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# -*- coding: utf-8 -*-
"""Mayavi/traits GUI for setting MRI fiducials."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import map
from mayavi.core.ui.mayavi_scene import MayaviScene
from mayavi.tools.mlab_scene_model import MlabSceneModel
import numpy as np
from pyface.api import confirm, error, FileDialog, OK, YES
from traits.api import (HasTraits, HasPrivateTraits, on_trait_change,
cached_property, DelegatesTo, Event, Instance,
Property, Array, Bool, Button, Enum)
from traitsui.api import HGroup, Item, VGroup, View, Handler, ArrayEditor
from traitsui.menu import NoButtons
from tvtk.pyface.scene_editor import SceneEditor
from ..coreg import fid_fname, _find_fiducials_files, _find_head_bem
from ..defaults import DEFAULTS
from ..io import write_fiducials
from ..io.constants import FIFF
from ..surface import complete_surface_info, decimate_surface
from ..utils import get_subjects_dir, logger, warn
from ..viz._3d import _toggle_mlab_render
from ._file_traits import (SurfaceSource, fid_wildcard, FiducialsSource,
MRISubjectSource, SubjectSelectorPanel,
Surf)
from ._viewer import (HeadViewController, PointObject, SurfaceObject,
headview_borders, _BUTTON_WIDTH,
_MRI_FIDUCIALS_WIDTH, _MM_WIDTH,
_RESET_LABEL, _RESET_WIDTH, _mm_fmt)
defaults = DEFAULTS['coreg']
class MRIHeadWithFiducialsModel(HasPrivateTraits):
"""Represent an MRI head shape (high and low res) with fiducials.
Attributes
----------
points : array (n_points, 3)
MRI head surface points.
tris : array (n_tris, 3)
Triangles based on points.
lpa : array (1, 3)
Left peri-auricular point coordinates.
nasion : array (1, 3)
Nasion coordinates.
rpa : array (1, 3)
Right peri-auricular point coordinates.
"""
subject_source = Instance(MRISubjectSource, ())
bem_low_res = Instance(SurfaceSource, ())
bem_high_res = Instance(SurfaceSource, ())
fid = Instance(FiducialsSource, ())
fid_file = DelegatesTo('fid', 'file')
fid_fname = DelegatesTo('fid', 'fname')
fid_points = DelegatesTo('fid', 'points')
subjects_dir = DelegatesTo('subject_source')
subject = DelegatesTo('subject_source')
subject_has_bem = DelegatesTo('subject_source')
lpa = Array(float, (1, 3))
nasion = Array(float, (1, 3))
rpa = Array(float, (1, 3))
reset = Event(desc="Reset fiducials to the file.")
# info
can_save = Property(depends_on=['file', 'can_save_as'])
can_save_as = Property(depends_on=['lpa', 'nasion', 'rpa'])
can_reset = Property(depends_on=['file', 'fid.points', 'lpa', 'nasion',
'rpa'])
fid_ok = Property(depends_on=['lpa', 'nasion', 'rpa'], desc="All points "
"are set")
default_fid_fname = Property(depends_on=['subjects_dir', 'subject'],
desc="the default file name for the "
"fiducials fif file")
# switch for the GUI (has no effect in the model)
lock_fiducials = Bool(False, desc="Used by GIU, has no effect in the "
"model.")
@on_trait_change('fid_points')
def reset_fiducials(self): # noqa: D102
if self.fid_points is not None:
self.lpa = self.fid_points[0:1]
self.nasion = self.fid_points[1:2]
self.rpa = self.fid_points[2:3]
def save(self, fname=None):
"""Save the current fiducials to a file.
Parameters
----------
fname : str
Destination file path. If None, will use the current fid filename
if available, or else use the default pattern.
"""
if fname is None:
fname = self.fid_file
if not fname:
fname = self.default_fid_fname
dig = [{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_LPA,
'r': np.array(self.lpa[0])},
{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_NASION,
'r': np.array(self.nasion[0])},
{'kind': FIFF.FIFFV_POINT_CARDINAL,
'ident': FIFF.FIFFV_POINT_RPA,
'r': np.array(self.rpa[0])}]
write_fiducials(fname, dig, FIFF.FIFFV_COORD_MRI)
self.fid_file = fname
@cached_property
def _get_can_reset(self):
if not self.fid_file:
return False
elif np.any(self.lpa != self.fid.points[0:1]):
return True
elif np.any(self.nasion != self.fid.points[1:2]):
return True
elif np.any(self.rpa != self.fid.points[2:3]):
return True
return False
@cached_property
def _get_can_save_as(self):
can = not (np.all(self.nasion == self.lpa) or
np.all(self.nasion == self.rpa) or
np.all(self.lpa == self.rpa))
return can
@cached_property
def _get_can_save(self):
if not self.can_save_as:
return False
elif self.fid_file:
return True
elif self.subjects_dir and self.subject:
return True
else:
return False
@cached_property
def _get_default_fid_fname(self):
fname = fid_fname.format(subjects_dir=self.subjects_dir,
subject=self.subject)
return fname
@cached_property
def _get_fid_ok(self):
return all(np.any(pt) for pt in (self.nasion, self.lpa, self.rpa))
def _reset_fired(self):
self.reset_fiducials()
# if subject changed because of a change of subjects_dir this was not
# triggered
@on_trait_change('subjects_dir,subject')
def _subject_changed(self):
subject = self.subject
subjects_dir = self.subjects_dir
if not subjects_dir or not subject:
return
# find high-res head model (if possible)
high_res_path = _find_head_bem(subject, subjects_dir, high_res=True)
low_res_path = _find_head_bem(subject, subjects_dir, high_res=False)
if high_res_path is None and low_res_path is None:
msg = 'No standard head model was found for subject %s' % subject
error(None, msg, "No head surfaces found")
raise RuntimeError(msg)
if high_res_path is not None:
self.bem_high_res.file = high_res_path
else:
self.bem_high_res.file = low_res_path
if low_res_path is None:
# This should be very rare!
warn('No low-resolution head found, decimating high resolution '
'mesh (%d vertices): %s' % (len(self.bem_high_res.surf.rr),
high_res_path,))
# Create one from the high res one, which we know we have
rr, tris = decimate_surface(self.bem_high_res.surf.rr,
self.bem_high_res.surf.tris,
n_triangles=5120)
surf = complete_surface_info(dict(rr=rr, tris=tris),
copy=False, verbose=False)
# directly set the attributes of bem_low_res
self.bem_low_res.surf = Surf(tris=surf['tris'], rr=surf['rr'],
nn=surf['nn'])
else:
self.bem_low_res.file = low_res_path
# find fiducials file
fid_files = _find_fiducials_files(subject, subjects_dir)
if len(fid_files) == 0:
self.fid.reset_traits(['file'])
self.lock_fiducials = False
else:
self.fid_file = fid_files[0].format(subjects_dir=subjects_dir,
subject=subject)
self.lock_fiducials = True
# does not seem to happen by itself ... so hard code it:
self.reset_fiducials()
class SetHandler(Handler):
"""Handler to change style when setting MRI fiducials."""
def object_set_changed(self, info): # noqa: D102
return self.object_locked_changed(info)
def object_locked_changed(self, info): # noqa: D102
if info.object.locked:
ss = ''
else:
ss = 'border-style: solid; border-color: red; border-width: 2px;'
# This will only work for Qt, but hopefully that's most users!
try:
_color_children(info.ui.info.ui.control, ss)
except AttributeError: # safeguard for wxpython
pass
def _color_children(obj, ss):
"""Qt helper."""
for child in obj.children():
if 'QRadioButton' in repr(child):
child.setStyleSheet(ss if child.isChecked() else '')
elif 'QLineEdit' in repr(child):
child.setStyleSheet(ss)
elif 'QWidget' in repr(child): # on Linux it's nested
_color_children(child, ss)
_SET_TOOLTIP = ('Click on the MRI image to set the position, '
'or enter values below')
class FiducialsPanel(HasPrivateTraits):
"""Set fiducials on an MRI surface."""
model = Instance(MRIHeadWithFiducialsModel)
fid_file = DelegatesTo('model')
fid_fname = DelegatesTo('model')
lpa = DelegatesTo('model')
nasion = DelegatesTo('model')
rpa = DelegatesTo('model')
can_save = DelegatesTo('model')
can_save_as = DelegatesTo('model')
can_reset = DelegatesTo('model')
fid_ok = DelegatesTo('model')
locked = DelegatesTo('model', 'lock_fiducials')
set = Enum('LPA', 'Nasion', 'RPA')
current_pos_mm = Array(float, (1, 3))
save_as = Button(label='Save as...')
save = Button(label='Save')
reset_fid = Button(label=_RESET_LABEL)
headview = Instance(HeadViewController)
hsp_obj = Instance(SurfaceObject)
picker = Instance(object)
# the layout of the dialog created
view = View(VGroup(
HGroup(Item('fid_file', width=_MRI_FIDUCIALS_WIDTH,
tooltip='MRI fiducials file'), show_labels=False),
HGroup(Item('set', width=_MRI_FIDUCIALS_WIDTH,
format_func=lambda x: x, style='custom',
tooltip=_SET_TOOLTIP), show_labels=False),
HGroup(Item('current_pos_mm',
editor=ArrayEditor(width=_MM_WIDTH, format_func=_mm_fmt),
tooltip='MRI fiducial position (mm)'), show_labels=False),
HGroup(Item('save', enabled_when='can_save',
tooltip="If a filename is currently specified, save to "
"that file, otherwise save to the default file name",
width=_BUTTON_WIDTH),
Item('save_as', enabled_when='can_save_as',
width=_BUTTON_WIDTH),
Item('reset_fid', enabled_when='can_reset', width=_RESET_WIDTH,
tooltip='Reset to file values (if available)'),
show_labels=False),
enabled_when="locked==False", show_labels=False), handler=SetHandler())
def __init__(self, *args, **kwargs): # noqa: D102
super(FiducialsPanel, self).__init__(*args, **kwargs)
@on_trait_change('current_pos_mm')
def _update_pos(self):
attr = self.set.lower()
if not np.allclose(getattr(self, attr), self.current_pos_mm * 1e-3):
setattr(self, attr, self.current_pos_mm * 1e-3)
@on_trait_change('model:lpa')
def _update_lpa(self, name):
if self.set == 'LPA':
self.current_pos_mm = self.lpa * 1000
@on_trait_change('model:nasion')
def _update_nasion(self, name):
if self.set.lower() == 'Nasion':
self.current_pos_mm = self.nasion * 1000
@on_trait_change('model:rpa')
def _update_rpa(self, name):
if self.set.lower() == 'RPA':
self.current_pos_mm = self.rpa * 1000
def _reset_fid_fired(self):
self.model.reset = True
def _save_fired(self):
self.model.save()
def _save_as_fired(self):
if self.fid_file:
default_path = self.fid_file
else:
default_path = self.model.default_fid_fname
dlg = FileDialog(action="save as", wildcard=fid_wildcard,
default_path=default_path)
dlg.open()
if dlg.return_code != OK:
return
path = dlg.path
if not path.endswith('.fif'):
path = path + '.fif'
if os.path.exists(path):
answer = confirm(None, "The file %r already exists. Should it "
"be replaced?", "Overwrite File?")
if answer != YES:
return
self.model.save(path)
def _on_pick(self, picker):
if self.locked:
return
self.picker = picker
n_pos = len(picker.picked_positions)
if n_pos == 0:
logger.debug("GUI: picked empty location")
return
if picker.actor is self.hsp_obj.surf.actor.actor:
idxs = []
idx = None
pt = [picker.pick_position]
elif self.hsp_obj.surf.actor.actor in picker.actors:
idxs = [i for i in range(n_pos) if picker.actors[i] is
self.hsp_obj.surf.actor.actor]
idx = idxs[-1]
pt = [picker.picked_positions[idx]]
else:
logger.debug("GUI: picked object other than MRI")
def round_(x):
return round(x, 3)
poss = [map(round_, pos) for pos in picker.picked_positions]
pos = map(round_, picker.pick_position)
msg = ["Pick Event: %i picked_positions:" % n_pos]
line = str(pos)
if idx is None:
line += " <-pick_position"
msg.append(line)
for i, pos in enumerate(poss):
line = str(pos)
if i == idx:
line += " <- MRI mesh"
elif i in idxs:
line += " (<- also MRI mesh)"
msg.append(line)
logger.debug(os.linesep.join(msg))
if self.set == 'Nasion':
self.nasion = pt
elif self.set == 'LPA':
self.lpa = pt
elif self.set == 'RPA':
self.rpa = pt
else:
raise ValueError("set = %r" % self.set)
@on_trait_change('set')
def _on_set_change(self, obj, name, old, new):
if new == 'Nasion':
self.current_pos_mm = self.nasion * 1000
self.headview.front = True
elif new == 'LPA':
self.current_pos_mm = self.lpa * 1000
self.headview.left = True
elif new == 'RPA':
self.current_pos_mm = self.rpa * 1000
self.headview.right = True
# FiducialsPanel view that allows manipulating all coordinates numerically
view2 = View(VGroup(Item('fid_file', label='Fiducials File'),
Item('fid_fname', show_label=False, style='readonly'),
Item('set', style='custom'), 'lpa', 'nasion', 'rpa',
HGroup(Item('save', enabled_when='can_save'),
Item('save_as', enabled_when='can_save_as'),
Item('reset_fid', enabled_when='can_reset'),
show_labels=False),
enabled_when="locked==False"))
class FiducialsFrame(HasTraits):
"""GUI for interpolating between two KIT marker files.
Parameters
----------
subject : None | str
Set the subject which is initially selected.
subjects_dir : None | str
Override the SUBJECTS_DIR environment variable.
"""
model = Instance(MRIHeadWithFiducialsModel, ())
scene = Instance(MlabSceneModel, ())
headview = Instance(HeadViewController)
spanel = Instance(SubjectSelectorPanel)
panel = Instance(FiducialsPanel)
mri_obj = Instance(SurfaceObject)
point_scale = float(defaults['mri_fid_scale'])
lpa_obj = Instance(PointObject)
nasion_obj = Instance(PointObject)
rpa_obj = Instance(PointObject)
def _headview_default(self):
return HeadViewController(scene=self.scene, system='RAS')
def _panel_default(self):
panel = FiducialsPanel(model=self.model, headview=self.headview)
panel.trait_view('view', view2)
return panel
def _spanel_default(self):
return SubjectSelectorPanel(model=self.model.subject_source)
view = View(HGroup(Item('scene',
editor=SceneEditor(scene_class=MayaviScene),
dock='vertical'),
VGroup(headview_borders,
VGroup(Item('spanel', style='custom'),
label="Subject", show_border=True,
show_labels=False),
VGroup(Item('panel', style="custom"),
label="Fiducials", show_border=True,
show_labels=False),
show_labels=False),
show_labels=False),
resizable=True,
buttons=NoButtons)
def __init__(self, subject=None, subjects_dir=None,
**kwargs): # noqa: D102
super(FiducialsFrame, self).__init__(**kwargs)
subjects_dir = get_subjects_dir(subjects_dir)
if subjects_dir is not None:
self.spanel.subjects_dir = subjects_dir
if subject is not None:
if subject in self.spanel.subjects:
self.spanel.subject = subject
@on_trait_change('scene.activated')
def _init_plot(self):
_toggle_mlab_render(self, False)
lpa_color = defaults['lpa_color']
nasion_color = defaults['nasion_color']
rpa_color = defaults['rpa_color']
# bem
color = defaults['mri_color']
self.mri_obj = SurfaceObject(points=self.model.points, color=color,
tri=self.model.tris, scene=self.scene)
self.model.on_trait_change(self._on_mri_src_change, 'tris')
self.panel.hsp_obj = self.mri_obj
# fiducials
self.lpa_obj = PointObject(scene=self.scene, color=lpa_color,
has_norm=True,
point_scale=self.point_scale)
self.panel.sync_trait('lpa', self.lpa_obj, 'points', mutual=False)
self.sync_trait('point_scale', self.lpa_obj, mutual=False)
self.nasion_obj = PointObject(scene=self.scene, color=nasion_color,
has_norm=True,
point_scale=self.point_scale)
self.panel.sync_trait('nasion', self.nasion_obj, 'points',
mutual=False)
self.sync_trait('point_scale', self.nasion_obj, mutual=False)
self.rpa_obj = PointObject(scene=self.scene, color=rpa_color,
has_norm=True,
point_scale=self.point_scale)
self.panel.sync_trait('rpa', self.rpa_obj, 'points', mutual=False)
self.sync_trait('point_scale', self.rpa_obj, mutual=False)
self.headview.left = True
_toggle_mlab_render(self, True)
# picker
self.scene.mayavi_scene.on_mouse_pick(self.panel._on_pick, type='cell')
def _on_mri_src_change(self):
if (not np.any(self.model.points)) or (not np.any(self.model.tris)):
self.mri_obj.clear()
return
self.mri_obj.points = self.model.points
self.mri_obj.tri = self.model.tris
self.mri_obj.plot()
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