def merge(self):
merge_points = vtk.vtkMergePoints()
merge_points.InitPointInsertion(self.points, self.points.GetBounds())
id = vtk.reference(0)
for i in range(self.vertice_number):
merge_points.InsertUniquePoint(self.points.GetPoint(i), id)
with open(self.files[self.Count], 'r') as f:
for line in f.readlines():
line = str.split(line, ' ')
inserted = merge_points.InsertUniquePoint(
[float(line[0]),
float(line[1]),
float(line[2])], id)
if inserted == 1:
self.vertice_number += 1
self.points = merge_points.GetPoints()
self.Count += 1
renderers = self.interactor.GetRenderWindow().GetRenderers()
renderers.InitTraversal()
points_renderer = renderers.GetNextItem()
points_renderer.RemoveActor(self.points_actor)
self.points_actor = create_points_actor(points)
points_renderer.AddActor(self.points_actor)
surface_renderer = renderers.GetNextItem()
surface_renderer.RemoveActor(self.surface_actor)
self.surface_actor = create_surface_actor(points)
surface_renderer.AddActor(self.surface_actor)
self.interactor.GetRenderWindow().Render()
def merge(self):
merge_points = vtk.vtkMergePoints()
merge_points.InitPointInsertion(self.points, self.points.GetBounds())
id = vtk.reference(0)
for i in range(self.vertice_number):
merge_points.InsertUniquePoint(self.points.GetPoint(i), id)
for i in range(self.Count,
min(self.Count + self.interval, len(self.vertices))):
inserted = merge_points.InsertUniquePoint(self.vertices[i], id)
if inserted == 1:
self.vertice_number += 1
if self.Count + self.interval < len(self.vertices):
self.Count = self.Count + self.interval
else:
self.Count = len(self.vertices)
self.points = merge_points.GetPoints()
self.interactor.GetRenderWindow().GetRenderers().GetFirstRenderer(
).RemoveActor(self.actor)
self.actor = create_points_actor(self.points)
self.interactor.GetRenderWindow().GetRenderers().GetFirstRenderer(
).AddActor(self.actor)
self.interactor.GetRenderWindow().Render()
def setVtkWidget(vtkWidget):
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
ren1 = vtk.vtkRenderer()
vtkWidget.GetRenderWindow().AddRenderer(ren1)
iren = vtkWidget.GetRenderWindow().GetInteractor()
reader = vtk.vtkMetaImageReader()
reader.SetFileName('FullHead.mha')
reader.Update()
locator = vtk.vtkMergePoints()
locator.SetDivisions(396, 396, 24)
locator.SetNumberOfPointsPerBucket(1)
locator.AutomaticOff()
iso = vtk.vtkMarchingCubes()
iso.SetInputConnection(reader.GetOutputPort())
iso.ComputeGradientsOn()
iso.ComputeScalarsOff()
iso.SetValue(0, 1)
iso.SetLocator(locator)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetColor(colors.GetColor3d("Wheat"))
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# Add the actors to the renderer, set the background and size.
#
ren1.AddActor(outlineActor)
ren1.AddActor(isoActor)
ren1.SetBackground(colors.GetColor3d("Black"))
ren1.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren1.GetActiveCamera().SetPosition(0, -1, 0)
ren1.GetActiveCamera().SetViewUp(0, 0, -1)
ren1.ResetCamera()
ren1.GetActiveCamera().Dolly(1.5)
ren1.ResetCameraClippingRange()
iren.Initialize()
def merge(feature_points_path, segment_points_path, merge_points_path):
'''
feature_points_path:str， 特征点的文件路径
segment_points_path:str, 分割后网格的顶点的文件路径
merge_points_path:str， 合并后的顶点存储路径
'''
# 读取feature_points
vertice_number = 0
feature_vertices = []
with open(feature_points_path, 'r') as f1:
for line in f1.readlines():
line = str.split(line, ' ')
vertice_number = vertice_number + 1
feature_vertices.append(
[float(line[0]),
float(line[1]),
float(line[2])])
points = vtk.vtkPoints()
points.SetNumberOfPoints(vertice_number)
for i in range(vertice_number):
points.SetPoint(i, feature_vertices[i])
# 初始化合并的顶点集
merge_points = vtk.vtkMergePoints()
# merge_points.SetDataSet(points)
merge_points.InitPointInsertion(points, points.GetBounds())
id = vtk.reference(0)
for i in range(vertice_number):
merge_points.InsertUniquePoint(points.GetPoint(i), id)
vertice_number = 0
segment_points = []
with open(segment_points_path, 'r') as f2:
for line in f2.readlines():
line = str.split(line, ' ')
if line[0] == 'v':
segment_points.append(
[float(line[1]),
float(line[2]),
float(line[3])])
vertice_number = vertice_number + 1
else:
break
id = vtk.reference(0)
replated_points_id = []
for i in range(vertice_number):
inserted = merge_points.InsertUniquePoint(segment_points[i], id)
if inserted == 0:
replated_points_id.append([id, i])
result = merge_points.GetPoints()
with open(merge_points_path, 'w') as f3:
for i in range(result.GetNumberOfPoints()):
pointTemp = result.GetPoint(i)
f3.write("%f %f %f\n" % (pointTemp[0], pointTemp[1], pointTemp[2]))
print("Replicated points number: %d" % len(replated_points_id))
return len(replated_points_id)
def create_merge_points(program_data):
merge_points = vtk.vtkMergePoints()
points = vtk.vtkPoints()
top_level_box = program_data['grid_desc']['create_box']
bounds = []
bounds.append(top_level_box['xlo'])
bounds.append(top_level_box['xhi'])
bounds.append(top_level_box['ylo'])
bounds.append(top_level_box['yhi'])
bounds.append(top_level_box['zlo'])
bounds.append(top_level_box['zhi'])
merge_points.InitPointInsertion(points, bounds)
return merge_points
def OnEndHeader(self):
"""Get ready to add blocks
"""
self.TotalFluidSites = self.Domain.BlockFluidSiteCounts.sum()
# Efficiently add the voxel corner points
self.Locator = vtk.vtkMergePoints()
self.Points = vtk.vtkPoints()
# Compute the bounds of the voxel corner points
# Initially in a shape == (3,2) array [[0, nSites[x]], ... ]
bounds = np.concatenate(
(np.zeros(3, dtype=int), self.Domain.SiteCounts)).reshape(
(2, 3)).transpose()
# shift half a voxel down, scale and then translate
bounds = self.Domain.VoxelSize*(bounds - 0.5) + \
self.Domain.Origin[:, np.newaxis]
# Since we know how the points will be arranged, use that information
# to tune the vtkMergePoints
self.Locator.SetDivisions(*self.Domain.BlockCounts)
self.Locator.InitPointInsertion(self.Points, bounds.flatten(),
self.TotalFluidSites)
# This is what we're trying to construct. Allocate data (we know how
# many cells (= TotalFluidSites) but not how many points, as we don't
# know the number of surface sites.
self.Grid = vtk.vtkUnstructuredGrid()
self.Grid.Allocate(self.TotalFluidSites, 1000)
self.Grid.SetPoints(self.Points)
# Array of offsets from a point to the corners of its cell.
self.deltas = 0.5 * self.Domain.VoxelSize * \
np.array([[ 1, 1, 1],
[ 1, 1,-1],
[ 1,-1, 1],
[ 1,-1,-1],
[-1, 1, 1],
[-1, 1,-1],
[-1,-1, 1],
[-1,-1,-1]],
dtype=float)
# Used as a working array.
self.vox = vtk.vtkVoxel()
return
def OnEndHeader(self):
"""Get ready to add blocks
"""
self.TotalFluidSites = self.Domain.BlockFluidSiteCounts.sum()
# Efficiently add the voxel corner points
self.Locator = vtk.vtkMergePoints()
self.Points = vtk.vtkPoints()
# Compute the bounds of the voxel corner points
# Initially in a shape == (3,2) array [[0, nSites[x]], ... ]
bounds = np.concatenate((np.zeros(3,dtype=int),
self.Domain.SiteCounts)).reshape((2,3)).transpose()
# shift half a voxel down, scale and then translate
bounds = self.Domain.VoxelSize*(bounds - 0.5) + \
self.Domain.Origin[:, np.newaxis]
# Since we know how the points will be arranged, use that information
# to tune the vtkMergePoints
self.Locator.SetDivisions(*self.Domain.BlockCounts)
self.Locator.InitPointInsertion(self.Points, bounds.flatten(),
self.TotalFluidSites)
# This is what we're trying to construct. Allocate data (we know how
# many cells (= TotalFluidSites) but not how many points, as we don't
# know the number of surface sites.
self.Grid = vtk.vtkUnstructuredGrid()
self.Grid.Allocate(self.TotalFluidSites, 1000)
self.Grid.SetPoints(self.Points)
# Array of offsets from a point to the corners of its cell.
self.deltas = 0.5 * self.Domain.VoxelSize * \
np.array([[ 1, 1, 1],
[ 1, 1,-1],
[ 1,-1, 1],
[ 1,-1,-1],
[-1, 1, 1],
[-1, 1,-1],
[-1,-1, 1],
[-1,-1,-1]],
dtype=float)
# Used as a working array.
self.vox = vtk.vtkVoxel()
return
def clean_unstructured_grid(ugrid):
"""Collapse a vtu produced from a discontinuous grid back down to the continuous space.
Args:
ugrid (vtkUnstructuredGrid): the input discontinuous grid
Results
out_grid (vtkUnstructuredGrid): A continuous grid"""
merge_points = vtk.vtkMergePoints()
out_grid = vtk.vtkUnstructuredGrid()
for i in range(ugrid.GetNumberOfPoints()):
merge_points.InsertUniquePoint(ugrid.GetPoints().GetPoint(i))
merge_points.BuildLocator()
pts = vtk.vtkPoints()
pts.DeepCopy(merge_points.GetPoints())
out_grid.SetPoints(pts)
for i in range(ugrid.GetNumberOfCells()):
cell = ugrid.GetCell(i)
cell_ids = cell.GetPointIds()
for j in range(cell.GetNumberOfPoints()):
original_point = cell.GetPoints().GetPoint(j)
cell_ids.SetId(j,
merge_points.FindClosestInsertedPoint(original_point))
out_grid.InsertNextCell(cell.GetCellType(), cell.GetPointIds())
out_grid.GetCellData().DeepCopy(ugrid.GetCellData())
return out_grid
def GenerateTetrInFile(self):
self.PrintLog('Generating Tetr .in file.')
f = open(self.OutputFileName, 'w')
line = '$title' + '\n'
f.write(line)
line = self.OutputFileName + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$compress' + '\n'
f.write(line)
line = 'gzip -f' + '\n'
f.write(line)
line = '\n'
f.write(line)
self.NormalizationTransform.Identity()
if (self.NormalizationEntity != ''):
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
self.NormalizationEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.Execute()
self.NormalizationRadius = sectionProperties.Radius
if (self.NormalizationRadius != 0.0) & (self.NormalizationRadius !=
1.0):
self.NormalizationTransform.Scale(1.0 / self.NormalizationRadius,
1.0 / self.NormalizationRadius,
1.0 / self.NormalizationRadius)
line = '$radius' + '\n'
f.write(line)
line = str(self.NormalizationRadius) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$viscosity' + '\n'
f.write(line)
line = str(0.035) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$density' + '\n'
f.write(line)
line = str(1.06) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$red' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$alpha' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$nsolve' + '\n'
f.write(line)
line = '22' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$Uzawa_PC' + '\n'
f.write(line)
line = '1' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$node' + '\n'
f.write(line)
line = str(self.Mesh.GetNumberOfPoints()) + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = [0.0, 0.0, 0.0]
self.NormalizationTransform.TransformPoint(self.Mesh.GetPoint(i),
point)
line = str(i + 1) + ' ' + str(point[0]) + ' ' + str(
point[1]) + ' ' + str(point[2]) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$elem' + '\n'
f.write(line)
quadratidTetraCellType = 24
quadraticTetraCellIds = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(quadratidTetraCellType,
quadraticTetraCellIds)
line = str(quadraticTetraCellIds.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(quadraticTetraCellIds.GetNumberOfTuples()):
line = str(i + 1) + ' '
cell = self.Mesh.GetCell(quadraticTetraCellIds.GetValue(i))
line += str(cell.GetPointId(0) + 1) + ' '
line += str(cell.GetPointId(4) + 1) + ' '
line += str(cell.GetPointId(1) + 1) + ' '
line += str(cell.GetPointId(5) + 1) + ' '
line += str(cell.GetPointId(2) + 1) + ' '
line += str(cell.GetPointId(6) + 1) + ' '
line += str(cell.GetPointId(7) + 1) + ' '
line += str(cell.GetPointId(8) + 1) + ' '
line += str(cell.GetPointId(9) + 1) + ' '
line += str(cell.GetPointId(3) + 1) + ' '
line += '\n'
f.write(line)
# inletEntities = self.InletEntities
# reversedInlets = self.ReverseInlets
# inletEntitiesReversed = zip(inletEntities,reversedInlets)
# for inletEntityReversed in inletEntitiesReversed:
# inletEntity = inletEntityReversed[0]
# reversedInlet = inletEntityReversed[1]
# if (inletEntity == ''):
# continue
for inletEntity in self.InletEntities:
reversedInlet = inletEntity in self.ReverseInletEntities
line = '\n'
f.write(line)
line = '$binlet' + ' (' + inletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(inletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
inletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
if not reversedInlet:
sectionProperties.FlipOutwardNormal = 1
else:
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(
sectionProperties.Origin[1]) + ' ' + str(
sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(
sectionProperties.Normal[1]) + ' ' + str(
sectionProperties.Normal[2]) + '\n'
f.write(line)
#TODO: for every inlet insert fourier coefficients given points of waveform (spline-interpolate points beforehands to get them equispaced).
if (self.OutletEntity != ''):
line = '\n'
f.write(line)
line = '$boutlet' + ' (' + self.OutletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.OutletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
self.OutletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(
sectionProperties.Origin[1]) + ' ' + str(
sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(
sectionProperties.Normal[1]) + ' ' + str(
sectionProperties.Normal[2]) + '\n'
f.write(line)
if (self.WallEntity != ''):
line = '\n'
f.write(line)
line = '$bwall' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.WallEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
wallPointIdsMap = vtk.vtkIdList()
if (self.WriteWNodeSection == 1):
line = '\n'
f.write(line)
line = '$wnode' + '\n'
f.write(line)
line = str(numberOfEntityNodes) + '\n'
f.write(line)
count = 0
wallPointIdsMap.SetNumberOfIds(entityArray.GetNumberOfTuples())
extractSurface = vtk.vtkGeometryFilter()
extractSurface.SetInputData(self.Mesh)
extractSurface.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputConnection(
extractSurface.GetOutputPort())
normalsFilter.AutoOrientNormalsOn()
normalsFilter.ConsistencyOn()
normalsFilter.Update()
normalsSurface = normalsFilter.GetOutput()
locator = vtk.vtkMergePoints()
locator.SetDataSet(normalsSurface)
locator.BuildLocator()
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
wallPointIdsMap.SetId(i, -1)
continue
wallPointIdsMap.SetId(i, count)
point = self.Mesh.GetPoint(i)
surfacePointId = locator.FindClosestPoint(point)
normal = normalsSurface.GetPointData().GetNormals(
).GetTuple3(surfacePointId)
line = str(count + 1) + ' ' + str(i + 1) + ' ' + str(
normal[0]) + ' ' + str(normal[1]) + ' ' + str(
normal[2]) + '\n'
f.write(line)
count += 1
if (self.WriteWElemSection == 1):
line = '\n'
f.write(line)
line = '$welem' + '\n'
f.write(line)
dataArray = vtk.vtkIntArray()
dataArray.SetNumberOfComponents(8)
for i in range(self.Mesh.GetNumberOfCells()):
qtetra = self.Mesh.GetCell(i)
for j in range(qtetra.GetNumberOfFaces()):
face = qtetra.GetFace(j)
isBoundaryFace = 1
for k in range(face.GetNumberOfPoints()):
if (entityArray.GetComponent(
face.GetPointId(k), 0) != 1.0):
isBoundaryFace = 0
break
if (isBoundaryFace == 0):
continue
dataArray.InsertNextValue(i)
dataArray.InsertNextValue(j)
for k in range(face.GetNumberOfPoints()):
dataArray.InsertNextValue(face.GetPointId(k))
line = str(dataArray.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(dataArray.GetNumberOfTuples()):
line = str(i + 1) + ' '
line += str(int(dataArray.GetComponent(i, 0)) + 1) + ' '
faceId = int(dataArray.GetComponent(i, 1))
newTetrFaceIdsMap = [2, 4, 3, 1]
line += str(newTetrFaceIdsMap[faceId]) + ' '
for j in range(2, dataArray.GetNumberOfComponents()):
line += str(
wallPointIdsMap.GetId(
int(dataArray.GetComponent(i, j))) + 1) + ' '
line += '\n'
f.write(line)
if (self.HistoryEntity != ''):
line = '\n'
f.write(line)
line = '$history' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.HistoryEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
self.WriteTimeSteps(f)
def GenerateTetrInFile(self):
self.PrintLog('Generating Tetr .in file.')
f=open(self.OutputFileName, 'w')
line = '$title' + '\n'
f.write(line)
line = self.OutputFileName + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$compress' + '\n'
f.write(line)
line = 'gzip -f' + '\n'
f.write(line)
line = '\n'
f.write(line)
self.NormalizationTransform.Identity()
if (self.NormalizationEntity != ''):
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(self.NormalizationEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.Execute()
self.NormalizationRadius = sectionProperties.Radius
if (self.NormalizationRadius != 0.0) & (self.NormalizationRadius != 1.0):
self.NormalizationTransform.Scale(1.0/self.NormalizationRadius,1.0/self.NormalizationRadius,1.0/self.NormalizationRadius)
line = '$radius' + '\n'
f.write(line)
line = str(self.NormalizationRadius) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$viscosity' + '\n'
f.write(line)
line = str(0.035) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$density' + '\n'
f.write(line)
line = str(1.06) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$red' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$alpha' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$nsolve' + '\n'
f.write(line)
line = '22' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$Uzawa_PC' + '\n'
f.write(line)
line = '1' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$node' + '\n'
f.write(line)
line = str(self.Mesh.GetNumberOfPoints()) + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = [0.0,0.0,0.0]
self.NormalizationTransform.TransformPoint(self.Mesh.GetPoint(i),point)
line = str(i+1) + ' ' + str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2]) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$elem' + '\n'
f.write(line)
quadratidTetraCellType = 24
quadraticTetraCellIds = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(quadratidTetraCellType,quadraticTetraCellIds)
line = str(quadraticTetraCellIds.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(quadraticTetraCellIds.GetNumberOfTuples()):
line = str(i+1) + ' '
cell = self.Mesh.GetCell(quadraticTetraCellIds.GetValue(i))
line += str(cell.GetPointId(0)+1) + ' '
line += str(cell.GetPointId(4)+1) + ' '
line += str(cell.GetPointId(1)+1) + ' '
line += str(cell.GetPointId(5)+1) + ' '
line += str(cell.GetPointId(2)+1) + ' '
line += str(cell.GetPointId(6)+1) + ' '
line += str(cell.GetPointId(7)+1) + ' '
line += str(cell.GetPointId(8)+1) + ' '
line += str(cell.GetPointId(9)+1) + ' '
line += str(cell.GetPointId(3)+1) + ' '
line += '\n'
f.write(line)
# inletEntities = self.InletEntities
# reversedInlets = self.ReverseInlets
# inletEntitiesReversed = zip(inletEntities,reversedInlets)
# for inletEntityReversed in inletEntitiesReversed:
# inletEntity = inletEntityReversed[0]
# reversedInlet = inletEntityReversed[1]
# if (inletEntity == ''):
# continue
for inletEntity in self.InletEntities:
reversedInlet = inletEntity in self.ReverseInletEntities
line = '\n'
f.write(line)
line = '$binlet' + ' (' + inletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(inletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(inletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
if not reversedInlet:
sectionProperties.FlipOutwardNormal = 1
else:
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(sectionProperties.Origin[1]) + ' ' + str(sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(sectionProperties.Normal[1]) + ' ' + str(sectionProperties.Normal[2]) + '\n'
f.write(line)
#TODO: for every inlet insert fourier coefficients given points of waveform (spline-interpolate points beforehands to get them equispaced).
if (self.OutletEntity != ''):
line = '\n'
f.write(line)
line = '$boutlet' + ' (' + self.OutletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.OutletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(self.OutletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(sectionProperties.Origin[1]) + ' ' + str(sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(sectionProperties.Normal[1]) + ' ' + str(sectionProperties.Normal[2]) + '\n'
f.write(line)
if (self.WallEntity != ''):
line = '\n'
f.write(line)
line = '$bwall' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.WallEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
wallPointIdsMap = vtk.vtkIdList()
if (self.WriteWNodeSection == 1):
line = '\n'
f.write(line)
line = '$wnode' + '\n'
f.write(line)
line = str(numberOfEntityNodes) + '\n'
f.write(line)
count = 0
wallPointIdsMap.SetNumberOfIds(entityArray.GetNumberOfTuples())
extractSurface = vtk.vtkGeometryFilter()
extractSurface.SetInput(self.Mesh)
extractSurface.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInput(extractSurface.GetOutput())
normalsFilter.AutoOrientNormalsOn()
normalsFilter.ConsistencyOn()
normalsFilter.Update()
normalsSurface = normalsFilter.GetOutput()
locator = vtk.vtkMergePoints()
locator.SetDataSet(normalsSurface)
locator.BuildLocator()
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
wallPointIdsMap.SetId(i,-1)
continue
wallPointIdsMap.SetId(i,count)
point = self.Mesh.GetPoint(i)
surfacePointId = locator.FindClosestPoint(point)
normal = normalsSurface.GetPointData().GetNormals().GetTuple3(surfacePointId)
line = str(count+1) + ' ' + str(i+1) + ' ' + str(normal[0]) + ' ' + str(normal[1]) + ' ' + str(normal[2]) + '\n'
f.write(line)
count += 1
if (self.WriteWElemSection == 1):
line = '\n'
f.write(line)
line = '$welem' + '\n'
f.write(line)
dataArray = vtk.vtkIntArray()
dataArray.SetNumberOfComponents(8)
for i in range(self.Mesh.GetNumberOfCells()):
qtetra = self.Mesh.GetCell(i)
for j in range(qtetra.GetNumberOfFaces()):
face = qtetra.GetFace(j)
isBoundaryFace = 1
for k in range(face.GetNumberOfPoints()):
if (entityArray.GetComponent(face.GetPointId(k),0) != 1.0):
isBoundaryFace = 0
break
if (isBoundaryFace == 0):
continue
dataArray.InsertNextValue(i)
dataArray.InsertNextValue(j)
for k in range(face.GetNumberOfPoints()):
dataArray.InsertNextValue(face.GetPointId(k))
line = str(dataArray.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(dataArray.GetNumberOfTuples()):
line = str(i+1) + ' '
line += str(int(dataArray.GetComponent(i,0))+1) + ' '
faceId = int(dataArray.GetComponent(i,1))
newTetrFaceIdsMap = [2, 4, 3, 1]
line += str(newTetrFaceIdsMap[faceId]) + ' '
for j in range(2,dataArray.GetNumberOfComponents()):
line += str(wallPointIdsMap.GetId(int(dataArray.GetComponent(i,j)))+1) + ' '
line += '\n'
f.write(line)
if (self.HistoryEntity != ''):
line = '\n'
f.write(line)
line = '$history' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.HistoryEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
self.WriteTimeSteps(f)
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64,64)
v16.GetOutput().SetOrigin(0.0,0.0,0.0)
v16.SetDataByteOrderToLittleEndian()
v16.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
v16.SetImageRange(1,93)
v16.SetDataSpacing(3.2,3.2,1.5)
v16.Update()
myLocator = vtk.vtkMergePoints()
isoXY = vtk.vtkMarchingSquares()
isoXY.SetInputConnection(v16.GetOutputPort())
isoXY.GenerateValues(2,600,1200)
isoXY.SetImageRange(0,32,32,63,45,45)
isoXY.SetLocator(myLocator)
isoXYMapper = vtk.vtkPolyDataMapper()
isoXYMapper.SetInputConnection(isoXY.GetOutputPort())
isoXYMapper.SetScalarRange(600,1200)
isoXYActor = vtk.vtkActor()
isoXYActor.SetMapper(isoXYMapper)
isoYZ = vtk.vtkMarchingSquares()
isoYZ.SetInputConnection(v16.GetOutputPort())
isoYZ.GenerateValues(2,600,1200)
isoYZ.SetImageRange(32,32,32,63,46,92)
isoYZMapper = vtk.vtkPolyDataMapper()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64,64)
v16.GetOutput().SetOrigin(0.0,0.0,0.0)
v16.SetDataByteOrderToLittleEndian()
v16.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
v16.SetImageRange(1,93)
v16.SetDataSpacing(3.2,3.2,1.5)
v16.Update()
myLocator = vtk.vtkMergePoints()
isoXY = vtk.vtkMarchingSquares()
isoXY.SetInputConnection(v16.GetOutputPort())
isoXY.GenerateValues(2,600,1200)
isoXY.SetImageRange(0,32,32,63,45,45)
isoXY.SetLocator(myLocator)
isoXYMapper = vtk.vtkPolyDataMapper()
isoXYMapper.SetInputConnection(isoXY.GetOutputPort())
isoXYMapper.SetScalarRange(600,1200)
isoXYActor = vtk.vtkActor()
isoXYActor.SetMapper(isoXYMapper)
isoYZ = vtk.vtkMarchingSquares()
isoYZ.SetInputConnection(v16.GetOutputPort())
isoYZ.GenerateValues(2,600,1200)
isoYZ.SetImageRange(32,32,32,63,46,92)
isoYZMapper = vtk.vtkPolyDataMapper()
def _shellSolidify(surfacePd, shellThickness, shellOffsetDirection):
"""Create a thick shell from a surface by extruding in surface normal direction"""
# remove double vertices
cleanPolyData = vtk.vtkCleanPolyData()
cleanPolyData.SetInputData(surfacePd)
# create normals
normals = vtk.vtkPolyDataNormals()
normals.SetComputeCellNormals(1)
normals.SetInputConnection(cleanPolyData.GetOutputPort())
normals.SplittingOff()
if shellOffsetDirection == SHELL_OFFSET_OUTSIDE:
normals.FlipNormalsOn()
normals.Update()
surfacePd = vtk.vtkPolyData()
surfacePd.DeepCopy(normals.GetOutput())
numberOfPoints = surfacePd.GetNumberOfPoints()
# get boundary edges, used later
featureEdges = vtk.vtkFeatureEdges()
featureEdges.BoundaryEdgesOn()
featureEdges.ColoringOff()
featureEdges.FeatureEdgesOff()
featureEdges.NonManifoldEdgesOff()
featureEdges.ManifoldEdgesOff()
featureEdges.SetInputData(normals.GetOutput())
featureEdges.Update()
addingPoints = []
addingPolys = []
allNormalsArray = surfacePd.GetCellData().GetArray('Normals')
for pointID in range(numberOfPoints):
cellIDs = vtk.vtkIdList()
surfacePd.GetPointCells(pointID, cellIDs)
normalsArray = []
# ilterate through all cells/faces which contain point
for i in range(cellIDs.GetNumberOfIds()):
n = allNormalsArray.GetTuple3(cellIDs.GetId(i))
normalsArray.append(np.array(n))
# calculate position of new vert
dir_vec = np.zeros(3)
for n in normalsArray:
dir_vec = dir_vec + np.array(n)
dir_vec_norm = dir_vec / np.linalg.norm(dir_vec)
proj_length = np.dot(dir_vec_norm, np.array(normalsArray[0]))
dir_vec_finallenght = dir_vec_norm * proj_length
vertex_neu = np.array(surfacePd.GetPoint(pointID)) + (
dir_vec_finallenght * shellThickness)
# append point
addingPoints.append(vertex_neu)
for cellID in range(surfacePd.GetNumberOfCells()):
pointIDs = vtk.vtkIdList()
surfacePd.GetCellPoints(cellID, pointIDs)
newPointIDs = vtk.vtkIdList()
for i in reversed(range(pointIDs.GetNumberOfIds())):
newPointIDs.InsertNextId(
int(pointIDs.GetId(i) + numberOfPoints))
addingPolys.append(newPointIDs)
doubleSurfacePoints = vtk.vtkPoints()
doubleSurfacePolys = vtk.vtkCellArray()
doubleSurfacePoints.DeepCopy(surfacePd.GetPoints())
doubleSurfacePolys.DeepCopy(surfacePd.GetPolys())
for p in addingPoints:
doubleSurfacePoints.InsertNextPoint(p)
for p in addingPolys:
doubleSurfacePolys.InsertNextCell(p)
doubleSurfacePD = vtk.vtkPolyData()
doubleSurfacePD.SetPoints(doubleSurfacePoints)
doubleSurfacePD.SetPolys(doubleSurfacePolys)
# add faces to boundary edges
mergePoints = vtk.vtkMergePoints()
mergePoints.InitPointInsertion(doubleSurfacePD.GetPoints(),
doubleSurfacePD.GetBounds())
mergePoints.SetDataSet(doubleSurfacePD)
mergePoints.BuildLocator()
manifoldPolys = vtk.vtkCellArray()
manifoldPolys.DeepCopy(doubleSurfacePD.GetPolys())
manifoldPoints = vtk.vtkPoints()
manifoldPoints.DeepCopy(doubleSurfacePD.GetPoints())
for e in range(featureEdges.GetOutput().GetNumberOfCells()):
pointIDs = vtk.vtkIdList()
featureEdges.GetOutput().GetCellPoints(e, pointIDs)
if pointIDs.GetNumberOfIds() == 2: # -> Edge
matchingPointIDs = []
newPointIDs = vtk.vtkIdList()
for p in range(2):
matchingPointIDs.append(
mergePoints.IsInsertedPoint(
featureEdges.GetOutput().GetPoint(
pointIDs.GetId(p))))
if not (
-1
) in matchingPointIDs: # edge vertex not found in original pd, should not happen
newPointIDs.InsertNextId(matchingPointIDs[1])
newPointIDs.InsertNextId(matchingPointIDs[0])
newPointIDs.InsertNextId(matchingPointIDs[0] +
numberOfPoints)
newPointIDs.InsertNextId(matchingPointIDs[1] +
numberOfPoints)
manifoldPolys.InsertNextCell(newPointIDs)
manifoldPD = vtk.vtkPolyData()
manifoldPD.SetPoints(manifoldPoints)
manifoldPD.SetPolys(manifoldPolys)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(manifoldPD)
# Compute normals to make the result look smooth
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(triangleFilter.GetOutputPort())
normals.Update()
return normals.GetOutput()
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Create the pipeline.
#
reader = vtk.vtkMetaImageReader()
reader.SetFileName(fileName)
reader.Update()
locator = vtk.vtkMergePoints()
locator.SetDivisions(64, 64, 92)
locator.SetNumberOfPointsPerBucket(2)
locator.AutomaticOff()
iso = vtk.vtkMarchingCubes()
iso.SetInputConnection(reader.GetOutputPort())
iso.ComputeGradientsOn()
iso.ComputeScalarsOff()
iso.SetValue(0, 1150)
iso.SetLocator(locator)
isoMapper = vtk.vtkPolyDataMapper()
isoMapper.SetInputConnection(iso.GetOutputPort())
isoMapper.ScalarVisibilityOff()
isoActor = vtk.vtkActor()
isoActor.SetMapper(isoMapper)
isoActor.GetProperty().SetColor(colors.GetColor3d("Wheat"))
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# Add the actors to the renderer, set the background and size.
#
ren1.AddActor(outlineActor)
ren1.AddActor(isoActor)
ren1.SetBackground(colors.GetColor3d("SlateGray"))
ren1.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren1.GetActiveCamera().SetPosition(0, -1, 0)
ren1.GetActiveCamera().SetViewUp(0, 0, -1)
ren1.ResetCamera()
ren1.GetActiveCamera().Dolly(1.5)
ren1.ResetCameraClippingRange()
renWin.SetSize(640, 480)
renWin.Render()
iren.Start()
def main():
# vtkFlyingEdges3D was introduced in VTK >= 8.2
use_flying_edges = vtk_version_ok(8, 2, 0)
file_name = get_program_parameters()
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
# Create the pipeline.
#
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_name)
reader.Update()
locator = vtk.vtkMergePoints()
locator.SetDivisions(64, 64, 92)
locator.SetNumberOfPointsPerBucket(2)
locator.AutomaticOff()
if use_flying_edges:
try:
using_marching_cubes = False
iso = vtk.vtkDiscreteFlyingEdges3D()
except AttributeError:
using_marching_cubes = True
iso = vtk.vtkDiscreteMarchingCubes()
else:
using_marching_cubes = True
iso = vtk.vtkDiscreteMarchingCubes()
iso.SetInputConnection(reader.GetOutputPort())
iso.ComputeGradientsOn()
iso.ComputeScalarsOff()
iso.SetValue(0, 1150)
if using_marching_cubes:
iso.SetLocator(locator)
iso_mapper = vtk.vtkPolyDataMapper()
iso_mapper.SetInputConnection(iso.GetOutputPort())
iso_mapper.ScalarVisibilityOff()
iso_actor = vtk.vtkActor()
iso_actor.SetMapper(iso_mapper)
iso_actor.GetProperty().SetColor(colors.GetColor3d('Ivory'))
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outline_actor = vtk.vtkActor()
outline_actor.SetMapper(outline_mapper)
# Add the actors to the renderer, set the background and size.
#
ren.AddActor(outline_actor)
ren.AddActor(iso_actor)
ren.SetBackground(colors.GetColor3d('SlateGray'))
ren.GetActiveCamera().SetFocalPoint(0, 0, 0)
ren.GetActiveCamera().SetPosition(0, -1, 0)
ren.GetActiveCamera().SetViewUp(0, 0, -1)
ren.ResetCamera()
ren.GetActiveCamera().Dolly(1.5)
ren.ResetCameraClippingRange()
ren_win.SetSize(640, 480)
ren_win.SetWindowName('HeadBone')
ren_win.Render()
iren.Start()
