scalars=(4**scalars-1)/3
#scalars**=2
nodes.glyph.scale_mode = 'scale_by_vector'
nodes.glyph.glyph.scale_factor = 12
nodes.mlab_source.dataset.point_data.vectors = (np.tile(
scalars[ixes], (3, 1)).T)
else:
nodes.glyph.scale_mode = 'data_scaling_off'
nodes.glyph.glyph.scale_factor = 3
#set node color -- we dont care about ds.node_colors for mayavi
if (self.ds.display_mode == 'normal'
or (self.ds.display_mode == 'scalar' and not nc) or
(self.ds.display_mode in ['module_single', 'module_multi']
and self.ds.opts.modules_on_surface)):
scalars = np.tile(.3, nr)
set_lut(nodes, self.ds.opts.default_map)
set_color_range(nodes, (0., 1.))
nodes.mlab_source.dataset.point_data.scalars = scalars
elif self.ds.display_mode == 'scalar': #and nc must be true
scalars = self.ds.node_scalars[nc]
set_lut(nodes, self.ds.opts.scalar_map)
set_color_range(nodes, scalars)
nodes.mlab_source.dataset.point_data.scalars = scalars[ixes]
elif self.ds.display_mode == 'module_single':
scalars = np.tile(.3, self.ds.nr_labels)
scalars[self.ds.get_module()] = .8
set_lut(nodes, self.ds.opts.default_map)
set_color_range(nodes, (0., 1.))
nodes.mlab_source.dataset.point_data.scalars = scalars[ixes]
elif self.ds.display_mode == 'module_multi':
new_colors = np.array(
self.ds.module_colors[:self.ds.nr_modules + 1])
manager = nodes.module_manager.scalar_lut_manager
#set the mayavi object to the dummy cmap that we hide from user
#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
#set the mayavi scalars to be fractions between 0 and 1
import bct
nodes.mlab_source.dataset.point_data.scalars = (bct.ls2ci(
self.ds.modules, zeroindexed=True))[ixes] + 1
set_color_range(nodes, (0., self.ds.nr_modules + 1))
mlab.draw()
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_nodes(self):
nc=self.ds.scalar_display_settings.node_color
ns=self.ds.scalar_display_settings.node_size
lhn=self.nodes_lh; lhn_ix=self.ds.lhnodes
rhn=self.nodes_rh; rhn_ix=self.ds.rhnodes
for nodes,ixes in ((lhn,lhn_ix),(rhn,rhn_ix)):
nr=len(ixes)
#set node size
if self.ds.display_mode=='scalar' and ns:
scalars = self.ds.node_scalars[ns]
#for node size, the scalars need to be scaled to 0-1
scalars = (scalars-np.min(scalars)) / (np.max(scalars)-np.min(scalars))
#logarithmic scaling does a better job of differentiating large nodes
scalars = (np.exp(scalars*np.log(2))-1)/(np.e-1)
#scalars=(4**(scalars*np.log(3)/np.log(4))-1)/3
#scalars=(4**scalars-1)/3
#scalars**=2
nodes.glyph.scale_mode='scale_by_vector'
nodes.glyph.glyph.scale_factor=12
nodes.mlab_source.dataset.point_data.vectors=(
np.tile(scalars[ixes],(3,1)).T)
else:
nodes.glyph.scale_mode='data_scaling_off'
nodes.glyph.glyph.scale_factor=3
#set node color -- we dont care about ds.node_colors for mayavi
if (self.ds.display_mode=='normal' or
(self.ds.display_mode=='scalar' and not nc) or
(self.ds.display_mode in ['module_single',
'module_multi'] and self.ds.opts.modules_on_surface)):
scalars = np.tile(.3, nr)
set_lut(nodes, self.ds.opts.default_map)
set_color_range(nodes, (0.,1.))
nodes.mlab_source.dataset.point_data.scalars = scalars
elif self.ds.display_mode=='scalar': #and nc must be true
scalars = self.ds.node_scalars[nc]
set_lut(nodes, self.ds.opts.scalar_map)
set_color_range(nodes, scalars)
nodes.mlab_source.dataset.point_data.scalars = scalars[ixes]
elif self.ds.display_mode=='module_single':
scalars = np.tile(.3, self.ds.nr_labels)
scalars[self.ds.get_module()]=.8
set_lut(nodes, self.ds.opts.default_map)
set_color_range(nodes, (0.,1.))
nodes.mlab_source.dataset.point_data.scalars = scalars[ixes]
elif self.ds.display_mode=='module_multi':
new_colors=np.array(self.ds.module_colors[
:self.ds.nr_modules+1])
manager=nodes.module_manager.scalar_lut_manager
#set the mayavi object to the dummy cmap that we hide from user
#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
#set the mayavi scalars to be fractions between 0 and 1
import bct
nodes.mlab_source.dataset.point_data.scalars=(bct.ls2ci(
self.ds.modules,zeroindexed=True))[ixes]+1
set_color_range(nodes, (0., self.ds.nr_modules+1))
mlab.draw()
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
