# -*- coding: utf-8 -*- """Mayavi/traits GUI for setting MRI fiducials.""" # Authors: Christian Brodbeck # # 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()