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Surface_Utilities.py
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Surface_Utilities.py
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'''
Created on Apr 1, 2016
@author: roger
'''
import openmesh as om
import SimpleITK as sitk
import vtk
import os
#This line is for using a 3D viewer with itk images we need to set the env var
os.environ["SITK_SHOW_3D_COMMAND"] = "/home/roger/Downloads/Slicer-4.5.0-1-linux-amd64/Slicer"
def DisplayVTKMesh(meshi,windowname):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(meshi)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetInterpolationToPhong()
actor.GetProperty().SetAmbient(0.2)
actor.GetProperty().SetDiffuse(0.7)
actor.GetProperty().SetSpecular(0.6)
actor.GetProperty().SetSpecularPower(100)
actor.GetProperty().SetColor(0.8,0.8,1)
ren1 = vtk.vtkRenderer()
ren1.AddActor(actor)
ren1.SetBackground(0, 0, 0)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.SetSize(300, 300)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
style = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
iren.Initialize()
renWin.SetWindowName(windowname)
iren.Start()
def compute_info_mesh(mesh):
vertices= mesh.GetNumberOfPoints()
triangles= mesh.GetNumberOfCells()
extractEdges = vtk.vtkExtractEdges()
extractEdges.SetInputData(mesh)
extractEdges.Update()
lines=extractEdges.GetOutput()
edges=lines.GetNumberOfCells()
print "triangles: ",triangles
print "vertices: ",vertices
print "edges: ",edges
return vertices,triangles
def clean_itkbin(imgitk,validlabel=1,variance=0.1,showimage=False):
imgbin=imgitk==validlabel#only consider 1 valid label
connectedfilter=sitk.ConnectedComponentImageFilter()
morfilter=sitk.BinaryMorphologicalOpeningImageFilter()
imgbin=morfilter.Execute(imgbin)
gfilter=sitk.DiscreteGaussianImageFilter()
gfilter.SetVariance(variance)
imgbin=gfilter.Execute(imgbin)
imgconn=connectedfilter.Execute(imgbin)
imgconn=imgconn==1
holesfilter=sitk.BinaryFillholeImageFilter()
imgfin=holesfilter.Execute(imgconn,True,1.0)
if showimage:
sitk.Show(imgfin)
return imgfin
def generate_mesh(imgbinitk):
sitk.WriteImage( imgbinitk,'label_cleaned_tmp.mha')
reader=vtk.vtkMetaImageReader()
reader.SetFileName('label_cleaned_tmp.mha')
reader.Update()
imgbin=reader.GetOutput()
dmc = vtk.vtkDiscreteMarchingCubes()
dmc.SetInputData(imgbin)
dmc.ComputeNormalsOn()
dmc.GenerateValues(1, 1, 1)
dmc.Update()
meshout=dmc.GetOutput()
#DisplayVTKMesh(meshout,"mesh from marchin cubes")
return meshout
def Decimate_mesh(meshvtk,name_vtkmesh,nvertices=2000):
print 'test'
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName('meshdecimated.stl')
stlWriter.SetInputData(meshvtk)
stlWriter.Write()
mesh_om = om.PolyMesh()
Result=om.read_mesh(mesh_om, "meshdecimated.stl")
print Result
deci_om=om.PolyMeshDecimater(mesh_om)
mh=om.PolyMeshModQuadricHandle()
deci_om.add(mh)
deci_om.initialize()
deci_om.decimate_to(nvertices)
mesh_om.garbage_collection()
assert mesh_om.n_vertices()==nvertices, 'vertices goal not acomplished; nvertices={0:d}'.format(mesh_om.n_vertices())
print "Decimation to {0} vertices Sucessful".format(nvertices)
om.write_mesh(mesh_om,'meshdecimated.stl')
stlReader = vtk.vtkSTLReader()
stlReader.SetFileName('meshdecimated.stl')
stlReader.Update()
vtkwrite=vtk.vtkPolyDataWriter()
vtkwrite.SetInputData(stlReader.GetOutput())
vtkwrite.SetFileName(name_vtkmesh)
vtkwrite.Write()
print "enters"
def LoadVTKMesh(filename):
reader = vtk.vtkPolyDataReader()
reader.SetFileName(filename)
reader.Update()
return reader.GetOutput()
def LoadSTLMesh(filename):
stlReader = vtk.vtkSTLReader()
stlReader.SetFileName(filename)
stlReader.Update()
return stlReader.GetOutput()
def WriteSTLMesh(meshvtk,filename):
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName(filename)
stlWriter.SetInputData(meshvtk)
stlWriter.Write()
def WriteVTKMesh(meshvtk,filename):
vtkwrite=vtk.vtkPolyDataWriter()
vtkwrite.SetInputData(meshvtk)
vtkwrite.SetFileName(filename)
vtkwrite.Write()
def Compute_Normals(vtkmesh):
normfilter=vtk.vtkPolyDataNormals()
normfilter.SetInputData(vtkmesh)
normfilter.ComputePointNormalsOn()
normfilter.ComputeCellNormalsOff
normfilter.SplittingOff()
normfilter.Update()
return normfilter.GetOutput()
def MakeGlyphs(src):
'''
Glyph the normals on the surface.
You may need to adjust the parameters for maskPts, arrow and glyph for a
nice appearance.
:param: src - the surface to glyph.
:param: reverseNormals - if True the normals on the surface are reversed.
:return: The glyph object.
'''
# Sometimes the contouring algorithm can create a volume whose gradient
# vector and ordering of polygon (using the right hand rule) are
# inconsistent. vtkReverseSense cures this problem.
# Choose a random subset of points.
maskPts = vtk.vtkMaskPoints()
maskPts.SetOnRatio(2)
maskPts.RandomModeOn()
maskPts.SetInputData(src)
# Source for the glyph filter
arrow = vtk.vtkArrowSource()
arrow.SetTipResolution(16)
arrow.SetTipLength(0.3)
arrow.SetTipRadius(0.1)
glyph = vtk.vtkGlyph3D()
glyph.SetSourceConnection(arrow.GetOutputPort())
glyph.SetInputConnection(maskPts.GetOutputPort())
glyph.SetVectorModeToUseNormal()
glyph.SetScaleFactor(1)
glyph.SetColorModeToColorByVector()
glyph.SetScaleModeToScaleByVector()
glyph.OrientOn()
glyph.Update()
return glyph
def Display_Normal_Mesh(meshi,glyph,windowname):
print ('test')
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(meshi)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetInterpolationToPhong()
actor.GetProperty().SetAmbient(0.2)
actor.GetProperty().SetDiffuse(0.7)
actor.GetProperty().SetSpecular(0.6)
actor.GetProperty().SetSpecularPower(100)
actor.GetProperty().SetColor(0.8,0.8,1)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyph.GetOutputPort())
glyphMapper.SetScalarModeToUsePointFieldData()
glyphMapper.SetColorModeToMapScalars()
glyphMapper.ScalarVisibilityOn()
glyphMapper.SelectColorArray('Elevation')
# Colour by scalars.
scalarRange = glyph.GetOutput().GetScalarRange()
glyphMapper.SetScalarRange(scalarRange)
glyphActor = vtk.vtkActor()
glyphActor.SetMapper(glyphMapper)
ren1 = vtk.vtkRenderer()
ren1.AddActor(actor)
ren1.AddViewProp(glyphActor)
ren1.SetBackground(0, 0, 0)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.SetSize(300, 300)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
style = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
iren.Initialize()
renWin.SetWindowName(windowname)
iren.Start()
if __name__ == '__main__':
inpath='/media/roger/48BCFC2BBCFC1562/dataset/labels_registered_mha/label_warped10.mha'
nvertices=2000
imgitk = sitk.ReadImage(inpath)
imgclean=clean_itkbin(imgitk,validlabel=2)
meshvtk=generate_mesh(imgclean)
_,_=compute_info_mesh(meshvtk)
WriteSTLMesh(meshvtk, 'meshdecimated.stl')
#===============================================================================
#
# This part should be in a function but it crashes duw to openmesh :/
#===============================================================================
mesh_om = om.PolyMesh()
Result=om.read_mesh(mesh_om, "meshdecimated.stl")
assert Result, "Open mesh could not read file"
deci_om=om.PolyMeshDecimater(mesh_om)
mh=om.PolyMeshModQuadricHandle()
deci_om.add(mh)
deci_om.initialize()
deci_om.decimate_to(nvertices)
mesh_om.garbage_collection()
assert mesh_om.n_vertices()==nvertices, 'vertices goal not acomplished; nvertices={0:d}'.format(mesh_om.n_vertices())
print "Decimation to {0} vertices Sucessful".format(nvertices)
om.write_mesh(mesh_om,'meshdecimated.stl')
################################################################################
meshvtktmp=LoadSTLMesh('meshdecimated.stl')
WriteVTKMesh(meshvtktmp,"mymesh.vtk")
meshvtk_dec=LoadVTKMesh('mymesh.vtk')
compute_info_mesh(meshvtk_dec)
norms=Compute_Normals(meshvtk_dec)
glyph = MakeGlyphs(norms)
Display_Normal_Mesh(meshvtk_dec,glyph,"arrows")