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 lA2spreadsheet(lAfilename,textoutputfilename):
lA = lA2array.calc(lAfilename)
f = open('/tmp/'+textoutputfilename+'.csv', 'w')
for i in lA.labels:
f.write(i+',')
f.write('\n')
for i in arange(shape(lA.dips)[0]):
lA.dips[i].tofile(f,sep=',',format='%s')
f.write('\n')
f.close()
print('finished writing /tmp/'+textoutputfilename+'.csv')
def startdensity(self, widget):
from meg import density
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)
try:
points = self.data_selected
except AttributeError:
from pdf2py import lA2array, readwrite
from numpy import array, append, size
from meg import dipole
datafile = self.builder.get_object("filechooserbutton1").get_filename()
print 'datafile=',datafile
#if datafile[-2:] == 'lA':
try:
lA = lA2array.calc(datafile)
except AttributeError: #probably not an MEG 4D file, try parsereport
lA = dipole.parsereport(datafile)
#lA.points = array([])
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)
session = p.data.session
run = p.data.run
datafilename = p.data.filename
f = open(fileoutput, 'w')
f.write('Patient:\t'+pid+'\n')
f.write('Scan:\t'+scan+'\n')
f.write('Session:\t'+session+'\n')
f.write('Run:\t'+run+'\n')
f.write('Localization File:\t'+datafilename+'\n')
f.write('Grid Size:\t'+dfa_info)
f.write('Latency\tX\tY\tZ\tQx\tQy\tQz\tRadius\t||\tQ\t||\tRms\tCorr\tGof\tIter\n')
f.write('(msec)\t(cm)\t(nAm)\t(cm)\t(nAm)\tfT\n')
f.write('EPOCH 1\n')
d = lA2array.calc(fn)
d.dips[:,0] = d.dips[:,0]*1000 #latency
d.dips[:,1:4] = d.dips[:,1:4]*100
d.dips[:,4:7] = d.dips[:,4:7]*1e+9
d.dips[:,7] = d.dips[:,7]*100
d.dips[:,8] = d.dips[:,8]*1e+9
d.dips[:,9] = d.dips[:,9]*1e+15
dips = d.dips[:,0:13]
#fwrite(f, dips.shape[], device_data.Xfm, 'd', 1);
for i in range(0,size(dips,0)):
for j in range(0, size(dips,1)):
f.write(str(round(dips[i,j],3))+'\t')
f.write('\n')
f.close()
