def get(self,label):
"""
Get either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
"""
cell_data = self.vtk_data.GetCellData()
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
return vtk_to_np(cell_data.GetArray(a))
point_data = self.vtk_data.GetPointData()
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
return vtk_to_np(point_data.GetArray(a))
raise ValueError(f'Array "{label}" not found.')
def vtkReadVTKfile(self, filename):
""" Lecture d'un fichier vtk"""
# Read the source file.
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update() # Needed because of GetScalarRange
surface_filter = vtk.vtkDataSetSurfaceFilter()
surface_filter.SetInputConnection(reader.GetOutputPort())
self.meshNormals = vtk.vtkPolyDataNormals()
self.meshNormals.SetInputConnection(surface_filter.GetOutputPort())
self.meshNormals.SetFeatureAngle(60.0)
self.meshNormals.ComputeCellNormalsOn()
self.meshNormals.ComputePointNormalsOn()
self.meshNormals.ConsistencyOn()
self.meshNormals.AutoOrientNormalsOn()
self.meshNormals.Update()
# Sauvegarde des proprietes maillage GMSH pour calcul centerline
self.gmeshNode = vtk_to_np(surface_filter.GetOutput().GetPoints().GetData())
self.gmeshTable = vtk_to_np(surface_filter.GetOutput().GetPolys().GetData())
# The quadric has nasty discontinuities from the way the edges are generated
# so let's pass it though a CleanPolyDataFilter and merge any points which
# are coincident, or very close
self.outputMesh = vtk.vtkCleanPolyData()
self.outputMesh.SetInputConnection(surface_filter.GetOutputPort())
self.outputMesh.SetTolerance(0.001)
def vtkCreateFilterIsoContour(self):
""" Fonction pour le filtrage du contour"""
#-----------------------------------------
# Application d'un filtre de subdivision
#-----------------------------------------
self.subdiviseAneurysm = vtk.vtkLoopSubdivisionFilter()
self.subdiviseAneurysm.SetNumberOfSubdivisions(self.valFilter)
self.subdiviseAneurysm.SetInputConnection(self.aneurysmNormals.GetOutputPort())
#-----------------------------------------
# Application d'un filtre decimate et smooth
#-----------------------------------------
self.aneurysmDecimator = vtk.vtkDecimatePro()
self.aneurysmDecimator.SetInputConnection(self.subdiviseAneurysm.GetOutputPort())
self.aneurysmDecimator.SetTargetReduction(self.valDecimate)
self.aneurysmDecimator.PreserveTopologyOn()
self.smoothAneurysm = vtk.vtkSmoothPolyDataFilter()
self.smoothAneurysm.SetInputConnection(self.aneurysmDecimator.GetOutputPort())
self.smoothAneurysm.SetNumberOfIterations(self.valSmoothIter)
self.smoothAneurysm.SetRelaxationFactor(0.07)
self.smoothAneurysm.SetFeatureAngle(90)
self.smoothAneurysm.FeatureEdgeSmoothingOn()
#-----------------------------------------
# Sauvegarde des datas pour le calcul des centerlines
#-----------------------------------------
surface_filter = vtk.vtkDataSetSurfaceFilter()
surface_filter.SetInputConnection(self.smoothAneurysm.GetOutputPort())
meshNormals = vtk.vtkPolyDataNormals()
meshNormals.SetInputConnection(surface_filter.GetOutputPort())
meshNormals.Update()
self.surfNode = vtk_to_np(self.smoothAneurysm.GetOutput().GetPoints().GetData())
self.surfTable = vtk_to_np(self.smoothAneurysm.GetOutput().GetPolys().GetData())
#-----------------------------------------
# Realisation du mapper ppour affichage
#-----------------------------------------
self.aneurysmStripper = vtk.vtkStripper()
self.aneurysmStripper.SetInputConnection(self.smoothAneurysm.GetOutputPort())
self.aneurysmMapper = vtk.vtkPolyDataMapper()
self.aneurysmMapper.SetInputConnection(self.aneurysmStripper.GetOutputPort())
self.aneurysmMapper.ScalarVisibilityOff()
self.aneurysmMapper.SetScalarRange(self.min_pixel_value, self.max_pixel_value)
self.aneurysmMapper.SetScalarModeToUsePointData()
self.aneurysmMapper.SetLookupTable(self.bwLut)
def get(self, label):
"""
Get either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
Returns
-------
data : numpy.ndarray
Data stored under the given label.
"""
cell_data = self.vtk_data.GetCellData()
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
try:
return vtk_to_np(cell_data.GetArray(a))
except AttributeError:
vtk_array = cell_data.GetAbstractArray(a) # string array
point_data = self.vtk_data.GetPointData()
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
try:
return vtk_to_np(point_data.GetArray(a))
except AttributeError:
vtk_array = point_data.GetAbstractArray(a) # string array
try:
# string array
return np.array([
vtk_array.GetValue(i)
for i in range(vtk_array.GetNumberOfValues())
]).astype(str)
except UnboundLocalError:
raise ValueError(f'Array "{label}" not found.')
def vtkReadVolumAll(self, filename):
""" Chargement des fichiers images dicom"""
#-----------------------------------------
# Creation de la donnee volumique
#-----------------------------------------
self.vtkVolumAll = vtk.vtkVolume16Reader()
self.vtkVolumAll.SetDataDimensions(self.col, self.lig)
self.vtkVolumAll.SetDataByteOrderToLittleEndian()
self.vtkVolumAll.SetFilePrefix(filename)
self.vtkVolumAll.SetImageRange(1, self.nb_coupe)
self.vtkVolumAll.SetDataSpacing(self.pixel_spacing_x, self.pixel_spacing_y, self.slice_spacing)
self.SizeOfVolum = np.array([self.lig*self.pixel_spacing_x,self.col*self.pixel_spacing_y,self.slice_spacing*self.nb_coupe])
self.NumpyData = np.zeros((self.lig,self.col,self.nb_coupe),int)
for i in range(self.nb_coupe):
self.NumpyData[:,:,i] = vtk_to_np(self.vtkVolumAll.GetImage(i+1).GetPointData().GetArray(0)).reshape(self.lig,self.col)
def load(fname):
"""
Load from VTK rectilinear grid file.
Parameters
----------
fname : str or or pathlib.Path
Grid file to read. Valid extension is .vtr, which will be appended
if not given.
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
"""
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname) +
'.vtr')
comments = v.get_comments()
cells = np.array(v.vtk_data.GetDimensions()) - 1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3, 2).T
for i, c in enumerate([
v.vtk_data.GetXCoordinates(),
v.vtk_data.GetYCoordinates(),
v.vtk_data.GetZCoordinates()
]):
if not np.allclose(
vtk_to_np(c),
np.linspace(bbox[0][i], bbox[1][i], cells[i] + 1)):
raise ValueError('regular grid spacing violated')
return Grid(material=v.get('material').reshape(cells, order='F'),
size=bbox[1] - bbox[0],
origin=bbox[0],
comments=comments)