def RequestData(self, vtkself, request, inputs, output):
vtkin = vtkImageData.GetData(inputs[0])
vtkout = vtkImageData.GetData(output)
vtkout.CopyStructure(vtkin)
indata = dsa.WrapDataObject(vtkin)
outdata = dsa.WrapDataObject(vtkout)
for k in indata.PointData.keys():
arr = indata.PointData[k]
arr *= self.params['a']
outdata.PointData.append(arr, "{}*{}".format(k, self.params['a']))
def getSlice(vol, volShape, y):
# Create slice
slicer = Slice(Input=vol)
slicer.SliceType = 'Plane'
slicer.SliceOffsetValues = [0.0]
slicer.Crinkleslice = 0
slicer.Triangulatetheslice = 1
slicer.Mergeduplicatedpointsintheslice = 1
# Get slice through chosen Y value
slicer.SliceType.Origin = [0, y, 0]
# Get Y slices
slicer.SliceType.Normal = [0, 1, 0]
# Update pipeline
slicer.UpdatePipeline()
# Convert slice to numpy array
slice_numpy = sm.Fetch(slicer)
slice_numpy = dsa.WrapDataObject(slice_numpy)
slice_numpy = slice_numpy.PointData[0]
# Re-shape vector into 2D slice
# Re-shaping with transpose because the other way messes up the layout
# Should probably read into how striding works in NumPy...
slice_numpy = np.array(slice_numpy).reshape((volShape[2], volShape[0])).T
# Convert from int16 back to LVF as float
slice_numpy = slice_numpy.astype('float32') / 1000
return slice_numpy
def extractVTK(vtk_path, clipVal):
vol = XMLImageDataReader(FileName=vtk_path)
vol.UpdatePipeline()
# Get extents (voxels) and bounds (mm)
extents = vol.GetDataInformation().GetExtent()
bounds = vol.GetDataInformation().GetBounds()
volShape = np.array(extents[1::2]) + 1
# Get slices
slice_jets = getSlice(vol, volShape, y=-3)
slice_impingement = getSlice(vol, volShape, y=1)
slice_near = getSlice(vol, volShape, y=5)
slice_far = getSlice(vol, volShape, y=9)
slices = [slice_jets, slice_impingement, slice_near, slice_far]
# Get smoothed surface
surface = getSurface(vol, clipVal)
# Get grid information as vectors for X/Y/Z (mm)
grid = [None] * 3
grid[0] = np.linspace(bounds[0], bounds[1], volShape[0])
grid[1] = np.linspace(bounds[2], bounds[3], volShape[1])
grid[2] = np.linspace(bounds[4], bounds[5], volShape[2])
# Get dx/dy/dz
dx = np.abs(grid[0][1] - grid[0][0])
dy = np.abs(grid[1][1] - grid[1][0])
dz = np.abs(grid[2][1] - grid[2][0])
# Get volume mass
mass = dsa.WrapDataObject(sm.Fetch(vol)).PointData[0].sum()
mass *= (dx * dy * dz)
return slices, grid, surface, mass
def asdf_to_mbds(self, tree, mbds):
def shape_3d(shape):
if len(shape) == 3:
return shape
elif len(shape) == 2:
return (1, ) + shape
elif len(shape) == 1:
return (1, 1) + shape
else:
return (1, 1, np.prod(shape))
# mbds = vtk.MultiBlockDataSet()
for (i, k) in enumerate(tree):
obj = tree[k]
# print(obj)
if isinstance(obj, dict):
child_mbds = vtk.vtkMultiBlockDataSet()
self.asdf_to_mbds(obj, child_mbds)
mbds.SetBlock(i, child_mbds)
mbds.GetMetaData(i).Set(vtk.vtkCompositeDataSet.NAME(), k)
elif hasattr(obj, 'shape'):
vtkdata = vtk.vtkImageData()
dim = tuple(reversed(shape_3d(obj.shape[0:-1])))
arr = obj[:]
arr.shape = (np.prod(dim), arr.shape[-1])
vtkdata.SetDimensions(dim)
data = dsa.WrapDataObject(vtkdata)
data.PointData.append(arr, k)
mbds.SetBlock(i, vtkdata)
mbds.GetMetaData(i).Set(vtk.vtkCompositeDataSet.NAME(), k)
def h5_to_mbds(self, group, mbds):
def shape_3d(shape):
if len(shape) == 3:
return shape
elif len(shape) == 2:
return (1,) + shape
elif len(shape) == 1:
return (1, 1) + shape
else:
return (0, 0, 0)
# mbds = vtk.MultiBlockDataSet()
for (i, k) in enumerate(group):
obj = group[k]
# print(obj)
if isinstance(obj, h5py.Group):
child_mbds = vtk.vtkMultiBlockDataSet()
self.h5_to_mbds(obj, child_mbds)
mbds.SetBlock(i, child_mbds)
mbds.GetMetaData(i).Set(vtk.vtkCompositeDataSet.NAME(), k)
elif isinstance(obj, h5py.Dataset):
vtkdata = vtk.vtkImageData()
shape = tuple(reversed(shape_3d(obj.shape)))
# print(shape)
vtkdata.SetDimensions(shape)
data = dsa.WrapDataObject(vtkdata)
arr = obj[:].flatten()
# print(arr)
data.PointData.append(arr, k)
mbds.SetBlock(i, vtkdata)
mbds.GetMetaData(i).Set(vtk.vtkCompositeDataSet.NAME(), k)
def generateSinData(self, vtkdata, s):
params = self.params
t = np.arange(params['t0'], params['t1'], 1.0/params['fs'])
print('t: {}'.format(t))
x = np.sin(2*np.pi*params['f']*t)
data = dsa.WrapDataObject(vtkdata)
vtkdata.SetDimensions((x.size, 1, 1))
vtkdata.SetOrigin((params['t0'], 0, 0))
vtkdata.SetSpacing(1/params['fs'], 0, 0)
data.PointData.append(x*s, 'sin')
data.PointData.append(t, 't')
def RequestData(self, vtkself, request, inputs, output):
params = self.params
N = int((params['t1'] - params['t0']) * params['fs'])
vtkdata = output.GetInformationObject(0).Get(vtkDataObject.DATA_OBJECT())
t = np.arange(params['t0'], params['t1'], 1.0/params['fs'])
x = np.sin(2*np.pi*params['f']*t)
data = dsa.WrapDataObject(vtkdata)
vtkdata.SetDimensions((x.size, 1, 1))
vtkdata.SetOrigin((params['t0'], 0, 0))
vtkdata.SetSpacing(1/params['fs'], 0, 0)
data.PointData.append(x, 'sin')
def point_data(self):
vtk_object = sm.Fetch(self.filter)
vtk_object = dsa.WrapDataObject(vtk_object)
pd_df = pd.DataFrame()
for key in self.point_keys:
temp_dataset = np.array(vtk_object.PointData[key]).transpose()
if len(temp_dataset.shape) != 1:
# The dataset is a vector:
for idx, vector_element in enumerate(temp_dataset):
new_key = f"{key}{self.vector_keys[idx]}"
pd_df[new_key] = vector_element
else:
pd_df[key] = temp_dataset
return pd_df.dropna()
def data_values(self):
_vtk_object = sm.Fetch(self.vtk_file)
_vtk_object = dsa.WrapDataObject(_vtk_object)
return _vtk_object.PointData
def values(self):
_vtk_object = sm.Fetch(self.current_array)
_vtk_object = dsa.WrapDataObject(_vtk_object)
return _vtk_object.PointData
import numpy as np
from paraview.vtk.numpy_interface import dataset_adapter as dsa
# Script to get total volume of a thresholded tumor of all timesteps
# Pipeline: Input -> Threshold -> GroupTimeSteps -> ProgrammableFilter with this script
# Output: Outputs the #cells and the total volume of these cells per time-step
input = inputs[0]
print("Found input with keys ", dsa.WrapDataObject(input).PointData.keys())
if input.IsA("vtkCompositeDataSet"):
numTimesteps = input.GetNumberOfBlocks()
# process block
for i in range(numTimesteps):
print("Process timestep ", i)
# get block
block = input.GetBlock(
i) # type vtkCommonDataModelPython.vtkUnstructuredGrid
block_np = dsa.WrapDataObject(
input.GetBlock(i)
) # type paraview.vtk.numpy_interface.dataset_adapter.UnstructuredGrid
# get volumes
numTets = block.GetNumberOfCells()
volumeArray = np.empty(numTets, dtype=np.float64)
for j in range(numTets):
cell = block.GetCell(j)
p1 = block.GetPoint(cell.GetPointId(0))
p2 = block.GetPoint(cell.GetPointId(1))
p3 = block.GetPoint(cell.GetPointId(2))
p4 = block.GetPoint(cell.GetPointId(3))
volumeArray[j] = abs(vtk.vtkTetra.ComputeVolume(p1, p2, p3, p4))
def field_keys(self):
vtk_object = sm.Fetch(self.filter)
vtk_object = dsa.WrapDataObject(vtk_object)
return vtk_object.FieldData.keys()
def point_keys(self):
vtk_object = sm.Fetch(self.filter)
vtk_object = dsa.WrapDataObject(vtk_object)
return vtk_object.PointData.keys()
def cell_keys(self):
vtk_object = sm.Fetch(self.filter)
vtk_object = dsa.WrapDataObject(vtk_object)
return vtk_object.CellData.keys()
zSlice.SliceOffsetValues = [0.0]
zSlice.SliceType.Origin = [0.0, 0.0, spanwise_locations_m[i]]
zSlice.SliceType.Normal = [0.0, 0.0, 1.0]
UpdatePipeline()
sortedLine = PlotOnSortedLines(Input=zSlice)
UpdatePipeline()
mergeBlocks2 = MergeBlocks(Input=sortedLine)
UpdatePipeline()
# stick data into useful array
rawData = servermanager.Fetch(mergeBlocks2)
data = dsa.WrapDataObject(rawData)
results[i] = {}
results[i]['spanwise_pctg'] = spanwise_locations_pctg[i]
results[i]['spanwise_m'] = spanwise_locations_m[i]
results[i]['p'] = data.PointData['p']
results[i]['y'] = data.Points[:, 1]
v_local = np.linalg.norm([omega * spanwise_locations_m[i], 15])
print(v_local)
results[i]['cp'] = np.zeros_like(results[i]['p'])
results[i]['y/x'] = np.zeros_like(results[i]['y'])
results[i]['cp'] = [(p - p_inf) / (0.5 * rho_inf * v_local ** 2) for p in results[i]['p']]