def get_tilt_angles(dataobject):
# Get the tilt angles array
do = dsa.WrapDataObject(dataobject)
rawarray = do.FieldData.GetArray('tilt_angles')
vtkarray = dsa.vtkDataArrayToVTKArray(rawarray, do)
vtkarray.Association = dsa.ArrayAssociation.FIELD
return vtkarray
def get_scalars(dataobject):
do = dsa.WrapDataObject(dataobject)
# get the first
rawarray = do.PointData.GetScalars()
vtkarray = dsa.vtkDataArrayToVTKArray(rawarray, do)
vtkarray.Association = dsa.ArrayAssociation.POINT
return vtkarray
def pointIsNear(locations, distance, inputs):
array = vtk.vtkDoubleArray()
array.SetNumberOfComponents(3)
array.SetNumberOfTuples(len(locations))
for i in range(len(locations)):
array.SetTuple(i, locations[i])
node = vtk.vtkSelectionNode()
node.SetFieldType(vtk.vtkSelectionNode.POINT)
node.SetContentType(vtk.vtkSelectionNode.LOCATIONS)
node.GetProperties().Set(vtk.vtkSelectionNode.EPSILON(), distance)
node.SetSelectionList(array)
selection = vtk.vtkSelection()
selection.AddNode(node)
from vtk.vtkFiltersExtraction import vtkExtractSelectedLocations
pointsNear = vtkExtractSelectedLocations()
pointsNear.SetInputData(0, inputs[0].VTKObject)
pointsNear.SetInputData(1, selection)
pointsNear.Update()
extractedPoints = pointsNear.GetOutput()
numPoints = inputs[0].GetNumberOfPoints()
result = np.zeros((numPoints, ), dtype=np.int8)
extracted = dsa.WrapDataObject(extractedPoints)
pointIds = extracted.PointData.GetArray('vtkOriginalPointIds')
result[pointIds] = 1
import vtk.util.numpy_support as np_s
vtkarray = np_s.numpy_to_vtk(result, deep=True)
return dsa.vtkDataArrayToVTKArray(vtkarray)
def get_scalars(dataobject):
do = dsa.WrapDataObject(dataobject)
# get the first
rawarray = do.PointData.GetScalars()
vtkarray = dsa.vtkDataArrayToVTKArray(rawarray, do)
vtkarray.Association = dsa.ArrayAssociation.POINT
return vtkarray
def cellContainsPoint(inputs, locations):
array = vtk.vtkDoubleArray()
array.SetNumberOfComponents(3)
array.SetNumberOfTuples(len(locations))
for i in range(len(locations)):
array.SetTuple(i, locations[i])
node = vtk.vtkSelectionNode()
node.SetFieldType(vtk.vtkSelectionNode.CELL)
node.SetContentType(vtk.vtkSelectionNode.LOCATIONS)
node.SetSelectionList(array)
selection = vtk.vtkSelection()
selection.AddNode(node)
from vtk.vtkFiltersExtraction import vtkExtractSelectedLocations
cellsNear = vtkExtractSelectedLocations()
cellsNear.SetInputData(0, inputs[0].VTKObject)
cellsNear.SetInputData(1, selection)
cellsNear.Update()
extractedCells = cellsNear.GetOutput()
numCells = inputs[0].GetNumberOfCells()
result = np.zeros((numCells, ), dtype=np.int8)
extracted = dsa.WrapDataObject(extractedCells)
cellIds = extracted.CellData.GetArray('vtkOriginalCellIds')
if isinstance(cellIds, dsa.VTKCompositeDataArray):
for a in cellIds.GetArrays():
result[a] = 1
else:
result[cellIds] = 1
import vtk.util.numpy_support as np_s
vtkarray = np_s.numpy_to_vtk(result, deep=True)
return dsa.vtkDataArrayToVTKArray(vtkarray)
def get_tilt_angles(dataobject):
# Get the tilt angles array
do = dsa.WrapDataObject(dataobject)
rawarray = do.FieldData.GetArray('tilt_angles')
vtkarray = dsa.vtkDataArrayToVTKArray(rawarray, do)
vtkarray.Association = dsa.ArrayAssociation.FIELD
return vtkarray
def getEdges(pd):
""" Extracts edges from polydata with correct point ids. """
# Store the original point ids
idf = v.vtkIdFilter()
idf.PointIdsOn()
idf.SetIdsArrayName('PointIds')
idf.SetInputData(pd.VTKObject)
# Extract the edges
edgeFilter = v.vtkExtractEdges()
edgeFilter.SetInputConnection(idf.GetOutputPort())
edgeFilter.Update()
# Now make a new cell array mapping to the old ids
edges = v.vtkCellArray()
badEdges = edgeFilter.GetOutput().GetLines()
badEdges.InitTraversal()
origIds = edgeFilter.GetOutput().GetPointData().GetArray('PointIds')
ptIds = v.vtkIdList()
while (badEdges.GetNextCell(ptIds)):
edges.InsertNextCell(2)
edges.InsertCellPoint(int(origIds.GetTuple1(ptIds.GetId(0))))
edges.InsertCellPoint(int(origIds.GetTuple1(ptIds.GetId(1))))
# Convert the cell array into a numpy array
conn = dsa.vtkDataArrayToVTKArray(edges.GetData()).reshape(
(edges.GetNumberOfCells(), 3))[:, 1:]
return conn
def get_scalars(dataobject, name=None):
do = dsa.WrapDataObject(dataobject)
if name is not None:
rawarray = do.PointData.GetAbstractArray(name)
else:
rawarray = do.PointData.GetScalars()
vtkarray = dsa.vtkDataArrayToVTKArray(rawarray, do)
vtkarray.Association = dsa.ArrayAssociation.POINT
return vtkarray
def RequestData(self, request, inInfo, outInfo):
info = inInfo[0].GetInformationObject(0)
inp = dsa.WrapDataObject(vtk.vtkDataSet.GetData(info))
if self.Cache is not None:
self.DoParticle(self.Cache, inp)
# print('data request')
else:
# First time step. Initialize.
# This is where we will store the coordinates of all points
# at all times
self.OutputPoints = np.zeros(
(len(self.TimeValues) * self.NumPts, 3))
# First time step uses the seed locations as the particle points
pts = vtk.vtkPoints()
pts.DeepCopy(self.Source.GetOutput().GetPoints())
self.Points = dsa.vtkDataArrayToVTKArray(pts.GetData())
self.OutputPoints[0:self.NumPts, :] = self.Points
# This will be a point array showing the time value of each
# output point. This is necessary to differentiate output
# points since we store all timesteps in the output.
self.TimeValuesArray = np.empty(len(self.TimeValues) * self.NumPts)
self.TimeValuesArray[0:self.NumPts] = self.TimeValues[0]
if self.UpdateTimeIndex < len(self.TimeValues) - 1:
# If we are not done, ask the pipeline to re-execute us.
self.UpdateTimeIndex += 1
request.Set(
vtk.vtkStreamingDemandDrivenPipeline.CONTINUE_EXECUTING(), 1)
c = inp.NewInstance()
c.ShallowCopy(inp.VTKObject)
c = dsa.WrapDataObject(c)
self.Cache = c
else:
# Stop execution
request.Remove(
vtk.vtkStreamingDemandDrivenPipeline.CONTINUE_EXECUTING())
# Reset for next potential execution.
self.UpdateTimeIndex = 0
# Create output
outputPts = dsa.numpyTovtkDataArray(self.OutputPoints)
pts = vtk.vtkPoints()
pts.SetData(outputPts)
output = dsa.WrapDataObject(
vtk.vtkUnstructuredGrid.GetData(outInfo))
output.SetPoints(pts)
tvs = dsa.numpyTovtkDataArray(self.TimeValuesArray)
tvs.SetName("Time Values")
output.GetPointData().SetScalars(tvs)
# Clean up
self.Cache = None
self.OutputPoints = None
self.Points = None
return 1
def wrap_vtk_array(a):
if isinstance(a, vtk.vtkIdList):
return _idlist_to_numpy(a)
if isinstance(a, (vtk.vtkStringArray, vtk.vtkUnicodeStringArray)):
return _string_to_numpy(a)
if isinstance(a, vtk.vtkVariantArray):
return _variant_to_numpy(a)
if isinstance(a, vtk.vtkDataArray):
return dsa.vtkDataArrayToVTKArray(a)
raise ValueError('Unsupported array type: {0}'.format(type(a)))
def testNumpyReduce(self):
"Test that reducing methods return scalars."
vtk_array = vtk.vtkLongArray()
for i in range(0, 10):
vtk_array.InsertNextValue(i)
numpy_vtk_array = dsa.vtkDataArrayToVTKArray(vtk_array)
s = numpy_vtk_array.sum()
self.assertEqual(s, 45)
self.assertTrue(isinstance(s, numpy.signedinteger))
m = numpy_vtk_array.mean()
self.assertEqual(m, 4.5)
self.assertTrue(isinstance(m, numpy.floating))
def testNumpyReduce(self):
"Test that reducing methods return scalars."
vtk_array = vtk.vtkLongArray()
for i in range(0, 10):
vtk_array.InsertNextValue(i)
numpy_vtk_array = dsa.vtkDataArrayToVTKArray(vtk_array)
s = numpy_vtk_array.sum()
self.assertEqual(s, 45)
self.assertEqual(type(s), numpy.int64)
m = numpy_vtk_array.mean()
self.assertEqual(m, 4.5)
self.assertEqual(type(m), numpy.float64)
def triangulate(sphereXyz):
"""
Generates a triangle mesh for a spherical point cloud.
"""
sphereXyz = np.around(sphereXyz, decimals=2)
sphereArr = dsa.numpyTovtkDataArray(sphereXyz, name='SpherePts')
pts = v.vtkPoints()
pts.SetData(sphereArr)
sphere = v.vtkPolyData()
sphere.SetPoints(pts)
# Store the original point ids
idf = v.vtkIdFilter()
idf.SetIdsArrayName('PointIds')
idf.PointIdsOn()
idf.SetInputData(sphere)
# Delaunay3D to make a convex hull
d3d = v.vtkDelaunay3D()
d3d.SetInputConnection(idf.GetOutputPort())
# Extract the surface
surf = v.vtkDataSetSurfaceFilter()
surf.SetInputConnection(d3d.GetOutputPort())
surf.Update()
# Now make a new cell array mapping to the old ids
polyCells = v.vtkCellArray()
sphereCells = surf.GetOutput().GetPolys()
sphereCells.InitTraversal()
origIds = surf.GetOutput().GetPointData().GetArray('PointIds')
ptIds = v.vtkIdList()
while (sphereCells.GetNextCell(ptIds)):
polyCells.InsertNextCell(3)
polyCells.InsertCellPoint(int(origIds.GetTuple1(ptIds.GetId(0))))
polyCells.InsertCellPoint(int(origIds.GetTuple1(ptIds.GetId(1))))
polyCells.InsertCellPoint(int(origIds.GetTuple1(ptIds.GetId(2))))
connectivity = dsa.vtkDataArrayToVTKArray(polyCells.GetData())
return connectivity
def main(argv):
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from vtk.numpy_interface import algorithms as algs
import numpy as np
### get parameters
import os
if not os.path.exists(OD):
os.makedirs(OD)
print '!!!Output to DIR: ',OD
if not read_fields_from_file:
### Readin stage
# using parallel openfoam reader
ofr = vtk.vtkPOpenFOAMReader()
# set reader's options
ofr.SetFileName(ID+IF)
print '!!!open file: ',ID+IF
ofr.SetDecomposePolyhedra(0)
ofr.CacheMeshOn()
ofr.SetCreateCellToPoint(0)
ofr.DisableAllCellArrays()
ofr.SetCellArrayStatus(fieldname,1)
ofr.Update()
# VTKArray is same as numpy array
times = dsa.vtkDataArrayToVTKArray( ofr.GetTimeValues() ,ofr)
# select the timestep between t0 and tf
times = [t for t in times if t>=t0 and t<=tf]
print '!!!available time steps: ',times
N = len(times)
np.save(times_filename,times)
# using CellQuality to get cell's volumes as weight
cq = vtk.vtkCellQuality()
cq.SetInputConnection(0,ofr.GetOutputPort(0))
cq.SetQualityMeasureToVolume()
cq.Update()
# cq is a composite dataset so I need GetBlock(0)
geom = cq.GetOutputDataObject(0).GetBlock(0)
# get volumes of cells V, size = L (number of cells)
V = np.copy(dsa.WrapDataObject(geom).CellData['CellQuality'])
# normalize it as weight
Vtotal = sum(V)
V /= Vtotal
# delete all other CellDataArray in geom DataSet, preserve its mesh structure and topology structure
for i in range(geom.GetCellData().GetNumberOfArrays()):
geom.GetCellData().RemoveArray(0)
# add volume weight to it for saving
geom.GetCellData().AddArray(dsa.numpyTovtkDataArray(V,'vol_weight'))
# using *.vtu file format to save the vol_weight
ugw = vtk.vtkXMLUnstructuredGridWriter()
ugw.SetInputDataObject(geom)
print '!!!Output vol_weight to file: ',geom_filename
ugw.SetFileName(geom_filename)
# using binary format
ugw.SetDataModeToBinary()
# enable compression
ugw.SetCompressorTypeToZLib()
# write to the file
ugw.Write()
# disconnect cq and ofr in order to isolate this dataset object from Update()
cq.RemoveAllInputConnections(0)
L = V.size # number of cells
N = len(times) #number of timesteps
# vector data is larger in size
if field_is_vector == True:
fields = np.zeros([N,L,3])
else:
fields = np.zeros([N,L])
pipepout = ofr
for i in range(N):
t = times[i]
print '!!!reading time:{}'.format(t)
# set time value
pipepout.GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_TIME_STEP(),t)
# read in field data of new timestep
pipepout.Update()
#
d = dsa.WrapDataObject(pipepout.GetOutput().GetBlock(0))
print '!!!reading field:{}'.format(fieldname)
field = d.CellData[fieldname]
# get the first component of composite dataset, it is the internalField
fields[i]=np.copy(field)
# write data to file
print '!!!write field data to file:',fields_filename
np.savez(fields_filename,fields)
else: #read fields from file
fields = np.load(fields_filename)['arr_0']
ugr = vtk.vtkXMLUnstructuredGridReader()
ugr.SetFileName(geom_filename)
ugr.Update()
geom = ugr.GetOutputDataObject(0)
V = np.copy(dsa.WrapDataObject(geom).CellData['vol_weight'])
times = np.load(times_filename)
assert times.shape[0] == fields.shape[0]
assert fields.shape[1] == V.shape[0]
N = times.shape[0]
L = fields.shape[1]
print 'Read in dataset complete'
### POD section
# calculate average
field_avg = np.average(fields, axis=0)
if subtractAvg:
fields = fields - field_avg
import modred as mr
if do_POD:
# if field is a vector, reshape the fields and corresponding volument weight
if field_is_vector:
shp_vec = fields.shape
shp_flat = (fields.shape[0],fields.shape[1]*fields.shape[2])
fields = fields.reshape(shp_flat)
V = np.tile(V,shp_vec[2])
# POD
print '!!!Doing POD analysis'
modes, eigen_vals, eigen_vecs, correlation_mat = mr.compute_POD_matrices_snaps_method(fields.T,range(M),inner_product_weights=V,return_all=True)
# if field is a vector, reshape the output matrix
if field_is_vector:
fields = fields.reshape(shp_vec)
modes = np.asarray(modes).T.reshape((modes.shape[1],shp_vec[1],shp_vec[2]))
V = V[:shp_vec[1]]
if output_correlation_matrix:
print "!!!output POD correlation matrix",POD_cm_filename
np.savetxt(POD_cm_filename,correlation_mat,delimiter=',')
if output_POD_temporal_modes:
print "!!!output POD temporal modes",POD_tm_filename
# output temporal modes
singular_vals = eigen_vals**0.5
POD_mode_energy_normalized = eigen_vals/correlation_mat.trace()[0,0]
cumsum_POD_mode_energy_normalized = np.cumsum(POD_mode_energy_normalized)
# generate header string
header_str = 'temporal modes\n'
header_str += 'time,eigen value,singular value,normalized eigen value,accumulated normalized eigen value'
for i in range(N-1):
header_str += ',Mode{}'.format(i)
header_str += '\n'
for i in range(N-1):
header_str += ',SV ={}'.format(singular_vals[i])
header_str += '\n'
for i in range(N-1):
header_str += ',EV ={}'.format(eigen_vals[i])
header_str += '\n'
for i in range(N-1):
header_str += ',NEnergy ={}'.format(POD_mode_energy_normalized[i])
header_str += '\n'
for i in range(N-1):
header_str += ',CumsumEnergy ={}'.format(cumsum_POD_mode_energy_normalized[i])
header_str += '\n'
np.savetxt(POD_tm_filename, \
np.c_[times, \
eigen_vecs], \
delimiter = ',', \
header = header_str)
if output_POD_spatial_modes:
print "!!!output POD spatial Modes to ",POD_sm_filename
#output to xml vtk unstructured grid file
ugcd = geom.GetCellData()
ugcd.Reset()
ugcd.CopyAllOff()
for i in range(ugcd.GetNumberOfArrays()):
ugcd.RemoveArray(0)
# import POD mode
for i in range(M):
ugcd.AddArray(dsa.numpyTovtkDataArray(modes[i],prefix+'_POD_mode_{}_{}'.format(fieldname,i)))
# add average field
ugcd.AddArray(dsa.numpyTovtkDataArray(field_avg,'field_{}_avg'.format(fieldname)))
ugw = vtk.vtkXMLUnstructuredGridWriter()
ugw.SetInputDataObject(geom)
ugw.SetFileName(POD_sm_filename)
ugw.Write()
if doReconstruction:
print "!!! do Reconstrution with {} POD modes at time {}".format(MR,ReconTime)
#get an empty mesh
ugcd = geom.GetCellData()
ugcd.Reset()
ugcd.CopyAllOff()
for i in range(ugcd.GetNumberOfArrays()):
ugcd.RemoveArray(0)
# reconstruct from first MR POD modes
#
ReconN = np.searchsorted(times,ReconTime)
print "!!!actually, reconstruction is done at time {} rather than time {}".format(times[ReconN],ReconTime)
recon_field = np.einsum("i...,i,i",modes[:MR],eigen_vals[:MR]**0.5,np.asarray(eigen_vecs)[ReconN,:MR])+field_avg;
ugcd.AddArray(dsa.numpyTovtkDataArray(recon_field,prefix+'_POD_{}_Reconstructed_{}_{}'.format(MR,fieldname,ReconTime)))
ugw = vtk.vtkXMLUnstructuredGridWriter()
ugw.SetInputDataObject(geom)
ugw.SetFileName(POD_reconstruction_filename)
ugw.Write()
if do_DMD:
print "!!!Begin to calculate DMD modes"
# if field is a vector, reshape the fields and corresponding volument weight
if field_is_vector:
shp_vec = fields.shape
shp_flat = (fields.shape[0],fields.shape[1]*fields.shape[2])
fields = fields.reshape(shp_flat)
V = np.tile(V,shp_vec[2])
# DMD, I do not know which mode is important, so I have to discard modes_
modes_, ritz_vals, mode_norms, build_coeffs = mr.compute_DMD_matrices_snaps_method(fields.T,[],inner_product_weights=V,return_all=True)
# if field is a vector, reshape the fields, V and output matrix
if field_is_vector:
fields = fields.reshape(shp_vec)
V = V[:shp_vec[1]]
# sorting
eorder = np.argsort(mode_norms)[::-1]
# re-order the outputs
ritz_vals = ritz_vals[eorder]
mode_norms = mode_norms[eorder]
build_coeffs = build_coeffs[:,eorder]
#build the DMD_modes
DMD_modes = np.einsum('ijk,il->ljk', fields,build_coeffs[:,:M_DMD])
if output_DMD_info:
print "!!!output DMD info to :",DMD_info_filename
# output modes info
header_str = 'DMD modes info\n'
header_str += 'ritz_vals.real,ritz_vals.imag,growth_rate, frequency, mode_norms\n'
header_str += r'AU,AU,1/s, Hz, AU'
dt = np.average(times[1:]-times[:-1]) #time step
np.savetxt(DMD_info_filename, \
np.c_[ np.real(ritz_vals), \
np.imag(ritz_vals), \
np.log(np.abs(ritz_vals))/dt, \
np.angle(ritz_vals)/dt, \
mode_norms], \
delimiter = ',', \
header = header_str)
if output_DMD_build_coeffs:
print "!!!output DMD build coeffs. to :",DMD_build_coeffs_filename
np.savez(DMD_build_coeffs_filename, build_coeffs)
if output_DMD_spatial_modes:
print "!!!output DMD info to :",DMD_sm_filename
#output to xml vtk unstructured grid file
ugcd = geom.GetCellData()
ugcd.Reset()
ugcd.CopyAllOff()
for i in range(ugcd.GetNumberOfArrays()):
ugcd.RemoveArray(0)
#import pi
from numpy import pi
for i in range(M_DMD):
ugcd.AddArray(dsa.numpyTovtkDataArray(np.abs(DMD_modes[i]),prefix+'_DMD_mode_abs_{}_{}'.format(fieldname,i)))
ugcd.AddArray(dsa.numpyTovtkDataArray(np.angle(DMD_modes[i])*180/pi,prefix+'_DMD_mode_angle_{}_{}'.format(fieldname,i)))
ugw = vtk.vtkXMLUnstructuredGridWriter()
ugw.SetInputDataObject(geom)
ugw.SetFileName(DMD_sm_filename)
ugw.Write()
def numpy2vtk(arr,dset,aa):
vtkdata = dsa.numpyTovtkDataArray(arr)
vtkarray = dsa.vtkDataArrayToVTKArray(vtkdata,dset)
vtkarray.Association = aa
return vtkarray
def GetLines(self):
"""Returns the lines as a 1D VTKArray instance."""
if not self.VTKObject.GetLines():
return None
return dsa.vtkDataArrayToVTKArray(self.VTKObject.GetLines().GetData(),
self)