def volume (dataset) :
"Returns the volume of each cell in a dataset."
#def _cell_quality (dataset, quality) :
if not dataset : raise RuntimeError('Need a dataset to compute volume')
# create a dataset with only our array but the same geometry/topology
ds = dataset.NewInstance()
ds.UnRegister(None)
ds.CopyStructure(dataset.VTKObject)
filter = vtk.vtkCellSizeFilter()
filter.SetInputData(ds)
filter.ComputePointOff()
filter.ComputeLengthOff()
filter.ComputeAreaOff()
filter.Update()
varray = filter.GetOutput().GetCellData().GetArray("size")
varray.SetName("CellQuality")
ans = dsa.vtkDataArrayToVTKArray(varray, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = dsa.ArrayAssociation.CELL
return ans
def calc_cluster_sizes(self):
for cluster_idx, cluster_key in enumerate(self.clusters.keys()):
cluster_mesh = self.clusters[cluster_key]['mesh']
cell_size_filter = vtk.vtkCellSizeFilter()
cell_size_filter.SetInputData(cluster_mesh)
cell_size_filter.ComputeAreaOn()
cell_size_filter.ComputeSumOn()
cell_size_filter.Update()
cell_area_mesh = cell_size_filter.GetOutput()
total_cluster_area = vtk_to_numpy(
cell_area_mesh.GetFieldData().GetAbstractArray('Area'))
self.clusters[cluster_key]['area'] = total_cluster_area[0]
def compute_cell_sizes(dataset, length=False, area=True, volume=True):
"""This filter computes sizes for 1D (length), 2D (area) and 3D (volume)
cells.
Parameters
----------
length : bool
Specify whether or not to compute the length of 1D cells.
area : bool
Specify whether or not to compute the area of 2D cells.
volume : bool
Specify whether or not to compute the volume of 3D cells.
"""
alg = vtk.vtkCellSizeFilter()
alg.SetInputDataObject(dataset)
alg.SetComputeArea(area)
alg.SetComputeVolume(volume)
alg.SetComputeLength(length)
alg.SetComputeVertexCount(False)
alg.Update()
return _get_output(alg)
stdParentBaselineWSS = parentBaselineWssWithin1cm.std()
meanParentAdjustedWSS = parentAdjustedWssWithin1cm.mean()
stdParentAdjustedWSS = parentAdjustedWssWithin1cm.std()
baselineLowShearThreshold = meanParentBaselineWSS - stdParentBaselineWSS
baselineLowShear = (baselineWSS < baselineLowShearThreshold).astype(np.uint8)
adjustedLowShearThreshold = meanParentAdjustedWSS - stdParentAdjustedWSS
adjustedLowShear = (adjustedWSS < adjustedLowShearThreshold).astype(np.uint8)
baselineLowShearArrayName = f'LowShearArea_{baselineTag}'
adjustedLowShearArrayName = f'LowShearArea_{adjustedTag}'
aneurysm_dsa.PointData.append(baselineLowShear, baselineLowShearArrayName)
aneurysm_dsa.PointData.append(adjustedLowShear, adjustedLowShearArrayName)
#%% plot lsas
cellSizer = vtk.vtkCellSizeFilter()
cellSizer.SetInputData(aneurysm)
cellSizer.ComputeLengthOff()
cellSizer.ComputeVertexCountOff()
cellSizer.ComputeVolumeOff()
cellSizer.Update()
aneurysm = cellSizer.GetOutput()
aneurysm_dsa = wdo(aneurysm)
cellAreas = aneurysm_dsa.CellData['Area'] # in mm2
aneurysmArea = cellAreas.sum()
baselineLsaSurface = vtkext.pyvtk.threshold(aneurysm, baselineLowShearArrayName,
lo=1, allScalars=True)
baselineLsaSurface_dsa = wdo(baselineLsaSurface)
baselineLSA = baselineLsaSurface_dsa.CellData['Area'].sum()/aneurysmArea
def measure_average_edge_length(self):
print('Average edge length')
size = vtk.vtkCellSizeFilter()
size.SetInputConnection(self.mesh.GetOutputPort())
size.Update()
print(size)