def set_props(self, props):
if props is None:
self.props = None
else:
self.props = vtk.vtkPropCollection()
for prop in props:
self.props.AddItem(prop)
def ColorByOrientation(self, colorScheme=None):
if NoBacteria(): return
bacilli, filaments, bdots, fdots, sRes = communityOrientationStats()
bdots = [map(abs, bdots[i]) for i in range(3)]
fdots = [map(abs, fdots[i]) for i in range(3)]
if colorScheme is None:
colorScheme = Vec3f(2,1,0)
for i, a in enumerate(bacilli):
aColl = vtk.vtkPropCollection()
a.GetActors(aColl)
aColl.InitTraversal()
actors = [aColl.GetNextProp() for _ in range(aColl.GetNumberOfItems())]
for actor in actors:
actor.GetProperty().SetDiffuseColor(bdots[colorScheme.x][i],
bdots[colorScheme.y][i],
bdots[colorScheme.z][i])
for j, fID in enumerate(filaments):
fColl = vtk.vtkPropCollection()
DataStore.BacteriaActors()[fID].GetActors(fColl)
fColl.InitTraversal()
factors = [fColl.GetNextProp() for _ in range(fColl.GetNumberOfItems())]
# Set color LUT for filament spline based on marker positions
colorTransferFunction = vtk.vtkColorTransferFunction()
fdotIdx = sum(sRes[:j])
for k in range(0, sRes[j]):
colorTransferFunction.AddRGBPoint(k,fdots[colorScheme.x][fdotIdx+k],
fdots[colorScheme.y][fdotIdx+k],
fdots[colorScheme.z][fdotIdx+k])
# print 'RGB:',fdots[colorScheme.x][fdotIdx+k],fdots[colorScheme.y][fdotIdx+k],fdots[colorScheme.z][fdotIdx+k]
# filament spline
factors[1].GetMapper().SetLookupTable(colorTransferFunction)
factors[1].GetMapper().ScalarVisibilityOn()
factors[1].GetMapper().SetColorModeToMapScalars()
factors[1].GetMapper().InterpolateScalarsBeforeMappingOff()
# sphere caps
self.setColor(factors[0], fdotIdx, fdots, colorScheme)
self.setColor(factors[-1], fdotIdx+k, fdots, colorScheme)
self.iren.Render()
def init(self):
self.renderer = vtkRenderer()
self.renderer.SetUseDepthPeeling(1); ####
self.renderer.SetBackground(1,1,1)
self.renderWindow = vtkGenericOpenGLRenderWindow()
self.renderWindow.SetAlphaBitPlanes(True) ####
self.renderWindow.AddRenderer(self.renderer)
self.SetRenderWindow(self.renderWindow)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.actors = vtkPropCollection()
def init(self):
self.renderer = vtkRenderer()
self.renderer.SetUseDepthPeeling(1); ####
self.renderer.SetBackground(1,1,1)
self.renderWindow = vtkGenericOpenGLRenderWindow()
self.renderWindow.SetAlphaBitPlanes(True) ####
self.renderWindow.AddRenderer(self.renderer)
self.SetRenderWindow(self.renderWindow)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.actors = vtkPropCollection()
def get_wall_actors(renderers, blocks):
# Returns a list of just the actor components from the wall cube props
# Setup the list to collect the actors
actorsList = []
# A vtkPropCollection, populate it with the props from the blocks renderer
propCollection = vtkPropCollection()
propCollection = renderers[blocks].GetViewProps()
# Get the number of props so we know how many items to iterate over
numberProps = propCollection.GetNumberOfItems()
# Initiate traversal over the collection
propCollection.InitTraversal()
# Now iterate over each of the props
for prop in range(numberProps):
# Move to the next prop in the collection and get the number of actors in that prop
currentProp = propCollection.GetNextProp()
# We're just interested in wall objects, not floor objects
# So only scan this prop further if it is a prop and not an actor
typeBool = currentProp.IsTypeOf("vtkPropAssembly")
if typeBool == 1:
# The prop doesn't list any positional attributes so we're going to need to loop over the component actors to find the cube actor which does have positional attributes
# Get the number of actors in this prop so we know how many iterations to make
numberOfActors = currentProp.GetNumberOfPaths()
# Setup a vtkPropAssembly to store the assembly of parts that make up the current prop, and populate it
actorCollection = vtkPropAssembly()
actorCollection = currentProp.GetParts()
# and initiate traversal over the collection of parts/actors
actorCollection.InitTraversal()
for actor in range(numberOfActors):
# Now iterate over each actor.
# Move to the next actor in the collection.
currentActor = actorCollection.GetNextProp()
# Check if the actor is an OpenGL type, which is used for the wall and floor objects, as opposed to a CaptionActor type which is the component used for the captioning
# method returns a 1 if the type of the actor matches the argument, otherwise returns a 0
typeBool = currentActor.IsTypeOf("vtkOpenGLActor")
if typeBool == 1:
# This actor is a wall or floor actor
# check the height of the actor ... if it's less than 1 then this actor is floor
actorHeight = currentActor.GetBounds(
)[3] - currentActor.GetBounds()[2]
if actorHeight >= 1:
# This is a wall actor
actorsList.append(currentActor)
return actorsList
def get_floor_actors(renderers, blocks):
# Returns a list of just the floor panel actors
# Setup the list to be returned
actorsList = []
# Setup a vtkPropCollection, get populate it with the props from the blocks renderer
propCollection = vtkPropCollection()
propCollection = renderers[blocks].GetViewProps()
# Get the number of props so we know how many items to iterate over
numberProps = propCollection.GetNumberOfItems()
# Initiate traversal over the collection
propCollection.InitTraversal()
# now iterate over each of the props
for prop in range(numberProps):
# Move to the next prop in the collection and get the number of actors in that prop
currentProp = propCollection.GetNextProp()
# Check if this prop is an OpenGLActor
typeBool = currentProp.IsTypeOf("vtkOpenGLActor")
if typeBool == 1:
# This is an actor, which means its part of the floor.
actorsList.append(currentProp)
return actorsList
def get_wall_props(renderers, blocks):
# Returns a list of the vtkPropAssembly props which are wall and obstacle objects with embedded captions
# Setup the list to collect the props
propsList = []
# A vtkPropCollection, populate it with the props from the blocks renderer
propCollection = vtkPropCollection()
propCollection = renderers[blocks].GetViewProps()
# Get the number of props so we know how many items to iterate over
numberProps = propCollection.GetNumberOfItems()
# Initiate traversal over the collection
propCollection.InitTraversal()
# Now iterate over each of the props
for prop in range(numberProps):
# Move to the next prop in the collection and get the number of actors in that prop
currentProp = propCollection.GetNextProp()
# We're just interested in wall objects, not floor objects
# So only scan this prop further if it is a prop and not an actor
typeBool = currentProp.IsTypeOf("vtkPropAssembly")
if typeBool == 1:
# This is a wall object prop
propsList.append(currentProp)
return propsList
def UpdateColor(self, color):
"""
Set the color of all actors.
:@type color: render.basic.Color
:@param color: The new color to use.
"""
self.color = color
for marker in DataStore.Markers():
marker.GetProperty().SetDiffuseColor(color.r,
color.g,
color.b)
for bact in DataStore.BacteriaActors():
aColl = vtk.vtkPropCollection()
bact.GetActors(aColl)
aColl.InitTraversal()
actors = [aColl.GetNextProp() for _ in range(aColl.GetNumberOfItems())]
for actor in actors:
actor.GetProperty().SetDiffuseColor(color.r,
color.g,
color.b)
self.renwin_update_callback()
def printInfo(obj):
"""Print information about a vtk object."""
def printvtkactor(actor, tab=""):
if not actor.GetPickable():
return
mapper = actor.GetMapper()
if hasattr(actor, "polydata"):
poly = actor.polydata()
else:
poly = mapper.GetInput()
pro = actor.GetProperty()
pos = actor.GetPosition()
bnds = actor.GetBounds()
col = pro.GetColor()
colr = precision(col[0], 3)
colg = precision(col[1], 3)
colb = precision(col[2], 3)
alpha = pro.GetOpacity()
npt = poly.GetNumberOfPoints()
ncl = poly.GetNumberOfCells()
npl = poly.GetNumberOfPolys()
print(tab, end="")
colors.printc("vtkActor", c="g", bold=1, invert=1, dim=1, end=" ")
if hasattr(actor, "_legend") and actor._legend:
colors.printc("legend: ", c="g", bold=1, end="")
colors.printc(actor._legend, c="g", bold=0)
else:
print()
if hasattr(actor, "filename") and actor.filename:
colors.printc(tab + " file: ", c="g", bold=1, end="")
colors.printc(actor.filename, c="g", bold=0)
if not actor.GetMapper().GetScalarVisibility():
colors.printc(tab + " color: ", c="g", bold=1, end="")
#colors.printc("defined by point or cell data", c="g", bold=0)
#else:
colors.printc(colors.getColorName(col) + ', rgb=(' + colr + ', ' +
colg + ', ' + colb + '), alpha=' + str(alpha),
c='g',
bold=0)
if actor.GetBackfaceProperty():
bcol = actor.GetBackfaceProperty().GetDiffuseColor()
bcolr = precision(bcol[0], 3)
bcolg = precision(bcol[1], 3)
bcolb = precision(bcol[2], 3)
colors.printc(tab + ' back color: ', c='g', bold=1, end='')
colors.printc(colors.getColorName(bcol) + ', rgb=(' + bcolr +
', ' + bcolg + ', ' + bcolb + ')',
c='g',
bold=0)
colors.printc(tab + " points: ", c="g", bold=1, end="")
colors.printc(npt, c="g", bold=0)
colors.printc(tab + " cells: ", c="g", bold=1, end="")
colors.printc(ncl, c="g", bold=0)
colors.printc(tab + " polygons: ", c="g", bold=1, end="")
colors.printc(npl, c="g", bold=0)
colors.printc(tab + " position: ", c="g", bold=1, end="")
colors.printc(pos, c="g", bold=0)
if hasattr(actor, "polydata") and actor.N():
colors.printc(tab + " c. of mass: ", c="g", bold=1, end="")
cm = tuple(actor.centerOfMass())
colors.printc(precision(cm, 3), c="g", bold=0)
colors.printc(tab + " ave. size: ", c="g", bold=1, end="")
colors.printc(precision(actor.averageSize(), 6), c="g", bold=0)
colors.printc(tab + " diag. size: ", c="g", bold=1, end="")
colors.printc(precision(actor.diagonalSize(), 6), c="g", bold=0)
_area = actor.area()
if _area:
colors.printc(tab + " area: ", c="g", bold=1, end="")
colors.printc(precision(_area, 6), c="g", bold=0)
_vol = actor.volume()
if _vol:
colors.printc(tab + " volume: ", c="g", bold=1, end="")
colors.printc(precision(_vol, 6), c="g", bold=0)
colors.printc(tab + " bounds: ", c="g", bold=1, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="g", bold=0, end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="g", bold=0, end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="g", bold=0)
arrtypes = dict()
arrtypes[vtk.VTK_UNSIGNED_CHAR] = "UNSIGNED_CHAR"
arrtypes[vtk.VTK_SIGNED_CHAR] = "SIGNED_CHAR"
arrtypes[vtk.VTK_UNSIGNED_INT] = "UNSIGNED_INT"
arrtypes[vtk.VTK_INT] = "INT"
arrtypes[vtk.VTK_CHAR] = "CHAR"
arrtypes[vtk.VTK_SHORT] = "SHORT"
arrtypes[vtk.VTK_LONG] = "LONG"
arrtypes[vtk.VTK_ID_TYPE] = "ID"
arrtypes[vtk.VTK_FLOAT] = "FLOAT"
arrtypes[vtk.VTK_DOUBLE] = "DOUBLE"
ptdata = poly.GetPointData()
cldata = poly.GetCellData()
colors.printc(tab + " scalar mode:", c="g", bold=1, end=" ")
colors.printc(mapper.GetScalarModeAsString(),
' coloring =',
mapper.GetColorModeAsString(),
c="g",
bold=0)
if ptdata.GetNumberOfArrays() + cldata.GetNumberOfArrays():
colors.printc(tab + " active scalars: ", c="g", bold=1, end="")
if ptdata.GetScalars():
colors.printc(ptdata.GetScalars().GetName(),
"(point data) ",
c="g",
bold=0,
end="")
if cldata.GetScalars():
colors.printc(cldata.GetScalars().GetName(),
"(cell data)",
c="g",
bold=0,
end="")
print()
for i in range(ptdata.GetNumberOfArrays()):
name = ptdata.GetArrayName(i)
if name and ptdata.GetArray(i):
colors.printc(tab + " point data: ", c="g", bold=1, end="")
try:
tt = arrtypes[ptdata.GetArray(i).GetDataType()]
except:
tt = str(ptdata.GetArray(i).GetDataType())
ncomp = str(ptdata.GetArray(i).GetNumberOfComponents())
colors.printc("name=" + name,
"(" + ncomp + " " + tt + "),",
c="g",
bold=0,
end="")
rng = ptdata.GetArray(i).GetRange()
colors.printc(" range=(" + precision(rng[0], 4) + ',' +
precision(rng[1], 4) + ')',
c="g",
bold=0)
for i in range(cldata.GetNumberOfArrays()):
name = cldata.GetArrayName(i)
if name and cldata.GetArray(i):
colors.printc(tab + " cell data: ", c="g", bold=1, end="")
try:
tt = arrtypes[cldata.GetArray(i).GetDataType()]
except:
tt = str(cldata.GetArray(i).GetDataType())
ncomp = str(cldata.GetArray(i).GetNumberOfComponents())
colors.printc("name=" + name,
"(" + ncomp + " " + tt + "),",
c="g",
bold=0,
end="")
rng = cldata.GetArray(i).GetRange()
colors.printc(" range=(" + precision(rng[0], 4) + ',' +
precision(rng[1], 4) + ')',
c="g",
bold=0)
if not obj:
return
elif isinstance(obj, vtk.vtkActor):
colors.printc("_" * 65, c="g", bold=0)
printvtkactor(obj)
elif isinstance(obj, vtk.vtkAssembly):
colors.printc("_" * 65, c="g", bold=0)
colors.printc("vtkAssembly", c="g", bold=1, invert=1, end=" ")
if hasattr(obj, "_legend"):
colors.printc("legend: ", c="g", bold=1, end="")
colors.printc(obj._legend, c="g", bold=0)
else:
print()
pos = obj.GetPosition()
bnds = obj.GetBounds()
colors.printc(" position: ", c="g", bold=1, end="")
colors.printc(pos, c="g", bold=0)
colors.printc(" bounds: ", c="g", bold=1, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="g", bold=0, end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="g", bold=0, end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="g", bold=0)
cl = vtk.vtkPropCollection()
obj.GetActors(cl)
cl.InitTraversal()
for i in range(obj.GetNumberOfPaths()):
act = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
if isinstance(act, vtk.vtkActor):
printvtkactor(act, tab=" ")
elif isinstance(obj, vtk.vtkVolume):
colors.printc("_" * 65, c="b", bold=0)
colors.printc("vtkVolume", c="b", bold=1, invert=1, end=" ")
if hasattr(obj, "_legend") and obj._legend:
colors.printc("legend: ", c="b", bold=1, end="")
colors.printc(obj._legend, c="b", bold=0)
else:
print()
pos = obj.GetPosition()
bnds = obj.GetBounds()
img = obj.GetMapper().GetInput()
colors.printc(" position: ", c="b", bold=1, end="")
colors.printc(pos, c="b", bold=0)
colors.printc(" dimensions: ", c="b", bold=1, end="")
colors.printc(img.GetDimensions(), c="b", bold=0)
colors.printc(" spacing: ", c="b", bold=1, end="")
colors.printc(img.GetSpacing(), c="b", bold=0)
colors.printc(" data dimension: ", c="b", bold=1, end="")
colors.printc(img.GetDataDimension(), c="b", bold=0)
colors.printc(" memory size: ", c="b", bold=1, end="")
colors.printc(int(img.GetActualMemorySize() / 1024),
'Mb',
c="b",
bold=0)
colors.printc(" scalar #bytes: ", c="b", bold=1, end="")
colors.printc(img.GetScalarSize(), c="b", bold=0)
colors.printc(" bounds: ", c="b", bold=1, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="b", bold=0, end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="b", bold=0, end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="b", bold=0)
colors.printc(" scalar range: ", c="b", bold=1, end="")
colors.printc(img.GetScalarRange(), c="b", bold=0)
printHistogram(obj,
horizontal=True,
logscale=True,
bins=8,
height=15,
c='b',
bold=0)
elif hasattr(obj, "interactor"): # dumps Plotter info
axtype = {
0: "(no axes)",
1: "(three customizable gray grid walls)",
2: "(cartesian axes from origin",
3: "(positive range of cartesian axes from origin",
4: "(axes triad at bottom left)",
5: "(oriented cube at bottom left)",
6: "(mark the corners of the bounding box)",
7: "(ruler at the bottom of the window)",
8: "(the vtkCubeAxesActor object)",
9: "(the bounding box outline)",
10: "(circles of maximum bounding box range)",
}
bns, totpt = [], 0
for a in obj.actors:
b = a.GetBounds()
if a.GetBounds() is not None:
if isinstance(a, vtk.vtkActor):
totpt += a.GetMapper().GetInput().GetNumberOfPoints()
bns.append(b)
if len(bns) == 0:
return
acts = obj.getActors()
colors.printc("_" * 65, c="c", bold=0)
colors.printc("Plotter", invert=1, dim=1, c="c", end=" ")
otit = obj.title
if not otit:
otit = None
colors.printc(" title:", otit, bold=0, c="c")
colors.printc(" active renderer:",
obj.renderers.index(obj.renderer),
bold=0,
c="c")
colors.printc(" nr. of actors:", len(acts), bold=0, c="c", end="")
colors.printc(" (" + str(totpt), "vertices)", bold=0, c="c")
max_bns = np.max(bns, axis=0)
min_bns = np.min(bns, axis=0)
colors.printc(" max bounds: ", c="c", bold=0, end="")
bx1, bx2 = precision(min_bns[0], 3), precision(max_bns[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="c", bold=0, end="")
by1, by2 = precision(min_bns[2], 3), precision(max_bns[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="c", bold=0, end="")
bz1, bz2 = precision(min_bns[4], 3), precision(max_bns[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="c", bold=0)
if isinstance(obj.axes, dict): obj.axes = 1
colors.printc(" axes type:",
obj.axes,
axtype[obj.axes],
bold=0,
c="c")
for a in obj.getVolumes():
if a.GetBounds() is not None:
img = a.GetMapper().GetDataSetInput()
colors.printc('_' * 65, c='b', bold=0)
colors.printc('Volume', invert=1, dim=1, c='b')
colors.printc(' scalar range:',
np.round(img.GetScalarRange(), 4),
c='b',
bold=0)
bnds = a.GetBounds()
colors.printc(" bounds: ", c="b", bold=0, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")",
c="b",
bold=0,
end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")",
c="b",
bold=0,
end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="b", bold=0)
colors.printc(" Click actor and press i for Actor info.", c="c")
else:
colors.printc("_" * 65, c="g", bold=0)
colors.printc(type(obj), c="g", invert=1)
from pymicro.crystal.lattice import Lattice, HklDirection
s3d = Scene3D(display=False, ren_size=(600, 600))
s3d.name = 'euler_angles_and_orientation_matrix'
euler_angles = np.array([142.8, 32.0, 214.4])
(phi1, Phi, phi2) = euler_angles
orientation = Orientation.from_euler(euler_angles)
g = orientation.orientation_matrix()
lab_frame = axes_actor(1, fontSize=50)
lab_frame.SetCylinderRadius(0.02)
s3d.add(lab_frame)
crystal_frame = axes_actor(0.6, fontSize=50, axisLabels=None)
crystal_frame.SetCylinderRadius(0.05)
collection = vtk.vtkPropCollection()
crystal_frame.GetActors(collection)
for i in range(collection.GetNumberOfItems()):
collection.GetItemAsObject(i).GetProperty().SetColor(0.0, 0.0, 0.0)
apply_orientation_to_actor(crystal_frame, orientation)
s3d.add(crystal_frame)
a = 1.0
l = Lattice.face_centered_cubic(a)
fcc_lattice = lattice_3d(l, crystal_orientation=orientation)
set_opacity(fcc_lattice, 0.3)
s3d.add(fcc_lattice)
# arrow to show 111 lattice vector
Vc = np.array([a, a, a])
Vs = np.dot(g.T, Vc)
def reset_camera(self):
self.ren.ResetCamera()
self.ren.ResetCameraClippingRange()
if self.experiment is not None:
calib = self.experiment.calibration_points
focal_point = self.experiment.sphere_center
view_up = calib["vertex"]-focal_point
mid_point = (calib["nasion"]*0.7+calib["vertex"]*0.3)
pos_vec = mid_point - focal_point
pos = focal_point+pos_vec*15
cam = self.ren.GetActiveCamera()
cam.SetFocalPoint(focal_point)
cam.SetPosition(pos)
cam.SetViewUp(view_up)
self.light.SetFocalPoint(focal_point)
self.light2.SetFocalPoint(focal_point)
self.light3.SetFocalPoint(focal_point)
left_mid_point= (calib["vertex"]+calib["left"])/2
right_mid_point= (calib["vertex"]+calib["right"])/2
#top_left_pos = focal_point + (left_mid_point-focal_point)*5
#top_right_pos = focal_point + (right_mid_point-focal_point)*5
right_pos = focal_point + (calib["right"]-focal_point)*15
top_pos = focal_point+(calib["vertex"]-focal_point)*15
top_front_pos = focal_point+((calib["nasion"]+calib["vertex"])/2-focal_point)*15
#self.light.SetPosition(top_left_pos)
#self.light2.SetPosition(top_right_pos)
trans = vtk.vtkTransform()
view_up_uni = view_up/np.linalg.norm(view_up)
n1 = calib["nasion"]-focal_point
n1 = n1 - (np.dot(n1, view_up_uni) * view_up_uni)
n1 /= np.linalg.norm(n1)
n2 = np.array((0,0,1))
n2 = n2 - (np.dot(n2, view_up_uni) * view_up_uni)
n2 /= np.linalg.norm(n2)
v2 = np.cross(n2,n1)
angle2 = np.arcsin(np.linalg.norm(v2))
angle2_deg = 180*angle2/np.pi
v1 = np.cross((0,1,0),view_up_uni)
angle1 = np.arcsin(np.linalg.norm(v1))
angle1_deg = 180*angle1/np.pi
trans.RotateWXYZ(angle2_deg,view_up_uni)
trans.RotateWXYZ(angle1_deg,*v1)
acs = vtk.vtkPropCollection()
self.axes_actor.GetActors(acs)
for i in xrange(acs.GetNumberOfItems()):
ac = acs.GetItemAsObject(i)
mapper = ac.GetMapper()
source_con = mapper.GetInputConnection(0,0)
source = source_con.GetProducer()
if not isinstance(source,vtk.vtkTransformFilter):
trans_filter = vtk.vtkTransformFilter()
trans_filter.SetInputConnection(source.GetOutputPort())
trans_filter.SetTransform(trans)
mapper.SetInputConnection(trans_filter.GetOutputPort())
else:
source.SetTransform(trans)
#self.axes_actor.RotateY(180)
self.light.SetPosition(top_pos)
self.light2.SetPosition(top_front_pos)
self.light3.SetPosition(right_pos)
self.light3.SetIntensity(0.5)
self.ren.ResetCameraClippingRange()
m1.SetInput(s1.GetOutput())
s2 = vtk.vtkConeSource()
m2 = vtk.vtkPolyDataMapper()
a2 = vtk.vtkActor()
a2.SetMapper(m2)
m2.SetInput(s2.GetOutput())
as1 = vtk.vtkAssembly()
as1.AddPart(a1)
as1.AddPart(a2)
t1 = vtk.vtkTransform()
t1.PostMultiply()
t1.Translate(5.0, 0.0, 0.0)
pc1 = vtk.vtkPropCollection()
as1.GetActors(pc1)
pc1.InitTraversal()
for i in xrange(pc1.GetNumberOfItems()):
pc1.GetNextProp().GetProperty().SetColor(255.0, 0.0, 0.0)
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
ren.AddActor(as1)
renWin.AddRenderer(ren)
iren.SetRenderWindow(renWin)
iren.Initialize()
iren.Start()
def printInfo(obj):
'''Print information about a vtkActor or vtkAssembly.'''
print([obj])
def printvtkactor(actor, tab=''):
poly = actor.polydata()
pro = actor.GetProperty()
pos = actor.GetPosition()
bnds = actor.GetBounds()
col = pro.GetColor()
colr = to_precision(col[0], 3)
colg = to_precision(col[1], 3)
colb = to_precision(col[2], 3)
alpha = pro.GetOpacity()
npt = poly.GetNumberOfPoints()
ncl = poly.GetNumberOfCells()
print(tab, end='')
colors.printc('vtkActor', c='g', bold=1, invert=1, dim=1, end=' ')
if hasattr(actor, 'legend') and actor.legend:
colors.printc('legend: ', c='g', bold=1, end='')
colors.printc(actor.legend, c='g', bold=0)
else:
print()
if hasattr(actor, 'filename'):
colors.printc(tab+' file: ', c='g', bold=1, end='')
colors.printc(actor.filename, c='g', bold=0)
colors.printc(tab+' color: ', c='g', bold=1, end='')
if actor.GetMapper().GetScalarVisibility():
colors.printc('defined by point or cell data', c='g', bold=0)
else:
colors.printc(colors.getColorName(col) + ', rgb=('+colr+', '
+ colg+', '+colb+'), alpha='+str(alpha), c='g', bold=0)
if actor.GetBackfaceProperty():
bcol = actor.GetBackfaceProperty().GetDiffuseColor()
bcolr = to_precision(bcol[0], 3)
bcolg = to_precision(bcol[1], 3)
bcolb = to_precision(bcol[2], 3)
colors.printc(tab+' back color: ', c='g', bold=1, end='')
colors.printc(colors.getColorName(bcol) + ', rgb=('+bcolr+', '
+ bcolg+', ' + bcolb+')', c='g', bold=0)
colors.printc(tab+' points: ', c='g', bold=1, end='')
colors.printc(npt, c='g', bold=0)
colors.printc(tab+' cells: ', c='g', bold=1, end='')
colors.printc(ncl, c='g', bold=0)
colors.printc(tab+' position: ', c='g', bold=1, end='')
colors.printc(pos, c='g', bold=0)
colors.printc(tab+' c. of mass: ', c='g', bold=1, end='')
colors.printc(actor.centerOfMass(), c='g', bold=0)
colors.printc(tab+' ave. size: ', c='g', bold=1, end='')
colors.printc(to_precision(actor.averageSize(), 4), c='g', bold=0)
colors.printc(tab+' diag. size: ', c='g', bold=1, end='')
colors.printc(actor.diagonalSize(), c='g', bold=0)
#colors.printc(' clicked point:', obj.picked3d, bold=0, c='c')
colors.printc(tab+' bounds: ', c='g', bold=1, end='')
bx1, bx2 = to_precision(bnds[0], 3), to_precision(bnds[1], 3)
colors.printc('x=('+bx1+', '+bx2+')', c='g', bold=0, end='')
by1, by2 = to_precision(bnds[2], 3), to_precision(bnds[3], 3)
colors.printc(' y=('+by1+', '+by2+')', c='g', bold=0, end='')
bz1, bz2 = to_precision(bnds[4], 3), to_precision(bnds[5], 3)
colors.printc(' z=('+bz1+', '+bz2+')', c='g', bold=0)
colors.printc(tab+' area: ', c='g', bold=1, end='')
colors.printc(to_precision(actor.area(), 8), c='g', bold=0)
colors.printc(tab+' volume: ', c='g', bold=1, end='')
colors.printc(to_precision(actor.volume(), 8), c='g', bold=0)
arrtypes = dict()
arrtypes[vtk.VTK_UNSIGNED_CHAR] = 'VTK_UNSIGNED_CHAR'
arrtypes[vtk.VTK_UNSIGNED_INT] = 'VTK_UNSIGNED_INT'
arrtypes[vtk.VTK_FLOAT] = 'VTK_FLOAT'
arrtypes[vtk.VTK_DOUBLE] = 'VTK_DOUBLE'
if poly.GetPointData():
ptdata = poly.GetPointData()
for i in range(ptdata.GetNumberOfArrays()):
name = ptdata.GetArrayName(i)
if name:
colors.printc(tab+' point data: ',
c='g', bold=1, end='')
try:
tt = arrtypes[ptdata.GetArray(i).GetDataType()]
colors.printc('name='+name, 'type='+tt, c='g', bold=0)
except:
tt = ptdata.GetArray(i).GetDataType()
colors.printc('name='+name, 'type=', tt, c='g', bold=0)
if poly.GetCellData():
cldata = poly.GetCellData()
for i in range(cldata.GetNumberOfArrays()):
name = cldata.GetArrayName(i)
if name:
colors.printc(tab+' cell data: ',
c='g', bold=1, end='')
try:
tt = arrtypes[cldata.GetArray(i).GetDataType()]
colors.printc('name='+name, 'type='+tt, c='g', bold=0)
except:
tt = cldata.GetArray(i).GetDataType()
colors.printc('name='+name, 'type=', tt, c='g', bold=0)
if not obj:
return
elif isinstance(obj, vtk.vtkActor):
colors.printc('_'*60, c='g', bold=0)
printvtkactor(obj)
elif isinstance(obj, vtk.vtkAssembly):
colors.printc('_'*60, c='g', bold=0)
colors.printc('vtkAssembly', c='g', bold=1, invert=1, end=' ')
if hasattr(obj, 'legend'):
colors.printc('legend: ', c='g', bold=1, end='')
colors.printc(obj.legend, c='g', bold=0)
else:
print()
pos = obj.GetPosition()
bnds = obj.GetBounds()
colors.printc(' position: ', c='g', bold=1, end='')
colors.printc(pos, c='g', bold=0)
colors.printc(' bounds: ', c='g', bold=1, end='')
bx1, bx2 = to_precision(bnds[0], 3), to_precision(bnds[1], 3)
colors.printc('x=('+bx1+', '+bx2+')', c='g', bold=0, end='')
by1, by2 = to_precision(bnds[2], 3), to_precision(bnds[3], 3)
colors.printc(' y=('+by1+', '+by2+')', c='g', bold=0, end='')
bz1, bz2 = to_precision(bnds[4], 3), to_precision(bnds[5], 3)
colors.printc(' z=('+bz1+', '+bz2+')', c='g', bold=0)
cl = vtk.vtkPropCollection()
obj.GetActors(cl)
cl.InitTraversal()
for i in range(obj.GetNumberOfPaths()):
act = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
if isinstance(act, vtk.vtkActor):
printvtkactor(act, tab=' ')
elif hasattr(obj, 'interactor'): # dumps Plotter info
axtype = {0 : '(no axes)',
1 : '(three gray grid walls)',
2 : '(cartesian axes from origin',
3 : '(positive range of cartesian axes from origin',
4 : '(axes triad at bottom left)',
5 : '(oriented cube at bottom left)',
6 : '(mark the corners of the bounding box)',
7 : '(ruler at the bottom of the window)',
8 : '(the vtkCubeAxesActor object)',
9 : '(the bounding box outline)'}
bns, totpt = [], 0
for a in obj.actors:
b = a.GetBounds()
if b is not None:
if isinstance(obj, vtk.vtkVolume): # dumps Volume info
colors.printc('Volume', invert=1, dim=1, c='b')
colors.printc(' scalar range:',
np.round(obj.GetScalarRange(),4), c='b', bold=0)
bnds = obj.GetBounds()
colors.printc(' bounds: ', c='g', bold=1, end='')
bx1, bx2 = to_precision(bnds[0], 3), to_precision(bnds[1], 3)
colors.printc('x=('+bx1+', '+bx2+')', c='g', bold=0, end='')
by1, by2 = to_precision(bnds[2], 3), to_precision(bnds[3], 3)
colors.printc(' y=('+by1+', '+by2+')', c='g', bold=0, end='')
bz1, bz2 = to_precision(bnds[4], 3), to_precision(bnds[5], 3)
colors.printc(' z=('+bz1+', '+bz2+')', c='g', bold=0)
elif isinstance(obj, vtk.vtkActor):
totpt += a.GetMapper().GetInput().GetNumberOfPoints()
bns.append(b)
if len(bns) == 0:
return
acts = obj.getActors()
colors.printc('_'*60, c='c', bold=0)
colors.printc('Plotter', invert=1, dim=1, c='c', end=' ')
otit = obj.title
if not otit:
otit = None
colors.printc(' title:', otit, bold=0, c='c')
colors.printc(' active renderer:', obj.renderers.index(obj.renderer), bold=0, c='c')
colors.printc(' nr. of actors:', len(acts), bold=0, c='c', end='')
colors.printc(' ('+str(totpt), 'vertices)', bold=0, c='c')
max_bns = np.max(bns, axis=0)
min_bns = np.min(bns, axis=0)
colors.printc(' max bounds: ', c='c', bold=0, end='')
bx1, bx2 = to_precision(min_bns[0], 3), to_precision(max_bns[1], 3)
colors.printc('x=('+bx1+', '+bx2+')', c='c', bold=0, end='')
by1, by2 = to_precision(min_bns[2], 3), to_precision(max_bns[3], 3)
colors.printc(' y=('+by1+', '+by2+')', c='c', bold=0, end='')
bz1, bz2 = to_precision(min_bns[4], 3), to_precision(max_bns[5], 3)
colors.printc(' z=('+bz1+', '+bz2+')', c='c', bold=0)
colors.printc(' axes type:', obj.axes, axtype[obj.axes], bold=0, c='c')
colors.printc(' click actor and press i for more info.', c='c')
else:
colors.printc('_'*60, c='g', bold=0)
colors.printc(obj, c='g')
colors.printc(type(obj), c='g', invert=1)
def polydata(obj, rebuild=True, index=0):
'''
Returns the vtkPolyData of a vtkActor or vtkAssembly.
If rebuild=True returns a copy of polydata
that corresponds to the current actor's position in space.
If a vtkAssembly is passed, return the polydata of component index.
'''
if isinstance(obj, vtk.vtkActor):
if not rebuild:
if hasattr(obj, 'poly'):
if obj.poly: return obj.poly
else:
setattr(obj, 'poly', None)
obj.poly = obj.GetMapper().GetInput() #cache it for speed
return obj.poly
M = obj.GetMatrix()
if isIdentity(M):
if hasattr(obj, 'poly'):
if obj.poly: return obj.poly
else:
setattr(obj, 'poly', None)
obj.poly = obj.GetMapper().GetInput() #cache it for speed
return obj.poly
# if identity return the original polydata
# otherwise make a copy that corresponds to
# the actual position in space of the actor
transform = vtk.vtkTransform()
transform.SetMatrix(M)
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
if vtkMV: tp.SetInputData(obj.GetMapper().GetInput())
else: tp.SetInput(obj.GetMapper().GetInput())
tp.Update()
return tp.GetOutput()
elif isinstance(obj, vtk.vtkAssembly):
cl = vtk.vtkPropCollection()
obj.GetActors(cl)
cl.InitTraversal()
for i in range(index + 1):
act = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
pd = act.GetMapper().GetInput() #not optimized
if not rebuild: return pd
M = act.GetMatrix()
if isIdentity(M): return pd
# if identity return the original polydata
# otherwise make a copy that corresponds to
# the actual position in space of the actor
transform = vtk.vtkTransform()
transform.SetMatrix(M)
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
if vtkMV: tp.SetInputData(pd)
else: tp.SetInput(pd)
tp.Update()
return tp.GetOutput()
elif isinstance(obj, vtk.vtkPolyData):
return obj
elif isinstance(obj, vtk.vtkActor2D):
return obj.GetMapper().GetInput()
elif isinstance(obj, vtk.vtkImageActor):
return obj.GetMapper().GetInput()
elif obj is None:
return None
colors.printc("Fatal Error in polydata(): ", 'r', end='')
colors.printc(("input is neither a vtkActor nor vtkAssembly.", [obj]), 'r')
exit(1)
def view(image=None, # noqa: C901
label_image=None, # noqa: C901
label_image_names=None, # noqa: C901
label_image_weights=None, # noqa: C901
label_image_blend=0.5,
cmap=None,
lut='glasbey',
select_roi=False,
interpolation=True,
gradient_opacity=0.22, opacity_gaussians=None, channels=None,
slicing_planes=False, shadow=True, blend_mode='composite',
point_sets=[],
point_set_colors=[], point_set_opacities=[],
point_set_representations=[], point_set_sizes=[],
geometries=[],
geometry_colors=[], geometry_opacities=[],
ui_collapsed=False, rotate=False, annotations=True, mode='v',
**kwargs):
"""View the image and/or point sets and/or geometries.
Creates and returns an ipywidget to visualize an image, and/or point sets
and/or geometries .
The image can be 2D or 3D. A label map that corresponds to the image can
also be provided. The image and label map must have the same size.
The type of the image can be an numpy.array, itk.Image,
vtk.vtkImageData, pyvista.UniformGrid, imglyb.ReferenceGuardingRandomAccessibleInterval,
or a NumPy array-like, e.g. a Dask array.
A point set or a sequence of points sets can be visualized. The type of the
point set can be an numpy.array (Nx3 array of point positions).
A geometry or a sequence of geometries can be visualized. The type of the
geometry can be an itk.Mesh.
Parameters
----------
General Interface
^^^^^^^^^^^^^^^^^
ui_collapsed : bool, default: False
Collapse the native widget user interface.
rotate : bool, default: False
Continuously rotate the camera around the scene in volume rendering
mode.
annotations : bool, default: True
Display annotations describing orientation and the value of a
mouse-position-based data probe.
mode: 'x', 'y', 'z', or 'v', default: 'v'
Only relevant for 3D scenes.
Viewing mode:
'x': x-plane
'y': y-plane
'z': z-plane
'v': volume rendering
camera: 3x3 numpy float32 array
Camera parameters:
[[position_x, position_y, position_z],
[focal_point_x, focal_point_y, focal_point_z],
[view_up_x, view_up_y, view_up_z]]
background: (red, green, blue) tuple, components from 0.0 to 1.0
Background color. Default is based on the current Jupyter theme.
Images
^^^^^^
image : array_like, itk.Image, or vtk.vtkImageData
The 2D or 3D image to visualize.
label_image : array_like, itk.Image, or vtk.vtkImageData
The 2D or 3D label map to visualize. If an image is also provided, the
label map must have the same size.
label_image_names : OrderedDict of (label_value, label_name)
String names associated with the integer label values.
label_image_weights : 1D numpy float32 array, default: None
Rendering weights, from 0.0 to 1.0, associated labels in the label map.
label_image_blend : float, default: 0.5
Label map blend with intensity image, from 0.0 to 1.0.
vmin: list of floats, default: Minimum of the image pixel buffer
Value that maps to the minimum of image colormap. A single value
can be provided or a list for multi-component images.
vmax: list of floats, default: Maximum of the image pixel buffer
Value that maps to the minimum of image colormap. A single value can
be provided or a list for multi-component images.
cmap: list of colormaps
default:
- single component: 'viridis', 'grayscale' with a label map,
- two components: 'BkCy', 'BkMa'
- three components: 'BkRd', 'BkGn', 'BkBu'
Colormap for each image component. Some valid values available at
itkwidgets.cm.*
Colormaps can also be Nx3 float NumPy arrays from 0.0 to 1.0 for the
red, green, blue points on the map or a
matplotlib.colors.LinearSegmentedColormap.
lut: lookup table, default: 'glasbey'
Lookup table for the label map. Some valid values available at
itkwidgets.lut.*
select_roi: bool, default: False
Enable an interactive region of interest widget for the image.
slicing_planes: bool, default: False
Enable slicing planes on the volume rendering.
x_slice: float, default: None
World-space position of the X slicing plane.
y_slice: float, default: None
World-space position of the Y slicing plane.
z_slice: float, default: None
World-space position of the Z slicing plane.
interpolation: bool, default: True
Linear as opposed to nearest neighbor interpolation for image slices.
Note: Interpolation is not currently supported with label maps.
gradient_opacity: float, default: 0.22
Gradient opacity for composite volume rendering, in the range (0.0, 1.0].
opacity_gaussians: list of list of dict
Volume rendering opacity transfer function Gaussian parameters. For each
image component, multiple Gaussians can be specified.
Default Gaussian parameters:
{'position': 0.5, 'height': 1, 'width': 0.5, 'xBias': 0.51, 'yBias': 0.4}
channels: list of booleans
For multi-component images, the components or channels that are enabled.
shadow: bool, default: True
Use shadowing with composite volume rendering.
blend_mode: 'composite', 'max', 'min', or 'average', default: 'composite'
Volume rendering blend mode.
Point Sets
^^^^^^^^^^
point_sets: point set, or sequence of point sets
The point sets to visualize.
point_set_colors: list of (r, g, b) colors
Colors for the N points. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
point_set_opacities: array of floats, default: [1.0,]*n
Opacity for the point sets, in the range (0.0, 1.0].
point_set_sizes: array of unsigned integers, default: [3,]*n
Sizes for the point sets, in pixel size units.
point_set_representations: list of strings, default: ['points',]*n
How to represent the point set. One of 'hidden', 'points', or 'spheres'.
Geometries
^^^^^^^^^^
geometries: geometries, or sequence of geometries
The geometries to visualize.
geometry_colors: list of RGB colors
Colors for the N geometries. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
geometry_opacities: list of floats, default: [1.0,]*n
Opacity for the point sets, in the range (0.0, 1.0].
Other Parameters
----------------
units: string, default: ''
Units to display in the scale bar.
actors: vtkActor, vtkAssembly, vtkVolume, default: None
List of standard vtk objects, colors are extracted from their properties
size_limit_2d: 2x1 numpy int64 array, default: [1024, 1024]
Size limit for 2D image visualization. If the roi is larger than this
size, it will be downsampled for visualization
size_limit_3d: 3x1 numpy int64 array, default: [192, 192, 192]
Size limit for 3D image visualization. If the roi is larger than this
size, it will be downsampled for visualization.
sample_distance: float, default: 0.25
Sampling distance for volume rendering, normalized from 0.0 to 1.0.
Lower values result in a higher quality rendering. High values improve
the framerate.
Returns
-------
viewer : ipywidget
Display by placing at the end of a Jupyter cell or calling
IPython.display.display. Query or set properties on the object to change
the visualization or retrieve values created by interacting with the
widget.
"""
# this block allows the user to pass already formed vtkActor vtkVolume
# objects
actors = kwargs.pop("actors", None)
if have_vtk and actors is not None:
if not isinstance(actors, (list, tuple)
): # passing the object directly, so make it a list
actors = [actors]
images = []
for a in actors:
if have_mayavi:
from mayavi.modules import surface
from mayavi.modules import iso_surface
from tvtk.api import tvtk
if isinstance(a, surface.Surface):
a = tvtk.to_vtk(a.actor.actor)
elif isinstance(a, iso_surface.IsoSurface):
a = tvtk.to_vtk(a.actor.actor)
if isinstance(a, vtk.vtkAssembly): # unpack assemblies
cl = vtk.vtkPropCollection()
a.GetActors(cl)
cl.InitTraversal()
for i in range(a.GetNumberOfPaths()):
ac = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
apoly = ac.GetMapper().GetInput()
prop = ac.GetProperty()
transform = vtk.vtkTransform()
transform.SetMatrix(ac.GetMatrix())
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
tp.SetInputData(apoly)
tp.Update()
poly = tp.GetOutput()
if poly.GetNumberOfPolys():
geometries.insert(0, poly)
geometry_colors.insert(0, prop.GetColor())
geometry_opacities.insert(0, prop.GetOpacity())
else:
point_sets.insert(0, poly)
point_set_colors.insert(0, prop.GetColor())
point_set_opacities.insert(0, prop.GetOpacity())
elif isinstance(a, vtk.vtkActor):
apoly = a.GetMapper().GetInput()
transform = vtk.vtkTransform()
transform.SetMatrix(a.GetMatrix())
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
tp.SetInputData(apoly)
tp.Update()
poly = tp.GetOutput()
prop = a.GetProperty()
if poly.GetNumberOfPolys() or poly.GetNumberOfStrips() or poly.GetNumberOfLines():
geometries.insert(0, poly)
geometry_colors.insert(0, prop.GetColor())
geometry_opacities.insert(0, prop.GetOpacity())
else:
point_sets.insert(0, poly)
point_set_colors.insert(0, prop.GetColor())
point_set_opacities.insert(0, prop.GetOpacity())
elif isinstance(a, vtk.vtkVolume):
images.append(a.GetMapper().GetInput())
if image is None and len(images): # only one image is rendered
image = images[0]
viewer = Viewer(image=image,
label_image=label_image,
label_image_names=label_image_names,
label_image_blend=label_image_blend,
label_image_weights=label_image_weights,
cmap=cmap,
lut=lut,
select_roi=select_roi,
interpolation=interpolation,
gradient_opacity=gradient_opacity,
opacity_gaussians=opacity_gaussians,
slicing_planes=slicing_planes,
shadow=shadow, blend_mode=blend_mode,
point_sets=point_sets,
point_set_colors=point_set_colors,
point_set_opacities=point_set_opacities,
point_set_representations=point_set_representations,
point_set_sizes=point_set_sizes,
geometries=geometries, geometry_colors=geometry_colors, geometry_opacities=geometry_opacities,
rotate=rotate, ui_collapsed=ui_collapsed, annotations=annotations, mode=mode,
**kwargs)
return viewer
def view(image=None, # noqa: C901
cmap=cm.viridis,
select_roi=False,
interpolation=True,
gradient_opacity=0.22, slicing_planes=False, shadow=True, blend='composite',
point_sets=[],
point_set_colors=[], point_set_opacities=[], point_set_representations=[],
# point_set_sizes=[],
geometries=[],
geometry_colors=[], geometry_opacities=[],
ui_collapsed=False, rotate=False, annotations=True, mode='v',
**kwargs):
"""View the image and/or point sets and/or geometries.
Creates and returns an ipywidget to visualize an image, and/or point sets
and/or geometries .
The image can be 2D or 3D.
The type of the image can be an numpy.array, itk.Image,
vtk.vtkImageData, pyvista.UniformGrid, imglyb.ReferenceGuardingRandomAccessibleInterval,
or a NumPy array-like, e.g. a Dask array.
A point set or a sequence of points sets can be visualized. The type of the
point set can be an numpy.array (Nx3 array of point positions).
A geometry or a sequence of geometries can be visualized. The type of the
geometry can be an itk.Mesh.
Parameters
----------
General Interface
^^^^^^^^^^^^^^^^^
ui_collapsed : bool, optional, default: False
Collapse the native widget user interface.
rotate : bool, optional, default: False
Continuously rotate the camera around the scene in volume rendering
mode.
annotations : bool, optional, default: True
Display annotations describing orientation and the value of a
mouse-position-based data probe.
mode: 'x', 'y', 'z', or 'v', optional, default: 'v'
Only relevant for 3D scenes.
Viewing mode:
'x': x-plane
'y': y-plane
'z': z-plane
'v': volume rendering
camera: 3x3 numpy float32 array, optional
Camera parameters:
[[position_x, position_y, position_z],
[focal_point_x, focal_point_y, focal_point_z],
[view_up_x, view_up_y, view_up_z]]
Images
^^^^^^
image : array_like, itk.Image, or vtk.vtkImageData
The 2D or 3D image to visualize.
vmin: float, optional, default: None
Value that maps to the minimum of image colormap. Defaults to minimum of
the image pixel buffer.
vmax: float, optional, default: None
Value that maps to the minimum of image colormap. Defaults to maximum of
the image pixel buffer.
cmap: string, optional, default: 'Viridis (matplotlib)'
Colormap. Some valid values available at itkwidgets.cm.*
select_roi: bool, optional, default: False
Enable an interactive region of interest widget for the image.
slicing_planes: bool, optional, default: False
Enable slicing planes on the volume rendering.
x_slice: float, optional, default: None
World-space position of the X slicing plane.
y_slice: float, optional, default: None
World-space position of the Y slicing plane.
z_slice: float, optional, default: None
World-space position of the Z slicing plane.
interpolation: bool, optional, default: True
Linear as opposed to nearest neighbor interpolation for image slices.
gradient_opacity: float, optional, default: 0.22
Gradient opacity for composite volume rendering, in the range (0.0, 1.0].
shadow: bool, optional, default: True
Use shadowing with composite volume rendering.
blend: 'composite', 'max', 'min', or 'average', optional, default: 'composite'
Volume rendering blend mode.
Point Sets
^^^^^^^^^^
point_sets: point set, or sequence of point sets, optional
The point sets to visualize.
point_set_colors: list of RGB colors, optional
Colors for the N geometries. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
point_set_opacities: list of floats, optional, default: [0.5,]*n
Opacity for the point sets, in the range (0.0, 1.0].
point_set_representations: list of strings, optional, default: ['points',]*n
How to represent the point set. One of 'hidden', 'points', or 'spheres'.
Geometries
^^^^^^^^^^
geometries: geometries, or sequence of geometries, optional
The geometries to visualize.
geometry_colors: list of RGB colors, optional
Colors for the N geometries. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
geometry_opacities: list of floats, optional, default: [1.0,]*n
Opacity for the point sets, in the range (0.0, 1.0].
Other Parameters
----------------
units: string, optional, default: ''
Units to display in the scale bar.
actors: vtkActor, vtkAssembly, vtkVolume, optional, default: None
List of standard vtk objects, colors are extracted from their properties
size_limit_2d: 2x1 numpy int64 array, optional, default: [1024, 1024]
Size limit for 2D image visualization. If the roi is larger than this
size, it will be downsampled for visualization
size_limit_3d: 3x1 numpy int64 array, optional, default: [192, 192, 192]
Size limit for 3D image visualization. If the roi is larger than this
size, it will be downsampled for visualization.
Returns
-------
viewer : ipywidget
Display by placing at the end of a Jupyter cell or calling
IPython.display.display. Query or set properties on the object to change
the visualization or retrieve values created by interacting with the
widget.
"""
# this block allows the user to pass already formed vtkActor vtkVolume
# objects
actors = kwargs.pop("actors", None)
if have_vtk and actors is not None:
if not isinstance(actors, (list, tuple)
): # passing the object directly, so make it a list
actors = [actors]
images = []
for a in actors:
if have_mayavi:
from mayavi.modules import surface
from mayavi.modules import iso_surface
from tvtk.api import tvtk
if isinstance(a, surface.Surface):
a = tvtk.to_vtk(a.actor.actor)
elif isinstance(a, iso_surface.IsoSurface):
a = tvtk.to_vtk(a.actor.actor)
if isinstance(a, vtk.vtkAssembly): # unpack assemblies
cl = vtk.vtkPropCollection()
a.GetActors(cl)
cl.InitTraversal()
for i in range(a.GetNumberOfPaths()):
ac = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
apoly = ac.GetMapper().GetInput()
prop = ac.GetProperty()
transform = vtk.vtkTransform()
transform.SetMatrix(ac.GetMatrix())
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
tp.SetInputData(apoly)
tp.Update()
poly = tp.GetOutput()
if poly.GetNumberOfPolys():
geometries.insert(0, poly)
geometry_colors.insert(0, prop.GetColor())
geometry_opacities.insert(0, prop.GetOpacity())
else:
point_sets.insert(0, poly)
point_set_colors.insert(0, prop.GetColor())
point_set_opacities.insert(0, prop.GetOpacity())
elif isinstance(a, vtk.vtkActor):
apoly = a.GetMapper().GetInput()
transform = vtk.vtkTransform()
transform.SetMatrix(a.GetMatrix())
tp = vtk.vtkTransformPolyDataFilter()
tp.SetTransform(transform)
tp.SetInputData(apoly)
tp.Update()
poly = tp.GetOutput()
prop = a.GetProperty()
if poly.GetNumberOfPolys() or poly.GetNumberOfStrips() or poly.GetNumberOfLines():
geometries.insert(0, poly)
geometry_colors.insert(0, prop.GetColor())
geometry_opacities.insert(0, prop.GetOpacity())
else:
point_sets.insert(0, poly)
point_set_colors.insert(0, prop.GetColor())
point_set_opacities.insert(0, prop.GetOpacity())
elif isinstance(a, vtk.vtkVolume):
images.append(a.GetMapper().GetInput())
if image is None and len(images): # only one image is rendered
image = images[0]
viewer = Viewer(image=image,
cmap=cmap,
select_roi=select_roi,
interpolation=interpolation,
gradient_opacity=gradient_opacity, slicing_planes=slicing_planes,
shadow=shadow, blend=blend,
point_sets=point_sets,
point_set_colors=point_set_colors,
point_set_opacities=point_set_opacities,
point_set_representations=point_set_representations,
geometries=geometries, geometry_colors=geometry_colors, geometry_opacities=geometry_opacities,
rotate=rotate, ui_collapsed=ui_collapsed, annotations=annotations, mode=mode,
**kwargs)
return viewer
def getActors(self, obj=None, renderer=None):
"""
Return an actors list.
If ``obj`` is:
``None``, return actors of current renderer
``int``, return actors in given renderer number
``vtkAssembly`` return the contained actors
``string``, return actors matching legend name
:param int,vtkRenderer renderer: specify which renederer to look into.
"""
if renderer is None:
renderer = self.renderer
elif isinstance(renderer, int):
renderer = self.renderers.index(renderer)
else:
return []
if obj is None or isinstance(obj, int):
if obj is None:
acs = renderer.GetActors()
elif obj >= len(self.renderers):
colors.printc(
"~timesError in getActors: non existing renderer",
obj,
c=1)
return []
else:
acs = self.renderers[obj].GetActors()
actors = []
acs.InitTraversal()
for i in range(acs.GetNumberOfItems()):
a = acs.GetNextItem()
if a.GetPickable():
r = self.renderers.index(renderer)
if a == self.axes_exist[r]:
continue
actors.append(a)
return actors
elif isinstance(obj, vtk.vtkAssembly):
cl = vtk.vtkPropCollection()
obj.GetActors(cl)
actors = []
cl.InitTraversal()
for i in range(obj.GetNumberOfPaths()):
act = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
if act.GetPickable():
actors.append(act)
return actors
elif isinstance(obj, str): # search the actor by the legend name
actors = []
for a in self.actors:
if hasattr(a, "_legend") and obj in a._legend:
actors.append(a)
return actors
elif isinstance(obj, vtk.vtkActor):
return [obj]
if self.verbose:
colors.printc(
"~lightning Warning in getActors: unexpected input type",
obj,
c=1)
return []
def set_props(self, props):
self.props = vtk.vtkPropCollection()
for prop in props:
self.props.AddItem(prop)
def printInfo(obj):
"""Print information about a vtk object."""
def printvtkactor(actor, tab=""):
if not actor.GetPickable():
return
if hasattr(actor, "polydata"):
poly = actor.polydata()
else:
poly = actor.GetMapper().GetInput()
pro = actor.GetProperty()
pos = actor.GetPosition()
bnds = actor.GetBounds()
col = pro.GetColor()
colr = precision(col[0], 3)
colg = precision(col[1], 3)
colb = precision(col[2], 3)
alpha = pro.GetOpacity()
npt = poly.GetNumberOfPoints()
ncl = poly.GetNumberOfCells()
print(tab, end="")
colors.printc("vtkActor", c="g", bold=1, invert=1, dim=1, end=" ")
if hasattr(actor, "_legend") and actor._legend:
colors.printc("legend: ", c="g", bold=1, end="")
colors.printc(actor._legend, c="g", bold=0)
else:
print()
if hasattr(actor, "filename") and actor.filename:
colors.printc(tab + " file: ", c="g", bold=1, end="")
colors.printc(actor.filename, c="g", bold=0)
colors.printc(tab + " color: ", c="g", bold=1, end="")
if actor.GetMapper().GetScalarVisibility():
colors.printc("defined by point or cell data", c="g", bold=0)
else:
colors.printc(colors.getColorName(col) + ', rgb=(' + colr + ', ' +
colg + ', ' + colb + '), alpha=' + str(alpha),
c='g',
bold=0)
if actor.GetBackfaceProperty():
bcol = actor.GetBackfaceProperty().GetDiffuseColor()
bcolr = precision(bcol[0], 3)
bcolg = precision(bcol[1], 3)
bcolb = precision(bcol[2], 3)
colors.printc(tab + ' back color: ', c='g', bold=1, end='')
colors.printc(colors.getColorName(bcol) + ', rgb=(' + bcolr +
', ' + bcolg + ', ' + bcolb + ')',
c='g',
bold=0)
colors.printc(tab + " points: ", c="g", bold=1, end="")
colors.printc(npt, c="g", bold=0)
colors.printc(tab + " cells: ", c="g", bold=1, end="")
colors.printc(ncl, c="g", bold=0)
colors.printc(tab + " position: ", c="g", bold=1, end="")
colors.printc(pos, c="g", bold=0)
if hasattr(actor, "polydata"):
colors.printc(tab + " c. of mass: ", c="g", bold=1, end="")
colors.printc(actor.centerOfMass(), c="g", bold=0)
colors.printc(tab + " ave. size: ", c="g", bold=1, end="")
colors.printc(precision(actor.averageSize(), 4), c="g", bold=0)
colors.printc(tab + " diag. size: ", c="g", bold=1, end="")
colors.printc(actor.diagonalSize(), c="g", bold=0)
colors.printc(tab + " area: ", c="g", bold=1, end="")
colors.printc(precision(actor.area(), 8), c="g", bold=0)
colors.printc(tab + " volume: ", c="g", bold=1, end="")
colors.printc(precision(actor.volume(), 8), c="g", bold=0)
colors.printc(tab + " bounds: ", c="g", bold=1, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="g", bold=0, end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="g", bold=0, end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="g", bold=0)
arrtypes = dict()
arrtypes[vtk.VTK_UNSIGNED_CHAR] = "VTK_UNSIGNED_CHAR"
arrtypes[vtk.VTK_UNSIGNED_INT] = "VTK_UNSIGNED_INT"
arrtypes[vtk.VTK_FLOAT] = "VTK_FLOAT"
arrtypes[vtk.VTK_DOUBLE] = "VTK_DOUBLE"
if poly.GetPointData():
ptdata = poly.GetPointData()
for i in range(ptdata.GetNumberOfArrays()):
name = ptdata.GetArrayName(i)
if name:
colors.printc(tab + " point data: ",
c="g",
bold=1,
end="")
try:
tt = arrtypes[ptdata.GetArray(i).GetDataType()]
colors.printc("name=" + name,
"type=" + tt,
c="g",
bold=0)
except:
tt = ptdata.GetArray(i).GetDataType()
colors.printc("name=" + name,
"type=",
tt,
c="g",
bold=0)
if poly.GetCellData():
cldata = poly.GetCellData()
for i in range(cldata.GetNumberOfArrays()):
name = cldata.GetArrayName(i)
if name:
colors.printc(tab + " cell data: ",
c="g",
bold=1,
end="")
try:
tt = arrtypes[cldata.GetArray(i).GetDataType()]
colors.printc("name=" + name,
"type=" + tt,
c="g",
bold=0)
except:
tt = cldata.GetArray(i).GetDataType()
colors.printc("name=" + name,
"type=",
tt,
c="g",
bold=0)
if not obj:
return
elif isinstance(obj, vtk.vtkActor):
colors.printc("_" * 60, c="g", bold=0)
printvtkactor(obj)
elif isinstance(obj, vtk.vtkAssembly):
colors.printc("_" * 60, c="g", bold=0)
colors.printc("vtkAssembly", c="g", bold=1, invert=1, end=" ")
if hasattr(obj, "_legend"):
colors.printc("legend: ", c="g", bold=1, end="")
colors.printc(obj._legend, c="g", bold=0)
else:
print()
pos = obj.GetPosition()
bnds = obj.GetBounds()
colors.printc(" position: ", c="g", bold=1, end="")
colors.printc(pos, c="g", bold=0)
colors.printc(" bounds: ", c="g", bold=1, end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="g", bold=0, end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="g", bold=0, end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="g", bold=0)
cl = vtk.vtkPropCollection()
obj.GetActors(cl)
cl.InitTraversal()
for i in range(obj.GetNumberOfPaths()):
act = vtk.vtkActor.SafeDownCast(cl.GetNextProp())
if isinstance(act, vtk.vtkActor):
printvtkactor(act, tab=" ")
elif hasattr(obj, "interactor"): # dumps Plotter info
axtype = {
0: "(no axes)",
1: "(three gray grid walls)",
2: "(cartesian axes from origin",
3: "(positive range of cartesian axes from origin",
4: "(axes triad at bottom left)",
5: "(oriented cube at bottom left)",
6: "(mark the corners of the bounding box)",
7: "(ruler at the bottom of the window)",
8: "(the vtkCubeAxesActor object)",
9: "(the bounding box outline)",
}
bns, totpt = [], 0
for a in obj.actors:
b = a.GetBounds()
if a.GetBounds() is not None:
if isinstance(a, vtk.vtkActor):
totpt += a.GetMapper().GetInput().GetNumberOfPoints()
bns.append(b)
if len(bns) == 0:
return
acts = obj.getActors()
colors.printc("_" * 60, c="c", bold=0)
colors.printc("Plotter", invert=1, dim=1, c="c", end=" ")
otit = obj.title
if not otit:
otit = None
colors.printc(" title:", otit, bold=0, c="c")
colors.printc(" active renderer:",
obj.renderers.index(obj.renderer),
bold=0,
c="c")
colors.printc(" nr. of actors:", len(acts), bold=0, c="c", end="")
colors.printc(" (" + str(totpt), "vertices)", bold=0, c="c")
max_bns = np.max(bns, axis=0)
min_bns = np.min(bns, axis=0)
colors.printc(" max bounds: ", c="c", bold=0, end="")
bx1, bx2 = precision(min_bns[0], 3), precision(max_bns[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")", c="c", bold=0, end="")
by1, by2 = precision(min_bns[2], 3), precision(max_bns[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")", c="c", bold=0, end="")
bz1, bz2 = precision(min_bns[4], 3), precision(max_bns[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")", c="c", bold=0)
colors.printc(" axes type:",
obj.axes,
axtype[obj.axes],
bold=0,
c="c")
for a in obj.actors:
if a.GetBounds() is not None:
if isinstance(a, vtk.vtkVolume): # dumps Volume info
img = a.GetMapper().GetDataSetInput()
colors.printc('_' * 60, c='b', bold=0)
colors.printc('Volume', invert=1, dim=1, c='b')
colors.printc(' scalar range:',
np.round(img.GetScalarRange(), 4),
c='b',
bold=0)
bnds = a.GetBounds()
colors.printc(" bounds: ",
c="b",
bold=0,
end="")
bx1, bx2 = precision(bnds[0], 3), precision(bnds[1], 3)
colors.printc("x=(" + bx1 + ", " + bx2 + ")",
c="b",
bold=0,
end="")
by1, by2 = precision(bnds[2], 3), precision(bnds[3], 3)
colors.printc(" y=(" + by1 + ", " + by2 + ")",
c="b",
bold=0,
end="")
bz1, bz2 = precision(bnds[4], 3), precision(bnds[5], 3)
colors.printc(" z=(" + bz1 + ", " + bz2 + ")",
c="b",
bold=0)
colors.printc(" Click actor and press i for Actor info.", c="c")
else:
colors.printc("_" * 60, c="g", bold=0)
colors.printc(obj, c="g")
colors.printc(type(obj), c="g", invert=1)
