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detail.py
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import vtk
import numpy as np
from vtk.util.vtkConstants import *
import matplotlib.pyplot as plt
from IPython.display import Image
Red=(1,0,0)
Blue=(0,0,1)
Green=(0,1,0)
Yellow=(1,1,0)
Magenta=(1,0,1)
Cyan=(0,1,1)
Purple=(0.5,0,0.5)
Orange=(1,0.5,0)
Brown=(0.6,0.5,0.1)
Black=(0,0,0)
White=(1,1,1)
Gray=(0.5,0.5,0.5)
def vtk_show(renderer, width=400, height=300):
"""
Takes vtkRenderer instance and returns an IPython Image with the rendering.
"""
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetOffScreenRendering(1)
renderWindow.AddRenderer(renderer)
renderWindow.SetSize(width, height)
renderWindow.Render()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renderWindow)
windowToImageFilter.Update()
writer = vtk.vtkPNGWriter()
writer.SetWriteToMemory(1)
writer.SetInputConnection(windowToImageFilter.GetOutputPort())
writer.Write()
data = str(buffer(writer.GetResult()))
return Image(data)
def SetColor(actor,c):
actor.GetProperty().SetColor(c[0],c[1],c[2])
def SetLineWidth(actor,w):
actor.GetProperty().SetLineWidth(w)
def MarchingCubes(img_data,isolevel):
importer = vtk.vtkImageImport()
img_string = img_data.tostring(order='F')
dim = img_data.shape
importer.CopyImportVoidPointer(img_string, len(img_string))
importer.SetDataScalarType(VTK_UNSIGNED_CHAR)
importer.SetNumberOfScalarComponents(1)
extent = importer.GetDataExtent()
importer.SetDataExtent(extent[0], extent[0] + dim[0] - 1,
extent[2], extent[2] + dim[1] - 1,
extent[4], extent[4] + dim[2] - 1)
importer.SetWholeExtent(extent[0], extent[0] + dim[0] - 1,
extent[2], extent[2] + dim[1] - 1,
extent[4], extent[4] + dim[2] - 1)
#importer.SetDataSpacing( dset.pixel_spacing[0], dset.pixel_spacing[1], dset.pixel_spacing[2])
outlineData=vtk.vtkOutlineFilter()
outlineData.SetInputConnection(importer.GetOutputPort())
mapOutline=vtk.vtkPolyDataMapper()
mapOutline.SetInputConnection(outlineData.GetOutputPort())
outline=vtk.vtkActor()
outline.SetMapper(mapOutline)
skinExtractor=vtk.vtkContourFilter()
skinExtractor.SetInputConnection(importer.GetOutputPort())
skinExtractor.SetValue(0,isolevel)
skinExtractor.Update()
tri=vtk.vtkTriangleFilter()
tri.SetInputConnection(skinExtractor.GetOutputPort())
tri.Update()
# deci=vtk.vtkQuadricDecimation()
# deci.SetInputConnection(tri.GetOutputPort())
# deci.SetTargetReduction(0.95)
# # deci-$obj PreserveTopologyOn
# deci.Update()
skinNormals=vtk.vtkPolyDataNormals()
# skinNormals SetInputConnection [skinExtractor GetOutputPort]
skinNormals.SetInputConnection(tri.GetOutputPort())
skinNormals.SetFeatureAngle( 60.0)
skinMapper=vtk.vtkPolyDataMapper()
skinMapper.SetInputConnection(skinNormals.GetOutputPort())
# skinMapper SetInputConnection [deci GetOutputPort]
#skinMapper.ScalarVisibilityOff()
skin=vtk.vtkActor()
skin.SetMapper(skinMapper)
return outline,skin
def MakeAxes(point,length):
xpts=vtk.vtkPoints()
xlines=vtk.vtkCellArray()
xpts.InsertNextPoint(point)
xpts.InsertNextPoint((point[0]+length,point[1],point[2]))
xlines.InsertNextCell(2)
xlines.InsertCellPoint(0)
xlines.InsertCellPoint(1)
xpoly=vtk.vtkPolyData()
xpoly.SetPoints(xpts)
xpoly.SetLines(xlines)
xpolyMapper=vtk.vtkPolyDataMapper()
xpolyMapper.SetInputData(xpoly)
xpolyActor=vtk.vtkActor()
xpolyActor.SetMapper(xpolyMapper)
SetColor(xpolyActor,Red)
SetLineWidth(xpolyActor,2)
ypts=vtk.vtkPoints()
ylines=vtk.vtkCellArray()
ypts.InsertNextPoint(point)
ypts.InsertNextPoint((point[0],point[1]+length,point[2]))
ylines.InsertNextCell(2)
ylines.InsertCellPoint(0)
ylines.InsertCellPoint(1)
ypoly=vtk.vtkPolyData()
ypoly.SetPoints(ypts)
ypoly.SetLines(ylines)
ypolyMapper=vtk.vtkPolyDataMapper()
ypolyMapper.SetInputData(ypoly)
ypolyActor=vtk.vtkActor()
ypolyActor.SetMapper(ypolyMapper)
SetColor(ypolyActor,Green)
SetLineWidth(ypolyActor,2)
zpts=vtk.vtkPoints()
zlines=vtk.vtkCellArray()
zpts.InsertNextPoint(point)
zpts.InsertNextPoint((point[0],point[1],point[2]+length))
zlines.InsertNextCell(2)
zlines.InsertCellPoint(0)
zlines.InsertCellPoint(1)
zpoly=vtk.vtkPolyData()
zpoly.SetPoints(zpts)
zpoly.SetLines(zlines)
zpolyMapper=vtk.vtkPolyDataMapper()
zpolyMapper.SetInputData(zpoly)
zpolyActor=vtk.vtkActor()
zpolyActor.SetMapper(zpolyMapper)
SetColor(zpolyActor,Blue)
SetLineWidth(zpolyActor,2)
return xpolyActor,ypolyActor,zpolyActor
def RenderActors(actors,interactive=True,bgcolor=(1.,1,1)):
renderer=vtk.vtkRenderer()
for a in actors:
renderer.AddActor(a)
renderer.SetBackground(bgcolor[0],bgcolor[1],bgcolor[2])
if interactive:
renderWindow=vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetStereoTypeToRedBlue() #Anaglyphic FTW
renderWindowInteractor=vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.Start()
renderWindow.Finalize()
renderWindowInteractor.TerminateApp()
del renderWindow,renderWindowInteractor
return renderer
def MakePrimalGrid(img_data):
pts=vtk.vtkPoints()
lines=vtk.vtkCellArray()
sz=img_data.shape
for i in range(sz[0]):
for j in range(sz[1]):
for k in range(sz[2]):
pts.InsertNextPoint((i,j,k))
for i in range(sz[0]):
for j in range(sz[1]):
for k in range(sz[2]):
if i<sz[0]-1:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2])*(sz[1])+j*(sz[2])+k)
lines.InsertCellPoint((i+1)*(sz[2])*(sz[1])+j*(sz[2])+k)
if j<sz[1]-1:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2])*(sz[1])+j*(sz[2])+k)
lines.InsertCellPoint(i*(sz[2])*(sz[1])+(j+1)*(sz[2])+k)
if k<sz[2]-1:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2])*(sz[1])+j*(sz[2])+k)
lines.InsertCellPoint(i*(sz[2])*(sz[1])+j*(sz[2])+k+1)
primal=vtk.vtkPolyData()
primal.SetPoints(pts)
primal.SetLines(lines)
scalars=vtk.vtkDoubleArray()
scalars.SetNumberOfValues(sz[0]*sz[1]*sz[2])
c=0
for i in range(sz[0]):
for j in range(sz[1]):
for k in range(sz[2]):
scalars.SetValue(c,(img_data[i,j,k]/255.)*0.2+0.03)
c=c+1
primal.GetPointData().SetScalars(scalars)
primalMapper=vtk.vtkPolyDataMapper()
primalMapper.SetInputData(primal)
primalMapper.ScalarVisibilityOff()
# skinMapper SetInputConnection [deci GetOutputPort]
#skinMapper.ScalarVisibilityOff()
primalActor=vtk.vtkActor()
primalActor.SetMapper(primalMapper)
primalglyph=vtk.vtkSphereSource()
primalglyph.SetRadius(0.5)
primalglyph.SetThetaResolution(12)
primalglyph.SetPhiResolution(12)
primalPoints=vtk.vtkGlyph3D()
primalPoints.SetInputData(primal)
primalPoints.SetSourceConnection(primalglyph.GetOutputPort())
primalPointMapper=vtk.vtkPolyDataMapper()
primalPointMapper.SetInputConnection(primalPoints.GetOutputPort())
primalPointMapper.ScalarVisibilityOff()
primalPointActor=vtk.vtkActor()
primalPointActor.SetMapper(primalPointMapper)
return primalActor,primalPointActor
def MakeDualGrid(img_data):
pts=vtk.vtkPoints()
lines=vtk.vtkCellArray()
sz=img_data.shape
for i in range(sz[0]+1):
for j in range(sz[1]+1):
for k in range(sz[2]+1):
pts.InsertNextPoint((i-0.5,j-0.5,k-0.5))
for i in range(sz[0]+1):
for j in range(sz[1]+1):
for k in range(sz[2]+1):
if i<sz[0]:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2]+1)*(sz[1]+1)+j*(sz[2]+1)+k)
lines.InsertCellPoint((i+1)*(sz[2]+1)*(sz[1]+1)+j*(sz[2]+1)+k)
if j<sz[1]:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2]+1)*(sz[1]+1)+j*(sz[2]+1)+k)
lines.InsertCellPoint(i*(sz[2]+1)*(sz[1]+1)+(j+1)*(sz[2]+1)+k)
if k<sz[2]:
lines.InsertNextCell(2)
lines.InsertCellPoint(i*(sz[2]+1)*(sz[1]+1)+j*(sz[2]+1)+k)
lines.InsertCellPoint(i*(sz[2]+1)*(sz[1]+1)+j*(sz[2]+1)+k+1)
dual=vtk.vtkPolyData()
dual.SetPoints(pts)
dual.SetLines(lines)
dualMapper=vtk.vtkPolyDataMapper()
dualMapper.SetInputData(dual)
dualActor=vtk.vtkActor()
dualActor.SetMapper(dualMapper)
dualglyph=vtk.vtkSphereSource()
dualglyph.SetRadius(0.03)
dualglyph.SetThetaResolution(12)
dualglyph.SetPhiResolution(12)
dualPoints=vtk.vtkGlyph3D()
dualPoints.SetInputData(dual)
dualPoints.SetSourceConnection(dualglyph.GetOutputPort())
dualPointMapper=vtk.vtkPolyDataMapper()
dualPointMapper.SetInputConnection(dualPoints.GetOutputPort())
dualPointActor=vtk.vtkActor()
dualPointActor.SetMapper(dualPointMapper)
return dualActor,dualPointActor
def DrawQEFProblem(ax,cs,ps,ns):
corners=[(0.,0.),(0.,1.),(1.,0.),(1.,1.)]
A=[]
b=[]
for i in range(4):
#print "i:",ps[i][0]
if not np.isnan(ps[i][0]):
A.append(ns[i])
b.append(np.dot(ns[i],ps[i]))
A=np.array(A)
b=np.array(b)
q,res,rank,s=np.linalg.lstsq(A,b.T)
#print q
#print "res",res
#print "rank",rank
#print "s",s
#try:
# qq=np.dot(np.linalg.inv(A),b.T)
# print qq
#except:
# print "singular"
def map2axis(pin):
return (2+pin[0]*6.,2+pin[1]*6.)
def qef(x,y):
q=0.0
for i in range(4):
if not np.isnan(ps[i][0]):
v=(ps[i][0]-x,ps[i][1]-y)
nv=ns[i][0]*v[0]+ns[i][1]*v[1]
q=q+nv**2
return q
# quadratic error functions QEF
ax.axis("equal")
ax.set_xlim([0,10])
ax.set_ylim([0,10])
x,y=np.meshgrid(np.linspace(0,1,20),np.linspace(0,1,20))
xqef=np.zeros_like(x)
yqef=np.zeros_like(y)
zqef=np.zeros_like(x)
for i in range(x.shape[0]):
for j in range(x.shape[1]):
xqef[i,j],yqef[i,j]=map2axis((x[i,j],y[i,j]))
zqef[i,j]=qef(x[i,j],y[i,j])
plt.contour(xqef,yqef,zqef)
ax.plot([1,9],[2,2],'b-')
ax.plot([2,2],[1,9],'b-')
ax.plot([1,9],[8,8],'b-')
ax.plot([8,8],[1,9],'b-')
z=map2axis(q)
ax.plot(z[0],z[1],'ro')
for i in range(4):
#corners
z1=map2axis(corners[i])
ax.plot(z1[0],z1[1],'bo',markersize=10) if cs[i]>0 else ax.plot(z1[0],z1[1],marker='o',markersize=10, markerfacecolor='none')
ax.plot([q[0],])
#points
z2=map2axis(ps[i])
#ax.plot([z1[0],z2[0]],[z1[1],z2[1]],'k-')
ax.plot(z2[0],z2[1],'ko')
ax.arrow(z2[0],z2[1],ns[i][0],ns[i][1],head_width=0.25,head_length=0.5,ec='k',fc='k')
if not np.isnan(z2[0]):
ax.plot([z[0],z2[0]],[z[1],z2[1]],c='silver')