def do_label_automatically(self, info):
#figure out c1, c2, c3
# c1,c2,c3 = 3*(None,)
# for e in self.electrodes:
# if len(e.corner) == 0:
# continue
# elif len(e.corner) > 1:
# error_dialog('Wrong corners specified, check again')
# return
#
# elif 'corner 1' in e.corner:
# c1 = e
# elif 'corner 2' in e.corner:
# c2 = e
# elif 'corner 3' in e.corner:
# c3 = e
#
# if c1 is None or c2 is None or c3 is None:
# error_dialog('Not all corners were specified')
# return
cur_geom = self.model._grid_geom[self.cur_grid]
if cur_geom == 'user-defined' and self.naming_convention != 'line':
from color_utils import mayavi2traits_color
from name_holder import GeometryNameHolder, GeomGetterWindow
nameholder = GeometryNameHolder(
geometry=cur_geom,
color=mayavi2traits_color(self.model._colors[self.cur_grid]))
geomgetterwindow = GeomGetterWindow(holder=nameholder)
if geomgetterwindow.edit_traits().result:
cur_geom = geomgetterwindow.geometry
else:
error_dialog("User did not specify any geometry")
return
import pipeline as pipe
if self.naming_convention == 'line':
pipe.fit_grid_to_line(
self.electrodes,
#c1.asiso(), c2.asiso(), c3.asiso(), cur_geom,
delta=self.labeling_delta,
rho_loose=self.labeling_rho + 10,
epsilon=self.labeling_epsilon)
else:
pipe.fit_grid_by_fixed_points(self.electrodes,
cur_geom,
delta=self.labeling_delta,
rho=self.labeling_rho,
rho_strict=self.labeling_rho - 10,
rho_loose=self.labeling_rho + 15,
epsilon=self.labeling_epsilon,
mindist=0,
maxdist=36)
self.naming_following_labeling(cur_geom=cur_geom)
def do_label_automatically(self, info):
#figure out c1, c2, c3
# c1,c2,c3 = 3*(None,)
# for e in self.electrodes:
# if len(e.corner) == 0:
# continue
# elif len(e.corner) > 1:
# error_dialog('Wrong corners specified, check again')
# return
#
# elif 'corner 1' in e.corner:
# c1 = e
# elif 'corner 2' in e.corner:
# c2 = e
# elif 'corner 3' in e.corner:
# c3 = e
#
# if c1 is None or c2 is None or c3 is None:
# error_dialog('Not all corners were specified')
# return
cur_geom = self.model._grid_geom[self.cur_grid]
if cur_geom=='user-defined' and self.naming_convention != 'line':
from color_utils import mayavi2traits_color
from name_holder import GeometryNameHolder, GeomGetterWindow
nameholder = GeometryNameHolder(
geometry=cur_geom,
color=mayavi2traits_color(
self.model._colors[self.cur_grid]))
geomgetterwindow = GeomGetterWindow(holder=nameholder)
if geomgetterwindow.edit_traits().result:
cur_geom = geomgetterwindow.geometry
else:
error_dialog("User did not specify any geometry")
return
import pipeline as pipe
if self.naming_convention == 'line':
pipe.fit_grid_to_line(self.electrodes,
#c1.asiso(), c2.asiso(), c3.asiso(), cur_geom,
delta=self.labeling_delta,
rho_loose=self.labeling_rho+10,
epsilon=self.labeling_epsilon)
else:
pipe.fit_grid_by_fixed_points(self.electrodes, cur_geom,
delta=self.labeling_delta,
rho=self.labeling_rho,
rho_strict=self.labeling_rho-10,
rho_loose=self.labeling_rho+15,
epsilon=self.labeling_epsilon,
mindist=0, maxdist=36)
self.naming_following_labeling(cur_geom=cur_geom)
def _postprocessing_effect_electrode_reposition(self):
if self.cur_sel is None:
error_dialog("No electrode specified to move")
return
pd = self.model.panel2d
image_name = pd.currently_showing.name
px,py,pz,_ = pd.pins[image_name][pd.current_pin]
if image_name=='t1':
px,py,pz = pd.map_cursor((px,py,pz), pd.images['t1'][2])
self.model.move_electrode( self.cur_sel, (px,py,pz),
in_ras=(image_name=='t1'), as_postprocessing=True )
def do_linear_interpolation(self, info):
#TODO does not feed back coordinates to model,
#which is important for snapping
if self.cur_sel is None:
return
elif self.cur_sel.special_name == '':
return
if len(self.cur_sel.geom_coords) == 0:
error_dialog("Specify geom_coords before linear interpolation")
return
x,y = self.cur_sel.geom_coords
x_low = self._find_closest_neighbor(self.cur_sel, 'x', '-')
x_hi = self._find_closest_neighbor(self.cur_sel, 'x', '+')
y_low = self._find_closest_neighbor(self.cur_sel, 'y', '-')
y_hi = self._find_closest_neighbor(self.cur_sel, 'y', '+')
loc = None
#handle simplest case of electrode directly in between others
if x_low is not None and x_hi is not None:
xl = x_low.geom_coords[0]
xh = x_hi.geom_coords[0]
ratio = (x - xl) / (xh - xl)
loc = np.array(x_low.iso_coords) + (np.array(x_hi.iso_coords)-
np.array(x_low.iso_coords))*ratio
elif y_low is not None and y_hi is not None:
yl = y_low.geom_coords[1]
yh = y_hi.geom_coords[1]
ratio = (y - yl) / (yh - yl)
loc = np.array(y_low.iso_coords) + (np.array(y_hi.iso_coords)-
np.array(y_low.iso_coords))*ratio
#handle poorer case of electrode on end of line
if x_low is not None and loc is None:
x_lower = self._find_closest_neighbor(x_low, 'x', '-')
xl = x_low.geom_coords[0]
xll = x_lower.geom_coords[0]
if xl == xll+1:
loc = 2*np.array(x_low.iso_coords) - np.array(
x_lower.iso_coords)
if x_hi is not None and loc is None:
x_higher = self._find_closest_neighbor(x_hi, 'x', '+')
xh = x_hi.geom_coords[0]
xhh = x_higher.geom_coords[0]
if xh == xhh-1:
loc = 2*np.array(x_hi.iso_coords) - np.array(
x_higher.iso_coords)
#import pdb
#pdb.set_trace()
if y_low is not None and loc is None:
y_lower = self._find_closest_neighbor(y_low, 'y', '-')
yl = y_low.geom_coords[1]
yll = y_lower.geom_coords[1]
if yl == yll+1:
loc = 2*np.array(y_low.iso_coords) - np.array(
y_lower.iso_coords)
if y_hi is not None and loc is None:
y_higher = self._find_closest_neighbor(y_hi, 'y', '+')
yh = y_hi.geom_coords[1]
yhh = y_higher.geom_coords[1]
if yh == yhh-1:
loc = 2*np.array(y_hi.iso_coords) - np.array(
y_higher.iso_coords)
if loc is not None:
self.cur_sel.iso_coords = tuple(loc)
self.cur_sel.special_name = 'Linearly interpolated electrode'
else:
error_dialog('No line for simple linear interpolation\n'
'Better algorithm needed')
# translate the electrode into RAS space
import pipeline as pipe
aff = self.model.acquire_affine()
pipe.translate_electrodes_to_surface_space( [self.cur_sel], aff,
subjects_dir=self.model.subjects_dir, subject=self.model.subject)
pipe.linearly_transform_electrodes_to_isotropic_coordinate_space(
[self.cur_sel], self.model.ct_scan,
isotropization_type = ('deisotropize' if self.model.isotropize
else 'copy_to_ct'))
# add this electrode to the grid model so that it can be visualized
self.model.add_electrode_to_grid(self.cur_sel, self.cur_grid)
def do_label_automatically(self, info):
#figure out c1, c2, c3
c1,c2,c3 = 3*(None,)
for e in self.electrodes:
if len(e.corner) == 0:
continue
elif len(e.corner) > 1:
error_dialog('Wrong corners specified, check again')
return
elif 'corner 1' in e.corner:
c1 = e
elif 'corner 2' in e.corner:
c2 = e
elif 'corner 3' in e.corner:
c3 = e
if c1 is None or c2 is None or c3 is None:
error_dialog('Not all corners were specified')
return
cur_geom = self.model._grid_geom[self.cur_grid]
if cur_geom=='user-defined' and self.naming_convention != 'line':
from color_utils import mayavi2traits_color
from name_holder import GeometryNameHolder, GeomGetterWindow
nameholder = GeometryNameHolder(
geometry=cur_geom,
color=mayavi2traits_color(
self.model._colors[self.cur_grid]))
geomgetterwindow = GeomGetterWindow(holder=nameholder)
if geomgetterwindow.edit_traits().result:
cur_geom = geomgetterwindow.geometry
else:
error_dialog("User did not specify any geometry")
return
import pipeline as pipe
if self.naming_convention == 'line':
pipe.fit_grid_to_line(self.electrodes, c1.asct(), c2.asct(),
c3.asct(), cur_geom, delta=self.model.delta,
rho_loose=self.model.rho_loose)
#do actual labeling
for elec in self.model._grids[self.cur_grid]:
_,y = elec.geom_coords
index = y+1
elec.name = '%s%i'%(self.name_stem, index)
else:
pipe.fit_grid_to_plane(self.electrodes, c1.asct(), c2.asct(),
c3.asct(), cur_geom)
#do actual labeling
for elec in self.model._grids[self.cur_grid]:
x,y = elec.geom_coords
if self.naming_convention=='grid':
#index = y*np.max(cur_geom) + x + 1
index = x*np.min(cur_geom) + y + 1
else: #reverse_grid
#index = x*np.min(cur_geom) + y + 1
index = y*np.max(cur_geom) + x + 1
elec.name = '%s%i'%(self.name_stem, index)