def _test(self, fname):
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(VTK_DATA_ROOT + fname)
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(reader.GetOutputPort())
elev.SetLowPoint(-0.05, 0.05, 0)
elev.SetHighPoint(0.05, 0.05, 0)
grad = vtk.vtkGradientFilter()
grad.SetInputConnection(elev.GetOutputPort())
grad.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS, "Elevation")
grad.Update()
vals = (10, 0, 0)
for i in range(3):
r = grad.GetOutput().GetPointData().GetArray("Gradients").GetRange(i)
self.assertTrue(abs(r[0] - vals[i]) < 1E-4)
self.assertTrue(abs(r[1] - vals[i]) < 1E-4)
elev.SetLowPoint(0.05, -0.05, 0)
elev.SetHighPoint(0.05, 0.05, 0)
grad.Update()
vals = (0, 10, 0)
for i in range(3):
r = grad.GetOutput().GetPointData().GetArray("Gradients").GetRange(i)
self.assertTrue(abs(r[0] - vals[i]) < 1E-4)
self.assertTrue(abs(r[1] - vals[i]) < 1E-4)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkGradientFilter(), 'Processing.',
('vtkDataSet',), ('vtkDataSet',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def test_contours(self):
cell = vtk.vtkUnstructuredGrid()
cell.ShallowCopy(self.Cell)
np = self.Cell.GetNumberOfPoints()
ncomb = pow(2, np)
scalar = vtk.vtkDoubleArray()
scalar.SetName("scalar")
scalar.SetNumberOfTuples(np)
cell.GetPointData().SetScalars(scalar)
incorrectCases = []
for i in range(1, ncomb - 1):
c = Combination(np, i)
for p in range(np):
scalar.SetTuple1(p, c[p])
gradientFilter = vtk.vtkGradientFilter()
gradientFilter.SetInputData(cell)
gradientFilter.SetInputArrayToProcess(0, 0, 0, 0, 'scalar')
gradientFilter.SetResultArrayName('grad')
gradientFilter.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(gradientFilter.GetOutputPort())
contourFilter.SetNumberOfContours(1)
contourFilter.SetValue(0, 0.5)
contourFilter.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputConnection(contourFilter.GetOutputPort())
normalsFilter.SetConsistency(0)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetSplitting(0)
calcFilter = vtk.vtkArrayCalculator()
calcFilter.SetInputConnection(normalsFilter.GetOutputPort())
calcFilter.SetAttributeTypeToPointData()
calcFilter.AddVectorArrayName('grad')
calcFilter.AddVectorArrayName('Normals')
calcFilter.SetResultArrayName('dir')
calcFilter.SetFunction('dot(grad,Normals)')
calcFilter.Update()
out = vtk.vtkUnstructuredGrid()
out.ShallowCopy(calcFilter.GetOutput())
numPts = out.GetNumberOfPoints()
if numPts > 0:
dirArray = out.GetPointData().GetArray('dir')
for p in range(numPts):
if (dirArray.GetTuple1(p) >
0.0): # all normals are reversed
incorrectCases.append(i)
break
self.assertEquals(','.join([str(i) for i in incorrectCases]), '')
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkGradientFilter(),
'Processing.', ('vtkDataSet', ),
('vtkDataSet', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def test_contours(self):
cell = vtk.vtkUnstructuredGrid()
cell.ShallowCopy(self.Cell)
np = self.Cell.GetNumberOfPoints()
ncomb = pow(2, np)
scalar = vtk.vtkDoubleArray()
scalar.SetName("scalar")
scalar.SetNumberOfTuples(np)
cell.GetPointData().SetScalars(scalar)
incorrectCases = []
for i in range(1,ncomb-1):
c = Combination(np, i)
for p in range(np):
scalar.SetTuple1(p, c[p])
gradientFilter = vtk.vtkGradientFilter()
gradientFilter.SetInputData(cell)
gradientFilter.SetInputArrayToProcess(0,0,0,0,'scalar')
gradientFilter.SetResultArrayName('grad')
gradientFilter.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(gradientFilter.GetOutputPort())
contourFilter.SetNumberOfContours(1)
contourFilter.SetValue(0, 0.5)
contourFilter.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputConnection(contourFilter.GetOutputPort())
normalsFilter.SetConsistency(0)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetSplitting(0)
calcFilter = vtk.vtkArrayCalculator()
calcFilter.SetInputConnection(normalsFilter.GetOutputPort())
calcFilter.SetAttributeTypeToPointData()
calcFilter.AddVectorArrayName('grad')
calcFilter.AddVectorArrayName('Normals')
calcFilter.SetResultArrayName('dir')
calcFilter.SetFunction('grad.Normals')
calcFilter.Update()
out = vtk.vtkUnstructuredGrid()
out.ShallowCopy(calcFilter.GetOutput())
numPts = out.GetNumberOfPoints()
if numPts > 0:
dirArray = out.GetPointData().GetArray('dir')
for p in range(numPts):
if(dirArray.GetTuple1(p) > 0.0): # all normals are reversed
incorrectCases.append(i)
break
self.assertEquals(','.join([str(i) for i in incorrectCases]), '')
def gradient(polydata, inputarray, outputarray, iscelldata=False):
"""Compute the gradient of a scalar or vector field."""
gradients = vtk.vtkGradientFilter()
gradients.SetInput(polydata)
fieldassociation = 1 if iscelldata == True else 0
gradients.SetInputScalars(fieldassociation, inputarray)
gradients.SetResultArrayName(outputarray)
gradients.Update()
return gradients.GetOutput()
def gradient(polydata, inputarray, outputarray, iscelldata=False):
"""Compute the gradient of a scalar or vector field."""
gradients = vtk.vtkGradientFilter()
gradients.SetInput(polydata)
fieldassociation = 1 if iscelldata == True else 0
gradients.SetInputScalars(fieldassociation, inputarray)
gradients.SetResultArrayName(outputarray)
gradients.Update()
return gradients.GetOutput()
def computeVarGradient(data_outVTK, var):
# test if the field "var" is present
if data_outVTK.GetPointData().HasArray(var) != 1:
raise ValueError("Error : field %s not present" % var)
gradientFilter = vtk.vtkGradientFilter()
gradientFilter.SetInputData(data_outVTK)
gradientFilter.SetInputArrayToProcess(0, 0, 0, 0, var)
gradientFilter.SetResultArrayName('GRAD_%s' % var)
gradientFilter.Update()
data_outVTK = gradientFilter.GetOutput()
return data_outVTK
def vtk_compute_normal_gradients(cell_normals, use_faster_approximation=False):
"""
Compute gradients of the normals
Args:
cell_normals (vtkPolyData): Surface to compute normals on
use_faster_approximation (bool): Use a less accurate algorithm that performs fewer calculations, but faster.
"""
gradient_filter = vtk.vtkGradientFilter()
gradient_filter.SetInputData(cell_normals)
gradient_filter.SetInputArrayToProcess(0, 0, 0, 1, "Normals")
if use_faster_approximation:
gradient_filter.FasterApproximationOn()
gradient_filter.Update()
gradients = gradient_filter.GetOutput()
return gradients
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
print " Gradient.execute, input Arrays: "
pointData = self.input().GetPointData()
for iA in range( pointData.GetNumberOfArrays() ):
array_name = pointData.GetArrayName(iA)
array = pointData.GetArray(iA)
print " Array %s: ntup = %d, ncomp = %d, type = %s, range = %s " % ( array_name, array.GetNumberOfTuples(), array.GetNumberOfComponents(), array.GetDataTypeAsString(), str(array.GetRange()) )
computeVorticity = wmod.forceGetInputFromPort( "computeVorticity", 1 )
self.gradient = vtk.vtkGradientFilter()
self.gradient.SetComputeVorticity( computeVorticity )
self.inputModule().inputToAlgorithm( self.gradient )
if computeVorticity: self.gradient.SetResultArrayName('vorticity')
self.set3DOutput( output=self.gradient.GetOutput() )
def compute_vorticity(dataset, scalars, vorticity_name='vorticity'):
"""(DEPRECATED) Compute Vorticity, only needed till my PR gets merged
.. deprecated::
Use the `compute_derivative` method in pyvista's `UnstructuredGrid` class
"""
warnings.warn(
"This function is deprecated. Use the 'compute_derivative'"
" method in pyvista's 'UnstructuredGrid' class", FutureWarning)
alg = vtk.vtkGradientFilter()
alg.SetComputeVorticity(True)
alg.SetVorticityArrayName(vorticity_name)
_, field = dataset.get_array(scalars, preference='point', info=True)
# args: (idx, port, connection, field, name)
alg.SetInputArrayToProcess(0, 0, 0, field.value, scalars)
alg.SetInputData(dataset)
alg.Update()
return pv.filters._get_output(alg)
def _test(self, fname):
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(VTK_DATA_ROOT + fname)
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(reader.GetOutputPort())
elev.SetLowPoint(-0.05, 0.05, 0)
elev.SetHighPoint(0.05, 0.05, 0)
grad = vtk.vtkGradientFilter()
grad.SetInputConnection(elev.GetOutputPort())
grad.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
"Elevation")
grad.Update()
vals = (10, 0, 0)
for i in range(3):
r = grad.GetOutput().GetPointData().GetArray("Gradients").GetRange(
i)
self.assertTrue(abs(r[0] - vals[i]) < 1E-4)
self.assertTrue(abs(r[1] - vals[i]) < 1E-4)
elev.SetLowPoint(0.05, -0.05, 0)
elev.SetHighPoint(0.05, 0.05, 0)
grad.Update()
vals = (0, 10, 0)
for i in range(3):
r = grad.GetOutput().GetPointData().GetArray("Gradients").GetRange(
i)
self.assertTrue(abs(r[0] - vals[i]) < 1E-4)
self.assertTrue(abs(r[1] - vals[i]) < 1E-4)
mesh_streeter = rd1.GetOutput()
print("Reading another mesh")
rd2 = vtk.vtkDataSetReader()
rd2.SetFileName(mesh_temp_longitudinal)
rd2.Update()
print("Reading yet another mesh")
rd3 = vtk.vtkDataSetReader()
rd3.SetFileName(mesh_complete)
rd3.Update()
mesh_full = rd3.GetOutput()
print("Gradient filter")
grad_filter = vtk.vtkGradientFilter()
grad_filter.SetInputData(rd2.GetOutput())
grad_filter.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
'temperature')
grad_filter.Update()
grad_mesh = grad_filter.GetOutput()
grad = grad_mesh.GetPointData().GetArray('Gradients')
fibers_full = vtk.vtkFloatArray()
fibers_full.SetName('Fibers')
fibers_full.SetNumberOfComponents(3)
fibers_full.SetNumberOfTuples(mesh_full.GetNumberOfPoints())
fibers_mask = numpy.zeros(mesh_full.GetNumberOfPoints(), dtype=numpy.int8)
def vis2hdf5_nosurface(fname, step_start, step_stop, step_step, mesh_fname):
# Command line arguments
# surface_fname = sys.argv[6]
compute_lambdatwo = 1
comm = mpi4py.MPI.COMM_WORLD
rank = comm.Get_rank()
def printRankZero(message):
if rank == 0:
print(message)
nprocs = comm.Get_size()
nsteps = old_div((step_stop-step_start+step_step),step_step)
nstepsperproc = old_div(nsteps,nprocs)
rest = nsteps % nprocs
if rest : nstepsperproc += 1
curstep_start = step_start
mesh_reader = vtk.vtkXMLUnstructuredGridReader()
mesh_reader.SetFileName(mesh_fname)
mesh_reader.Update()
# surface_reader = vtk.vtkXMLPolyDataReader()
# surface_reader.SetFileName(surface_fname)
# surface_reader.Update()
# surface_npts = surface_reader.GetOutput().GetNumberOfPoints()
npts = mesh_reader.GetOutput().GetNumberOfPoints()
ncells = mesh_reader.GetOutput().GetNumberOfCells()
# Open results file and in dictionary declare computed fields (name:n_of_components)
printRankZero("Preparing hdf5 file...")
fout = h5py.File("%s.h5" % fname,'w',driver='mpio',comm=comm)
groups = {"pressure":1,
"velocity":3,
"wall shear stress":3,
"traction":3,
"displacement":3,
"frobenius":1,
"lambda two":1,
}
# Create groups and datasets
# Creating group and datasets are collective operations, all processes need to do it
for group in groups:
fout.create_group(group)
for i in range(step_start,step_stop+step_step,step_step):
fout[group].create_dataset("%d" % i, (npts,groups[group]),dtype='float64')
# Create Mesh topology and coordinates
printRankZero("Adding mesh data to hdf5 file...")
fout.create_group("Mesh")
fout["Mesh"].create_dataset("topology", (ncells,4), dtype='int64')
fout["Mesh"].create_dataset("coordinates", (npts,3),dtype='float64')
curnsteps=nstepsperproc
if rank >= rest and rest:
curnsteps -= 1
curstep_start += rest*(curnsteps+1)*step_step+(rank-rest)*curnsteps*step_step
else:
curstep_start += rank*curnsteps*step_step
tmp_tawss = np.zeros(npts)
tmp_wssint = np.zeros((npts,3))
tmp_lambdatwo = np.zeros((npts,1))
tmp_frobenius = np.zeros((npts,1))
#########################################################
####### PARSE VIS FILES #################################
#########################################################
for i in tqdm.trange(curstep_start,curstep_start+curnsteps*step_step,step_step):
currentVisFileName = "%s-%d.vis" % (fname,i)
tqdm.tqdm.write("Rank {} Reading file {}".format(rank, currentVisFileName))
fin = open(currentVisFileName,'r')
while True:
# Get Group Name
for line in fin:
line_split = line.split('"')
if (" analysis results " in line_split) : break
if line == '\n' : break # Reached end of file"
group_name = line_split[-2]
if group_name not in fout:
tqdm.tqdm.write("ERROR: GROUP '%s' IS NOT ON YOUR LIST" % group_name)
# Determine size of vector and initialize
line_split = (next(fin)).split()
npts = int(line_split[-1])
for line in fin:
line_split = line.split()
if "length" in line_split: break
ncols = int(line_split[-1])
tmp_vec = np.zeros((npts,ncols))
# Get to the data
for line in fin:
line_split = line.split()
if "data" in line_split: break
#for j in xrange(npts):
#tmp_vec[j] = [float(x) for x in fin.next().split()]
tmp_vec = np.genfromtxt(islice(fin,None,npts))
fout["/%s/%d" % (group_name, i)][:] = np.reshape(tmp_vec,(npts,ncols))
if group_name == "wall shear stress":
tmp_tawss += np.linalg.norm(tmp_vec,axis=1)
tmp_wssint += tmp_vec
if group_name == "velocity" and compute_lambdatwo==1:
# Compute gradient of velocity
tmp_vec_vtk = numpy_support.numpy_to_vtk(tmp_vec)
tmp_vec_vtk.SetName("tmp_velocity")
mesh_reader.GetOutput().GetPointData().AddArray(tmp_vec_vtk)
gradient_filter = vtk.vtkGradientFilter()
gradient_filter.SetInputConnection(mesh_reader.GetOutputPort())
gradient_filter.SetInputScalars(0,"tmp_velocity")
gradient_filter.SetResultArrayName("tmp_velocity_gradient")
gradient_filter.Update()
tmp_vel_gradient = numpy_support.vtk_to_numpy(gradient_filter.GetOutput().GetPointData().GetArray("tmp_velocity_gradient"))
tmp_vel_gradient = np.reshape(tmp_vel_gradient, (npts,3,3))
tmp_vel_gradient_t = np.transpose(tmp_vel_gradient, (0,2,1))
tmp_S = 0.5*(tmp_vel_gradient+tmp_vel_gradient_t)
tmp_W = 0.5*(tmp_vel_gradient-tmp_vel_gradient_t)
tmp_frobenius[:] = np.reshape(np.linalg.norm(tmp_S, axis=(1,2)),(npts,1))
tmp_S2 = np.einsum('abj,ajc->abc',tmp_S,tmp_S)
tmp_W2 = np.einsum('abj,ajc->abc',tmp_W,tmp_W)
eigvals = np.linalg.eigvals(tmp_S2+tmp_W2)
eigvals = np.sort(eigvals,axis=1)
tmp_lambdatwo = eigvals[:,1]
fout["/lambda two/%d" % (i,)][:] = np.reshape(tmp_lambdatwo,(npts,1))
fout["/frobenius/%d" % (i,)][:] = tmp_frobenius
fin.close()
####### END OF PARSING #################################
printRankZero("Finished reading vis files.")
# Average indices TAWSS and OSI can be conveniently computed through reduction operations
if rank == 0:
total_tawss = np.zeros(npts)
total_wssint = np.zeros((npts,3))
else:
total_tawss = None
total_wssint = None
comm.Reduce([tmp_tawss, mpi4py.MPI.DOUBLE],
[total_tawss, mpi4py.MPI.DOUBLE],
op = mpi4py.MPI.SUM,
root = 0)
comm.Reduce([tmp_wssint, mpi4py.MPI.DOUBLE],
[total_wssint, mpi4py.MPI.DOUBLE],
op = mpi4py.MPI.SUM,
root = 0)
printRankZero("Adding TAWSS and OSI data to hdf5 file...")
fout.create_group("TAWSS")
fout["TAWSS"].create_dataset("0", (npts,),dtype='float64')
fout.create_group("WSSINT")
fout["WSSINT"].create_dataset("0",(npts,3),dtype='float64')
fout.create_group("OSI")
fout["OSI"].create_dataset("0",(npts,),dtype='float64')
if rank == 0:
# Also add TAWSS and OSI to HDF5 file
total_tawss /= nsteps
total_wssint /= nsteps
idx_ok = np.where(total_tawss>1e-6)
total_wssint_norm = np.linalg.norm(total_wssint,axis=1)
total_osi = np.zeros(npts)
total_osi[idx_ok] = 0.5*(1.0-old_div(total_wssint_norm[idx_ok],total_tawss[idx_ok]))
fout["/TAWSS/0"][:] = total_tawss
fout["/OSI/0"][:] = total_osi
fout["/WSSINT/0"][:] = total_wssint
pts = numpy_support.vtk_to_numpy(mesh_reader.GetOutput().GetPoints().GetData())
cells = numpy_support.vtk_to_numpy(mesh_reader.GetOutput().GetCells().GetData())
cells = np.reshape(cells, (ncells,5))
cells = cells[:,1:]
fout["/Mesh/coordinates"][:] = pts
fout["/Mesh/topology"][:] = cells
mesh_locator = vtk.vtkPointLocator()
mesh_locator.SetDataSet(mesh_reader.GetOutput())
mesh_locator.BuildLocator()
# map_surface_to_mesh = np.zeros(surface_npts, dtype=np.int64)
# for i in xrange(surface_npts):
# pt = surface_reader.GetOutput().GetPoint(i)
# closept = mesh_locator.FindClosestPoint(pt)
# map_surface_to_mesh[i] = closept
# tawss_surface = total_tawss[map_surface_to_mesh]
# osi_surface = total_osi[map_surface_to_mesh]
# wssint_surface = total_wssint[map_surface_to_mesh]
# tawss_surface_vtk = numpy_support.numpy_to_vtk(tawss_surface)
# tawss_surface_vtk.SetName("TAWSS")
# osi_surface_vtk = numpy_support.numpy_to_vtk(osi_surface)
# osi_surface_vtk.SetName("OSI")
# wssint_surface_vtk = numpy_support.numpy_to_vtk(wssint_surface)
# wssint_surface_vtk.SetName("WSSINT")
# Save the WSS based indices in VTK polydata format
# surface_reader.GetOutput().GetPointData().AddArray(tawss_surface_vtk)
# surface_reader.GetOutput().GetPointData().AddArray(osi_surface_vtk)
# surface_reader.GetOutput().GetPointData().AddArray(wssint_surface_vtk)
# surface_writer = vtk.vtkXMLPolyDataWriter()
# surface_writer.SetInputConnection(surface_reader.GetOutputPort())
# surface_writer.SetFileName("%s-wss.vtp" %fname )
# surface_writer.Update()
# Write XDMF File for visualization in Paraview
xdmf_out = open("%s.xdmf" % fname, 'w')
# Header
xdmf_out.write("""<?xml version="1.0"?>
<Xdmf Version="2.0" xmlns:xi="http://www.w3.org/2001/XInclude">
<Domain>
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
<Time TimeType="List">\n""")
# Line of timesteps
timesteps_str = ' '.join(str(i) for i in range(step_start,step_stop+step_step,step_step))
xdmf_out.write('<DataItem Format="XML" Dimensions="%d">%s</DataItem>\n</Time>' %(nsteps,timesteps_str) )
# For each timestep point to grid topology and geometry, and attributes
for i in range(step_start,step_stop+step_step,step_step):
xdmf_out.write('<Grid Name="grid_%d" GridType="Uniform">\n' % i)
xdmf_out.write('<Topology NumberOfElements="%d" TopologyType="Tetrahedron">\n' % ncells)
xdmf_out.write('<DataItem Format="HDF" Dimensions="%d 4">%s.h5:/Mesh/topology</DataItem>\n'
% (ncells,fname))
xdmf_out.write('</Topology>\n<Geometry GeometryType="XYZ">\n')
xdmf_out.write('<DataItem Format="HDF" Dimensions="%d 3">%s.h5:/Mesh/coordinates</DataItem>\n'
% (npts, fname))
xdmf_out.write('</Geometry>\n')
for group in groups:
if groups[group] == 1:
xdmf_out.write('<Attribute Name="%s" AttributeType="Scalar" Center="Node">\n'
% group)
if groups[group] == 3:
xdmf_out.write('<Attribute Name="%s" AttributeType="Vector" Center="Node">\n'
% group)
xdmf_out.write('<DataItem Format="HDF" Dimensions="%d %d">%s.h5:/%s/%d</DataItem>\n'
% (npts,groups[group],fname,group,i))
xdmf_out.write('</Attribute>\n')
xdmf_out.write('</Grid>\n')
xdmf_out.write('</Grid>\n</Domain>\n</Xdmf>')
xdmf_out.close()
fout.close()
def main(filename):
print("Loading", filename)
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
edges = vtk.vtkExtractEdges()
edges.SetInputConnection(reader.GetOutputPort())
tubes = vtk.vtkTubeFilter()
tubes.SetInputConnection(edges.GetOutputPort())
tubes.SetRadius(0.0625)
tubes.SetVaryRadiusToVaryRadiusOff()
tubes.SetNumberOfSides(32)
tubesMapper = vtk.vtkPolyDataMapper()
tubesMapper.SetInputConnection(tubes.GetOutputPort())
tubesMapper.SetScalarRange(0.0, 26.0)
tubesActor = vtk.vtkActor()
tubesActor.SetMapper(tubesMapper)
gradients = vtk.vtkGradientFilter()
gradients.SetInputConnection(reader.GetOutputPort())
vectors = vtk.vtkAssignAttribute()
vectors.SetInputConnection(gradients.GetOutputPort())
vectors.Assign("Gradients", vtk.vtkDataSetAttributes.VECTORS, \
vtk.vtkAssignAttribute.POINT_DATA)
arrow = vtk.vtkArrowSource()
glyphs = vtk.vtkGlyph3D()
glyphs.SetInputConnection(0, vectors.GetOutputPort())
glyphs.SetInputConnection(1, arrow.GetOutputPort())
glyphs.ScalingOn()
glyphs.SetScaleModeToScaleByVector()
glyphs.SetScaleFactor(0.25)
glyphs.OrientOn()
glyphs.ClampingOff()
glyphs.SetVectorModeToUseVector()
glyphs.SetIndexModeToOff()
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphs.GetOutputPort())
glyphMapper.ScalarVisibilityOff()
glyphActor = vtk.vtkActor()
glyphActor.SetMapper(glyphMapper)
renderer = vtk.vtkRenderer()
renderer.AddActor(tubesActor)
renderer.AddActor(glyphActor)
renderer.SetBackground(0.328125, 0.347656, 0.425781)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(renderer)
renwin.SetSize(350, 500)
renderer.ResetCamera()
camera = renderer.GetActiveCamera()
camera.Elevation(-80.0)
camera.OrthogonalizeViewUp()
camera.Azimuth(135.0)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
iren.Initialize()
iren.Start()
return 1
def main(argv):
#Just get something working for testing...
try:
opts, args = getopt.getopt(argv, "hi:", ["ifile="])
except getopt.GetoptError as err:
print 'tviewer.py -i <inputfile.vtk>'
print(str(err))
for opt, arg in opts:
if opt == '-h':
print 'tviewer.py -i <inputfile.vtk>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
print("Going to load and view ", inputfile)
#Read data
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(inputfile)
reader.Update()
#lut = vtk.vtkLookupTable()
#lut.SetNumberOfColors(65535)
#lut.SetHueRange(0.0, 2.667)
#lut.SetVectorMode(vtk.vtkScalarsToColors.MAGNITUDE)
#lut.Build()
#Setup offscreen rendering
graphics_factory = vtk.vtkGraphicsFactory()
graphics_factory.SetOffScreenOnlyMode(1)
graphics_factory.SetUseMesaClasses(1)
#imaging_factory = vtk.vtkImagingFactory()
#imaging_factory.SetUseMesaClasses(1)
#Get image from reader
image = reader.GetOutput()
#image.SetSpacing(1,1,1)
#image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#Compute Q Criterion for texture mapping
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
#vorticity.SetComputeGradient(0)
vorticity.Update()
#Generate contour for comparison
c = vtk.vtkContourFilter()
#c.SetValue(0,1128)
c.SetValue(0, 450)
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
#contour.GetCellData().SetScalars(image.GetPointData().GetVectors("Velocity"))
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(contour)
normals.SetFeatureAngle(45) #?
normals.Update()
#print normals.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(normals.GetOutput())
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1, 1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
#print image
#print contour
#mapper.SelectColorArray("Q-criterion")
#mapper.SetLookupTable(lut)
#print mapper
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1, 1, 1)
ren.ResetCamera()
renWin = vtk.vtkRenderWindow()
renWin.SetSize(400, 400)
renWin.SetOffScreenRendering(1)
renWin.AddRenderer(ren)
renWin.Render()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
w.SetFileName("cube.png")
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
windowToImageFilter.Update()
writer = vtk.vtkPNGWriter()
writer.SetWriteToMemory(1)
writer.SetInputConnection(windowToImageFilter.GetOutputPort())
writer.Write()
data = str(buffer(writer.GetResult()))
return Image(data)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName("/home/stephenh/turbulence/sc/datasets/vtkscripts/iso64.vti")
reader.Update()
image = reader.GetOutput()
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.Update()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,1128)
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(contour)
normals.SetFeatureAngle(35) #?
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print ("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,1128)
if (comptype == "q"):
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3,3,3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
def vortmesh(args):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] +str(cubenum) + ".npy" #Used so we can set either npy input or h5 input
outputfile = p["outputfile"] + str(cubenum) + ".vtp" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
#In case file isn't here, catch this.
try:
vel = np.load(inputfile)
except:
p["message"] = "Failed to find file"
return p
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing TODO: Add to parameters
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,thresh)
if (comptype == "q"):
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
result = w.Write()
we = timeit.default_timer()
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
def vortmesh(args):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] + str(
cubenum) + ".npy" #Used so we can set either npy input or h5 input
outputfile = p["outputfile"] + str(
cubenum) + ".vtp" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
#In case file isn't here, catch this.
try:
vel = np.load(inputfile)
except:
p["message"] = "Failed to find file"
return p
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing TODO: Add to parameters
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, thresh)
if (comptype == "q"):
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
result = w.Write()
we = timeit.default_timer()
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we - rs)
return p #return the packet
def getvtkimage(self, webargs, timestep):
#Setup query
DBSTRING = os.environ['db_connection_string']
conn = pyodbc.connect(DBSTRING, autocommit=True)
cursor = conn.cursor()
#url = "http://localhost:8000/cutout/getcutout/"+ token + "/" + dataset + "/" + datafield + "/" + ts + "," +te + "/" + xs + "," + xe +"/" + ys + "," + ye +"/" + zs + "," + ze
w = webargs.split("/")
ts = int(w[3].split(',')[0])
te = int(w[3].split(',')[1])
xs = int(w[4].split(',')[0])
xe = int(w[4].split(',')[1])
ys = int(w[5].split(',')[0])
ye = int(w[5].split(',')[1])
zs = int(w[6].split(',')[0])
ze = int(w[6].split(',')[1])
extent = (xs, ys, zs, xe, ye, ze)
overlap = 2 #Used only on contours--vorticity and Q-criterion
#Look for step parameters
if (len(w) > 9):
step = True;
s = w[8].split(",")
tstep = s[0]
xstep = float(s[1])
ystep = float(s[2])
zstep = float(s[3])
filterwidth = w[9]
else:
step = False;
xstep = 1
ystep = 1
zstep = 1
filterwidth = 1
cfieldlist = w[2].split(",")
firstval = cfieldlist[0]
maxrange = self.getmaxrange(w[1])
if ((firstval == 'vo') or (firstval == 'qc') or (firstval == 'cvo') or (firstval == 'qcc')):
component = 'u'
computation = firstval #We are doing a computation, so we need to know which one.
#check to see if we have a threshold (only for contours)
if (len(cfieldlist) > 1):
threshold = float(cfieldlist[1])
else:
threshold = .6
#New: We need an expanded cutout if contouring. Push the cutout out by 2 in all directions (unless at boundary).
if ((firstval == 'cvo') or (firstval == 'qcc')):
newextent = self.expandcutout(extent, maxrange[0], maxrange[1], maxrange[2], overlap)
contour = True
else:
component = w[2] #There could be multiple components, so we will have to loop
computation = ''
#Split component into list and add them to the image
#Check to see if we have a value for vorticity or q contour
fieldlist = list(component)
for field in fieldlist:
print("Field = %s" % field)
cursor.execute("{CALL turbdev.dbo.GetAnyCutout(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)}",w[1], field, timestep, extent[0], extent[1], extent[2], xstep, ystep, zstep, 1,1,extent[3], extent[4], extent[5],filterwidth,1)
#If data spans across multiple servers, we get multiple sets, so concatenate them.
row = cursor.fetchone()
raw = row[0]
part = 0
print ("First part size is %d" % len(row[0]))
while(cursor.nextset()):
row = cursor.fetchone()
raw = raw + row[0]
part = part +1
print ("added part %d" % part)
print ("Part size is %d" % len(row[0]))
print ("Raw size is %d" % len(raw))
data = np.frombuffer(raw, dtype=np.float32)
conn.close()
vtkdata = numpy_support.numpy_to_vtk(data, deep=True, array_type=vtk.VTK_FLOAT)
components = self.numcomponents(field)
vtkdata.SetNumberOfComponents(components)
vtkdata.SetName(self.componentname(field))
image = vtk.vtkImageData()
if (step):
xes = int(extent[3])/int(xstep)-1
yes = int(extent[4])/int(ystep)-1
zes = int(extent[5])/int(zstep)-1
image.SetExtent(extent[0], extent[0]+extent[3], extent[1], extent[1]+extent[4], extent[2], extenet[2]+extenet[5])
print("Step extent=" +str(xes))
print("xs=" + str(xstep) + " ys = "+ str(ystep) +" zs = " + str(zstep))
else:
image.SetExtent(extent[0], extent[0]+extent[3]-1, extent[1], extent[1]+extent[4]-1, extent[2], extent[2]+extent[5]-1)
image.GetPointData().SetVectors(vtkdata)
if (step): #Magnify to original size
image.SetSpacing(xstep,ystep,zstep)
#Check if we need a rectilinear grid, and set it up if so.
if (w[1] == 'channel'):
ygrid = self.getygrid()
#print("Ygrid: ")
#print (ygrid)
rg = vtk.vtkRectilinearGrid()
#Not sure about contouring channel yet, so we are going back to original variables at this point.
rg.SetExtent(xs, xs+xe-1, ys, ys+ye-1, zs, zs+ze-1)
rg.GetPointData().SetVectors(vtkdata)
xg = np.arange(float(xs),float(xe))
zg = np.arange(float(zs),float(ze))
for x in xg:
xg[x] = 8*3.141592654/2048*x
for z in zg:
zg[z] = 3*3.141592654/2048*z
vtkxgrid=numpy_support.numpy_to_vtk(xg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkzgrid=numpy_support.numpy_to_vtk(zg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkygrid=numpy_support.numpy_to_vtk(ygrid,
deep=True, array_type=vtk.VTK_FLOAT)
rg.SetXCoordinates(vtkxgrid)
rg.SetZCoordinates(vtkzgrid)
rg.SetYCoordinates(vtkygrid)
image = rg #we rewrite the image since we may be doing a
#computation below
#See if we are doing a computation
if (computation == 'vo'):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
print("Computing Vorticity")
vorticity.Update()
elif (computation == 'cvo'):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
print("Computing Voricity")
vorticity.Update()
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
print("Computing magnitude")
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
c.SetInputData(mag.GetOutput())
print("Computing Contour")
c.Update()
#Now we need to clip out the overlap
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(xs, xs+xe-1, ys, ys+ye-1, zs,zs+ze-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
return cropdata
elif (computation == 'qcc'):
q = vtk.vtkGradientFilter()
q.SetInputData(image)
q.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
q.ComputeQCriterionOn()
q.Update()
#newimage = vtk.vtkImageData()
image.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mag = vtk.vtkImageMagnitude()
mag.SetInputData(image)
mag.Update()
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
c.SetInputData(mag.GetOutput())
c.Update()
#clip out the overlap here
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(xs, xs+xe-1, ys, ys+ye-1, zs,zs+ze-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
return cropdata
else:
return image
def main(argv):
try:
opts, args = getopt.getopt(argv,"hi:o:x:a:y:b:z:c:d:u:", ["ifile=","ofile=","sx=","ex=","sy=","ez=","dataset=","comp="])
except getopt.GetoptError as err:
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset -comptype'
print (str(err))
for opt, arg in opts:
if opt == '-h':
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-x", "--sx"):
sx = int(arg)
elif opt in ("-a", "--ex"):
ex = int(arg)
elif opt in ("-y", "--sy"):
sy = int(arg)
elif opt in ("-b", "--ey"):
ey = int(arg)
elif opt in ("-z", "--sz"):
sz = int(arg)
elif opt in ("-c", "--ez"):
ez = int(arg)
elif opt in ("-d", "--dataset"):
dataset = str(arg)
elif opt in ("-u", "--du"):
comptype = str(arg)
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print ("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
ve = timeit.default_timer()
print ("Generating contour")
ms = timeit.default_timer()
mag = vtk.vtkImageMagnitude()
for x in range (0,1):
start = timeit.default_timer()
threshold = (22.39 * (2.5))
if (comptype == "q"):
threshold= (783.3)
vort = vtk.vtkGradientFilter()
vort.SetInputData(image)
vort.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vort.ComputeQCriterionOn()
vort.Update()
image.GetPointData().SetScalars(vort.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
v = vtk.vtkCellDerivatives()
v.SetVectorModeToComputeVorticity()
v.SetTensorModeToPassTensors()
v.SetInputData(image)
v.Update()
vort = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(v.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
vort.SetInputData(image)
vort.Update()
#ni = vtk.vtkImageData()
#ni.SetSpacing(.006135923, .006135923, .006135923)
#ni.SetExtent(sx,ex,sy,ey,sz,ez)
#ni.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mend = timeit.default_timer()
me = mend
comptime = mend-start
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
if (comptype == "q"):
c.SetInputData(image)
else:
c.SetInputData(vort.GetOutput())
print("Computing Contour with threshold", threshold)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile + str(x) + ".vtp ")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
#print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, 1128)
if (comptype == "q"):
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(
cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0, 0, 0,
mag.GetOutput().FIELD_ASSOCIATION_POINTS,
"Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3, 3, 3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex - sx + 1)
w.GetCompressor().SetNy(ey - sy + 1)
w.GetCompressor().SetNz(ez - sz + 1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
print("Q Magnitude: %s" % str(me - ms))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Vorticity Magnitude: %s" % str(me - ms))
print("Threshold: %s" % str(te - ts))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
print("Reading another mesh")
rd2 = vtk.vtkDataSetReader()
rd2.SetFileName(mesh_temp_longitudinal)
rd2.Update()
print("Reading yet another mesh")
rd3 = vtk.vtkDataSetReader()
rd3.SetFileName(mesh_complete)
rd3.Update()
mesh_full = rd3.GetOutput()
print("Gradient filter")
grad_filter = vtk.vtkGradientFilter()
grad_filter.SetInputData(rd2.GetOutput())
grad_filter.SetInputArrayToProcess(0,0,0,vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,'temperature')
grad_filter.Update()
grad_mesh = grad_filter.GetOutput()
grad = grad_mesh.GetPointData().GetArray('Gradients')
fibers_full = vtk.vtkFloatArray()
fibers_full.SetName('Fibers')
fibers_full.SetNumberOfComponents(3)
fibers_full.SetNumberOfTuples(mesh_full.GetNumberOfPoints())
fibers_mask = numpy.zeros(mesh_full.GetNumberOfPoints(), dtype=numpy.int8)
fibers_mask.fill(0)
def vortvelvolume(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
#We use 0 for structured grid (vti) and 1 for unstructured grid (vtu)
if (p["param3"] != ''):
grid = 0
else:
grid = 1
if (p["param4"] != ''):
kernelsize = int(p["param4"])
else:
kernelsize = 3
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(kernelsize,kernelsize,kernelsize)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
if (grid == 0):
w = vtk.vtkXMLImageDataWriter()
else:
w = vtk.vtkXMLUnstructuredGridWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
#grid = reader.GetOutput()
#wallshear = grid.GetCellData().GetArray("x_wall_shear")
#print(wallshear)
calc1 = vtk.vtkArrayCalculator()
calc1.SetFunction("sqrt(x_wall_shear^2+y_wall_shear^2+y_wall_shear^2)")
calc1.AddScalarVariable("x_wall_shear", "x_wall_shear", 0)
calc1.AddScalarVariable("y_wall_shear", "y_wall_shear", 0)
calc1.AddScalarVariable("z_wall_shear", "z_wall_shear", 0)
calc1.SetResultArrayName("WSS")
calc1.SetInputConnection(reader.GetOutputPort())
calc1.SetAttributeModeToUsePointData()
#calc1.SetAttributeModeToUseCellData()
calc1.SetResultArrayType(vtk.VTK_FLOAT)
x_WSS_grad = vtk.vtkGradientFilter()
x_WSS_grad.SetInputConnection(calc1.GetOutputPort())
x_WSS_grad.ComputeGradientOn()
x_WSS_grad.FasterApproximationOff()
x_WSS_grad.SetResultArrayName("x_WSS_grad")
x_WSS_grad.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
"x_wall_shear")
y_WSS_grad = vtk.vtkGradientFilter()
y_WSS_grad.SetInputConnection(x_WSS_grad.GetOutputPort())
y_WSS_grad.ComputeGradientOn()
y_WSS_grad.FasterApproximationOff()
y_WSS_grad.SetResultArrayName("y_WSS_grad")
x_WSS_grad.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
def post_proc_cfd(dir_path, vtu_input, cell_type="point",
vtu_output_1="calc_test_node.vtu",
vtu_output_2="calc_test_node_stats.vtu", N_peak=3):
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(os.path.join(dir_path, vtu_input))
reader.Update()
N = reader.GetNumberOfTimeSteps()
print(N)
#N = test.GetNumberOfBlocks()ls
#block = test.GetBlock(0)
#for i in range(N):
# print(i, test.GetMetaData(i).Get(vtk.vtkCompositeDataSet.NAME()))
#grid = reader.GetOutput()
#wallshear = grid.GetCellData().GetArray("x_wall_shear")
#print(wallshear)
calc1 = vtk.vtkArrayCalculator()
calc1.SetFunction("sqrt(x_wall_shear^2+y_wall_shear^2+z_wall_shear^2)")
calc1.AddScalarVariable("x_wall_shear", "x_wall_shear",0)
calc1.AddScalarVariable("y_wall_shear", "y_wall_shear",0)
calc1.AddScalarVariable("z_wall_shear", "z_wall_shear",0)
calc1.SetResultArrayName("WSS")
calc1.SetInputConnection(reader.GetOutputPort())
if(cell_type == "cell"):
calc1.SetAttributeModeToUseCellData()
vtk_process = vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS
vtk_data_type = vtk.vtkDataObject.CELL
else:
calc1.SetAttributeModeToUsePointData()
vtk_process = vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS
vtk_data_type = vtk.vtkDataObject.POINT
calc1.SetResultArrayType(vtk.VTK_DOUBLE)
x_WSS_grad = vtk.vtkGradientFilter()
x_WSS_grad.SetInputConnection(calc1.GetOutputPort())
x_WSS_grad.ComputeGradientOn()
x_WSS_grad.FasterApproximationOff()
x_WSS_grad.SetResultArrayName("x_WSS_grad")
x_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "x_wall_shear")
y_WSS_grad = vtk.vtkGradientFilter()
y_WSS_grad.SetInputConnection(x_WSS_grad.GetOutputPort())
y_WSS_grad.ComputeGradientOn()
y_WSS_grad.FasterApproximationOff()
y_WSS_grad.SetResultArrayName("y_WSS_grad")
x_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "y_wall_shear")
z_WSS_grad = vtk.vtkGradientFilter()
z_WSS_grad.SetInputConnection(y_WSS_grad.GetOutputPort())
z_WSS_grad.ComputeGradientOn()
z_WSS_grad.FasterApproximationOff()
z_WSS_grad.SetResultArrayName("z_WSS_grad")
z_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "z_wall_shear")
calc2 = vtk.vtkArrayCalculator()
calc2.AddScalarVariable("x_component", "x_WSS_grad",0)
calc2.AddScalarVariable("y_component", "y_WSS_grad",1)
calc2.AddScalarVariable("z_component", "z_WSS_grad",2)
calc2.SetFunction("sqrt(x_component^2+y_component^2+z_component^2)")
calc2.SetResultArrayName("WSSG")
calc2.SetInputConnection(z_WSS_grad.GetOutputPort())
if(cell_type == "cell"):
calc2.SetAttributeModeToUseCellData()
else:
calc2.SetAttributeModeToUsePointData()
calc2.SetResultArrayType(vtk.VTK_DOUBLE)
# initialize the output to include the peak values
grid = vtk.vtkUnstructuredGrid()
#N_peak = 3
reader.SetTimeStep(N_peak)
print("loading {0}th timestep to copy data".format(N_peak))
calc2.Update()
grid.DeepCopy(calc2.GetOutput())
#grid.SetNumberOfTimeSteps(1)
#grid.SetTimeStep(0)
#grid.Update()
#sqrt((ddx({Wall shear-1}))**2 + (ddy({Wall shear-2}))**2 + (ddz({Wall shear-3}))**2)'
def init_zero(in_array, sz_array):
for i in range(sz_array):
in_array.SetValue(i,0.0)
def array_sum(out_array, in_array, sz_array):
for i in range(sz_array):
out_array.SetValue(i, out_array.GetValue(i) + in_array.GetValue(i))
def array_division(out_array, in_array, sz_array):
for i in range(sz_array):
out_array.SetValue(i, out_array.GetValue(i) / in_array.GetValue(i))
def array_avg(out_array, N):
float_N = float(N)
for i in range(N):
out_array.SetValue(i, out_array.GetValue(i) / float_N)
reader.SetTimeStep(0)
print("loading {0}th timestep for averaging initialization".format(0))
reader.Update()
calc2.Update()
if(cell_type == "cell"):
calc_data = calc2.GetOutput().GetCellData()
grid_data = grid.GetCellData()
n_sz = grid.GetNumberOfCells()
else:
calc_data = calc2.GetOutput().GetPointData()
grid_data = grid.GetPointData()
n_sz = grid.GetNumberOfPoints()
TAWSS = vtk.vtkDoubleArray()
TAWSS.DeepCopy(calc_data.GetArray("WSS"))
TAWSS.SetName("TAWSS")
TAWSSG = vtk.vtkDoubleArray()
TAWSSG.DeepCopy(calc_data.GetArray("WSSG"))
TAWSSG.SetName("TAWSSG")
x_shear_avg = vtk.vtkDoubleArray()
x_shear_avg.DeepCopy(calc_data.GetArray("x_wall_shear"))
x_shear_avg.SetName("x_shear_avg")
y_shear_avg = vtk.vtkDoubleArray()
y_shear_avg.DeepCopy(calc_data.GetArray("y_wall_shear"))
y_shear_avg.SetName("y_shear_avg")
z_shear_avg = vtk.vtkDoubleArray()
z_shear_avg.DeepCopy(calc_data.GetArray("z_wall_shear"))
z_shear_avg.SetName("z_shear_avg")
#TAWSSVector = vtk.vtkDoubleArray()
#TAWSSVector.DeepCopy(calc_data.GetArray("z_wall_shear"))
#TAWSSVector.SetName("TAWSSVector")
#grid_data.AddArray(TAWSSVector)
# def get_array_names(input):
# N_point_array = input.GetOutput().GetPointData().GetNumberOfArrays()
# N_WSS = 9999999
# for i in range(N_point_array):
# name_WSS = input.GetOutput().GetPointData().GetArrayName(i)
# if (name_WSS == "WSS"):
# N_WSS = i
# print(name_WSS)
#
# def array_sum(output, input_calc, N):
# for i in range(N):
# calc = output.GetValue(i) + input_calc.GetValue(i)
# output.SetValue(i, calc)
writer = vtk.vtkXMLUnstructuredGridWriter()
#writer.SetFileName(os.path.join(out_dir,'test_outfile.vtu'))
writer.SetFileName(os.path.join(dir_path, vtu_output_1))
writer.SetNumberOfTimeSteps(N)
#writer.SetTimeStepRange(0,len(filelist)-1)
writer.SetInputConnection(calc2.GetOutputPort())
writer.Start()
#avg_map = {"TAWSS":"WSS", "TAWSSG": "WSSG", "x_shear_avg":"x_wall_shear",
# "y_shear_avg":"y_wall_shear" , "z_shear_avg":"z_wall_shear"}
for i in range(1,N):
reader.SetTimeStep(i)
print("Time step {0} for average calc".format(i))
reader.Update()
calc2.Update()
if(cell_type == "cell"):
calc_data = calc2.GetOutput().GetCellData()
else:
calc_data = calc2.GetOutput().GetPointData()
#get_array_names(calc2)
array_sum(TAWSS, calc_data.GetArray("WSS"), n_sz)
array_sum(TAWSSG, calc_data.GetArray("WSSG"), n_sz)
array_sum(x_shear_avg, calc_data.GetArray("x_wall_shear"), n_sz)
array_sum(y_shear_avg, calc_data.GetArray("y_wall_shear"), n_sz)
array_sum(z_shear_avg, calc_data.GetArray("z_wall_shear"), n_sz)
writer.WriteNextTime(reader.GetTimeStep())
writer.Stop()
array_avg(TAWSS, N)
array_avg(TAWSSG, N)
array_avg(x_shear_avg, N)
array_avg(y_shear_avg, N)
array_avg(z_shear_avg, N)
WSS_peak2mean = vtk.vtkDoubleArray()
WSS_peak2mean.DeepCopy(grid_data.GetArray("WSS"))
WSS_peak2mean.SetName("WSS_peak2mean")
array_division(WSS_peak2mean, TAWSS, n_sz)
WSSG_peak2mean = vtk.vtkDoubleArray()
WSSG_peak2mean.DeepCopy(grid_data.GetArray("WSSG"))
WSSG_peak2mean.SetName("WSSG_peak2mean")
array_division(WSSG_peak2mean, TAWSSG, n_sz)
grid_data.AddArray(TAWSS)
grid_data.AddArray(TAWSSG)
grid_data.AddArray(x_shear_avg)
grid_data.AddArray(y_shear_avg)
grid_data.AddArray(z_shear_avg)
grid_data.AddArray(WSS_peak2mean)
grid_data.AddArray(WSSG_peak2mean)
print("got here")
calc3 = vtk.vtkArrayCalculator()
calc3.AddScalarVariable("x_shear_avg", "x_shear_avg",0)
calc3.AddScalarVariable("y_shear_avg", "y_shear_avg",0)
calc3.AddScalarVariable("z_shear_avg", "z_shear_avg",0)
calc3.SetFunction("sqrt(x_shear_avg^2+y_shear_avg^2+z_shear_avg^2)")
calc3.SetResultArrayName("TAWSSVector")
calc3.SetInputData(grid)
if(cell_type == "cell"):
calc3.SetAttributeModeToUseCellData()
else:
calc3.SetAttributeModeToUsePointData()
calc3.SetResultArrayType(vtk.VTK_DOUBLE)
calc3.Update()
calc4 = vtk.vtkArrayCalculator()
calc4.AddScalarVariable("TAWSSVector", "TAWSSVector",0)
calc4.AddScalarVariable("TAWSS", "TAWSS",0)
calc4.SetFunction("0.5*(1.0-(TAWSSVector/(TAWSS)))")
calc4.SetResultArrayName("OSI")
calc4.SetInputConnection(calc3.GetOutputPort())
if(cell_type == "cell"):
calc4.SetAttributeModeToUseCellData()
else:
calc4.SetAttributeModeToUsePointData()
calc4.SetResultArrayType(vtk.VTK_DOUBLE)
calc4.Update()
pass_filt = vtk.vtkPassArrays()
pass_filt.SetInputConnection(calc4.GetOutputPort())
pass_filt.AddArray(vtk_data_type, "WSS")
pass_filt.AddArray(vtk_data_type, "WSSG")
pass_filt.AddArray(vtk_data_type, "absolute_pressure")
pass_filt.AddArray(vtk_data_type, "TAWSS")
pass_filt.AddArray(vtk_data_type, "TAWSSG")
pass_filt.AddArray(vtk_data_type, "OSI")
pass_filt.AddArray(vtk_data_type, "WSS_peak2mean")
pass_filt.AddArray(vtk_data_type, "WSSG_peak2mean")
pass_filt.Update()
#if(cell_type == "cell"):
# print(pass_filt.GetOutput().GetCellData().GetArray("OSI").GetValue(0))
#else:
# print(pass_filt.GetOutput().GetPointData().GetArray("OSI").GetValue(0))
writer2 = vtk.vtkXMLUnstructuredGridWriter()
writer2.SetFileName(os.path.join(dir_path, vtu_output_2))
writer2.SetInputConnection(pass_filt.GetOutputPort())
writer2.Update()
def vortvelvolumei(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
print ("File Loaded")
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
print ("Beginning computation: " + comptype)
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
print("Initial calculation done")
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Generating screenshot")
c = vtk.vtkContourFilter()
c.SetValue(0,thresh)
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(contour)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
camera = vtk.vtkCamera()
ren.SetActiveCamera(camera)
ren.ResetCamera()
camera.Zoom(1.5) #This reduces the whitespace around the image
renWin = vtk.vtkRenderWindow()
renWin.SetSize(1024,1024)
renWin.AddRenderer(ren)
renWin.SetOffScreenRendering(1)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
pngfilename = p["outputfile"] + str(cubenum) + ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
#Shift camera angle and take snapshots around the cube.
for aznum in range(4):
camera.Azimuth(90)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-r" + str(aznum)+ ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(90) #Rotate camera to top
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-t1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(180) #Rotate camera to bottom
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-b1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold() #Dense represenation (0's included, structured grid)
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(4,4,4)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
#result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
def main(argv):
#Just get something working for testing...
try:
opts, args = getopt.getopt(argv,"hi:", ["ifile="])
except getopt.GetoptError as err:
print 'tviewer.py -i <inputfile.vtk>'
print (str(err))
for opt, arg in opts:
if opt == '-h':
print 'tviewer.py -i <inputfile.vtk>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
print("Going to load and view ", inputfile)
#Read data
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(inputfile)
reader.Update()
#lut = vtk.vtkLookupTable()
#lut.SetNumberOfColors(65535)
#lut.SetHueRange(0.0, 2.667)
#lut.SetVectorMode(vtk.vtkScalarsToColors.MAGNITUDE)
#lut.Build()
image = reader.GetOutput()
#image.SetSpacing(1,1,1)
#image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#Compute Q Criterion for texture mapping
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
#vorticity.SetComputeGradient(0)
vorticity.Update()
#Generate contour for comparison
c = vtk.vtkContourFilter()
#c.SetValue(0,1128)
c.SetValue(0,450)
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
#contour.GetCellData().SetScalars(image.GetPointData().GetVectors("Velocity"))
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(contour)
normals.SetFeatureAngle(45) #?
normals.Update()
print normals.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(normals.GetOutput())
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
#print image
#print contour
#mapper.SelectColorArray("Q-criterion")
#mapper.SetLookupTable(lut)
print mapper
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
ren.ResetCamera()
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600,600)
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
def MouseMove(self, data):
print("Load Cache %s" % data )
print ("Iren data")
#print iren
#addcube
#print ren
print ren.GetViewPoint()
print ren.GetDisplayPoint()
print ren.WorldToView()
print ren.ComputeVisiblePropBounds()
ysize = renWin.GetSize()[1]
c.SetValue(0,ysize)
c.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(c.GetOutput())
normals.SetFeatureAngle(25) #?
normals.Update()
normals.SetFeatureAngle(45) #?
normals.Update()
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputData(normals.GetOutput())
mapper2.ScalarVisibilityOn()
mapper2.SetScalarRange(-.5,1)
mapper2.SetScalarModeToUsePointFieldData()
mapper2.ColorByArrayComponent("Velocity", 0)
actor2 = vtk.vtkActor()
actor2.SetMapper(mapper2)
ren.AddActor(actor2)
iren.AddObserver("MiddleButtonPressEvent", MouseMove)
iren.SetRenderWindow(renWin)
iren.Initialize()
iren.Start()
#time.sleep(2)
print("adding another cube")
#iso64p2 iso64p2k1
#.006135923
import sys
import vtk
from vtk.util import numpy_support
r = vtk.vtkXMLImageDataReader()
r.SetFileName("iso128thresh.vti")
r.Update()
image = r.GetOutput()
#Copy velocity into vectors...
#image.GetPointData().SetCopyVectors(image.GetPointData().GetScalars())
threshold= (783.3)
vort = vtk.vtkGradientFilter()
vort.SetInputData(image)
vort.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vort.ComputeQCriterionOn()
vort.Update()
image.GetPointData().SetScalars(vort.GetOutput().GetPointData().GetArray("Q-criterion"))
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
c.SetInputData(image)
c.Update()
box = vtk.vtkBox()
#box.SetBounds(0,0.380427226,0,63,0,63)
box.SetBounds(0,64,0,64,0,64)
writer = vtk.vtkPNGWriter()
writer.SetWriteToMemory(1)
writer.SetInputConnection(windowToImageFilter.GetOutputPort())
writer.Write()
data = str(buffer(writer.GetResult()))
return Image(data)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(
"/home/stephenh/turbulence/sc/datasets/vtkscripts/iso64.vti")
reader.Update()
image = reader.GetOutput()
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.Update()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, 1128)
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(contour)
def main(argv):
try:
opts, args = getopt.getopt(argv, "hi:o:x:a:y:b:z:c:d:u:", [
"ifile=", "ofile=", "sx=", "ex=", "sy=", "ez=", "dataset=", "comp="
])
except getopt.GetoptError as err:
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset -comptype'
print(str(err))
for opt, arg in opts:
if opt == '-h':
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-x", "--sx"):
sx = int(arg)
elif opt in ("-a", "--ex"):
ex = int(arg)
elif opt in ("-y", "--sy"):
sy = int(arg)
elif opt in ("-b", "--ey"):
ey = int(arg)
elif opt in ("-z", "--sz"):
sz = int(arg)
elif opt in ("-c", "--ez"):
ez = int(arg)
elif opt in ("-d", "--dataset"):
dataset = str(arg)
elif opt in ("-u", "--du"):
comptype = str(arg)
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
ve = timeit.default_timer()
print("Generating contour")
ms = timeit.default_timer()
mag = vtk.vtkImageMagnitude()
for x in range(0, 1):
start = timeit.default_timer()
threshold = (22.39 * (2.5))
if (comptype == "q"):
threshold = (783.3)
vort = vtk.vtkGradientFilter()
vort.SetInputData(image)
vort.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vort.ComputeQCriterionOn()
vort.Update()
image.GetPointData().SetScalars(
vort.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
v = vtk.vtkCellDerivatives()
v.SetVectorModeToComputeVorticity()
v.SetTensorModeToPassTensors()
v.SetInputData(image)
v.Update()
vort = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(v.GetOutput())
cp.Update()
image.GetPointData().SetScalars(
cp.GetOutput().GetPointData().GetVectors())
vort.SetInputData(image)
vort.Update()
#ni = vtk.vtkImageData()
#ni.SetSpacing(.006135923, .006135923, .006135923)
#ni.SetExtent(sx,ex,sy,ey,sz,ez)
#ni.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mend = timeit.default_timer()
me = mend
comptime = mend - start
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0, threshold)
if (comptype == "q"):
c.SetInputData(image)
else:
c.SetInputData(vort.GetOutput())
print("Computing Contour with threshold", threshold)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile + str(x) + ".vtp ")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
print("Q Magnitude: %s" % str(me - ms))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Vorticity Magnitude: %s" % str(me - ms))
#print ("Threshold: %s" % str(te-ts))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
def main(argv):
#Just get something working for testing...
try:
opts, args = getopt.getopt(argv, "hi:", ["ifile="])
except getopt.GetoptError as err:
print 'tviewer.py -i <inputfile.vtk>'
print(str(err))
for opt, arg in opts:
if opt == '-h':
print 'tviewer.py -i <inputfile.vtk>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
print("Going to load and view ", inputfile)
#Read data
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(inputfile)
reader.Update()
#Setup offscreen rendering
graphics_factory = vtk.vtkGraphicsFactory()
graphics_factory.SetOffScreenOnlyMode(1)
graphics_factory.SetUseMesaClasses(1)
#Get image from reader
image = reader.GetOutput()
print("Image read in")
#compute q-criterion
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
print("Vorticity done")
#Get magnitude not sure we need it now. lets see.
#mag = vtk.vtkImageMagnitude()
#cp = vtk.vtkCellDataToPointData()
#cp.SetInputData(vorticity.GetOutput())
#cp.Update()
#image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
#mag.SetInputData(image)
#mag.Update()
#m = mag.GetOutput()
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
print image
#image.GetPointData().SetScalars(image.GetPointData().GetVectors("Velocity"))
c = vtk.vtkContourFilter()
#c.SetValue(0,1128)
c.SetValue(0, 600)
c.SetInputData(image)
c.Update()
#import pdb; pdb.set_trace()
contour = c.GetOutput()
#contour.GetCellData().SetScalars(image.GetPointData().GetVectors("Velocity"))
print "Contour done"
#normals = vtk.vtkPolyDataNormals()
#normals.SetInputData(contour)
#normals.SetFeatureAngle(45) #?
#normals.Update()
#print normals.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(contour)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1, 1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
#import pdb; pdb.set_trace()
print("mapped")
#print mapper
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1, 1, 1)
ren.ResetCamera()
#camera = vtk.vtkCamera()
#camera.SetPosition(0,0,0)
#camera.SetFocalPoint(0,0,0)
#ren.SetActiveCamera(camera)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 600)
renWin.AddRenderer(ren)
renWin.SetOffScreenRendering(1)
#import pdb; pdb.set_trace()
#iren = vtk.vtkRenderWindowInteractor()
#iren.SetRenderWindow(renWin)
#iren.Initialize()
#iren.Start()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
w.SetFileName("cube.png")
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
sorted_plap = final_plap[sort_indices]
output["PLAP/Final/%d" % (nprocs+1,)][:,1] = sorted_plap
output["PRT/Final/%d" % (nprocs+1,)][:,0] = final_indices[sort_indices]
sorted_prt = final_prt[sort_indices]
output["PRT/Final/%d" % (nprocs+1,)][:,1] = sorted_prt
coordinates_vtu_vtk = numpy_support.numpy_to_vtk(sorted_coordinates)
coordinates_vtu_vtk.SetName("Coordinates")
plap_vtu_vtk = numpy_support.numpy_to_vtk(sorted_plap)
plap_vtu_vtk.SetName("PLAP")
prt_vtu_vtk = numpy_support.numpy_to_vtk(sorted_prt)
prt_vtu_vtk.SetName("PRT")
domain_particles.GetOutput().GetPointData().AddArray(coordinates_vtu_vtk)
domain_particles.GetOutput().GetPointData().AddArray(plap_vtu_vtk)
domain_particles.GetOutput().GetPointData().AddArray(prt_vtu_vtk)
# Compute Right Cauchy Green tensor for FTLE
deformation_gradient = vtk.vtkGradientFilter()
deformation_gradient.SetInputConnection(domain_particles.GetOutputPort())
deformation_gradient.SetInputArrayToProcess(0,0,0,vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,"Coordinates")
deformation_gradient.Update()
deformation_gradient_tensor = numpy_support.vtk_to_numpy(deformation_gradient.GetOutput().GetPointData().GetArray("Gradients"))
deformation_gradient_tensor = np.reshape(deformation_gradient_tensor,(-1,3,3))
right_cauchy_green_tensor = np.einsum('abj,acj->abc',deformation_gradient_tensor,deformation_gradient_tensor)
eigvals = np.linalg.eigvals(right_cauchy_green_tensor)
eigvals = np.sort(eigvals,axis=1)
##### ADDED BY KEVIN ###############################################################################################
# Compute real part of eigenvalues, as VTK cannot accept complex numbers
# Occasionally the imaginary part is present, but equal to 0
real_eigvals = np.real(eigvals[:,2])
ftle = np.ascontiguousarray(np.log(real_eigvals))
##### END ##########################################################################################################
ftle_vtu_vtk = numpy_support.numpy_to_vtk(ftle)
def post_proc_cfd_diff(parameter_list):
dir_path = parameter_list[0]
vtu_input = parameter_list[1]
cell_type = parameter_list[1]
vtu_output_1 = parameter_list[3]
vtu_output_2 = parameter_list[4]
N_peak = parameter_list[5]
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(os.path.join(dir_path, vtu_input))
reader.Update()
N = reader.GetNumberOfTimeSteps()
print(N)
if (cell_type == "cell"):
vtk_process = vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS
vtk_data_type = vtk.vtkDataObject.CELL
else:
vtk_process = vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS
vtk_data_type = vtk.vtkDataObject.POINT
pass_arr = vtk.vtkPassArrays()
pass_arr.SetInputConnection(reader.GetOutputPort())
pass_arr.AddArray(vtk_data_type, "absolute_pressure")
pass_arr.AddArray(vtk_data_type, "x_wall_shear")
pass_arr.AddArray(vtk_data_type, "y_wall_shear")
pass_arr.AddArray(vtk_data_type, "z_wall_shear")
calc1 = vtk.vtkArrayCalculator()
calc1.SetFunction("sqrt(x_wall_shear^2+y_wall_shear^2+z_wall_shear^2)")
calc1.AddScalarVariable("x_wall_shear", "x_wall_shear", 0)
calc1.AddScalarVariable("y_wall_shear", "y_wall_shear", 0)
calc1.AddScalarVariable("z_wall_shear", "z_wall_shear", 0)
calc1.SetResultArrayName("WSS")
calc1.SetInputConnection(pass_arr.GetOutputPort())
if (cell_type == "cell"):
calc1.SetAttributeModeToUseCellData()
else:
calc1.SetAttributeModeToUsePointData()
calc1.SetResultArrayType(vtk.VTK_DOUBLE)
x_WSS_grad = vtk.vtkGradientFilter()
x_WSS_grad.SetInputConnection(calc1.GetOutputPort())
x_WSS_grad.ComputeGradientOn()
x_WSS_grad.FasterApproximationOff()
x_WSS_grad.ComputeDivergenceOff()
x_WSS_grad.ComputeVorticityOff()
x_WSS_grad.ComputeQCriterionOff()
x_WSS_grad.SetResultArrayName("x_WSS_grad")
x_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "x_wall_shear")
y_WSS_grad = vtk.vtkGradientFilter()
y_WSS_grad.SetInputConnection(x_WSS_grad.GetOutputPort())
y_WSS_grad.ComputeGradientOn()
y_WSS_grad.FasterApproximationOff()
y_WSS_grad.ComputeDivergenceOff()
y_WSS_grad.ComputeVorticityOff()
y_WSS_grad.ComputeQCriterionOff()
y_WSS_grad.SetResultArrayName("y_WSS_grad")
y_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "y_wall_shear")
z_WSS_grad = vtk.vtkGradientFilter()
z_WSS_grad.SetInputConnection(y_WSS_grad.GetOutputPort())
z_WSS_grad.ComputeGradientOn()
z_WSS_grad.FasterApproximationOff()
z_WSS_grad.ComputeDivergenceOff()
z_WSS_grad.ComputeVorticityOff()
z_WSS_grad.ComputeQCriterionOff()
z_WSS_grad.SetResultArrayName("z_WSS_grad")
z_WSS_grad.SetInputArrayToProcess(0, 0, 0, vtk_process, "z_wall_shear")
calc2 = vtk.vtkArrayCalculator()
calc2.AddScalarVariable("x_component", "x_WSS_grad", 0)
calc2.AddScalarVariable("y_component", "y_WSS_grad", 1)
calc2.AddScalarVariable("z_component", "z_WSS_grad", 2)
calc2.SetFunction("sqrt(x_component^2+y_component^2+z_component^2)")
calc2.SetResultArrayName("WSSG")
calc2.SetInputConnection(z_WSS_grad.GetOutputPort())
if (cell_type == "cell"):
calc2.SetAttributeModeToUseCellData()
else:
calc2.SetAttributeModeToUsePointData()
calc2.SetResultArrayType(vtk.VTK_DOUBLE)
# initialize the output to include the peak values
grid = vtk.vtkUnstructuredGrid()
#N_peak = 3
reader.SetTimeStep(N_peak)
calc2.Update()
print("loading peak: {0} timestep to copy data".format(
reader.GetTimeStep()))
grid.DeepCopy(calc2.GetOutput())
reader.SetTimeStep(0)
#reader.Update()
calc2.Update()
print("loading {0}th timestep for averaging initialization".format(
reader.GetTimeStep()))
stats = vtk.vtkTemporalStatistics()
stats.SetInputConnection(calc2.GetOutputPort())
stats.ComputeMaximumOff()
stats.ComputeMinimumOff()
stats.ComputeStandardDeviationOff()
stats.ComputeAverageOn()
stats.Update()
print("what's the time step after stats :{0}".format(reader.GetTimeStep()))
grid_out = vtk.vtkUnstructuredGrid()
grid_out.DeepCopy(stats.GetOutput())
if (cell_type == "cell"):
out_data = grid_out.GetCellData()
grid_data = grid.GetCellData()
else:
out_data = grid_out.GetPointData()
grid_data = grid.GetPointData()
print("update names")
out_data.AddArray(grid_data.GetArray("WSS"))
out_data.GetArray("WSS").SetName("WSS_peak")
out_data.AddArray(grid_data.GetArray("WSSG"))
out_data.GetArray("WSSG").SetName("WSSG_peak")
out_data.AddArray(grid_data.GetArray("absolute_pressure"))
out_data.GetArray("absolute_pressure").SetName("pressure_peak")
out_data.GetArray("WSS_average").SetName("TAWSS")
out_data.GetArray("WSSG_average").SetName("TAWSSG")
out_data.GetArray("absolute_pressure_average").SetName("pressure_average")
print("TAWSSVector")
calc3 = vtk.vtkArrayCalculator()
calc3.AddScalarVariable("x_wall_shear_average", "x_wall_shear_average", 0)
calc3.AddScalarVariable("y_wall_shear_average", "y_wall_shear_average", 0)
calc3.AddScalarVariable("z_wall_shear_average", "z_wall_shear_average", 0)
calc3.SetFunction(
"sqrt(x_wall_shear_average^2+y_wall_shear_average^2+z_wall_shear_average^2)"
)
calc3.SetResultArrayName("TAWSSVector")
calc3.SetInputData(grid_out)
if (cell_type == "cell"):
calc3.SetAttributeModeToUseCellData()
else:
calc3.SetAttributeModeToUsePointData()
calc3.SetResultArrayType(vtk.VTK_DOUBLE)
calc3.Update()
print("OSI")
calc4 = vtk.vtkArrayCalculator()
calc4.AddScalarVariable("TAWSSVector", "TAWSSVector", 0)
calc4.AddScalarVariable("TAWSS", "TAWSS", 0)
calc4.SetFunction("0.5*(1.0-(TAWSSVector/(TAWSS)))")
calc4.SetResultArrayName("OSI")
calc4.SetInputConnection(calc3.GetOutputPort())
if (cell_type == "cell"):
calc4.SetAttributeModeToUseCellData()
else:
calc4.SetAttributeModeToUsePointData()
calc4.SetResultArrayType(vtk.VTK_DOUBLE)
#calc4.Update()
# peak ratios
calc5 = vtk.vtkArrayCalculator()
calc5.AddScalarVariable("WSS_peak", "WSS_peak", 0)
calc5.AddScalarVariable("TAWSS", "TAWSS", 0)
calc5.SetFunction("WSS_peak/TAWSS")
calc5.SetResultArrayName("WSS_peak_q_TAWSS")
calc5.SetInputConnection(calc4.GetOutputPort())
if (cell_type == "cell"):
calc5.SetAttributeModeToUseCellData()
else:
calc5.SetAttributeModeToUsePointData()
calc5.SetResultArrayType(vtk.VTK_DOUBLE)
#calc5.Update()
calc6 = vtk.vtkArrayCalculator()
calc6.AddScalarVariable("WSSG_peak", "WSSG_peak", 0)
calc6.AddScalarVariable("TAWSSG", "TAWSSG", 0)
calc6.SetFunction("WSSG_peak/TAWSSG")
calc6.SetResultArrayName("WSSG_peak_q_TAWSSG")
calc6.SetInputConnection(calc5.GetOutputPort())
if (cell_type == "cell"):
calc6.SetAttributeModeToUseCellData()
else:
calc6.SetAttributeModeToUsePointData()
calc6.SetResultArrayType(vtk.VTK_DOUBLE)
calc7 = vtk.vtkArrayCalculator()
calc7.AddScalarVariable("pressure_peak", "pressure_peak", 0)
calc7.AddScalarVariable("pressure_average", "pressure_average", 0)
calc7.SetFunction("pressure_peak/pressure_average")
calc7.SetResultArrayName("pressure_peak_q_pressure_average")
calc7.SetInputConnection(calc6.GetOutputPort())
if (cell_type == "cell"):
calc7.SetAttributeModeToUseCellData()
else:
calc7.SetAttributeModeToUsePointData()
calc7.SetResultArrayType(vtk.VTK_DOUBLE)
pass_filt = vtk.vtkPassArrays()
pass_filt.SetInputConnection(calc7.GetOutputPort())
pass_filt.AddArray(vtk_data_type, "WSS_peak")
pass_filt.AddArray(vtk_data_type, "WSSG_peak")
pass_filt.AddArray(vtk_data_type, "pressure_peak")
pass_filt.AddArray(vtk_data_type, "pressure_average")
pass_filt.AddArray(vtk_data_type, "TAWSS")
pass_filt.AddArray(vtk_data_type, "TAWSSG")
pass_filt.AddArray(vtk_data_type, "OSI")
pass_filt.AddArray(vtk_data_type, "WSS_peak_q_TAWSS")
pass_filt.AddArray(vtk_data_type, "WSSG_peak_q_TAWSSG")
pass_filt.AddArray(vtk_data_type, "pressure_peak_q_pressure_average")
pass_filt.Update()
#if(cell_type == "cell"):
# print(pass_filt.GetOutput().GetCellData().GetArray("OSI").GetValue(0))
#else:
# print(pass_filt.GetOutput().GetPointData().GetArray("OSI").GetValue(0))
writer2 = vtk.vtkXMLUnstructuredGridWriter()
writer2.SetFileName(os.path.join(dir_path, vtu_output_2))
writer2.SetInputConnection(pass_filt.GetOutputPort())
writer2.Update()
def main(argv):
#Just get something working for testing...
try:
opts, args = getopt.getopt(argv,"hi:", ["ifile="])
except getopt.GetoptError as err:
print 'tviewer.py -i <inputfile.vtk>'
print (str(err))
for opt, arg in opts:
if opt == '-h':
print 'tviewer.py -i <inputfile.vtk>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
print("Going to load and view ", inputfile)
#Read data
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(inputfile)
reader.Update()
#lut = vtk.vtkLookupTable()
#lut.SetNumberOfColors(65535)
#lut.SetHueRange(0.0, 2.667)
#lut.SetVectorMode(vtk.vtkScalarsToColors.MAGNITUDE)
#lut.Build()
#Setup offscreen rendering
graphics_factory = vtk.vtkGraphicsFactory()
graphics_factory.SetOffScreenOnlyMode(1)
graphics_factory.SetUseMesaClasses(1)
#imaging_factory = vtk.vtkImagingFactory()
#imaging_factory.SetUseMesaClasses(1)
#Get image from reader
image = reader.GetOutput()
#image.SetSpacing(1,1,1)
#image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#Compute Q Criterion for texture mapping
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
#vorticity.SetComputeGradient(0)
vorticity.Update()
#Generate contour for comparison
c = vtk.vtkContourFilter()
#c.SetValue(0,1128)
c.SetValue(0,450)
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
#contour.GetCellData().SetScalars(image.GetPointData().GetVectors("Velocity"))
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(contour)
normals.SetFeatureAngle(45) #?
normals.Update()
#print normals.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(normals.GetOutput())
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
#print image
#print contour
#mapper.SelectColorArray("Q-criterion")
#mapper.SetLookupTable(lut)
#print mapper
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
ren.ResetCamera()
renWin = vtk.vtkRenderWindow()
renWin.SetSize(400,400)
renWin.SetOffScreenRendering(1)
renWin.AddRenderer(ren)
renWin.Render()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
w.SetFileName("cube.png")
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
def main(argv):
#Just get something working for testing...
try:
opts, args = getopt.getopt(argv,"hi:", ["ifile="])
except getopt.GetoptError as err:
print 'tviewer.py -i <inputfile.vtk>'
print (str(err))
for opt, arg in opts:
if opt == '-h':
print 'tviewer.py -i <inputfile.vtk>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
print("Going to load and view ", inputfile)
#Read data
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(inputfile)
reader.Update()
#Setup offscreen rendering
graphics_factory = vtk.vtkGraphicsFactory()
graphics_factory.SetOffScreenOnlyMode(1)
graphics_factory.SetUseMesaClasses(1)
#Get image from reader
image = reader.GetOutput()
print ("Image read in")
#compute q-criterion
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
print ("Vorticity done")
#Get magnitude not sure we need it now. lets see.
#mag = vtk.vtkImageMagnitude()
#cp = vtk.vtkCellDataToPointData()
#cp.SetInputData(vorticity.GetOutput())
#cp.Update()
#image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
#mag.SetInputData(image)
#mag.Update()
#m = mag.GetOutput()
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
print image
#image.GetPointData().SetScalars(image.GetPointData().GetVectors("Velocity"))
c = vtk.vtkContourFilter()
#c.SetValue(0,1128)
c.SetValue(0,600)
c.SetInputData(image)
c.Update()
#import pdb; pdb.set_trace()
contour = c.GetOutput()
#contour.GetCellData().SetScalars(image.GetPointData().GetVectors("Velocity"))
print "Contour done"
#normals = vtk.vtkPolyDataNormals()
#normals.SetInputData(contour)
#normals.SetFeatureAngle(45) #?
#normals.Update()
#print normals.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(contour)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
#import pdb; pdb.set_trace()
print ("mapped")
#print mapper
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
ren.ResetCamera()
#camera = vtk.vtkCamera()
#camera.SetPosition(0,0,0)
#camera.SetFocalPoint(0,0,0)
#ren.SetActiveCamera(camera)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600,600)
renWin.AddRenderer(ren)
renWin.SetOffScreenRendering(1)
#import pdb; pdb.set_trace()
#iren = vtk.vtkRenderWindowInteractor()
#iren.SetRenderWindow(renWin)
#iren.Initialize()
#iren.Start()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
w.SetFileName("cube.png")
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
def getvtkdata(self, ci, timestep):
PI= 3.141592654
contour=False
firstval = ci.datafields.split(',')[0]
#print ("First: ", firstval)
if ((firstval == 'vo') or (firstval == 'qc') or (firstval == 'cvo') or (firstval == 'pcvo') or (firstval == 'qcc')):
datafields = 'u'
computation = firstval #We are doing a computation, so we need to know which one.
if ((firstval == 'cvo') or (firstval == 'qcc') or (firstval == 'pcvo')):
overlap = 3 #This was 2, but due to rounding because of the spacing, 3 is required.
#Save a copy of the original request
oci = jhtdblib.CutoutInfo()
oci.xstart = ci.xstart
oci.ystart = ci.ystart
oci.zstart = ci.zstart
oci.xlen = ci.xlen
oci.ylen = ci.ylen
oci.zlen = ci.zlen
ci = self.expandcutout(ci, overlap) #Expand the cutout by the overlap
contour = True
else:
datafields = ci.datafields.split(',') #There could be multiple components, so we will have to loop
computation = ''
#Split component into list and add them to the image
#Check to see if we have a value for vorticity or q contour
fieldlist = list(datafields)
image = vtk.vtkImageData()
rg = vtk.vtkRectilinearGrid()
for field in fieldlist:
if (ci.xlen > 61 and ci.ylen > +61 and ci.zlen > 61 and ci.xstep ==1 and ci.ystep ==1 and ci.zstep ==1 and not contour):
#Do this if cutout is too large
#Note: we don't want to get cubed data if we are doing cubes for contouring.
data=GetData().getcubedrawdata(ci, timestep, field)
else:
data=GetData().getrawdata(ci, timestep, field)
vtkdata = numpy_support.numpy_to_vtk(data.flat, deep=True, array_type=vtk.VTK_FLOAT)
components = Datafield.objects.get(shortname=field).components
vtkdata.SetNumberOfComponents(components)
vtkdata.SetName(Datafield.objects.get(shortname=field).longname)
#We need to see if we need to subtract one on end of extent edges.
image.SetExtent(ci.xstart, ci.xstart+((ci.xlen+ci.xstep-1)/ci.xstep)-1, ci.ystart, ci.ystart+((ci.ylen+ci.ystep-1)/ci.ystep)-1, ci.zstart, ci.zstart+((ci.zlen+ci.zstep-1)/ci.zstep)-1)
#image.SetExtent(ci.xstart, ci.xstart+int(ci.xlen)-1, ci.ystart, ci.ystart+int(ci.ylen)-1, ci.zstart, ci.zstart+int(ci.zlen)-1)
image.GetPointData().AddArray(vtkdata)
if (Datafield.objects.get(shortname=field).longname == "Velocity"):
#Set the Velocity Array as vectors in the image.
image.GetPointData().SetVectors(image.GetPointData().GetArray("Velocity"))
#Get spacing from database and multiply it by the step. Don't do this on the contour--it is performed later on.
#if (contour):
#We need to scale the threshold to the spacing of the dataset. This is because we build the cubes
#on a 1 spacing cube in order to get proper overlap on the contours.
#ci.threshold = ci.threshold*Dataset.objects.get(dbname_text=ci.dataset).xspacing
#else:
xspacing = Dataset.objects.get(dbname_text=ci.dataset).xspacing
yspacing = Dataset.objects.get(dbname_text=ci.dataset).yspacing
zspacing = Dataset.objects.get(dbname_text=ci.dataset).zspacing
#Check if we need a rectilinear grid, and set it up if so.
if (ci.dataset == 'channel'):
ygrid = jhtdblib.JHTDBLib().getygrid()
#print("Ygrid: ")
#print (ygrid)
#Not sure about contouring channel yet, so we are going back to original variables at this point.
rg.SetExtent(ci.xstart, ci.xstart+((ci.xlen+ci.xstep-1)/ci.xstep)-1, ci.ystart, ci.ystart+((ci.ylen+ci.ystep-1)/ci.ystep)-1, ci.zstart, ci.zstart+((ci.zlen+ci.zstep-1)/ci.zstep)-1)
#components = Datafield.objects.get(shortname=field).components
#vtkdata.SetNumberOfComponents(components)
#vtkdata.SetName(Datafield.objects.get(shortname=field).longname)
rg.GetPointData().AddArray(vtkdata)
#import pdb;pdb.set_trace()
#This isn't possible--we will have to do something about this in the future.
#rg.SetSpacing(ci.xstep,ci.ystep,ci.zstep)
xg = np.arange(0,2047.0)
zg = np.arange(0,1535.0)
for x in xg:
xg[x] = 8*PI/2048*x
for z in zg:
zg[z] = 3*PI/2048*z
vtkxgrid=numpy_support.numpy_to_vtk(xg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkzgrid=numpy_support.numpy_to_vtk(zg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkygrid=numpy_support.numpy_to_vtk(ygrid,
deep=True, array_type=vtk.VTK_FLOAT)
rg.SetXCoordinates(vtkxgrid)
rg.SetZCoordinates(vtkzgrid)
rg.SetYCoordinates(vtkygrid)
image = rg #we rewrite the image since we may be doing a
#computation below
else:
image.SetSpacing(xspacing*ci.xstep,yspacing*ci.ystep,zspacing*ci.zstep)
#See if we are doing a computation
if (computation == 'vo'):
start = time.time()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
#print("Computing Vorticity")
vorticity.Update()
end = time.time()
comptime = end-start
print("Vorticity Computation time: " + str(comptime) + "s")
return image
elif (computation == 'cvo' or computation == 'pcvo'):
start = time.time()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
#print("Computing Voricity")
vorticity.Update()
vend = time.time()
comptime = vend-start
print("Vorticity Computation time: " + str(comptime) + "s")
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
#print("Computing magnitude")
cp.Update()
mend = time.time()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
comptime = mend-vend
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,ci.threshold)
c.SetInputData(mag.GetOutput())
print("Computing Contour with threshold", ci.threshold)
c.Update()
cend = time.time()
comptime = cend-mend
print("Contour Computation time: " + str(comptime) + "s")
#Now we need to clip out the overlap
box = vtk.vtkBox()
#set box to requested size
#The OCI deepcopy didn't seem to work. Manually taking the overlap again.
box.SetBounds(oci.xstart*xspacing, (oci.xstart+oci.xlen)*xspacing, oci.ystart*yspacing, (oci.ystart+oci.ylen)*yspacing, oci.zstart*yspacing,(oci.zstart+oci.zlen)*yspacing)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
#import pdb;pdb.set_trace()
cropdata = clip.GetOutput()
#Cleanup
image.ReleaseData()
#mag.ReleaseData()
#box.ReleaseData()
#clip.ReleaseData()
#image.Delete()
#box.Delete()
#vorticity.Delete()
end = time.time()
comptime = end-start
print("Total Computation time: " + str(comptime) + "s")
#return cropdata
#We need the output port for appending, so return the clip instead
return clip
elif (computation == 'qcc'):
start = time.time()
q = vtk.vtkGradientFilter()
q.SetInputData(image)
q.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
q.ComputeQCriterionOn()
q.Update()
image.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
#mag = vtk.vtkImageMagnitude()
#mag.SetInputData(image)
#mag.Update()
mend = time.time()
comptime = mend-start
#print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,ci.threshold)
c.SetInputData(image)
print("Computing Contour with threshold", ci.threshold)
c.Update()
cend = time.time()
comptime = cend-mend
print("Q Contour Computation time: " + str(comptime) + "s")
#clip out the overlap here
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(oci.xstart, oci.xstart+oci.xlen-1, oci.ystart, oci.ystart+oci.ylen-1, oci.zstart,oci.zstart+oci.zlen-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
end = time.time()
comptime = end-start
print("Computation time: " + str(comptime) + "s")
#return cropdata
return clip
else:
return image