def read_data_and_build_snapshot_matrix(x_min,x_max,y_min,y_max,z_min,z_max,snapshot_dir,file_list,\ num_snapshots,num_points,num_components,var_name, A): reader = vtk.vtkUnstructuredGridReader() reader.ReadAllScalarsOn() reader.ReadAllVectorsOn() extract_region = "false" if ( (x_min<x_max) and (y_min<y_max) and (z_min<z_max) ): extract_region = "true" extract = vtk.vtkExtractUnstructuredGrid() extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max) extract.MergingOn() u_temp_read = np.array(np.zeros((num_points,3), dtype=np.float64)) print '\n Reading data ...' for j in range(0,num_snapshots+1): print ' Reading file ', file_list[j].strip(), 'file number ', j, ' of ', num_snapshots reader.SetFileName(snapshot_dir + file_list[j].strip()) reader.Update() if (extract_region=="true"): extract.SetInput(reader.GetOutput()) extract.Update() u_temp_read = VN.vtk_to_numpy(extract.GetOutput().GetPointData().GetVectors(var_name)) else: u_temp_read = VN.vtk_to_numpy(reader.GetOutput().GetPointData().GetVectors(var_name)) for k in range(0,num_components): A[k*num_points:(k+1)*num_points,j] = u_temp_read[:,k]
def read_data_and_build_snapshot_matrix(x_min,x_max,y_min,y_max,z_min,z_max,snapshot_dir,file_list,\
num_snapshots,num_points,num_components,var_name, A):
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
extract_region = "false"
if ((x_min < x_max) and (y_min < y_max) and (z_min < z_max)):
extract_region = "true"
extract = vtk.vtkExtractUnstructuredGrid()
extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max)
extract.MergingOn()
u_temp_read = np.array(np.zeros((num_points, 3), dtype=np.float64))
print '\n Reading data ...'
for j in range(0, num_snapshots + 1):
print ' Reading file ', file_list[j].strip(
), 'file number ', j, ' of ', num_snapshots
reader.SetFileName(snapshot_dir + file_list[j].strip())
reader.Update()
if (extract_region == "true"):
extract.SetInput(reader.GetOutput())
extract.Update()
u_temp_read = VN.vtk_to_numpy(
extract.GetOutput().GetPointData().GetVectors(var_name))
else:
u_temp_read = VN.vtk_to_numpy(
reader.GetOutput().GetPointData().GetVectors(var_name))
for k in range(0, num_components):
A[k * num_points:(k + 1) * num_points, j] = u_temp_read[:, k]
def update(self):
"""
"""
appendFilter = vtkAppendFilter()
appendFilter.AddInput(self.input_)
appendFilter.Update()
extractGrid = vtkExtractUnstructuredGrid()
extractGrid.SetInput(appendFilter.GetOutput())
extractGrid.SetExtent(self.extent[0], self.extent[1], self.extent[2],
self.extent[3], self.extent[4], self.extent[5])
geom = vtkGeometryFilter()
geom.SetInputConnection(extractGrid.GetOutputPort())
geom.Update()
clean = vtkCleanPolyData()
clean.PointMergingOn()
clean.SetTolerance(0.01)
clean.SetInput(geom.GetOutput())
clean.Update()
self.output_ = clean.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExtractUnstructuredGrid(), 'Processing.',
('vtkUnstructuredGrid',), ('vtkUnstructuredGrid',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def Crop(self, min_x, max_x, min_y, max_y, min_z, max_z):
"""Trim off the edges defined by a bounding box."""
trimmer = vtk.vtkExtractUnstructuredGrid()
trimmer.SetInput(self.ugrid)
trimmer.SetExtent(min_x, max_x, min_y, max_y, min_z, max_z)
trimmer.Update()
trimmed_ug = trimmer.GetOutput()
self.ugrid = trimmed_ug
def Crop(self, min_x, max_x, min_y, max_y, min_z, max_z):
"""Trim off the edges defined by a bounding box."""
trimmer = vtk.vtkExtractUnstructuredGrid()
trimmer.SetInputData(self.ugrid)
trimmer.SetExtent(min_x, max_x, min_y, max_y, min_z, max_z)
trimmer.Update()
trimmed_ug = trimmer.GetOutput()
self.ugrid = trimmed_ug
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkExtractUnstructuredGrid(),
'Processing.',
('vtkUnstructuredGrid', ),
('vtkUnstructuredGrid', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def Crop(self, min_x, max_x, min_y, max_y, min_z, max_z):
"""Trim off the edges defined by a bounding box."""
trimmer = vtk.vtkExtractUnstructuredGrid()
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
trimmer.SetInput(self.ugrid)
else:
trimmer.SetInputData(self.ugrid)
trimmer.SetExtent(min_x, max_x, min_y, max_y, min_z, max_z)
trimmer.Update()
trimmed_ug = trimmer.GetOutput()
self.ugrid = trimmed_ug
def makeUnstructVTKVOIThres(vtkObj,extent,limits): """Make volume of interest and threshold for rectilinear grid.""" # Check for the input cellCore = vtk.vtkExtractUnstructuredGrid() cellCore.SetExtent(extent) cellCore.SetInput(vtkObj) cellThres = vtk.vtkThreshold() cellThres.AllScalarsOn() cellThres.SetInputConnection(cellCore.GetOutputPort()) cellThres.ThresholdBetween(limits[0],limits[1]) cellThres.Update() return cellThres.GetOutput(), cellCore.GetOutput()
def get_grid_template(x_min,x_max,y_min,y_max,z_min,z_max,filename,grid): reader = vtk.vtkUnstructuredGridReader() reader.ReadAllScalarsOn() reader.ReadAllVectorsOn() reader.SetFileName(filename) reader.Update() if ( (x_min<x_max) and (y_min<y_max) and (z_min<z_max) ): extract = vtk.vtkExtractUnstructuredGrid() extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max) extract.SetInput(reader.GetOutput()) extract.MergingOn() extract.Update() grid.DeepCopy(extract.GetOutput()) else: grid.DeepCopy(reader.GetOutput())
def get_cell_volumes(x_min,x_max,y_min,y_max,z_min,z_max,filename,cell_volume):
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.SetFileName(filename)
reader.Update()
if ( (x_min<x_max) and (y_min<y_max) and (z_min<z_max) ):
extract = vtk.vtkExtractUnstructuredGrid()
extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max)
extract.SetInput(reader.GetOutput())
extract.MergingOn()
extract.Update()
cell_volume = VN.vtk_to_numpy(extract.GetOutput().GetPointData().GetScalars("cell_volume"))
else:
cell_volume = VN.vtk_to_numpy(reader.GetOutput().GetPointData().GetScalars("cell_volume"))
def get_grid_template(x_min, x_max, y_min, y_max, z_min, z_max, filename,
grid):
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.SetFileName(filename)
reader.Update()
if ((x_min < x_max) and (y_min < y_max) and (z_min < z_max)):
extract = vtk.vtkExtractUnstructuredGrid()
extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max)
extract.SetInput(reader.GetOutput())
extract.MergingOn()
extract.Update()
grid.DeepCopy(extract.GetOutput())
else:
grid.DeepCopy(reader.GetOutput())
def get_number_of_points(x_min, x_max, y_min, y_max, z_min, z_max, filename):
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.SetFileName(filename)
reader.Update()
if ((x_min < x_max) and (y_min < y_max) and (z_min < z_max)):
extract = vtk.vtkExtractUnstructuredGrid()
extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max)
extract.SetInput(reader.GetOutput())
extract.MergingOn()
extract.Update()
num_points = extract.GetOutput().GetNumberOfPoints()
else:
num_points = reader.GetOutput().GetNumberOfPoints()
print ' Number of points = ', num_points
return num_points
def get_number_of_points(x_min,x_max,y_min,y_max,z_min,z_max,filename): reader = vtk.vtkUnstructuredGridReader() reader.ReadAllScalarsOn() reader.ReadAllVectorsOn() reader.SetFileName(filename) reader.Update() if ( (x_min<x_max) and (y_min<y_max) and (z_min<z_max) ): extract = vtk.vtkExtractUnstructuredGrid() extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max) extract.SetInput(reader.GetOutput()) extract.MergingOn() extract.Update() num_points = extract.GetOutput().GetNumberOfPoints() else: num_points = reader.GetOutput().GetNumberOfPoints() print ' Number of points = ', num_points return num_points
def get_cell_volumes(x_min, x_max, y_min, y_max, z_min, z_max, filename,
cell_volume):
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.SetFileName(filename)
reader.Update()
if ((x_min < x_max) and (y_min < y_max) and (z_min < z_max)):
extract = vtk.vtkExtractUnstructuredGrid()
extract.SetExtent(x_min, x_max, y_min, y_max, z_min, z_max)
extract.SetInput(reader.GetOutput())
extract.MergingOn()
extract.Update()
cell_volume = VN.vtk_to_numpy(
extract.GetOutput().GetPointData().GetScalars("cell_volume"))
else:
cell_volume = VN.vtk_to_numpy(
reader.GetOutput().GetPointData().GetScalars("cell_volume"))
def update(self):
"""
"""
appendFilter = vtkAppendFilter()
appendFilter.AddInput(self.input_)
appendFilter.Update()
extractGrid = vtkExtractUnstructuredGrid()
extractGrid.SetInput(appendFilter.GetOutput())
extractGrid.SetExtent(self.extent[0], self.extent[1], self.extent[2], self.extent[3], self.extent[4], self.extent[5])
geom = vtkGeometryFilter()
geom.SetInputConnection(extractGrid.GetOutputPort() )
geom.Update()
clean = vtkCleanPolyData()
clean.PointMergingOn()
clean.SetTolerance(0.01)
clean.SetInput(geom.GetOutput())
clean.Update()
self.output_ = clean.GetOutput()
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: no Mesh.')
## if (self.FOVNormal != [0.0, 0.0, 1.0]):
##
## translation = [-self.FOVCenter[0], -self.FOVCenter[1], -self.FOVCenter[2]]
##
## referenceNormal = [0.0, 0.0, 1.0]
## rotationAxis = [0.0, 0.0, 0.0]
## vtk.vtkMath.Normalize(self.FOVNormal)
## vtk.vtkMath.Cross(self.FOVNormal,referenceNormal,rotationAxis)
## angle = self.AngleBetweenNormals(referenceNormal,self.FOVNormal) / vtk.vtkMath.Pi() * 180.0
##
## transform = vtk.vtkTransform()
## transform.PostMultiply()
## transform.Translate(translation)
## transform.RotateWXYZ(angle,rotationAxis)
## transform.Translate(self.FOVCenter)
##
## transformFilter = vtk.vtkTransformFilter()
## transformFilter.SetInput(self.Mesh)
## transformFilter.SetTransform(transform)
## transformFilter.Update()
##
## acquiredMesh = transformFilter.GetOutput()
if (self.KSpaceDimensionality == 3) or not self.SliceModel:
origin = [self.FOVCenter[0] - self.FOV[0]/2.0,
self.FOVCenter[1] - self.FOV[1]/2.0,
self.FOVCenter[2] - self.FOV[2]/2.0]
spacing = [self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]]
self.KSpace = self.AcquireKSpace(self.Mesh,origin,spacing)
elif self.KSpaceDimensionality == 2:
kSpaceAppend = vtk.vtkImageAppend()
kSpaceAppend.SetAppendAxis(2)
sliceLocations = []
sliceLocation = self.FOVCenter[2] - self.FOV[2]/2.0
while (sliceLocation < self.FOVCenter[2] + self.FOV[2]/2.0):
sliceLocations.append(sliceLocation)
sliceLocation += self.SliceSpacing
spacing = [self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]]
bounds = self.Mesh.GetBounds()
for sliceLocation in sliceLocations:
self.PrintLog("Processing slice at" + float(sliceLocation))
origin = [self.FOVCenter[0] - self.FOV[0]/2.0,
self.FOVCenter[1] - self.FOV[1]/2.0,
sliceLocation]
clipper1 = vtk.vtkClipDataSet()
clipper1.SetInput(self.Mesh)
clipper1.InsideOutOff()
plane1 = vtk.vtkPlane()
plane1.SetNormal(0.0,0.0,1.0)
plane1.SetOrigin(0.0,0.0,sliceLocation - self.SliceThickness / 2.0)
clipper1.SetClipFunction(plane1)
clipper1.Update()
clipper2 = vtk.vtkClipDataSet()
clipper2.SetInput(clipper1.GetOutput())
clipper2.InsideOutOn()
plane2 = vtk.vtkPlane()
plane2.SetNormal(0.0,0.0,1.0)
plane2.SetOrigin(0.0,0.0,sliceLocation + self.SliceThickness / 2.0)
clipper2.SetClipFunction(plane2)
clipper2.Update()
clipper2Bounds = clipper2.GetOutput().GetBounds()
cleaner = vtk.vtkExtractUnstructuredGrid()
cleaner.SetInput(clipper2.GetOutput())
cleaner.ExtentClippingOn()
cleaner.SetExtent(clipper2Bounds[0],clipper2Bounds[1],
clipper2Bounds[2],clipper2Bounds[3],
sliceLocation-self.SliceThickness/2.0,sliceLocation+self.SliceThickness/2.0)
cleaner.Update()
tetraFilter = vtk.vtkDataSetTriangleFilter()
tetraFilter.SetInput(cleaner.GetOutput())
tetraFilter.Update()
sliceMesh = tetraFilter.GetOutput()
self.PrintLog("Number of integration elements:" + int(sliceMesh.GetNumberOfCells()))
sliceKSpace = self.AcquireKSpace(sliceMesh,origin,spacing)
kSpaceAppend.AddInput(sliceKSpace)
kSpaceAppend.Update()
self.KSpace = self.ComputeKSpaceOperation(kSpaceAppend.GetOutput())
def initialize (self):
debug ("In ExtractUnstructuredGrid::__init__ ()")
self.fil = vtk.vtkExtractUnstructuredGrid ()
self.fil.SetInput (self.prev_fil.GetOutput ())
self.fil.Update ()
def extract_mesh_subregion(mesh,regionBoundaries):
subregionAlgorithm = vtkExtractUnstructuredGrid()
subregionAlgorithm.SetInputData(mesh)
subregionAlgorithm.SetExtent(regionBoundaries)
subregionAlgorithm.Update()
return subregionAlgorithm.GetOutput()
def _makeSTL(self):
local_dir = self._gray_dir
surface_dir = self._vol_dir+'_surfaces'+self._path_dlm
try:
os.mkdir(surface_dir)
except:
pass
files = fnmatch.filter(sorted(os.listdir(local_dir)),'*.tif')
counter = re.search("[0-9]*\.tif", files[0]).group()
prefix = self._path_dlm+string.replace(files[0],counter,'')
counter = str(len(counter)-4)
prefixImageName = local_dir + prefix
### Create the renderer, the render window, and the interactor. The renderer
# The following reader is used to read a series of 2D slices (images)
# that compose the volume. The slice dimensions are set, and the
# pixel spacing. The data Endianness must also be specified. The reader
v16=vtk.vtkTIFFReader()
v16.SetFilePrefix(prefixImageName)
v16.SetDataExtent(0,100,0,100,1,len(files))
v16.SetFilePattern("%s%0"+counter+"d.tif")
v16.Update()
im = v16.GetOutput()
im.SetSpacing(self._pixel_dim[0],self._pixel_dim[1],self._pixel_dim[2])
v = vte.vtkImageExportToArray()
v.SetInputData(im)
n = np.float32(v.GetArray())
idx = np.argwhere(n)
(ystart,xstart,zstart), (ystop,xstop,zstop) = idx.min(0),idx.max(0)+1
I,J,K = n.shape
if ystart > 5:
ystart -= 5
else:
ystart = 0
if ystop < I-5:
ystop += 5
else:
ystop = I
if xstart > 5:
xstart -= 5
else:
xstart = 0
if xstop < J-5:
xstop += 5
else:
xstop = J
if zstart > 5:
zstart -= 5
else:
zstart = 0
if zstop < K-5:
zstop += 5
else:
zstop = K
a = n[ystart:ystop,xstart:xstop,zstart:zstop]
itk_img = sitk.GetImageFromArray(a)
itk_img.SetSpacing([self._pixel_dim[0],self._pixel_dim[1],self._pixel_dim[2]])
print "\n"
print "-------------------------------------------------------"
print "-- Applying Patch Based Denoising - this can be slow --"
print "-------------------------------------------------------"
print "\n"
pb = sitk.PatchBasedDenoisingImageFilter()
pb.KernelBandwidthEstimationOn()
pb.SetNoiseModel(3) #use a Poisson noise model since this is confocal
pb.SetNoiseModelFidelityWeight(1)
pb.SetNumberOfSamplePatches(20)
pb.SetPatchRadius(4)
pb.SetNumberOfIterations(10)
fimg = pb.Execute(itk_img)
b = sitk.GetArrayFromImage(fimg)
intensity = b.max()
#grad = sitk.GradientMagnitudeRecursiveGaussianImageFilter()
#grad.SetSigma(0.05)
gf = sitk.GradientMagnitudeImageFilter()
gf.UseImageSpacingOn()
grad = gf.Execute(fimg)
edge = sitk.Cast(sitk.BoundedReciprocal( grad ),sitk.sitkFloat32)
print "\n"
print "-------------------------------------------------------"
print "---- Thresholding to deterimine initial level sets ----"
print "-------------------------------------------------------"
print "\n"
t = 0.5
seed = sitk.BinaryThreshold(fimg,t*intensity)
#Opening (Erosion/Dilation) step to remove islands smaller than 2 voxels in radius)
seed = sitk.BinaryMorphologicalOpening(seed,2)
seed = sitk.BinaryFillhole(seed!=0)
#Get connected regions
r = sitk.ConnectedComponent(seed)
labels = sitk.GetArrayFromImage(r)
ids = sorted(np.unique(labels))
N = len(ids)
if N > 2:
i = np.copy(N)
while i == N and (t-self._tratio)>-1e-7:
t -= 0.01
seed = sitk.BinaryThreshold(fimg,t*intensity)
#Opening (Erosion/Dilation) step to remove islands smaller than 2 voxels in radius)
seed = sitk.BinaryMorphologicalOpening(seed,2)
seed = sitk.BinaryFillhole(seed!=0)
#Get connected regions
r = sitk.ConnectedComponent(seed)
labels = sitk.GetArrayFromImage(r)
i = len(np.unique(labels))
if i > N:
N = np.copy(i)
t+=0.01
else:
t = np.copy(self._tratio)
seed = sitk.BinaryThreshold(fimg,t*intensity)
#Opening (Erosion/Dilation) step to remove islands smaller than 2 voxels in radius)
seed = sitk.BinaryMorphologicalOpening(seed,2)
seed = sitk.BinaryFillhole(seed!=0)
#Get connected regions
r = sitk.ConnectedComponent(seed)
labels = sitk.GetArrayFromImage(r)
labels = np.unique(labels)[1:]
'''
labels[labels==0] = -1
labels = sitk.GetImageFromArray(labels)
labels.SetSpacing([self._pixel_dim[0],self._pixel_dim[1],self._pixel_dim[2]])
#myshow3d(labels,zslices=range(20))
#plt.show()
ls = sitk.ScalarChanAndVeseDenseLevelSetImageFilter()
ls.UseImageSpacingOn()
ls.SetLambda2(1.5)
#ls.SetCurvatureWeight(1.0)
ls.SetAreaWeight(1.0)
#ls.SetReinitializationSmoothingWeight(1.0)
ls.SetNumberOfIterations(100)
seg = ls.Execute(sitk.Cast(labels,sitk.sitkFloat32),sitk.Cast(fimg,sitk.sitkFloat32))
seg = sitk.Cast(seg,sitk.sitkUInt8)
seg = sitk.BinaryMorphologicalOpening(seg,1)
seg = sitk.BinaryFillhole(seg!=0)
#Get connected regions
#r = sitk.ConnectedComponent(seg)
contours = sitk.BinaryContour(seg)
myshow3d(sitk.LabelOverlay(sitk.Cast(fimg,sitk.sitkUInt8),contours),zslices=range(fimg.GetSize()[2]))
plt.show()
'''
segmentation = sitk.Image(r.GetSize(),sitk.sitkUInt8)
segmentation.SetSpacing([self._pixel_dim[0],self._pixel_dim[1],self._pixel_dim[2]])
for l in labels:
d = sitk.SignedMaurerDistanceMap(r==l,insideIsPositive=False,squaredDistance=True,useImageSpacing=True)
#d = sitk.BinaryThreshold(d,-1000,0)
#d = sitk.Cast(d,edge.GetPixelIDValue() )*-1+0.5
#d = sitk.Cast(d,edge.GetPixelIDValue() )
seg = sitk.GeodesicActiveContourLevelSetImageFilter()
seg.SetPropagationScaling(1.0)
seg.SetAdvectionScaling(1.0)
seg.SetCurvatureScaling(0.5)
seg.SetMaximumRMSError(0.01)
levelset = seg.Execute(d,edge)
levelset = sitk.BinaryThreshold(levelset,-1000,0)
segmentation = sitk.Add(segmentation,levelset)
print ("RMS Change for Cell %d: "% l,seg.GetRMSChange())
print ("Elapsed Iterations for Cell %d: "% l, seg.GetElapsedIterations())
'''
contours = sitk.BinaryContour(segmentation)
myshow3d(sitk.LabelOverlay(sitk.Cast(fimg,sitk.sitkUInt8),contours),zslices=range(fimg.GetSize()[2]))
plt.show()
'''
n[ystart:ystop,xstart:xstop,zstart:zstop] = sitk.GetArrayFromImage(segmentation)*100
i = vti.vtkImageImportFromArray()
i.SetDataSpacing([self._pixel_dim[0],self._pixel_dim[1],self._pixel_dim[2]])
i.SetDataExtent([0,100,0,100,1,len(files)])
i.SetArray(n)
i.Update()
thres=vtk.vtkImageThreshold()
thres.SetInputData(i.GetOutput())
thres.ThresholdByLower(0)
thres.ThresholdByUpper(101)
iso=vtk.vtkImageMarchingCubes()
iso.SetInputConnection(thres.GetOutputPort())
iso.SetValue(0,1)
regions = vtk.vtkConnectivityFilter()
regions.SetInputConnection(iso.GetOutputPort())
regions.SetExtractionModeToAllRegions()
regions.ColorRegionsOn()
regions.Update()
N = regions.GetNumberOfExtractedRegions()
for i in xrange(N):
r = vtk.vtkConnectivityFilter()
r.SetInputConnection(iso.GetOutputPort())
r.SetExtractionModeToSpecifiedRegions()
r.AddSpecifiedRegion(i)
g = vtk.vtkExtractUnstructuredGrid()
g.SetInputConnection(r.GetOutputPort())
geo = vtk.vtkGeometryFilter()
geo.SetInputConnection(g.GetOutputPort())
geo.Update()
t = vtk.vtkTriangleFilter()
t.SetInputConnection(geo.GetOutputPort())
t.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(t.GetOutputPort())
s = vtk.vtkSmoothPolyDataFilter()
s.SetInputConnection(cleaner.GetOutputPort())
s.SetNumberOfIterations(50)
dl = vtk.vtkDelaunay3D()
dl.SetInputConnection(s.GetOutputPort())
dl.Update()
self.cells.append(dl)
for i in xrange(N):
g = vtk.vtkGeometryFilter()
g.SetInputConnection(self.cells[i].GetOutputPort())
t = vtk.vtkTriangleFilter()
t.SetInputConnection(g.GetOutputPort())
#get the surface points of the cells and save to points attribute
v = t.GetOutput()
points = []
for j in xrange(v.GetNumberOfPoints()):
p = [0,0,0]
v.GetPoint(j,p)
points.append(p)
self.points.append(points)
#get the volume of the cell
vo = vtk.vtkMassProperties()
vo.SetInputConnection(t.GetOutputPort())
self.volumes.append(vo.GetVolume())
stl = vtk.vtkSTLWriter()
stl.SetInputConnection(t.GetOutputPort())
stl.SetFileName(surface_dir+'cell%02d.stl' % (i+self._counter))
stl.Write()
if self._display:
skinMapper = vtk.vtkDataSetMapper()
skinMapper.SetInputConnection(regions.GetOutputPort())
skinMapper.SetScalarRange(regions.GetOutput().GetPointData().GetArray("RegionId").GetRange())
skinMapper.SetColorModeToMapScalars()
#skinMapper.ScalarVisibilityOff()
skinMapper.Update()
skin = vtk.vtkActor()
skin.SetMapper(skinMapper)
#skin.GetProperty().SetColor(0,0,255)
# An outline provides context around the data.
#
outlineData = vtk.vtkOutlineFilter()
outlineData.SetInputConnection(v16.GetOutputPort())
mapOutline = vtk.vtkPolyDataMapper()
mapOutline.SetInputConnection(outlineData.GetOutputPort())
outline = vtk.vtkActor()
#outline.SetMapper(mapOutline)
#outline.GetProperty().SetColor(0,0,0)
colorbar = vtk.vtkScalarBarActor()
colorbar.SetLookupTable(skinMapper.GetLookupTable())
colorbar.SetTitle("Cells")
colorbar.SetNumberOfLabels(N)
# Create the renderer, the render window, and the interactor. The renderer
# draws into the render window, the interactor enables mouse- and
# keyboard-based interaction with the data within the render window.
#
aRenderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(aRenderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# It is convenient to create an initial view of the data. The FocalPoint
# and Position form a vector direction. Later on (ResetCamera() method)
# this vector is used to position the camera to look at the data in
# this direction.
aCamera = vtk.vtkCamera()
aCamera.SetViewUp (0, 0, -1)
aCamera.SetPosition (0, 1, 0)
aCamera.SetFocalPoint (0, 0, 0)
aCamera.ComputeViewPlaneNormal()
# Actors are added to the renderer. An initial camera view is created.
# The Dolly() method moves the camera towards the FocalPoint,
# thereby enlarging the image.
aRenderer.AddActor(outline)
aRenderer.AddActor(skin)
aRenderer.AddActor(colorbar)
aRenderer.SetActiveCamera(aCamera)
aRenderer.ResetCamera ()
aCamera.Dolly(1.5)
# Set a background color for the renderer and set the size of the
# render window (expressed in pixels).
aRenderer.SetBackground(0.0,0.0,0.0)
renWin.SetSize(800, 600)
# Note that when camera movement occurs (as it does in the Dolly()
# method), the clipping planes often need adjusting. Clipping planes
# consist of two planes: near and far along the view direction. The
# near plane clips out objects in front of the plane the far plane
# clips out objects behind the plane. This way only what is drawn
# between the planes is actually rendered.
aRenderer.ResetCameraClippingRange()
im=vtk.vtkWindowToImageFilter()
im.SetInput(renWin)
iren.Initialize();
iren.Start();
#remove gray directory
shutil.rmtree(local_dir)
moldMapper.ScalarVisibilityOff() moldActor = vtk.vtkActor() moldActor.SetMapper(moldMapper) moldActor.GetProperty().SetColor(.2, .2, .2) moldActor.GetProperty().SetRepresentationToWireframe() # Another connectivity filter is used to extract the parison. connect2 = vtk.vtkConnectivityFilter() connect2.SetInputConnection(warp.GetOutputPort()) connect2.SetExtractionModeToSpecifiedRegions() connect2.AddSpecifiedRegion(2) # We use vtkExtractUnstructuredGrid because we are interested in # looking at just a few cells. We use cell clipping via cell id to # extract the portion of the grid we are interested in. extractGrid = vtk.vtkExtractUnstructuredGrid() extractGrid.SetInputConnection(connect2.GetOutputPort()) extractGrid.CellClippingOn() extractGrid.SetCellMinimum(0) extractGrid.SetCellMaximum(23) parison = vtk.vtkGeometryFilter() parison.SetInputConnection(extractGrid.GetOutputPort()) normals2 = vtk.vtkPolyDataNormals() normals2.SetInputConnection(parison.GetOutputPort()) normals2.SetFeatureAngle(60) lut = vtk.vtkLookupTable() lut.SetHueRange(0.0, 0.66667) parisonMapper = vtk.vtkPolyDataMapper() parisonMapper.SetInputConnection(normals2.GetOutputPort()) parisonMapper.SetLookupTable(lut) parisonMapper.SetScalarRange(0.12, 1.0)
connect.SetExtractionModeToSpecifiedRegions() connect.AddSpecifiedRegion(0) connect.AddSpecifiedRegion(1) moldMapper = vtk.vtkDataSetMapper() moldMapper.SetInputConnection(reader.GetOutputPort()) moldMapper.ScalarVisibilityOff() moldActor = vtk.vtkActor() moldActor.SetMapper(moldMapper) moldActor.GetProperty().SetColor(.2,.2,.2) moldActor.GetProperty().SetRepresentationToWireframe() # extract parison from mesh using connectivity connect2 = vtk.vtkConnectivityFilter() connect2.SetInputConnection(warp.GetOutputPort()) connect2.SetExtractionModeToSpecifiedRegions() connect2.AddSpecifiedRegion(2) extractGrid = vtk.vtkExtractUnstructuredGrid() extractGrid.SetInputConnection(connect2.GetOutputPort()) extractGrid.CellClippingOn() extractGrid.SetCellMinimum(0) extractGrid.SetCellMaximum(23) parison = vtk.vtkGeometryFilter() parison.SetInputConnection(extractGrid.GetOutputPort()) normals2 = vtk.vtkPolyDataNormals() normals2.SetInputConnection(parison.GetOutputPort()) normals2.SetFeatureAngle(60) lut = vtk.vtkLookupTable() lut.SetHueRange(0.0,0.66667) parisonMapper = vtk.vtkPolyDataMapper() parisonMapper.SetInputConnection(normals2.GetOutputPort()) parisonMapper.SetLookupTable(lut) parisonMapper.SetScalarRange(0.12,1.0)
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: no Mesh.')
## if (self.FOVNormal != [0.0, 0.0, 1.0]):
##
## translation = [-self.FOVCenter[0], -self.FOVCenter[1], -self.FOVCenter[2]]
##
## referenceNormal = [0.0, 0.0, 1.0]
## rotationAxis = [0.0, 0.0, 0.0]
## vtk.vtkMath.Normalize(self.FOVNormal)
## vtk.vtkMath.Cross(self.FOVNormal,referenceNormal,rotationAxis)
## angle = self.AngleBetweenNormals(referenceNormal,self.FOVNormal) / vtk.vtkMath.Pi() * 180.0
##
## transform = vtk.vtkTransform()
## transform.PostMultiply()
## transform.Translate(translation)
## transform.RotateWXYZ(angle,rotationAxis)
## transform.Translate(self.FOVCenter)
##
## transformFilter = vtk.vtkTransformFilter()
## transformFilter.SetInput(self.Mesh)
## transformFilter.SetTransform(transform)
## transformFilter.Update()
##
## acquiredMesh = transformFilter.GetOutput()
if (self.KSpaceDimensionality == 3) or not self.SliceModel:
origin = [
self.FOVCenter[0] - self.FOV[0] / 2.0,
self.FOVCenter[1] - self.FOV[1] / 2.0,
self.FOVCenter[2] - self.FOV[2] / 2.0
]
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]
]
self.KSpace = self.AcquireKSpace(self.Mesh, origin, spacing)
elif self.KSpaceDimensionality == 2:
kSpaceAppend = vtk.vtkImageAppend()
kSpaceAppend.SetAppendAxis(2)
sliceLocations = []
sliceLocation = self.FOVCenter[2] - self.FOV[2] / 2.0
while (sliceLocation < self.FOVCenter[2] + self.FOV[2] / 2.0):
sliceLocations.append(sliceLocation)
sliceLocation += self.SliceSpacing
spacing = [
self.FOV[0] / self.MatrixSize[0],
self.FOV[1] / self.MatrixSize[1],
self.FOV[2] / self.MatrixSize[2]
]
bounds = self.Mesh.GetBounds()
for sliceLocation in sliceLocations:
self.PrintLog("Processing slice at" + float(sliceLocation))
origin = [
self.FOVCenter[0] - self.FOV[0] / 2.0,
self.FOVCenter[1] - self.FOV[1] / 2.0, sliceLocation
]
clipper1 = vtk.vtkClipDataSet()
clipper1.SetInput(self.Mesh)
clipper1.InsideOutOff()
plane1 = vtk.vtkPlane()
plane1.SetNormal(0.0, 0.0, 1.0)
plane1.SetOrigin(0.0, 0.0,
sliceLocation - self.SliceThickness / 2.0)
clipper1.SetClipFunction(plane1)
clipper1.Update()
clipper2 = vtk.vtkClipDataSet()
clipper2.SetInput(clipper1.GetOutput())
clipper2.InsideOutOn()
plane2 = vtk.vtkPlane()
plane2.SetNormal(0.0, 0.0, 1.0)
plane2.SetOrigin(0.0, 0.0,
sliceLocation + self.SliceThickness / 2.0)
clipper2.SetClipFunction(plane2)
clipper2.Update()
clipper2Bounds = clipper2.GetOutput().GetBounds()
cleaner = vtk.vtkExtractUnstructuredGrid()
cleaner.SetInput(clipper2.GetOutput())
cleaner.ExtentClippingOn()
cleaner.SetExtent(clipper2Bounds[0], clipper2Bounds[1],
clipper2Bounds[2], clipper2Bounds[3],
sliceLocation - self.SliceThickness / 2.0,
sliceLocation + self.SliceThickness / 2.0)
cleaner.Update()
tetraFilter = vtk.vtkDataSetTriangleFilter()
tetraFilter.SetInput(cleaner.GetOutput())
tetraFilter.Update()
sliceMesh = tetraFilter.GetOutput()
self.PrintLog("Number of integration elements:" +
int(sliceMesh.GetNumberOfCells()))
sliceKSpace = self.AcquireKSpace(sliceMesh, origin, spacing)
kSpaceAppend.AddInput(sliceKSpace)
kSpaceAppend.Update()
self.KSpace = self.ComputeKSpaceOperation(kSpaceAppend.GetOutput())
