def startdensity(self, widget):
from meg import density
from mri import img_nibabel as img
from numpy import array, append, size, ones
#import nifti
gofscale = float(self.builder.get_object('entry1').get_text())
sigma = int(self.builder.get_object('entry2').get_text())
print self.builder.get_object("filechooserbutton2").get_filename()
self.mrfilename = self.builder.get_object("filechooserbutton2").get_filename()
#mr = nifti.NiftiImage(self.mrfilename)
mr = img.loadimage(self.mrfilename)
print 'loaded MRI',mr
if self.itemselected == 'manual':
points = array(eval(self.paired_item.get_text()))
gof = ones(size(points,0))
if self.itemselected == 'selected':
points = self.data_selected
if self.itemselected == 'fileopen':
from pdf2py import lA2array, readwrite
from meg import dipole
datafile = self.builder.get_object("fileopenitem").get_filename()
print 'datafile=',datafile
try:
lA = lA2array.calc(datafile)
except AttributeError: #probably not an MEG 4D file, try parsereport
lA = dipole.parsereport(datafile)
lA.dips[:,1:4] = lA.dips[:,1:4]/100 #xyz in meters (this is the units in the 4D,lA file)
points = lA.dips[:,1:4]*1000 # units in mm
gof_ind = lA.labels.index('GoF')
gof = lA.dips[:,gof_ind]
from meg import dipole2densitynifti
self.dipoledensityimage = dipole2densitynifti.handler(points,mr,gofscale,gof,sigma)
self.fcd = self.builder.get_object("filechooserdialog1")
self.fcd.show()
self.fcd.set_current_name('*dd.nii.gz')
filter = gtk.FileFilter()
filter.set_name("Nifti files")
filter.add_pattern("*nii.gz")
filter.add_pattern("*nii")
self.fcd.add_filter(filter)
#uridefault = self.fcd.set_uri(self.fcd.get_current_folder_uri())
self.fcd.set_uri('file://'+self.mrfilename)
uridefault = self.fcd.get_current_folder_uri()
print 'uri', uridefault
self.fcd.set_uri(uridefault)
def mrigrid(self,widget):
print 'computing MRI source space '
from numpy import shape
self.mr = img.loadimage(self.filename)
def gridthread():
if self.builder.get_object('radiobutton4').get_active() == True:
braintype = 'yes'
else:
braintype = 'no'
self.mr.decimate(int(self.builder.get_object('entry1').get_text()))
self.grid = (transform.scalesourcespace(self.headshape, self.mr.megxyz,
self.mr.lpa,self.mr.rpa,self.mr.nas,self.mr.pixdim,brain=braintype))
#except: print 'Error, aborting'; return
print 'grid shape', shape(self.grid) #shape(self.workspace_data.results.grid)
print self.callback
self.gridcallback()
MT = progressbar.MainThread()
MT.main(gridthread)
