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_pyvista.py
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_pyvista.py
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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 platform
import re
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, _cart_to_sph, _sph_to_cart
from ...utils import (
copy_base_doc_to_subclass_doc,
_check_option,
_require_version,
_validate_type,
warn,
deprecated,
)
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=DeprecationWarning)
import pyvista
from pyvista import Plotter, PolyData, Line, close_all, UnstructuredGrid
from pyvistaqt import BackgroundPlotter
try:
from pyvista.plotting.plotter import _ALL_PLOTTERS
except Exception: # PV < 0.40
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
_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
self.store["line_smoothing"] = True
self.store["polygon_smoothing"] = True
self.store["point_smoothing"] = True
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 = _SafeBackgroundPlotter
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"]
def _build(self):
if self.plotter is None:
if not self.notebook:
out = _init_mne_qtapp(enable_icon=True, 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
# TODO: This breaks trame "client" backend
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):
return hasattr(self.plotter, "ren_win")
class _Projection:
"""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 platform.system() == "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._toggle_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()
self.plotter.enable_rubber_band_2d_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=1.0,
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) / 255.0
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,
*,
backface_culling=False,
scalars=None,
colormap=None,
vmin=None,
vmax=None,
interpolate_before_map=True,
representation="surface",
line_width=1.0,
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=2.0,
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)
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, *, rigid=None):
return _get_3d_view(self.figure, rigid=rigid)
def set_camera(
self,
azimuth=None,
elevation=None,
distance=None,
focalpoint=None,
roll=None,
*,
rigid=None,
update=True,
reset_camera=None,
):
_set_3d_view(
self.figure,
azimuth=azimuth,
elevation=elevation,
distance=distance,
focalpoint=focalpoint,
roll=roll,
reset_camera=reset_camera,
rigid=rigid,
update=update,
)
@deprecated(
"reset_camera is deprecated and will be removed in 1.7, use "
"set_camera(distance='auto') instead"
)
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):
for plotter in self._all_plotters:
if self.depth_peeling:
plotter.enable_depth_peeling()
else:
plotter.disable_depth_peeling()
def _toggle_antialias(self):
"""Enable it everywhere except on systems with problematic OpenGL."""
# MESA can't seem to handle MSAA and depth peeling simultaneously, see
# https://github.com/pyvista/pyvista/issues/4867
bad_system = _is_mesa(self.plotter)
for plotter in self._all_plotters:
if bad_system or not self.antialias:
plotter.disable_anti_aliasing()
else:
if not bad_system:
plotter.enable_anti_aliasing(aa_type="msaa")
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(0.0)
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] / 255.0))
opacity_tf.AddPoint(loc, color[-1] * alpha / 255.0)
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
try:
grid = pyvista.ImageData()
except AttributeError: # PV < 0.40
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