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"""
Core visualization operations based on PyVista.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
# Joan Massich <mailsik@gmail.com>
#
# License: Simplified BSD
from contextlib import contextmanager
from inspect import signature
import os
import re
import sys
import warnings
import numpy as np
from ._abstract import _AbstractRenderer, Figure3D
from ._utils import (_get_colormap_from_array, _alpha_blend_background,
ALLOWED_QUIVER_MODES, _init_mne_qtapp)
from ...fixes import _compare_version
from ...transforms import apply_trans
from ...utils import (copy_base_doc_to_subclass_doc, _check_option,
_require_version, _validate_type, warn)
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
import pyvista
from pyvista import Plotter, PolyData, Line, close_all, UnstructuredGrid
try:
from pyvistaqt import BackgroundPlotter # noqa
except ImportError:
from pyvista import BackgroundPlotter
from pyvista.plotting.plotting import _ALL_PLOTTERS
from vtkmodules.vtkCommonCore import (
vtkCommand, vtkLookupTable, VTK_UNSIGNED_CHAR)
from vtkmodules.vtkCommonDataModel import VTK_VERTEX, vtkPiecewiseFunction
from vtkmodules.vtkCommonTransforms import vtkTransform
from vtkmodules.vtkFiltersCore import vtkCellDataToPointData, vtkGlyph3D
from vtkmodules.vtkFiltersGeneral import (
vtkTransformPolyDataFilter, vtkMarchingContourFilter)
from vtkmodules.vtkFiltersHybrid import vtkPolyDataSilhouette
from vtkmodules.vtkFiltersSources import (
vtkSphereSource, vtkConeSource, vtkCylinderSource, vtkArrowSource,
vtkPlatonicSolidSource, vtkGlyphSource2D)
from vtkmodules.vtkImagingCore import vtkImageReslice
from vtkmodules.vtkRenderingCore import (
vtkMapper, vtkActor, vtkCellPicker, vtkColorTransferFunction,
vtkPolyDataMapper, vtkVolume, vtkCoordinate, vtkDataSetMapper)
from vtkmodules.vtkRenderingVolumeOpenGL2 import vtkSmartVolumeMapper
from vtkmodules.util.numpy_support import numpy_to_vtk
try:
from vtkmodules.vtkCommonCore import VTK_VERSION
except Exception: # some bad versions of VTK
VTK_VERSION = '9.0'
VTK9 = _compare_version(VTK_VERSION, '>=', '9.0')
_FIGURES = dict()
class PyVistaFigure(Figure3D):
"""PyVista-based 3D Figure.
.. note:: This class should not be instantiated directly via
``mne.viz.PyVistaFigure(...)``. Instead, use
:func:`mne.viz.create_3d_figure`.
See Also
--------
mne.viz.create_3d_figure
"""
def __init__(self):
pass
def _init(self, plotter=None, show=False, title='PyVista Scene',
size=(600, 600), shape=(1, 1), background_color='black',
smooth_shading=True, off_screen=False, notebook=False,
splash=False, multi_samples=None):
self._plotter = plotter
self.display = None
self.background_color = background_color
self.smooth_shading = smooth_shading
self.notebook = notebook
self.title = title
self.splash = splash
self.store = dict()
self.store['window_size'] = size
self.store['shape'] = shape
self.store['off_screen'] = off_screen
self.store['border'] = False
self.store['multi_samples'] = multi_samples
if not self.notebook:
self.store['show'] = show
self.store['title'] = title
self.store['auto_update'] = False
self.store['menu_bar'] = False
self.store['toolbar'] = False
self.store['update_app_icon'] = False
self._plotter_class = BackgroundPlotter
if 'app_window_class' in signature(BackgroundPlotter).parameters:
from ._qt import _MNEMainWindow
self.store['app_window_class'] = _MNEMainWindow
else:
self._plotter_class = Plotter
self._nrows, self._ncols = self.store['shape']
self._azimuth = self._elevation = None
def _build(self):
if self.plotter is None:
if not self.notebook:
out = _init_mne_qtapp(
enable_icon=hasattr(self._plotter_class, 'set_icon'),
splash=self.splash)
# replace it with the Qt object
if self.splash:
self.splash = out[1]
app = out[0]
else:
app = out
self.store['app'] = app
plotter = self._plotter_class(**self.store)
plotter.background_color = self.background_color
self._plotter = plotter
if self.plotter.iren is not None:
self.plotter.iren.initialize()
_process_events(self.plotter)
_process_events(self.plotter)
return self.plotter
def _is_active(self):
if self.plotter is None:
return False
return hasattr(self.plotter, 'ren_win')
class _Projection(object):
"""Class storing projection information.
Attributes
----------
xy : array
Result of 2d projection of 3d data.
pts : None
Scene sensors handle.
"""
def __init__(self, *, xy, pts, plotter):
"""Store input projection information into attributes."""
self.xy = xy
self.pts = pts
self.plotter = plotter
def visible(self, state):
"""Modify visibility attribute of the sensors."""
self.pts.SetVisibility(state)
self.plotter.render()
@copy_base_doc_to_subclass_doc
class _PyVistaRenderer(_AbstractRenderer):
"""Class managing rendering scene.
Attributes
----------
plotter: Plotter
Main PyVista access point.
name: str
Name of the window.
"""
def __init__(self, fig=None, size=(600, 600), bgcolor='black',
name="PyVista Scene", show=False, shape=(1, 1),
notebook=None, smooth_shading=True, splash=False,
multi_samples=None):
from .._3d import _get_3d_option
_require_version('pyvista', 'use 3D rendering', '0.32')
multi_samples = _get_3d_option('multi_samples')
# multi_samples > 1 is broken on macOS + Intel Iris + volume rendering
if sys.platform == 'darwin':
multi_samples = 1
figure = PyVistaFigure()
figure._init(
show=show, title=name, size=size, shape=shape,
background_color=bgcolor, notebook=notebook,
smooth_shading=smooth_shading, splash=splash,
multi_samples=multi_samples)
self.font_family = "arial"
self.tube_n_sides = 20
self.antialias = _get_3d_option('antialias')
self.depth_peeling = _get_3d_option('depth_peeling')
self.smooth_shading = smooth_shading
if isinstance(fig, int):
saved_fig = _FIGURES.get(fig)
# Restore only active plotter
if saved_fig is not None and saved_fig._is_active():
self.figure = saved_fig
else:
self.figure = figure
_FIGURES[fig] = self.figure
elif fig is None:
self.figure = figure
else:
self.figure = fig
# Enable off_screen if sphinx-gallery or testing
if pyvista.OFF_SCREEN:
self.figure.store['off_screen'] = True
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
# pyvista theme may enable depth peeling by default so
# we disable it initially to better control the value afterwards
with _disabled_depth_peeling():
self.plotter = self.figure._build()
self._hide_axes()
self._enable_antialias()
self._enable_depth_peeling()
# FIX: https://github.com/pyvista/pyvistaqt/pull/68
if not hasattr(self.plotter, "iren"):
self.plotter.iren = None
self.update_lighting()
@property
def _all_plotters(self):
if self.figure.plotter is not None:
return [self.figure.plotter]
else:
return list()
@property
def _all_renderers(self):
if self.figure.plotter is not None:
return self.figure.plotter.renderers
else:
return list()
def _hide_axes(self):
for renderer in self._all_renderers:
renderer.hide_axes()
def _update(self):
for plotter in self._all_plotters:
plotter.update()
def _index_to_loc(self, idx):
_ncols = self.figure._ncols
row = idx // _ncols
col = idx % _ncols
return (row, col)
def _loc_to_index(self, loc):
_ncols = self.figure._ncols
return loc[0] * _ncols + loc[1]
def subplot(self, x, y):
x = np.max([0, np.min([x, self.figure._nrows - 1])])
y = np.max([0, np.min([y, self.figure._ncols - 1])])
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
self.plotter.subplot(x, y)
def scene(self):
return self.figure
def update_lighting(self):
# Inspired from Mayavi's version of Raymond Maple 3-lights illumination
for renderer in self._all_renderers:
lights = list(renderer.GetLights())
headlight = lights.pop(0)
headlight.SetSwitch(False)
# below and centered, left and above, right and above
az_el_in = ((0, -45, 0.7), (-60, 30, 0.7), (60, 30, 0.7))
for li, light in enumerate(lights):
if li < len(az_el_in):
light.SetSwitch(True)
light.SetPosition(_to_pos(*az_el_in[li][:2]))
light.SetIntensity(az_el_in[li][2])
else:
light.SetSwitch(False)
light.SetPosition(_to_pos(0.0, 0.0))
light.SetIntensity(0.0)
light.SetColor(1.0, 1.0, 1.0)
def set_interaction(self, interaction):
if not hasattr(self.plotter, "iren") or self.plotter.iren is None:
return
if interaction == "rubber_band_2d":
for renderer in self._all_renderers:
renderer.enable_parallel_projection()
if hasattr(self.plotter, 'enable_rubber_band_2d_style'):
self.plotter.enable_rubber_band_2d_style()
else:
from vtkmodules.vtkInteractionStyle import\
vtkInteractorStyleRubberBand2D
style = vtkInteractorStyleRubberBand2D()
self.plotter.interactor.SetInteractorStyle(style)
else:
for renderer in self._all_renderers:
renderer.disable_parallel_projection()
kwargs = dict()
if interaction == 'terrain':
kwargs['mouse_wheel_zooms'] = True
getattr(self.plotter, f'enable_{interaction}_style')(**kwargs)
def legend(self, labels, border=False, size=0.1, face='triangle',
loc='upper left'):
return self.plotter.add_legend(
labels, size=(size, size), face=face, loc=loc)
def polydata(self, mesh, color=None, opacity=1.0, normals=None,
backface_culling=False, scalars=None, colormap=None,
vmin=None, vmax=None, interpolate_before_map=True,
representation='surface', line_width=1.,
polygon_offset=None, **kwargs):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
rgba = False
if color is not None and len(color) == mesh.n_points:
if color.shape[1] == 3:
scalars = np.c_[color, np.ones(mesh.n_points)]
else:
scalars = color
scalars = (scalars * 255).astype('ubyte')
color = None
rgba = True
if isinstance(colormap, np.ndarray):
if colormap.dtype == np.uint8:
colormap = colormap.astype(np.float64) / 255.
from matplotlib.colors import ListedColormap
colormap = ListedColormap(colormap)
if normals is not None:
mesh.point_data["Normals"] = normals
mesh.GetPointData().SetActiveNormals("Normals")
else:
_compute_normals(mesh)
if 'rgba' in kwargs:
rgba = kwargs["rgba"]
kwargs.pop('rgba')
smooth_shading = self.smooth_shading
if representation == 'wireframe':
smooth_shading = False # never use smooth shading for wf
actor = _add_mesh(
plotter=self.plotter,
mesh=mesh, color=color, scalars=scalars, edge_color=color,
rgba=rgba, opacity=opacity, cmap=colormap,
backface_culling=backface_culling,
rng=[vmin, vmax], show_scalar_bar=False,
smooth_shading=smooth_shading,
interpolate_before_map=interpolate_before_map,
style=representation, line_width=line_width, **kwargs,
)
if polygon_offset is not None:
mapper = actor.GetMapper()
mapper.SetResolveCoincidentTopologyToPolygonOffset()
mapper.SetRelativeCoincidentTopologyPolygonOffsetParameters(
polygon_offset, polygon_offset)
return actor, mesh
def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
backface_culling=False, scalars=None, colormap=None,
vmin=None, vmax=None, interpolate_before_map=True,
representation='surface', line_width=1., normals=None,
polygon_offset=None, **kwargs):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
vertices = np.c_[x, y, z].astype(float)
triangles = np.c_[np.full(len(triangles), 3), triangles]
mesh = PolyData(vertices, triangles)
return self.polydata(
mesh=mesh,
color=color,
opacity=opacity,
normals=normals,
backface_culling=backface_culling,
scalars=scalars,
colormap=colormap,
vmin=vmin,
vmax=vmax,
interpolate_before_map=interpolate_before_map,
representation=representation,
line_width=line_width,
polygon_offset=polygon_offset,
**kwargs,
)
def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
vmin=None, vmax=None, colormap=None,
normalized_colormap=False, kind='line', color=None):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
if colormap is not None:
colormap = _get_colormap_from_array(colormap,
normalized_colormap)
vertices = np.array(surface['rr'])
triangles = np.array(surface['tris'])
n_triangles = len(triangles)
triangles = np.c_[np.full(n_triangles, 3), triangles]
mesh = PolyData(vertices, triangles)
mesh.point_data['scalars'] = scalars
contour = mesh.contour(isosurfaces=contours)
line_width = width
if kind == 'tube':
contour = contour.tube(radius=width, n_sides=self.tube_n_sides)
line_width = 1.0
actor = _add_mesh(
plotter=self.plotter,
mesh=contour,
show_scalar_bar=False,
line_width=line_width,
color=color,
rng=[vmin, vmax],
cmap=colormap,
opacity=opacity,
smooth_shading=self.smooth_shading,
)
return actor, contour
def surface(self, surface, color=None, opacity=1.0,
vmin=None, vmax=None, colormap=None,
normalized_colormap=False, scalars=None,
backface_culling=False, polygon_offset=None):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
normals = surface.get('nn', None)
vertices = np.array(surface['rr'])
triangles = np.array(surface['tris'])
triangles = np.c_[np.full(len(triangles), 3), triangles]
mesh = PolyData(vertices, triangles)
colormap = _get_colormap_from_array(colormap, normalized_colormap)
if scalars is not None:
mesh.point_data['scalars'] = scalars
return self.polydata(
mesh=mesh,
color=color,
opacity=opacity,
normals=normals,
backface_culling=backface_culling,
scalars=scalars,
colormap=colormap,
vmin=vmin,
vmax=vmax,
polygon_offset=polygon_offset,
)
def sphere(self, center, color, scale, opacity=1.0,
resolution=8, backface_culling=False,
radius=None):
from vtkmodules.vtkFiltersSources import vtkSphereSource
factor = 1.0 if radius is not None else scale
center = np.array(center, dtype=float)
if len(center) == 0:
return None, None
_check_option('center.ndim', center.ndim, (1, 2))
_check_option('center.shape[-1]', center.shape[-1], (3,))
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
sphere = vtkSphereSource()
sphere.SetThetaResolution(resolution)
sphere.SetPhiResolution(resolution)
if radius is not None:
sphere.SetRadius(radius)
sphere.Update()
geom = sphere.GetOutput()
mesh = PolyData(center)
glyph = mesh.glyph(orient=False, scale=False,
factor=factor, geom=geom)
actor = _add_mesh(
self.plotter,
mesh=glyph, color=color, opacity=opacity,
backface_culling=backface_culling,
smooth_shading=self.smooth_shading
)
return actor, glyph
def tube(self, origin, destination, radius=0.001, color='white',
scalars=None, vmin=None, vmax=None, colormap='RdBu',
normalized_colormap=False, reverse_lut=False):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
cmap = _get_colormap_from_array(colormap, normalized_colormap)
for (pointa, pointb) in zip(origin, destination):
line = Line(pointa, pointb)
if scalars is not None:
line.point_data['scalars'] = scalars[0, :]
scalars = 'scalars'
color = None
else:
scalars = None
tube = line.tube(radius, n_sides=self.tube_n_sides)
actor = _add_mesh(
plotter=self.plotter,
mesh=tube,
scalars=scalars,
flip_scalars=reverse_lut,
rng=[vmin, vmax],
color=color,
show_scalar_bar=False,
cmap=cmap,
smooth_shading=self.smooth_shading,
)
return actor, tube
def quiver3d(self, x, y, z, u, v, w, color, scale, mode, resolution=8,
glyph_height=None, glyph_center=None, glyph_resolution=None,
opacity=1.0, scale_mode='none', scalars=None, colormap=None,
backface_culling=False, line_width=2., name=None,
glyph_width=None, glyph_depth=None, glyph_radius=0.15,
solid_transform=None, *, clim=None):
_check_option('mode', mode, ALLOWED_QUIVER_MODES)
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
factor = scale
vectors = np.c_[u, v, w]
points = np.vstack(np.c_[x, y, z])
n_points = len(points)
cell_type = np.full(n_points, VTK_VERTEX)
cells = np.c_[np.full(n_points, 1), range(n_points)]
args = (cells, cell_type, points)
if not VTK9:
args = (np.arange(n_points) * 3,) + args
grid = UnstructuredGrid(*args)
if scalars is None:
scalars = np.ones((n_points,))
grid.point_data['scalars'] = np.array(scalars)
grid.point_data['vec'] = vectors
if mode == '2darrow':
return _arrow_glyph(grid, factor), grid
elif mode == 'arrow':
alg = _glyph(
grid,
orient='vec',
scalars='scalars',
factor=factor
)
mesh = pyvista.wrap(alg.GetOutput())
else:
tr = None
if mode == 'cone':
glyph = vtkConeSource()
glyph.SetCenter(0.5, 0, 0)
if glyph_radius is not None:
glyph.SetRadius(glyph_radius)
elif mode == 'cylinder':
glyph = vtkCylinderSource()
if glyph_radius is not None:
glyph.SetRadius(glyph_radius)
elif mode == 'oct':
glyph = vtkPlatonicSolidSource()
glyph.SetSolidTypeToOctahedron()
else:
assert mode == 'sphere', mode # guaranteed above
glyph = vtkSphereSource()
if mode == 'cylinder':
if glyph_height is not None:
glyph.SetHeight(glyph_height)
if glyph_center is not None:
glyph.SetCenter(glyph_center)
if glyph_resolution is not None:
glyph.SetResolution(glyph_resolution)
tr = vtkTransform()
tr.RotateWXYZ(90, 0, 0, 1)
elif mode == 'oct':
if solid_transform is not None:
assert solid_transform.shape == (4, 4)
tr = vtkTransform()
tr.SetMatrix(
solid_transform.astype(np.float64).ravel())
if tr is not None:
# fix orientation
glyph.Update()
trp = vtkTransformPolyDataFilter()
trp.SetInputData(glyph.GetOutput())
trp.SetTransform(tr)
glyph = trp
glyph.Update()
geom = glyph.GetOutput()
mesh = grid.glyph(orient='vec', scale=scale_mode == 'vector',
factor=factor, geom=geom)
actor = _add_mesh(
self.plotter,
mesh=mesh,
color=color,
opacity=opacity,
scalars=None,
colormap=colormap,
show_scalar_bar=False,
backface_culling=backface_culling,
clim=clim,
)
return actor, mesh
def text2d(self, x_window, y_window, text, size=14, color='white',
justification=None):
size = 14 if size is None else size
position = (x_window, y_window)
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
actor = self.plotter.add_text(text, position=position,
font_size=size,
color=color,
viewport=True)
if isinstance(justification, str):
if justification == 'left':
actor.GetTextProperty().SetJustificationToLeft()
elif justification == 'center':
actor.GetTextProperty().SetJustificationToCentered()
elif justification == 'right':
actor.GetTextProperty().SetJustificationToRight()
else:
raise ValueError('Expected values for `justification`'
'are `left`, `center` or `right` but '
'got {} instead.'.format(justification))
_hide_testing_actor(actor)
return actor
def text3d(self, x, y, z, text, scale, color='white'):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
kwargs = dict(
points=np.array([x, y, z]).astype(float),
labels=[text],
point_size=scale,
text_color=color,
font_family=self.font_family,
name=text,
shape_opacity=0,
)
if ('always_visible'
in signature(self.plotter.add_point_labels).parameters):
kwargs['always_visible'] = True
actor = self.plotter.add_point_labels(**kwargs)
_hide_testing_actor(actor)
return actor
def scalarbar(self, source, color="white", title=None, n_labels=4,
bgcolor=None, **extra_kwargs):
if isinstance(source, vtkMapper):
mapper = source
elif isinstance(source, vtkActor):
mapper = source.GetMapper()
else:
mapper = None
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
kwargs = dict(color=color, title=title, n_labels=n_labels,
use_opacity=False, n_colors=256, position_x=0.15,
position_y=0.05, width=0.7, shadow=False, bold=True,
label_font_size=22, font_family=self.font_family,
background_color=bgcolor, mapper=mapper)
kwargs.update(extra_kwargs)
actor = self.plotter.add_scalar_bar(**kwargs)
_hide_testing_actor(actor)
return actor
def show(self):
self.plotter.show()
def close(self):
_close_3d_figure(figure=self.figure)
def get_camera(self):
return _get_3d_view(self.figure)
def set_camera(self, azimuth=None, elevation=None, distance=None,
focalpoint='auto', roll=None, reset_camera=True,
rigid=None, update=True):
_set_3d_view(self.figure, azimuth=azimuth, elevation=elevation,
distance=distance, focalpoint=focalpoint, roll=roll,
reset_camera=reset_camera, rigid=rigid, update=update)
def reset_camera(self):
self.plotter.reset_camera()
def screenshot(self, mode='rgb', filename=None):
return _take_3d_screenshot(figure=self.figure, mode=mode,
filename=filename)
def project(self, xyz, ch_names):
xy = _3d_to_2d(self.plotter, xyz)
xy = dict(zip(ch_names, xy))
# pts = self.fig.children[-1]
pts = self.plotter.renderer.GetActors().GetLastItem()
return _Projection(xy=xy, pts=pts, plotter=self.plotter)
def _enable_depth_peeling(self):
if not self.depth_peeling:
return
if not self.figure.store['off_screen']:
for renderer in self._all_renderers:
renderer.enable_depth_peeling()
def _enable_antialias(self):
"""Enable it everywhere except Azure."""
if not self.antialias:
return
# XXX for some reason doing this on Azure causes access violations:
# ##[error]Cmd.exe exited with code '-1073741819'
# So for now don't use it there. Maybe has to do with setting these
# before the window has actually been made "active"...?
# For Mayavi we have an "on activated" event or so, we should look into
# using this for Azure at some point, too.
if self.figure._is_active():
# macOS, Azure
bad_system = (
sys.platform == 'darwin' or
os.getenv('AZURE_CI_WINDOWS', 'false').lower() == 'true')
bad_system |= _is_mesa(self.plotter)
if not bad_system:
for renderer in self._all_renderers:
renderer.enable_anti_aliasing()
for plotter in self._all_plotters:
plotter.ren_win.LineSmoothingOn()
def remove_mesh(self, mesh_data):
actor, _ = mesh_data
self.plotter.remove_actor(actor)
@contextmanager
def _disabled_interaction(self):
if not self.plotter.renderer.GetInteractive():
yield
else:
self.plotter.disable()
try:
yield
finally:
self.plotter.enable()
def _actor(self, mapper=None):
actor = vtkActor()
if mapper is not None:
actor.SetMapper(mapper)
_hide_testing_actor(actor)
return actor
def _process_events(self):
for plotter in self._all_plotters:
_process_events(plotter)
def _update_picking_callback(self,
on_mouse_move,
on_button_press,
on_button_release,
on_pick):
add_obs = self.plotter.iren.add_observer
add_obs(vtkCommand.RenderEvent, on_mouse_move)
add_obs(vtkCommand.LeftButtonPressEvent, on_button_press)
add_obs(vtkCommand.EndInteractionEvent, on_button_release)
self.plotter.picker = vtkCellPicker()
self.plotter.picker.AddObserver(
vtkCommand.EndPickEvent,
on_pick
)
self.plotter.picker.SetVolumeOpacityIsovalue(0.)
def _set_mesh_scalars(self, mesh, scalars, name):
# Catch: FutureWarning: Conversion of the second argument of
# issubdtype from `complex` to `np.complexfloating` is deprecated.
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
mesh.point_data[name] = scalars
def _set_colormap_range(self, actor, ctable, scalar_bar, rng=None,
background_color=None):
if rng is not None:
mapper = actor.GetMapper()
mapper.SetScalarRange(*rng)
lut = mapper.GetLookupTable()
lut.SetTable(numpy_to_vtk(ctable))
if scalar_bar is not None:
lut = scalar_bar.GetLookupTable()
if background_color is not None:
background_color = np.array(background_color) * 255
ctable = _alpha_blend_background(ctable, background_color)
lut.SetTable(numpy_to_vtk(ctable, array_type=VTK_UNSIGNED_CHAR))
lut.SetRange(*rng)
def _set_volume_range(self, volume, ctable, alpha, scalar_bar, rng):
color_tf = vtkColorTransferFunction()
opacity_tf = vtkPiecewiseFunction()
for loc, color in zip(np.linspace(*rng, num=len(ctable)), ctable):
color_tf.AddRGBPoint(loc, *(color[:-1] / 255.))
opacity_tf.AddPoint(loc, color[-1] * alpha / 255.)
color_tf.ClampingOn()
opacity_tf.ClampingOn()
prop = volume.GetProperty()
prop.SetColor(color_tf)
prop.SetScalarOpacity(opacity_tf)
prop.ShadeOn()
prop.SetInterpolationTypeToLinear()
if scalar_bar is not None:
lut = vtkLookupTable()
lut.SetRange(*rng)
lut.SetTable(numpy_to_vtk(ctable))
scalar_bar.SetLookupTable(lut)
def _sphere(self, center, color, radius):
from vtkmodules.vtkFiltersSources import vtkSphereSource
sphere = vtkSphereSource()
sphere.SetThetaResolution(8)
sphere.SetPhiResolution(8)
sphere.SetRadius(radius)
sphere.SetCenter(center)
sphere.Update()
mesh = pyvista.wrap(sphere.GetOutput())
actor = _add_mesh(
self.plotter,
mesh=mesh,
color=color
)
return actor, mesh
def _volume(self, dimensions, origin, spacing, scalars,
surface_alpha, resolution, blending, center):
# Now we can actually construct the visualization
grid = pyvista.UniformGrid()
grid.dimensions = dimensions + 1 # inject data on the cells
grid.origin = origin
grid.spacing = spacing
grid.cell_data['values'] = scalars
# Add contour of enclosed volume (use GetOutput instead of
# GetOutputPort below to avoid updating)
if surface_alpha > 0 or resolution is not None:
grid_alg = vtkCellDataToPointData()
grid_alg.SetInputDataObject(grid)
grid_alg.SetPassCellData(False)
grid_alg.Update()
else:
grid_alg = None
if surface_alpha > 0:
grid_surface = vtkMarchingContourFilter()
grid_surface.ComputeNormalsOn()
grid_surface.ComputeScalarsOff()
grid_surface.SetInputData(grid_alg.GetOutput())
grid_surface.SetValue(0, 0.1)
grid_surface.Update()
grid_mesh = vtkPolyDataMapper()
grid_mesh.SetInputData(grid_surface.GetOutput())
else:
grid_mesh = None
mapper = vtkSmartVolumeMapper()
if resolution is None: # native
mapper.SetScalarModeToUseCellData()
mapper.SetInputDataObject(grid)
else:
upsampler = vtkImageReslice()
upsampler.SetInterpolationModeToLinear() # default anyway
upsampler.SetOutputSpacing(*([resolution] * 3))
upsampler.SetInputConnection(grid_alg.GetOutputPort())
mapper.SetInputConnection(upsampler.GetOutputPort())
# Additive, AverageIntensity, and Composite might also be reasonable
remap = dict(composite='Composite', mip='MaximumIntensity')
getattr(mapper, f'SetBlendModeTo{remap[blending]}')()
volume_pos = vtkVolume()
volume_pos.SetMapper(mapper)
dist = grid.length / (np.mean(grid.dimensions) - 1)
volume_pos.GetProperty().SetScalarOpacityUnitDistance(dist)
if center is not None and blending == 'mip':
# We need to create a minimum intensity projection for the neg half
mapper_neg = vtkSmartVolumeMapper()
if resolution is None: # native
mapper_neg.SetScalarModeToUseCellData()
mapper_neg.SetInputDataObject(grid)
else:
mapper_neg.SetInputConnection(upsampler.GetOutputPort())
mapper_neg.SetBlendModeToMinimumIntensity()
volume_neg = vtkVolume()
volume_neg.SetMapper(mapper_neg)
volume_neg.GetProperty().SetScalarOpacityUnitDistance(dist)
else:
volume_neg = None
return grid, grid_mesh, volume_pos, volume_neg
def _silhouette(self, mesh, color=None, line_width=None, alpha=None,
decimate=None):
mesh = mesh.decimate(decimate) if decimate is not None else mesh
silhouette_filter = vtkPolyDataSilhouette()
silhouette_filter.SetInputData(mesh)
silhouette_filter.SetCamera(self.plotter.renderer.GetActiveCamera())
silhouette_filter.SetEnableFeatureAngle(0)
silhouette_mapper = vtkPolyDataMapper()
silhouette_mapper.SetInputConnection(
silhouette_filter.GetOutputPort())
actor, prop = self.plotter.add_actor(
silhouette_mapper, reset_camera=False, name=None,
culling=False, pickable=False, render=False)
if color is not None:
prop.SetColor(*color)
if alpha is not None:
prop.SetOpacity(alpha)
if line_width is not None:
prop.SetLineWidth(line_width)
_hide_testing_actor(actor)
return actor
def _compute_normals(mesh):
"""Patch PyVista compute_normals."""
if 'Normals' not in mesh.point_data:
mesh.compute_normals(
cell_normals=False,
consistent_normals=False,
non_manifold_traversal=False,
inplace=True,
)
def _add_mesh(plotter, *args, **kwargs):
"""Patch PyVista add_mesh."""
mesh = kwargs.get('mesh')
if 'smooth_shading' in kwargs:
smooth_shading = kwargs.pop('smooth_shading')
else:
smooth_shading = True
# disable rendering pass for add_mesh, render()
# is called in show()
if 'render' not in kwargs:
kwargs['render'] = False
actor = plotter.add_mesh(*args, **kwargs)
if smooth_shading and 'Normals' in mesh.point_data:
prop = actor.GetProperty()
prop.SetInterpolationToPhong()
_hide_testing_actor(actor)
return actor
def _hide_testing_actor(actor):
from . import renderer
if renderer.MNE_3D_BACKEND_TESTING:
actor.SetVisibility(False)
def _deg2rad(deg):
return deg * np.pi / 180.
def _rad2deg(rad):
return rad * 180. / np.pi
def _to_pos(azimuth, elevation):
theta = azimuth * np.pi / 180.0
phi = (90.0 - elevation) * np.pi / 180.0
x = np.sin(theta) * np.sin(phi)
y = np.cos(phi)
z = np.cos(theta) * np.sin(phi)
return x, y, z
def _mat_to_array(vtk_mat):
e = [vtk_mat.GetElement(i, j) for i in range(4) for j in range(4)]
arr = np.array(e, dtype=float)
arr.shape = (4, 4)
return arr
def _3d_to_2d(plotter, xyz):
# https://vtk.org/Wiki/VTK/Examples/Cxx/Utilities/Coordinate
coordinate = vtkCoordinate()
coordinate.SetCoordinateSystemToWorld()
xy = list()
for coord in xyz:
coordinate.SetValue(*coord)
xy.append(coordinate.GetComputedLocalDisplayValue(plotter.renderer))
xy = np.array(xy, float).reshape(-1, 2) # in case it's empty
return xy
def _close_all():
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
close_all()
_FIGURES.clear()
def _get_camera_direction(focalpoint, position):
x, y, z = position - focalpoint
r = np.sqrt(x * x + y * y + z * z)
theta = np.arccos(z / r)
phi = np.arctan2(y, x)
return r, theta, phi
def _get_3d_view(figure):
position = np.array(figure.plotter.camera_position[0])
focalpoint = np.array(figure.plotter.camera_position[1])
_, theta, phi = _get_camera_direction(focalpoint, position)
azimuth, elevation = _rad2deg(phi), _rad2deg(theta)
return (figure.plotter.camera.GetRoll(),
figure.plotter.camera.GetDistance(),
azimuth, elevation, focalpoint)
def _set_3d_view(figure, azimuth=None, elevation=None, focalpoint='auto',
distance=None, roll=None, reset_camera=True, rigid=None,
update=True):
rigid = np.eye(4) if rigid is None else rigid
position = np.array(figure.plotter.camera_position[0])
bounds = np.array(figure.plotter.renderer.ComputeVisiblePropBounds())
if reset_camera:
figure.plotter.reset_camera(render=False)
# focalpoint: if 'auto', we use the center of mass of the visible
# bounds, if None, we use the existing camera focal point otherwise
# we use the values given by the user
if isinstance(focalpoint, str):
_check_option('focalpoint', focalpoint, ('auto',),
extra='when a string')
focalpoint = (bounds[1::2] + bounds[::2]) * 0.5
elif focalpoint is None:
focalpoint = np.array(figure.plotter.camera_position[1])
else:
focalpoint = np.asarray(focalpoint)
# work in the transformed space
position = apply_trans(rigid, position)
focalpoint = apply_trans(rigid, focalpoint)
_, theta, phi = _get_camera_direction(focalpoint, position)
if azimuth is not None:
phi = _deg2rad(azimuth)
if elevation is not None:
theta = _deg2rad(elevation)
# set the distance
if distance is None:
distance = max(bounds[1::2] - bounds[::2]) * 2.0
# Now calculate the view_up vector of the camera. If the view up is
# close to the 'z' axis, the view plane normal is parallel to the
# camera which is unacceptable, so we use a different view up.
if elevation is None or 5. <= abs(elevation) <= 175.:
view_up = [0, 0, 1]
else:
view_up = [0, 1, 0]
position = [
distance * np.cos(phi) * np.sin(theta),
distance * np.sin(phi) * np.sin(theta),
distance * np.cos(theta)]
figure._azimuth = _rad2deg(phi)
figure._elevation = _rad2deg(theta)
# restore to the original frame
rigid = np.linalg.inv(rigid)
position = apply_trans(rigid, position)
focalpoint = apply_trans(rigid, focalpoint)
view_up = apply_trans(rigid, view_up, move=False)
figure.plotter.camera_position = [
position, focalpoint, view_up]
# We need to add the requested roll to the roll dictated by the
# transformed view_up
if roll is not None:
figure.plotter.camera.SetRoll(figure.plotter.camera.GetRoll() + roll)
if update:
figure.plotter.update()
_process_events(figure.plotter)
def _set_3d_title(figure, title, size=16):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
figure.plotter.add_text(title, font_size=size, color='white',
name='title')
figure.plotter.update()
_process_events(figure.plotter)
def _check_3d_figure(figure):
_validate_type(figure, PyVistaFigure, 'figure')
def _close_3d_figure(figure):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
# copy the plotter locally because figure.plotter is modified
plotter = figure.plotter
# close the window
plotter.close() # additional cleaning following signal_close
_process_events(plotter)
# free memory and deregister from the scraper
plotter.deep_clean() # remove internal references
_ALL_PLOTTERS.pop(plotter._id_name, None)
_process_events(plotter)
def _take_3d_screenshot(figure, mode='rgb', filename=None):
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
_process_events(figure.plotter)
return figure.plotter.screenshot(
transparent_background=(mode == 'rgba'),
filename=filename)
def _process_events(plotter):
if hasattr(plotter, 'app'):
with warnings.catch_warnings(record=True):
warnings.filterwarnings('ignore', 'constrained_layout')
plotter.app.processEvents()
def _add_camera_callback(camera, callback):
camera.AddObserver(vtkCommand.ModifiedEvent, callback)
def _arrow_glyph(grid, factor):
glyph = vtkGlyphSource2D()
glyph.SetGlyphTypeToArrow()
glyph.FilledOff()
glyph.Update()
# fix position
tr = vtkTransform()
tr.Translate(0.5, 0., 0.)
trp = vtkTransformPolyDataFilter()
trp.SetInputConnection(glyph.GetOutputPort())
trp.SetTransform(tr)
trp.Update()
alg = _glyph(
grid,
scale_mode='vector',
scalars=False,
orient='vec',
factor=factor,
geom=trp.GetOutputPort(),
)
mapper = vtkDataSetMapper()
mapper.SetInputConnection(alg.GetOutputPort())
return mapper
def _glyph(dataset, scale_mode='scalar', orient=True, scalars=True, factor=1.0,
geom=None, tolerance=0.0, absolute=False, clamping=False, rng=None):
if geom is None:
arrow = vtkArrowSource()
arrow.Update()
geom = arrow.GetOutputPort()
alg = vtkGlyph3D()
alg.SetSourceConnection(geom)
if isinstance(scalars, str):
dataset.active_scalars_name = scalars
if isinstance(orient, str):
dataset.active_vectors_name = orient
orient = True
if scale_mode == 'scalar':
alg.SetScaleModeToScaleByScalar()
elif scale_mode == 'vector':
alg.SetScaleModeToScaleByVector()
else:
alg.SetScaleModeToDataScalingOff()
if rng is not None:
alg.SetRange(rng)
alg.SetOrient(orient)
alg.SetInputData(dataset)
alg.SetScaleFactor(factor)
alg.SetClamping(clamping)
alg.Update()
return alg
@contextmanager
def _disabled_depth_peeling():
try:
from pyvista import global_theme
except Exception: # workaround for older PyVista
from pyvista import rcParams
depth_peeling = rcParams['depth_peeling']
else:
depth_peeling = global_theme.depth_peeling
depth_peeling_enabled = depth_peeling["enabled"]
depth_peeling["enabled"] = False
try:
yield
finally:
depth_peeling["enabled"] = depth_peeling_enabled
def _is_mesa(plotter):
# MESA (could use GPUInfo / _get_gpu_info here, but it takes
# > 700 ms to make a new window + report capabilities!)
# CircleCI's is: "Mesa 20.0.8 via llvmpipe (LLVM 10.0.0, 256 bits)"
gpu_info_full = plotter.ren_win.ReportCapabilities()
gpu_info = re.findall("OpenGL renderer string:(.+)\n", gpu_info_full)
gpu_info = ' '.join(gpu_info).lower()
is_mesa = 'mesa' in gpu_info.split()
if is_mesa:
# Try to warn if it's ancient
version = re.findall("mesa ([0-9.]+) .*", gpu_info) or \
re.findall("OpenGL version string: .* Mesa ([0-9.]+)\n",
gpu_info_full)
if version:
version = version[0]
if _compare_version(version, '<', '18.3.6'):
warn(f'Mesa version {version} is too old for translucent 3D '
'surface rendering, consider upgrading to 18.3.6 or '
'later.')
else:
raise RuntimeError
return is_mesa
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