def calculate_modules(self,thres):
import bct
thres_adj=self.adj.copy()
thres_adj[thres_adj < thres] = 0
self.verbose_msg('Threshold for modularity calculation: %s'%str(thres))
modvec,_=bct.modularity_und(thres_adj)
self.modules = bct.ci2ls(modvec)
self.nr_modules = len(self.modules)
def calculate_modules(self, thres):
import graph, bct
thres_adj = self.adj.copy()
thres_adj[thres_adj < thres] = 0
self.verbose_msg('Threshold for modularity calculation: %s' %
str(thres))
modvec = graph.calculate_modules(thres_adj)
self.modules = bct.ci2ls(modvec)
self.nr_modules = len(self.modules)
def load_modules_or_scalars(self, params):
if not params.mat:
self.error_dialog('You must specify a valid matrix file')
return
if params.whichkind == 'scalars' and not params.measure_name:
self.error_dialog('Cannot leave scalar name blank. cvu uses '
'this value as a dictionary index')
return
import preprocessing
try:
ci = preprocessing.loadmat(params.mat,
field=params.field_name,
is_adjmat=False)
except (CVUError, IOError) as e:
self.error_dialog(str(e))
return
if params.mat_order:
try:
init_ord, bads = preprocessing.read_ordering_file(
params.mat_order)
except (IndexError, UnicodeDecodeError) as e:
self.error_dialog(str(e))
return
#delete the bads
if not params.ignore_deletes:
ci = np.delete(ci, bads)
#perform the swapping
try:
ci_ord = preprocessing.adj_sort(init_ord, self.labnam)
except CVUError as e:
self.error_dialog(str(e))
return
except KeyError as e:
self.error_dialog('Field not found: %s' % str(e))
return
ci = ci[ci_ord]
try:
ci = np.reshape(ci, (self.nr_labels, ))
except ValueError as e:
self.error_dialog('The %s file is of size %i after deletions, but '
'the dataset has %i regions' %
(params.whichkind, len(ci), self.nr_labels))
return
if params.whichkind == 'modules':
import bct
self.modules = bct.ci2ls(ci)
self.nr_modules = len(self.modules)
elif params.whichkind == 'scalars':
self.save_scalar(params.measure_name, ci)
params._increment_scalar_count()
def load_modules_or_scalars(self,params):
if not params.mat:
self.error_dialog('You must specify a valid matrix file'); return
if params.whichkind=='scalars' and not params.measure_name:
self.error_dialog('Cannot leave scalar name blank. cvu uses '
'this value as a dictionary index'); return
import preprocessing
try:
ci=preprocessing.loadmat(params.mat, field=params.field_name,
is_adjmat=False)
except (CVUError,IOError) as e: self.error_dialog(str(e)); return
if params.mat_order:
try:
init_ord, bads = preprocessing.read_ordering_file(
params.mat_order)
except (IndexError,UnicodeDecodeError) as e:
self.error_dialog(str(e)); return
#delete the bads
if not params.ignore_deletes:
ci=np.delete(ci,bads)
#perform the swapping
try:
ci_ord = preprocessing.adj_sort(init_ord, self.labnam)
except CVUError as e: self.error_dialog(str(e)); return
except KeyError as e:
self.error_dialog('Field not found: %s'%str(e)); return
ci=ci[ci_ord]
try:
ci=np.reshape(ci,(self.nr_labels,))
except ValueError as e:
self.error_dialog('The %s file is of size %i after deletions, but '
'the dataset has %i regions' %
(params.whichkind, len(ci), self.nr_labels)); return
if params.whichkind=='modules':
import bct
self.modules=bct.ci2ls(ci)
self.nr_modules=len(self.modules)
elif params.whichkind=='scalars':
self.save_scalar(params.measure_name,ci)
params._increment_scalar_count()
