def coregistercheck(self,widget,filename=None):
print filename, 'fn'
if self.builder.get_object("filechooserbutton1").get_filename() == None:
pass
else:
filename = self.filename = self.builder.get_object("filechooserbutton1").get_filename()
print 'loading and checking coreg', filename
try: self.mr = nibabel.load(filename); print 'loaded', filename
except RuntimeError: print 'unsupported MR file'; return
self.prevdata['MRI'] = filename
readwrite.writedata(self.prevdata, os.getenv('HOME')+'/.pymegdata')
try:
xfm = readwrite.readdata(os.path.splitext(filename)[0]+'.pym')
print 'file previously coregistered', xfm
self.builder.get_object("button1").set_sensitive(True)
except:
print 'cant find fiducal file', os.path.splitext(filename)[0]+'.pym';
return
self.lpa = xfm['lpa']
self.rpa = xfm['rpa']
self.nas = xfm['nas']
def __init__(self):
self.builder = gtk.Builder()
self.builder.add_from_file(os.path.splitext(__file__)[0]+".glade")
self.window = self.builder.get_object("window")
#for j in self.builder.get_objects():
#n = gtk.Buildable.get_name(j)
try:
self.prefs = readwrite.readdata(os.getenv('HOME')+'/.pymeg.pym')
print 'reading pref file'
for i in self.prefs.keys():
try: self.builder.get_object(i).set_state(self.prefs[i])
except: pass
pass
#i.set_state(self.prefs[i])
except IOError:
print 'no pref set.'
self.prefs = {}
dic = {
"on_preference_toggled" : self.updateprefs,
}
self.builder.connect_signals(dic)
def __init__(self):
self.builder = gtk.Builder()
self.builder.add_from_file(os.path.splitext(__file__)[0]+".glade")
self.window = self.builder.get_object("window")
dic = {
"on_toolbutton_refresh_clicked" : self.generate_testdata,
"on_button1_clicked" : self.generate_testdata,
"on_vboxMain_button_press_event" : self.button_press_event,
"on_vboxMain_button_release_event" : self.button_release_event,
"on_vboxMain_drag" : self.drag_begin,
"on_vboxMain_motion_notify_event" : self.drag_begin,
"on_toolbar_clear_clicked" : self.clear_selections,
"on_toolbar_zoomin_clicked" : self.zoomin_time,
"on_toolbar_zoomout_clicked" : self.zoomout_time,
"on_go_back_clicked" : self.page_back,
"on_go_forward_clicked" : self.page_forward,
"on_toolbutton_setup_toggled" : self.preferences_open,
"on_button_channel_apply_clicked" : self.channel_selection_apply,
"set_channel_groups" : self.set_channel_groups,
"showpopupmenu" : self.showpopupmenu,
"on_toolbar_plot_clicked" : self.plot_contour,
"on_plot_contour_activate" : self.plot_contour,
"on_button_delete_selection_clicked" : self.event_selection_delete,
"gtk_widget_hide" : self.hideinsteadofdelete,
"on_button_display_apply_clicked": self.display_apply,
"on_go_up_clicked" : self.page_up,
"on_go_down_clicked" : self.page_down,
"on_toolbutton_load_clicked" : self.load_data,
"on_menu_offset_correct_clicked" : self.offset_correct,
"on_button_epoch_clicked" : self.add_selections_to_event_process,
"on_store_event_clicked" : self.store_event,
"on_menu_save_noise_activate" : self.store_noise,
"on_menu_save_event_activate" : self.store_event,
"on_key_press_event" : self.key_press_event,
}
self.builder.connect_signals(dic)
try: self.prefs = readwrite.readdata(os.getenv('HOME')+'/.pymeg.pym')
except IOError: self.prefs = {}; readwrite.writedata(self.prefs, os.getenv('HOME')+'/.pymeg')
try:
self.line_r,self.line_g,self.line_b = self.prefs['LineColor'][0],self.prefs['LineColor'][1],self.prefs['LineColor'][2]
self.back_r,self.back_g,self.back_b = self.prefs['BackColor'][0],self.prefs['BackColor'][1],self.prefs['BackColor'][2]
except:
self.line_r,self.line_g,self.line_b = 1.,1.,1.
self.back_r,self.back_g,self.back_b = .9,.9,.9
self.color = (self.line_r,self.line_g,self.line_b)
self.create_draw_frame('none')
self.create_spec_frame('none')
self.create_csd_frame('none')
self.space = 0
#self.generate_testdata(None)
self.preferences_open(None)
def retrievepythondata(fn):
from pdf2py import readwrite
pyd = readwrite.readdata(fn)
try:
data = pyd["data"]
chlabels = pyd["chlabels"]
samplerate = pyd["samplerate"]
sp = 1 / np.float32(samplerate)
timeaxes = np.arange(0, sp * np.size(data, 0), sp)
except AttributeError:
print "ae"
return data, timeaxes, chlabels, samplerate
def create_draw_frame(self,widget):
#ion()
self.fig = Figure(figsize=[200,200], dpi=100)
self.canvas = FigureCanvas(self.fig)
#self.canvas.connect("scroll_event", self.scroll_event)
#self.canvas.connect('button_press_event', self.button_press_event)
self.canvas.show()
self.figure = self.canvas.figure
self.axes = self.fig.add_axes([0.045, 0.05, 0.93, 0.925], axisbg='#FFFFCC')
self.axes.axis('off')
self.vb = self.builder.get_object("viewport1")
self.vb.add(self.canvas)
#self.vb.pack_start(self.canvas, gtk.TRUE, gtk.TRUE)
self.vb.show()
from pdf2py import readwrite
self.data = readwrite.readdata('/home/danc/vault/decrypted/programming/python/chanlocs.pym')
#self.data = np.arange(300)#np.random.randn(300)
self.axes.scatter(self.data[1],self.data[0],marker='o',facecolors='none');
def changed_cb(self, combobox):
model = combobox.get_model()
index = combobox.get_active()
if index > -1:
print model[index][0], 'selected','index',index
#self.chan_ind = index
self.color_sel = str(model[index][0])
#self.im1.axes.clear()
print 'debug'
self.im1.set_cmap(self.color_sel)
self.im1.axes.figure.canvas.draw()
self.im2.set_cmap(self.color_sel)
self.im2.axes.figure.canvas.draw()
self.im3.set_cmap(self.color_sel)
self.im3.axes.figure.canvas.draw()
try:
prefs = readwrite.readdata(os.getenv('HOME')+'/.pymeg.pym')
prefs['MRI_color'] = index
readwrite.writedata(prefs, os.getenv('HOME')+'/.pymeg')
except IOError: pass
return
def populate_combo(self, colorlabels=None):
print 'populating channel list'
#if colorlabels == None:
#colorlabels = arange(50)
combobox = self.builder.get_object("combobox1")
combobox.clear()
liststore = gtk.ListStore(str)
cell = gtk.CellRendererText()
combobox.pack_start(cell)
combobox.add_attribute(cell, 'text', 0)
combobox.set_wrap_width(int(ceil(sqrt(len(colorlabels)))))
for n in colorlabels: #range(50):
liststore.append([n])
combobox.set_model(liststore)
combobox.connect('changed', self.changed_cb)
try:
prefs = readwrite.readdata(os.getenv('HOME')+'/.pymeg.pym')
combobox.set_active(prefs['MRI_color'])
print 'Setting color scheme to last'
except:
combobox.set_active(0)
return
def __init__(self, filepath):
print 'reading',filepath
self.nifti = nibabel.load(filepath)
dirpath = os.path.dirname(filepath)
self.data = copy(self.nifti.get_data())#.T
#self.nifti.data = self.data
h = self.nifti.get_header()
self.pixdim = h['pixdim'][1:4]
self.gettransform(h)
#self.reorient()
xfm_fn = os.path.splitext(filepath)[0]+'.pym'
if os.path.isfile(xfm_fn) == True:
print('loading index points found in file',xfm_fn)
self.fiddata = readwrite.readdata(xfm_fn)
self.getfiducals(h)
else:
try: #This is a shitty way in which fiducal point were saved in descrip field in header, as there were no user avail fields to store the 3X3 matrix.
self.lpa = eval(str(h['descrip']))[0]
self.rpa = eval(str(h['descrip']))[1]
self.nas = eval(str(h['descrip']))[2]
print('got fiducal info from description field in header')
except NameError:
print 'no fiducal file or info found. you will not be able to perform any transforms with other data.'
def __init__(self):
MT = progressbar.MainThread()
self.datahandler()
self.builder = gtk.Builder()
self.builder.add_from_file(os.path.splitext(__file__)[0]+".glade")
self.window = self.builder.get_object("window1")
n = self.builder.get_object('notebook1')
self.statusbar = self.builder.get_object("statusbar1")
self.statusbar_cid = self.statusbar.get_context_id("")
#n.set_current_page(0)
dic = {
"on_mrigridcompute_clicked" : self.mrigrid,
"on_filechooserbutton1_file_set": self.coregistercheck,
"on_filechooserbutton2_file_set": self.pdfcheck,
"on_coregister_clicked" : self.coregister_handler,
"on_radiobutton_clicked" : self.gridtypechanged,
"on_button2_clicked" : self.manualgrid,
}
self.builder.connect_signals(dic)
try:
self.prevdata = readwrite.readdata(os.getenv('HOME')+'/.pymegdata.pym')
print 'previous data', self.prevdata
self.builder.get_object("filechooserbutton1").set_uri('file://'+self.prevdata['MRI'])
#self.builder.get_object("filechooserbutton1").set_filename(self.prevdata['MRI'])
#self.mr = img.loadimage(self.prevdata['brain.nii.gz'])
filename = self.filename = self.prevdata['MRI']
self.coregistercheck(None, filename)
self.statusbar.push(self.statusbar_cid, 'Loading Previous MRI.')
except (IOError, KeyError): #no last file
print 'no prev data'
self.prevdata = {}
except TypeError:
pass
m.show_all()
m.popup(None,None,None,3,0)
if event.button == 1:
ap = self.axes.get_position()
x,y = self.canvas.get_width_height()
posx = (event.x/x-.5)*(1/(ap.x1-ap.x0))*-1
posy = ((event.y/y-.5)*(1/(ap.y0-ap.y1)))
#posx = ((event.x/x)-ap.x0)*(1/(ap.x1-ap.x0))
#posy = ((event.y/y)-(1-ap.y0))*(1/(ap.y0-ap.y1))
print posx,posy
from meg import nearest
nx=nearest.nearest(self.data[0],posy)[0]
ny=nearest.nearest(self.data[1],posx)[0]
print nx,ny
def apply_selection(self, widget):
print 'Number of channels applied:',size(self.chanchecked,0)
self.result_handler(self.chanchecked)
return self.chanchecked
if __name__ == "__main__":
from pdf2py import readwrite
chanlocs = readwrite.readdata('/home/danc/python/chlocs.pym')
chanlabels = []
for i in arange(size(chanlocs,1)):
chanlabels = append(chanlabels, 'A'+str(i))
mainwindow = setup(chanlocs,chanlabels)
mainwindow.window.show()
print 'testing'
gtk.main()
def load_coregister_info(self, widget):
if os.path.isfile(filepath+'.pym') == True:
print('loading index points found in file',filepath+'.pym')
self.fiddata = readwrite.readdata(filepath+'.pym')
self.getfiducals(h)
