def addScalarBar(
self,
pos=(0.8, 0.05),
title="",
titleXOffset=0,
titleYOffset=15,
titleFontSize=12,
nlabels=None,
c=None,
horizontal=False,
useAlpha=True,
):
"""
Add a 2D scalar bar for the specified obj.
.. hint:: |mesh_coloring| |mesh_coloring.py|_ |scalarbars.py|_
"""
import vtkplotter.addons as addons
self.scalarbar = addons.addScalarBar(
self,
pos,
title,
titleXOffset,
titleYOffset,
titleFontSize,
nlabels,
c,
horizontal,
useAlpha,
)
return self
def buttonfunc():
global cmap
bu.switch()
cmap = bu.status()
for mesh in visibles:
if mesh:
mesh.pointColors(cmap=cmap)
vp.renderer.RemoveActor(mesh.scalarbar)
mesh.scalarbar = addons.addScalarBar(mesh,
pos=(0.04, 0.0),
horizontal=True,
titleFontSize=0)
vp.renderer.AddActor(mesh.scalarbar)
def addScalarBar(self,
actor=None,
c=None,
title="",
horizontal=False,
vmin=None,
vmax=None):
"""Add a 2D scalar bar for the specified actor.
If `actor` is ``None`` will add it to the last actor in ``self.actors``.
.. hint:: |mesh_bands| |mesh_bands.py|_
"""
return addons.addScalarBar(actor, c, title, horizontal, vmin, vmax)
def buttonfunc():
global _cmap_slicer
bu.switch()
_cmap_slicer = bu.status()
for mesh in visibles:
if mesh:
mesh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells:
mesh.mapPointsToCells()
vp.renderer.RemoveActor(mesh.scalarbar)
mesh.scalarbar = addScalarBar(mesh,
pos=(0.04, 0.0),
horizontal=True,
titleFontSize=0)
vp.renderer.AddActor(mesh.scalarbar)
def show(
self, *actors, **options
# at=None,
# axes=None,
# c=None,
# alpha=None,
# wire=False,
# bc=None,
# resetcam=True,
# zoom=False,
# interactive=None,
# rate=None,
# viewup="",
# azimuth=0,
# elevation=0,
# roll=0,
# interactorStyle=0,
# q=False,
):
"""
Render a list of actors.
Allowed input objects are: ``filename``, ``vtkPolyData``, ``vtkActor``,
``vtkActor2D``, ``vtkImageActor``, ``vtkAssembly`` or ``vtkVolume``.
If filename is given, its type is guessed based on its extension.
Supported formats are:
`vtu, vts, vtp, ply, obj, stl, 3ds, xml, neutral, gmsh, pcd, xyz, txt, byu,
tif, slc, vti, mhd, png, jpg`.
:param int at: number of the renderer to plot to, if more than one exists
:param int axes: set the type of axes to be shown
- 0, no axes,
- 1, draw three gray grid walls
- 2, show cartesian axes from (0,0,0)
- 3, show positive range of cartesian axes from (0,0,0)
- 4, show a triad at bottom left
- 5, show a cube at bottom left
- 6, mark the corners of the bounding box
- 7, draw a simple ruler at the bottom of the window
- 8, show the ``vtkCubeAxesActor`` object,
- 9, show the bounding box outLine,
- 10, show three circles representing the maximum bounding box
:param c: surface color, in rgb, hex or name formats
:param bc: set a color for the internal surface face
:param bool wire: show actor in wireframe representation
:param float azimuth/elevation/roll: move camera accordingly
:param str viewup: either ['x', 'y', 'z'] or a vector to set vertical direction
:param bool resetcam: re-adjust camera position to fit objects
:param bool interactive: pause and interact with window (True)
or continue execution (False)
:param float rate: maximum rate of `show()` in Hertz
:param int interactorStyle: set the type of interaction
- 0, TrackballCamera
- 1, TrackballActor
- 2, JoystickCamera
- 3, Unicam
- 4, Flight
- 5, RubberBand3D
- 6, RubberBandZoom
:param bool q: force program to quit after `show()` command returns.
"""
if not hasattr(self, 'window'):
return
at = options.pop("at", None)
axes = options.pop("axes", None)
c = options.pop("c", None)
alpha = options.pop("alpha", None)
wire = options.pop("wire", False)
bc = options.pop("bc", None)
resetcam = options.pop("resetcam", True)
zoom = options.pop("zoom", False)
interactive = options.pop("interactive", None)
rate = options.pop("rate", None)
viewup = options.pop("viewup", "")
azimuth = options.pop("azimuth", 0)
elevation = options.pop("elevation", 0)
roll = options.pop("roll", 0)
interactorStyle = options.pop("interactorStyle", 0)
q = options.pop("q", False)
if self.offscreen:
interactive = False
self.interactive = False
def scan(wannabeacts):
scannedacts = []
if not utils.isSequence(wannabeacts):
wannabeacts = [wannabeacts]
for a in wannabeacts: # scan content of list
if isinstance(a, vtk.vtkActor):
scannedacts.append(a)
if hasattr(a, 'trail'
) and a.trail and not a.trail in self.actors:
scannedacts.append(a.trail)
elif isinstance(a, vtk.vtkAssembly):
scannedacts.append(a)
if a.trail and not a.trail in self.actors:
scannedacts.append(a.trail)
elif isinstance(a, vtk.vtkActor2D):
if isinstance(a, vtk.vtkCornerAnnotation):
for a2 in settings.collectable_actors:
if isinstance(a2, vtk.vtkCornerAnnotation):
if at in a2.renderedAt: # remove old message
self.removeActor(a2)
scannedacts.append(a)
elif isinstance(a, vtk.vtkImageActor):
scannedacts.append(a)
elif isinstance(a, vtk.vtkVolume):
scannedacts.append(a)
elif isinstance(a, vtk.vtkImageData):
scannedacts.append(Volume(a))
elif isinstance(a, vtk.vtkPolyData):
scannedacts.append(Actor(a, c, alpha, wire, bc))
elif isinstance(a, str): # assume a filepath was given
out = vtkio.load(a, c, alpha, wire, bc)
if isinstance(out, str):
colors.printc("~times File not found:", out, c=1)
scannedacts.append(None)
else:
scannedacts.append(out)
elif "dolfin" in str(type(a)): # assume a dolfin.Mesh object
from vtkplotter.dolfin import MeshActor
out = MeshActor(a, c=c, alpha=alpha, wire=True, bc=bc)
scannedacts.append(out)
elif a is None:
pass
elif isinstance(a, vtk.vtkUnstructuredGrid):
gf = vtk.vtkGeometryFilter()
gf.SetInputData(a)
gf.Update()
scannedacts.append(
Actor(gf.GetOutput(), c, alpha, wire, bc))
elif isinstance(a, vtk.vtkStructuredGrid):
gf = vtk.vtkGeometryFilter()
gf.SetInputData(a)
gf.Update()
scannedacts.append(
Actor(gf.GetOutput(), c, alpha, wire, bc))
elif isinstance(a, vtk.vtkRectilinearGrid):
gf = vtk.vtkRectilinearGridGeometryFilter()
gf.SetInputData(a)
gf.Update()
scannedacts.append(
Actor(gf.GetOutput(), c, alpha, wire, bc))
elif isinstance(a, vtk.vtkMultiBlockDataSet):
for i in range(a.GetNumberOfBlocks()):
b = a.GetBlock(i)
if isinstance(b, vtk.vtkPolyData):
scannedacts.append(Actor(b, c, alpha, wire, bc))
elif isinstance(b, vtk.vtkImageData):
scannedacts.append(Volume(b))
else:
colors.printc("~!? Cannot understand input in show():",
type(a),
c=1)
scannedacts.append(None)
return scannedacts
if len(actors) == 0:
actors = None
elif len(actors) == 1:
actors = actors[0]
else:
actors = utils.flatten(actors)
if actors is not None:
self.actors = []
actors2show = scan(actors)
for a in actors2show:
if a not in self.actors:
self.actors.append(a)
else:
actors2show = scan(self.actors)
self.actors = list(actors2show)
if axes is not None:
self.axes = axes
if interactive is not None:
self.interactive = interactive
if at is None and len(self.renderers) > 1:
# in case of multiple renderers a call to show w/o specifing
# at which renderer will just render the whole thing and return
if self.interactor:
if zoom:
self.camera.Zoom(zoom)
self.interactor.Render()
if self.interactive:
self.interactor.Start()
return
if at is None:
at = 0
if at < len(self.renderers):
self.renderer = self.renderers[at]
else:
colors.printc("~times Error in show(): wrong renderer index",
at,
c=1)
return
if not self.camera:
self.camera = self.renderer.GetActiveCamera()
self.camera.SetParallelProjection(self.infinity)
if self.camThickness:
self.camera.SetThickness(self.camThickness)
if self.sharecam:
for r in self.renderers:
r.SetActiveCamera(self.camera)
if len(self.renderers) == 1:
self.renderer.SetActiveCamera(self.camera)
# rendering
for ia in actors2show: # add the actors that are not already in scene
if ia:
if isinstance(ia, vtk.vtkVolume):
self.renderer.AddVolume(ia)
else:
self.renderer.AddActor(ia)
if hasattr(ia, 'renderedAt'):
ia.renderedAt.add(at)
else:
colors.printc(
"~lightning Warning: Invalid actor in actors list, skip.",
c=5)
# remove the ones that are not in actors2show
for ia in self.getActors(at):
if ia not in actors2show:
self.renderer.RemoveActor(ia)
if hasattr(ia, 'renderedAt'):
ia.renderedAt.discard(at)
for c in self.scalarbars:
self.renderer.RemoveActor(c)
if hasattr(c, 'renderedAt'):
c.renderedAt.discard(at)
if self.axes is not None:
addons.addAxes()
addons.addLegend()
if self.showFrame and len(self.renderers) > 1:
addons.addFrame()
if resetcam or self.initializedIren == False:
self.renderer.ResetCamera()
if not self.initializedIren and self.interactor:
self.initializedIren = True
self.interactor.Initialize()
self.interactor.RemoveObservers("CharEvent")
if self.verbose and self.interactive:
docs.onelinetip()
self.initializedPlotter = True
if zoom:
self.camera.Zoom(zoom)
if azimuth:
self.camera.Azimuth(azimuth)
if elevation:
self.camera.Elevation(elevation)
if roll:
self.camera.Roll(roll)
if len(viewup):
if viewup == "x":
viewup = [1, 0, 0]
elif viewup == "y":
viewup = [0, 1, 0]
elif viewup == "z":
viewup = [0, 0, 1]
self.camera.Azimuth(60)
self.camera.Elevation(30)
self.camera.Azimuth(0.01) # otherwise camera gets locked
self.camera.SetViewUp(viewup)
self.renderer.ResetCameraClippingRange()
self.window.Render()
scbflag = False
for a in self.actors:
if (hasattr(a, "scalarbar") and a.scalarbar is not None
and utils.isSequence(a.scalarbar)):
if len(a.scalarbar) == 5: # addScalarBar
s1, s2, s3, s4, s5 = a.scalarbar
sb = addons.addScalarBar(a, s1, s2, s3, s4, s5)
scbflag = True
a.scalarbar = sb # save scalarbar actor
elif len(a.scalarbar) == 10: # addScalarBar3D
s0, s1, s2, s3, s4, s5, s6, s7, s8 = a.scalarbar
sb = addons.addScalarBar3D(a, at, s0, s1, s2, s3, s4, s5,
s6, s7, s8)
scbflag = True
a.scalarbar = sb # save scalarbar actor
if scbflag:
self.window.Render()
if settings.allowInteraction and not self.offscreen:
self.allowInteraction()
if settings.interactorStyle is not None:
interactorStyle = settings.interactorStyle
if interactorStyle == 0 or interactorStyle == "TrackballCamera":
pass # do nothing
elif interactorStyle == 1 or interactorStyle == "TrackballActor":
self.interactor.SetInteractorStyle(
vtk.vtkInteractorStyleTrackballActor())
elif interactorStyle == 2 or interactorStyle == "JoystickCamera":
self.interactor.SetInteractorStyle(
vtk.vtkInteractorStyleJoystickCamera())
elif interactorStyle == 3 or interactorStyle == "Unicam":
self.interactor.SetInteractorStyle(vtk.vtkInteractorStyleUnicam())
elif interactorStyle == 4 or interactorStyle == "Flight":
self.interactor.SetInteractorStyle(vtk.vtkInteractorStyleFlight())
elif interactorStyle == 5 or interactorStyle == "RubberBand3D":
self.interactor.SetInteractorStyle(
vtk.vtkInteractorStyleRubberBand3D())
elif interactorStyle == 6 or interactorStyle == "RubberBandZoom":
self.interactor.SetInteractorStyle(
vtk.vtkInteractorStyleRubberBandZoom())
if self.interactor and self.interactive:
self.interactor.Start()
if rate:
if self.clock is None: # set clock and limit rate
self._clockt0 = time.time()
self.clock = 0.0
else:
t = time.time() - self._clockt0
elapsed = t - self.clock
mint = 1.0 / rate
if elapsed < mint:
time.sleep(mint - elapsed)
self.clock = time.time() - self._clockt0
if q: # gracefully exit
if self.verbose:
print("q flag set to True. Exit.")
sys.exit(0)
def slicer(
volume,
alpha=1,
cmaps=('gist_ncar_r', "hot_r", "bone_r", "jet", "Spectral_r"),
map2cells=False, # buggy
clamp=True,
useSlider3D=False,
size=(850, 700),
screensize="auto",
title="",
bg="white",
bg2="lightblue",
axes=1,
showHisto=True,
showIcon=True,
draggable=False,
verbose=True,
):
"""
Generate a ``Plotter`` window with slicing planes for the input Volume.
Returns the ``Plotter`` object.
:param float alpha: transparency of the slicing planes
:param list cmaps: list of color maps names to cycle when clicking button
:param bool map2cells: scalars are mapped to cells, not intepolated.
:param bool clamp: clamp scalar to reduce the effect of tails in color mapping
:param bool useSlider3D: show sliders attached along the axes
:param list size: rendering window size in pixels
:param list screensize: size of the screen can be specified
:param str title: window title
:param bg: background color
:param bg2: background gradient color
:param int axes: axis type number
:param bool showHisto: show histogram on bottom left
:param bool showIcon: show a small 3D rendering icon of the volume
:param bool draggable: make the icon draggable
"""
global _cmap_slicer
if verbose: printc("Slicer tool", invert=1, c="m")
################################
vp = Plotter(bg=bg,
bg2=bg2,
size=size,
screensize=screensize,
title=title,
interactive=False,
verbose=verbose)
################################
box = volume.box().wireframe().alpha(0)
vp.show(box, viewup="z", axes=axes)
if showIcon:
vp.showInset(volume,
pos=(.85, .85),
size=0.15,
c='w',
draggable=draggable)
# inits
la, ld = 0.7, 0.3 #ambient, diffuse
dims = volume.dimensions()
data = volume.getPointArray()
rmin, rmax = volume.imagedata().GetScalarRange()
sbwidth = 800
if clamp:
hdata, edg = np.histogram(data, bins=50)
logdata = np.log(hdata + 1)
# mean of the logscale plot
meanlog = np.sum(np.multiply(edg[:-1], logdata)) / np.sum(logdata)
rmax = min(rmax, meanlog + (meanlog - rmin) * 0.9)
rmin = max(rmin, meanlog - (rmax - meanlog) * 0.9)
if verbose:
printc('scalar range clamped to: (' + precision(rmin, 3) + ', ' +
precision(rmax, 3) + ')',
c='m',
bold=0)
_cmap_slicer = cmaps[0]
visibles = [None, None, None]
msh = volume.zSlice(int(dims[2] / 2))
msh.alpha(alpha).lighting('', la, ld, 0)
msh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells: msh.mapPointsToCells()
vp.renderer.AddActor(msh)
visibles[2] = msh
addScalarBar(msh,
pos=(0.04, 0.0),
horizontal=True,
width=sbwidth,
vmin=rmin,
vmax=rmax,
titleFontSize=0)
def sliderfunc_x(widget, event):
i = int(widget.GetRepresentation().GetValue())
msh = volume.xSlice(i).alpha(alpha).lighting('', la, ld, 0)
msh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells: msh.mapPointsToCells()
vp.renderer.RemoveActor(visibles[0])
if i and i < dims[0]: vp.renderer.AddActor(msh)
visibles[0] = msh
def sliderfunc_y(widget, event):
i = int(widget.GetRepresentation().GetValue())
msh = volume.ySlice(i).alpha(alpha).lighting('', la, ld, 0)
msh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells: msh.mapPointsToCells()
vp.renderer.RemoveActor(visibles[1])
if i and i < dims[1]: vp.renderer.AddActor(msh)
visibles[1] = msh
def sliderfunc_z(widget, event):
i = int(widget.GetRepresentation().GetValue())
msh = volume.zSlice(i).alpha(alpha).lighting('', la, ld, 0)
msh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells: msh.mapPointsToCells()
vp.renderer.RemoveActor(visibles[2])
if i and i < dims[2]: vp.renderer.AddActor(msh)
visibles[2] = msh
cx, cy, cz, ch = 'dr', 'dg', 'db', (0.3, 0.3, 0.3)
if np.sum(vp.renderer.GetBackground()) < 1.5:
cx, cy, cz = 'lr', 'lg', 'lb'
ch = (0.8, 0.8, 0.8)
if not useSlider3D:
vp.addSlider2D(sliderfunc_x,
0,
dims[0],
title='X',
pos=[(0.8, 0.12), (0.95, 0.12)],
showValue=False,
c=cx)
vp.addSlider2D(sliderfunc_y,
0,
dims[1],
title='Y',
pos=[(0.8, 0.08), (0.95, 0.08)],
showValue=False,
c=cy)
vp.addSlider2D(sliderfunc_z,
0,
dims[2],
title='Z',
value=int(dims[2] / 2),
pos=[(0.8, 0.04), (0.95, 0.04)],
showValue=False,
c=cz)
else: # 3d sliders attached to the axes bounds
bs = box.bounds()
vp.addSlider3D(
sliderfunc_x,
pos1=(bs[0], bs[2], bs[4]),
pos2=(bs[1], bs[2], bs[4]),
xmin=0,
xmax=dims[0],
t=box.diagonalSize() / mag(box.xbounds()) * 0.6,
c=cx,
showValue=False,
)
vp.addSlider3D(
sliderfunc_y,
pos1=(bs[1], bs[2], bs[4]),
pos2=(bs[1], bs[3], bs[4]),
xmin=0,
xmax=dims[1],
t=box.diagonalSize() / mag(box.ybounds()) * 0.6,
c=cy,
showValue=False,
)
vp.addSlider3D(
sliderfunc_z,
pos1=(bs[0], bs[2], bs[4]),
pos2=(bs[0], bs[2], bs[5]),
xmin=0,
xmax=dims[2],
value=int(dims[2] / 2),
t=box.diagonalSize() / mag(box.zbounds()) * 0.6,
c=cz,
showValue=False,
)
#################
def buttonfunc():
global _cmap_slicer
bu.switch()
_cmap_slicer = bu.status()
for mesh in visibles:
if mesh:
mesh.pointColors(cmap=_cmap_slicer, vmin=rmin, vmax=rmax)
if map2cells:
mesh.mapPointsToCells()
vp.renderer.RemoveActor(mesh.scalarbar)
mesh.scalarbar = addScalarBar(mesh,
pos=(0.04, 0.0),
horizontal=True,
width=sbwidth,
vmin=rmin,
vmax=rmax,
titleFontSize=0)
vp.renderer.AddActor(mesh.scalarbar)
bu = vp.addButton(
buttonfunc,
pos=(0.27, 0.005),
states=cmaps,
c=["db"] * len(cmaps),
bc=["lb"] * len(cmaps), # colors of states
size=14,
bold=True,
)
#################
hist = None
if showHisto:
hist = cornerHistogram(data,
s=0.2,
bins=25,
logscale=1,
pos=(0.02, 0.02),
c=ch,
bg=ch,
alpha=0.7)
# vp.backgroundRenderer = vtk.vtkRenderer()
# vp.backgroundRenderer.SetLayer(1)
# vp.backgroundRenderer.InteractiveOff()
# actor = histogram(data, logscale=1, alpha=0.8).scale(4/150)
# vp.window.AddRenderer(vp.backgroundRenderer)
# vp.backgroundRenderer.AddActor(actor)
# cam = vtk.vtkCamera()
# cam.SetPosition( -10,-10, 40)
# #actor.SetPosition(-4,-4, 0)
# actor.SetOrigin(-8,-8,0)
# cam.SetParallelScale(1)
# vp.backgroundRenderer.SetActiveCamera(cam)
# vp.backgroundRenderer.ResetCameraClippingRange()
comment = None
if verbose:
comment = Text2D(
"Use sliders to slice volume\nClick button to change colormap",
font='Montserrat',
s=0.8)
vp.show(msh, hist, comment, interactive=False)
vp.interactive = True
if verbose:
printc("Press button to cycle through color maps:\n", cmaps, c="m")
printc("Use sliders to select the slicing planes.", c="m")
return vp