def RayCaster(volume):
"""
Generate a ``Plotter`` window for Volume rendering using ray casting.
Returns the ``Plotter`` object.
"""
vp = settings.plotter_instance
if not vp:
vp = Plotter(axes=4, bg='bb')
volumeProperty = volume.GetProperty()
img = volume.imagedata()
if volume.dimensions()[2]<3:
print("Error in raycaster: not enough depth", volume.dimensions())
return vp
printc("GPU Ray-casting tool", c="b", invert=1)
smin, smax = img.GetScalarRange()
x0alpha = smin + (smax - smin) * 0.25
x1alpha = smin + (smax - smin) * 0.5
x2alpha = smin + (smax - smin) * 1.0
############################## color map slider
# Create transfer mapping scalar value to color
cmaps = ["jet",
"viridis",
"bone",
"hot",
"plasma",
"winter",
"cool",
"gist_earth",
"coolwarm",
"tab10",
]
cols_cmaps = []
for cm in cmaps:
cols = colorMap(range(0, 21), cm, 0, 20) # sample 20 colors
cols_cmaps.append(cols)
Ncols = len(cmaps)
csl = (0.9, 0.9, 0.9)
if sum(getColor(vp.renderer.GetBackground())) > 1.5:
csl = (0.1, 0.1, 0.1)
def sliderColorMap(widget, event):
sliderRep = widget.GetRepresentation()
k = int(sliderRep.GetValue())
sliderRep.SetTitleText(cmaps[k])
volume.color(cmaps[k])
w1 = vp.addSlider2D(
sliderColorMap,
0,
Ncols - 1,
value=0,
showValue=0,
title=cmaps[0],
c=csl,
pos=[(0.8, 0.05), (0.965, 0.05)],
)
w1.GetRepresentation().SetTitleHeight(0.018)
############################## alpha sliders
# Create transfer mapping scalar value to opacity
opacityTransferFunction = volumeProperty.GetScalarOpacity()
def setOTF():
opacityTransferFunction.RemoveAllPoints()
opacityTransferFunction.AddPoint(smin, 0.0)
opacityTransferFunction.AddPoint(smin + (smax - smin) * 0.1, 0.0)
opacityTransferFunction.AddPoint(x0alpha, _alphaslider0)
opacityTransferFunction.AddPoint(x1alpha, _alphaslider1)
opacityTransferFunction.AddPoint(x2alpha, _alphaslider2)
setOTF()
def sliderA0(widget, event):
global _alphaslider0
_alphaslider0 = widget.GetRepresentation().GetValue()
setOTF()
vp.addSlider2D(sliderA0, 0, 1,
value=_alphaslider0,
pos=[(0.84, 0.1), (0.84, 0.26)],
c=csl, showValue=0)
def sliderA1(widget, event):
global _alphaslider1
_alphaslider1 = widget.GetRepresentation().GetValue()
setOTF()
vp.addSlider2D(sliderA1, 0, 1,
value=_alphaslider1,
pos=[(0.89, 0.1), (0.89, 0.26)],
c=csl, showValue=0)
def sliderA2(widget, event):
global _alphaslider2
_alphaslider2 = widget.GetRepresentation().GetValue()
setOTF()
w2 = vp.addSlider2D(sliderA2, 0, 1,
value=_alphaslider2,
pos=[(0.96, 0.1), (0.96, 0.26)],
c=csl, showValue=0,
title="Opacity levels")
w2.GetRepresentation().SetTitleHeight(0.016)
# add a button
def buttonfuncMode():
s = volume.mode()
snew = (s + 1) % 2
volume.mode(snew)
bum.switch()
bum = vp.addButton(
buttonfuncMode,
pos=(0.7, 0.035),
states=["composite", "max proj."],
c=["bb", "gray"],
bc=["gray", "bb"], # colors of states
font="",
size=16,
bold=0,
italic=False,
)
bum.status(volume.mode())
def CheckAbort(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
vp.window.AddObserver("AbortCheckEvent", CheckAbort)
# add histogram of scalar
plot = cornerHistogram(volume.getPointArray(),
bins=25, logscale=1, c=(.7,.7,.7), bg=(.7,.7,.7), pos=(0.78, 0.065),
lines=True, dots=False,
)
# xbins = np.linspace(smin, smax, 25)
# yvals = volume.histogram(bins=25, logscale=1)
# plot = cornerPlot(np.c_[xbins, yvals],
# c=(.7,.7,.7), bg=(.7,.7,.7), pos=(0.78, 0.065), s=0.4,
# lines=True, dots=False,
# )
plot.GetPosition2Coordinate().SetValue(0.197, 0.20, 0)
plot.GetXAxisActor2D().SetFontFactor(0.7)
plot.GetProperty().SetOpacity(0.5)
vp.add([plot, volume])
return vp
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=7,
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,
)
################################
box = volume.box().wireframe().alpha(0)
vp.show(box, viewup="z", axes=axes)
if showIcon:
vp.addInset(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()
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.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, titleFontSize=0)
def sliderfunc_x(widget, event):
i = int(widget.GetRepresentation().GetValue())
msh = volume.xSlice(i).alpha(alpha).lighting('', la, ld, 0)
msh.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.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.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', titleSize=0.5,
pos=[(0.8,0.12), (0.95,0.12)], showValue=False, c=cx)
vp.addSlider2D(sliderfunc_y, 0, dims[1], title='Y', titleSize=0.5,
pos=[(0.8,0.08), (0.95,0.08)], showValue=False, c=cy)
vp.addSlider2D(sliderfunc_z, 0, dims[2], title='Z', titleSize=0.6,
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.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)
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)
comment = None
if verbose:
comment = Text2D("Use sliders to slice volume\nClick button to change colormap",
font='', s=0.8)
vp.show(msh, hist, comment, interactive=False)
vp.interactive = True
if verbose:
printc("Press button to cycle through color maps,", c="m")
printc("Use sliders to select the slicing planes.", c="m")
return vp