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# -*- coding: utf-8 -*-
"""Mayavi/traits GUI visualization elements."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import numpy as np
from mayavi.mlab import pipeline, text3d
from mayavi.modules.glyph import Glyph
from mayavi.modules.surface import Surface
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.tools.mlab_scene_model import MlabSceneModel
from traits.api import (HasTraits, HasPrivateTraits, on_trait_change,
Instance, Array, Bool, Button, Enum, Float, Int, List,
Range, Str, RGBColor, Property, cached_property)
from traitsui.api import (View, Item, HGroup, VGrid, VGroup, Spring,
TextEditor)
from tvtk.api import tvtk
from ..defaults import DEFAULTS
from ..surface import _project_onto_surface, _normalize_vectors
from ..source_space import _points_outside_surface
from ..utils import SilenceStdout
from ..viz._3d import _create_mesh_surf, _toggle_mlab_render
headview_borders = VGroup(Item('headview', style='custom', show_label=False),
show_border=True, label='View')
def _mm_fmt(x):
"""Format data in units of mm."""
return '%0.1f' % x
laggy_float_editor_mm = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.1f' % x)
laggy_float_editor_scale = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.1f' % x)
laggy_float_editor_headscale = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.3f' % x)
laggy_float_editor_weight = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.2f' % x)
laggy_float_editor_scale = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.1f' % x)
laggy_float_editor_deg = TextEditor(auto_set=False, enter_set=True,
evaluate=float,
format_func=lambda x: '%0.1f' % x)
_BUTTON_WIDTH = -80
_DEG_WIDTH = -50 # radian floats
_MM_WIDTH = _DEG_WIDTH # mm floats
_SCALE_WIDTH = _DEG_WIDTH # scale floats
_INC_BUTTON_WIDTH = -25 # inc/dec buttons
_DEG_STEP_WIDTH = -50
_MM_STEP_WIDTH = _DEG_STEP_WIDTH
_SCALE_STEP_WIDTH = _DEG_STEP_WIDTH
_WEIGHT_WIDTH = -60 # weight floats
_VIEW_BUTTON_WIDTH = -60
# width is optimized for macOS and Linux avoid a horizontal scroll-bar
# even when a vertical one is present
_COREG_WIDTH = -290
_TEXT_WIDTH = -260
_REDUCED_TEXT_WIDTH = _TEXT_WIDTH - 40 * np.sign(_TEXT_WIDTH)
_DIG_SOURCE_WIDTH = _TEXT_WIDTH - 50 * np.sign(_TEXT_WIDTH)
_MRI_FIDUCIALS_WIDTH = _TEXT_WIDTH - 60 * np.sign(_TEXT_WIDTH)
_SHOW_BORDER = True
_RESET_LABEL = u"↻"
_RESET_WIDTH = _INC_BUTTON_WIDTH
class HeadViewController(HasTraits):
"""Set head views for the given coordinate system.
Parameters
----------
system : 'RAS' | 'ALS' | 'ARI'
Coordinate system described as initials for directions associated with
the x, y, and z axes. Relevant terms are: Anterior, Right, Left,
Superior, Inferior.
"""
system = Enum("RAS", "ALS", "ARI", desc="Coordinate system: directions of "
"the x, y, and z axis.")
right = Button()
front = Button()
left = Button()
top = Button()
interaction = Enum('trackball', 'terrain')
scale = Float(0.16)
scene = Instance(MlabSceneModel)
view = View(VGroup(
VGrid('0', Item('top', width=_VIEW_BUTTON_WIDTH), '0',
Item('right', width=_VIEW_BUTTON_WIDTH),
Item('front', width=_VIEW_BUTTON_WIDTH),
Item('left', width=_VIEW_BUTTON_WIDTH),
columns=3, show_labels=False),
'_',
HGroup(Item('scale', label='Scale',
editor=laggy_float_editor_headscale,
width=_SCALE_WIDTH, show_label=True),
Item('interaction', tooltip='Mouse interaction mode',
show_label=False), Spring()),
show_labels=False))
@on_trait_change('scene.activated')
def _init_view(self):
self.scene.parallel_projection = True
# apparently scene,activated happens several times
if self.scene.renderer:
self.sync_trait('scale', self.scene.camera, 'parallel_scale')
# and apparently this does not happen by default:
self.on_trait_change(self.scene.render, 'scale')
self.interaction = self.interaction # could be delayed
@on_trait_change('interaction')
def on_set_interaction(self, _, interaction):
if self.scene is None or self.scene.interactor is None:
return
# Ensure we're in the correct orientation for the
# InteractorStyleTerrain to have the correct "up"
self.on_set_view('front', '')
self.scene.mlab.draw()
self.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain() if interaction == 'terrain' else \
tvtk.InteractorStyleTrackballCamera()
# self.scene.interactor.interactor_style.
self.on_set_view('front', '')
self.scene.mlab.draw()
@on_trait_change('top,left,right,front')
def on_set_view(self, view, _):
if self.scene is None:
return
system = self.system
kwargs = dict(ALS=dict(front=(0, 90, -90),
left=(90, 90, 180),
right=(-90, 90, 0),
top=(0, 0, -90)),
RAS=dict(front=(90., 90., 180),
left=(180, 90, 90),
right=(0., 90, 270),
top=(90, 0, 180)),
ARI=dict(front=(0, 90, 90),
left=(-90, 90, 180),
right=(90, 90, 0),
top=(0, 180, 90)))
if system not in kwargs:
raise ValueError("Invalid system: %r" % system)
if view not in kwargs[system]:
raise ValueError("Invalid view: %r" % view)
kwargs = dict(zip(('azimuth', 'elevation', 'roll'),
kwargs[system][view]))
kwargs['focalpoint'] = (0., 0., 0.)
with SilenceStdout():
self.scene.mlab.view(distance=None, reset_roll=True,
figure=self.scene.mayavi_scene, **kwargs)
class Object(HasPrivateTraits):
"""Represent a 3d object in a mayavi scene."""
points = Array(float, shape=(None, 3))
nn = Array(float, shape=(None, 3))
name = Str
scene = Instance(MlabSceneModel, ())
src = Instance(VTKDataSource)
# This should be Tuple, but it is broken on Anaconda as of 2016/12/16
color = RGBColor((1., 1., 1.))
# Due to a MESA bug, we use 0.99 opacity to force alpha blending
opacity = Range(low=0., high=1., value=0.99)
visible = Bool(True)
def _update_points(self):
"""Update the location of the plotted points."""
if hasattr(self.src, 'data'):
self.src.data.points = self.points
return True
class PointObject(Object):
"""Represent a group of individual points in a mayavi scene."""
label = Bool(False)
label_scale = Float(0.01)
projectable = Bool(False) # set based on type of points
orientable = Property(depends_on=['project_to_points'])
text3d = List
point_scale = Float(10, label='Point Scale')
# projection onto a surface
project_to_points = Array(float, shape=(None, 3))
project_to_tris = Array(int, shape=(None, 3))
project_to_surface = Bool(False, label='Project', desc='project points '
'onto the surface')
orient_to_surface = Bool(False, label='Orient', desc='orient points '
'toward the surface')
scale_by_distance = Bool(False, label='Dist.', desc='scale points by '
'distance from the surface')
mark_inside = Bool(False, label='Mark', desc='mark points inside the '
'surface in a different color')
inside_color = RGBColor((0., 0., 0.))
glyph = Instance(Glyph)
resolution = Int(8)
view = View(HGroup(Item('visible', show_label=False),
Item('color', show_label=False),
Item('opacity')))
def __init__(self, view='points', has_norm=False, *args, **kwargs):
"""Init.
Parameters
----------
view : 'points' | 'cloud'
Whether the view options should be tailored to individual points
or a point cloud.
has_norm : bool
Whether a norm can be defined; adds view options based on point
norms (default False).
"""
assert view in ('points', 'cloud', 'arrow')
self._view = view
self._has_norm = bool(has_norm)
super(PointObject, self).__init__(*args, **kwargs)
def default_traits_view(self): # noqa: D102
color = Item('color', show_label=False)
scale = Item('point_scale', label='Size', width=_SCALE_WIDTH,
editor=laggy_float_editor_headscale)
orient = Item('orient_to_surface',
enabled_when='orientable and not project_to_surface',
tooltip='Orient points toward the surface')
dist = Item('scale_by_distance',
enabled_when='orientable and not project_to_surface',
tooltip='Scale points by distance from the surface')
mark = Item('mark_inside',
enabled_when='orientable and not project_to_surface',
tooltip='Mark points inside the surface using a different '
'color')
if self._view == 'arrow':
visible = Item('visible', label='Show', show_label=False)
return View(HGroup(visible, scale, 'opacity', 'label', Spring()))
elif self._view == 'points':
visible = Item('visible', label='Show', show_label=True)
views = (visible, color, scale, 'label')
else:
assert self._view == 'cloud'
visible = Item('visible', show_label=False)
views = (visible, color, scale)
if not self._has_norm:
return View(HGroup(*views))
group2 = HGroup(dist, Item('project_to_surface', show_label=True,
enabled_when='projectable',
tooltip='Project points onto the surface '
'(for visualization, does not affect '
'fitting)'),
orient, mark, Spring(), show_left=False)
return View(HGroup(HGroup(*views), group2))
@on_trait_change('label')
def _show_labels(self, show):
_toggle_mlab_render(self, False)
while self.text3d:
text = self.text3d.pop()
text.remove()
if show and len(self.src.data.points) > 0:
fig = self.scene.mayavi_scene
if self._view == 'arrow': # for axes
x, y, z = self.src.data.points[0]
self.text3d.append(text3d(
x, y, z, self.name, scale=self.label_scale,
color=self.color, figure=fig))
else:
for i, (x, y, z) in enumerate(np.array(self.src.data.points)):
self.text3d.append(text3d(
x, y, z, ' %i' % i, scale=self.label_scale,
color=self.color, figure=fig))
_toggle_mlab_render(self, True)
@on_trait_change('visible')
def _on_hide(self):
if not self.visible:
self.label = False
@on_trait_change('scene.activated')
def _plot_points(self):
"""Add the points to the mayavi pipeline"""
if self.scene is None:
return
if hasattr(self.glyph, 'remove'):
self.glyph.remove()
if hasattr(self.src, 'remove'):
self.src.remove()
_toggle_mlab_render(self, False)
x, y, z = self.points.T
fig = self.scene.mayavi_scene
scatter = pipeline.scalar_scatter(x, y, z, fig=fig)
if not scatter.running:
# this can occur sometimes during testing w/ui.dispose()
return
# fig.scene.engine.current_object is scatter
mode = 'arrow' if self._view == 'arrow' else 'sphere'
glyph = pipeline.glyph(scatter, color=self.color,
figure=fig, scale_factor=self.point_scale,
opacity=1., resolution=self.resolution,
mode=mode)
glyph.actor.property.backface_culling = True
glyph.glyph.glyph.vector_mode = 'use_normal'
glyph.glyph.glyph.clamping = False
if mode == 'arrow':
glyph.glyph.glyph_source.glyph_position = 'tail'
glyph.actor.mapper.color_mode = 'map_scalars'
glyph.actor.mapper.scalar_mode = 'use_point_data'
glyph.actor.mapper.use_lookup_table_scalar_range = False
self.src = scatter
self.glyph = glyph
self.sync_trait('point_scale', self.glyph.glyph.glyph, 'scale_factor')
self.sync_trait('color', self.glyph.actor.property, mutual=False)
self.sync_trait('visible', self.glyph)
self.sync_trait('opacity', self.glyph.actor.property)
self.sync_trait('mark_inside', self.glyph.actor.mapper,
'scalar_visibility')
self.on_trait_change(self._update_points, 'points')
self._update_marker_scaling()
self._update_marker_type()
self._update_colors()
_toggle_mlab_render(self, True)
# self.scene.camera.parallel_scale = _scale
# don't put project_to_tris here, just always set project_to_points second
@on_trait_change('points,project_to_points,project_to_surface,mark_inside')
def _update_projections(self):
"""Update the styles of the plotted points."""
if not hasattr(self.src, 'data'):
return
if self._view == 'arrow':
self.src.data.point_data.normals = self.nn
self.src.data.point_data.update()
return
# projections
if len(self.project_to_points) <= 1 or len(self.points) == 0:
return
# Do the projections
pts = self.points
surf = dict(rr=np.array(self.project_to_points),
tris=np.array(self.project_to_tris))
method = 'accurate' if len(surf['rr']) <= 20484 else 'nearest'
proj_pts, proj_nn = _project_onto_surface(
pts, surf, project_rrs=True, return_nn=True,
method=method)[2:4]
vec = pts - proj_pts # point to the surface
if self.project_to_surface:
pts = proj_pts
nn = proj_nn
else:
nn = vec.copy()
_normalize_vectors(nn)
if self.mark_inside and not self.project_to_surface:
scalars = _points_outside_surface(pts, surf).astype(int)
else:
scalars = np.ones(len(pts))
# With this, a point exactly on the surface is of size point_scale
dist = np.linalg.norm(vec, axis=-1, keepdims=True)
self.src.data.point_data.normals = (250 * dist + 1) * nn
self.src.data.point_data.scalars = scalars
self.glyph.actor.mapper.scalar_range = [0., 1.]
self.src.data.points = pts # projection can change this
self.src.data.point_data.update()
@on_trait_change('color,inside_color')
def _update_colors(self):
if self.glyph is None:
return
# inside_color is the surface color, let's try to get far
# from that
inside = np.array(self.inside_color)
# if it's too close to gray, just use black:
if np.mean(np.abs(inside - 0.5)) < 0.2:
inside.fill(0.)
else:
inside = 1 - inside
colors = np.array([tuple(inside) + (1,),
tuple(self.color) + (1,)]) * 255.
self.glyph.module_manager.scalar_lut_manager.lut.table = colors
@on_trait_change('project_to_surface,orient_to_surface')
def _update_marker_type(self):
# not implemented for arrow
if self.glyph is None or self._view == 'arrow':
return
defaults = DEFAULTS['coreg']
gs = self.glyph.glyph.glyph_source
res = getattr(gs.glyph_source, 'theta_resolution',
getattr(gs.glyph_source, 'resolution', None))
if self.project_to_surface or self.orient_to_surface:
gs.glyph_source = tvtk.CylinderSource()
gs.glyph_source.height = defaults['eegp_height']
gs.glyph_source.center = (0., -defaults['eegp_height'], 0)
gs.glyph_source.resolution = res
else:
gs.glyph_source = tvtk.SphereSource()
gs.glyph_source.phi_resolution = res
gs.glyph_source.theta_resolution = res
@on_trait_change('scale_by_distance,project_to_surface')
def _update_marker_scaling(self):
if self.glyph is None:
return
if self.scale_by_distance and not self.project_to_surface:
self.glyph.glyph.scale_mode = 'scale_by_vector'
else:
self.glyph.glyph.scale_mode = 'data_scaling_off'
def _resolution_changed(self, new):
if not self.glyph:
return
gs = self.glyph.glyph.glyph_source.glyph_source
if isinstance(gs, tvtk.SphereSource):
gs.phi_resolution = new
gs.theta_resolution = new
elif isinstance(gs, tvtk.CylinderSource):
gs.resolution = new
else: # ArrowSource
gs.tip_resolution = new
gs.shaft_resolution = new
@cached_property
def _get_orientable(self):
return (len(self.project_to_points) > 0 and
len(self.project_to_tris) > 0)
class SurfaceObject(Object):
"""Represent a solid object in a mayavi scene.
Notes
-----
Doesn't automatically update plot because update requires both
:attr:`points` and :attr:`tris`. Call :meth:`plot` after updating both
attributes.
"""
rep = Enum("Surface", "Wireframe")
tris = Array(int, shape=(None, 3))
surf = Instance(Surface)
surf_rear = Instance(Surface)
view = View(HGroup(Item('visible', show_label=False),
Item('color', show_label=False),
Item('opacity')))
def __init__(self, block_behind=False, **kwargs): # noqa: D102
self._block_behind = block_behind
self._deferred_tri_update = False
super(SurfaceObject, self).__init__(**kwargs)
def clear(self): # noqa: D102
if hasattr(self.src, 'remove'):
self.src.remove()
if hasattr(self.surf, 'remove'):
self.surf.remove()
if hasattr(self.surf_rear, 'remove'):
self.surf_rear.remove()
self.reset_traits(['src', 'surf'])
@on_trait_change('scene.activated')
def plot(self):
"""Add the points to the mayavi pipeline"""
_scale = self.scene.camera.parallel_scale
self.clear()
if not np.any(self.tris):
return
fig = self.scene.mayavi_scene
surf = dict(rr=self.points, tris=self.tris)
normals = _create_mesh_surf(surf, fig=fig)
self.src = normals.parent
rep = 'wireframe' if self.rep == 'Wireframe' else 'surface'
# Add the opaque "inside" first to avoid the translucent "outside"
# from being occluded (gh-5152)
if self._block_behind:
surf_rear = pipeline.surface(
normals, figure=fig, color=self.color, representation=rep,
line_width=1)
surf_rear.actor.property.frontface_culling = True
self.surf_rear = surf_rear
self.sync_trait('color', self.surf_rear.actor.property,
mutual=False)
self.sync_trait('visible', self.surf_rear, 'visible')
self.surf_rear.actor.property.opacity = 1.
surf = pipeline.surface(
normals, figure=fig, color=self.color, representation=rep,
line_width=1)
surf.actor.property.backface_culling = True
self.surf = surf
self.sync_trait('visible', self.surf, 'visible')
self.sync_trait('color', self.surf.actor.property, mutual=False)
self.sync_trait('opacity', self.surf.actor.property)
self.scene.camera.parallel_scale = _scale
@on_trait_change('tris')
def _update_tris(self):
self._deferred_tris_update = True
@on_trait_change('points')
def _update_points(self):
if Object._update_points(self):
if self._deferred_tris_update:
self.src.data.polys = self.tris
self._deffered_tris_update = False
self.src.update() # necessary for SurfaceObject since Mayavi 4.5.0
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