I am using Julia to write .hdf files and I need to write a version with PolyData type. VTK File Formats - VTK documentation
The docs mention test_poly_data.hdf, I would like to have it as a file I can open. Please don’t tell me I have to compile the whole of Paraview for one file 
Can I find it on Gitlab/Github somewhere?
Kind regards
Thanks!
Do you know where I can find a multi-block example of vtkhdf using PolyData ?
I understand I can save multiple / time transient data in it?
Kind regards
Hello @AhmedSalih3d,
In the data from the link shared by mathieu there is only a PartitionDataSetCollection example named test_composite.hdf.
It contains polydata, imagedata and an unstructured grid.
However you can also generate a valid multiblock example from this repository: https://gitlab.kitware.com/keu-public/vtkhdf/vtkhdf-scripts. It contains several python scripts to generate valid VTKHDF file.
If you edit this line by replacing PartitionedDataSetCollection to MultiBlockDataSet, you should be able to generate a multiblock dataset with pvpython.
I understand I can save multiple / time transient data in it?
Yes!
Best,
Thanks!
I was able to install everything correctly and now able to generate the hdf file. I need a bit of help though. What I want to do is save a particle simulation (Smoothed Particle Hydrodynamics), i.e. no connectivity etc. I then want to update the particle position and properties over time in a single vtkhdf file. Currently I have:
import numpy as np
import h5py as h5
from vtkmodules.vtkCommonCore import vtkDoubleArray
from vtkmodules.vtkCommonDataModel import vtkPolyData
from vtkmodules.vtkFiltersCore import vtkAppendFilter
from vtkmodules.vtkFiltersGeometry import vtkGeometryFilter
from vtkmodules.vtkFiltersSources import vtkSphereSource
from vtkmodules.vtkIOXML import vtkXMLPolyDataWriter
import vtkmodules.numpy_interface.dataset_adapter as dsa
from vtkmodules.util.numpy_support import (numpy_to_vtk as npvtk, vtk_to_numpy as vtknp)
fType = 'f'
idType = 'i8'
connectivities = ['Vertices', 'Lines', 'Polygons', 'Strips']
# -----------------------------------------------------------------
def generate_geometry_structure(root):
root.attrs['Version'] = (2,1)
ascii_type = 'PolyData'.encode('ascii')
root.attrs.create('Type', ascii_type, dtype=h5.string_dtype('ascii', len(ascii_type)))
root.create_dataset('NumberOfPoints', (0,), maxshape=(None,), dtype=idType)
root.create_dataset('Points', (0,3), maxshape=(None,3), dtype=fType)
for connect in connectivities:
group = root.create_group(connect)
group.create_dataset('NumberOfConnectivityIds', (0,), maxshape=(None,), dtype=idType)
group.create_dataset('NumberOfCells', (0,), maxshape=(None,), dtype=idType)
group.create_dataset('Offsets', (0,), maxshape=(None,), dtype=idType)
group.create_dataset('Connectivity', (0,), maxshape=(None,), dtype=idType)
pData = root.create_group('PointData')
pData.create_dataset('Warping', (0,3), maxshape=(None,3), dtype=fType)
pData.create_dataset('Normals', (0,3), maxshape=(None,3), dtype=fType)
cData = root.create_group('CellData')
cData.create_dataset('Materials', (0,), maxshape=(None,), dtype=idType)
# -----------------------------------------------------------------
def generate_step_structure(root):
steps = root.create_group('Steps')
steps.attrs['NSteps'] = 0
steps.create_dataset('Values', (0,), maxshape=(None,), dtype=fType)
singleDSs = ['PartOffsets', 'NumberOfParts', 'PointOffsets']
for name in singleDSs:
steps.create_dataset(name, (0,), maxshape=(None,), dtype=idType)
nTopoDSs = ['CellOffsets', 'ConnectivityIdOffsets']
for name in nTopoDSs:
steps.create_dataset(name, (0,4), maxshape=(None,4), dtype=idType)
pData = steps.create_group('PointDataOffsets')
pData.create_dataset('Warping', (0,), maxshape=(None,), dtype=idType)
pData.create_dataset('Normals', (0,), maxshape=(None,), dtype=idType)
cData = steps.create_group('CellDataOffsets')
cData.create_dataset('Materials', (0,), maxshape=(None,), dtype=idType)
# -----------------------------------------------------------------
def append_data(root, poly_data, newStep=None, geometryOffset=None):
if not newStep == None:
steps = root['Steps']
steps.attrs['NSteps'] = steps.attrs['NSteps'] + 1
append_dataset(steps['Values'], np.array([newStep]))
geomOffs = []
if geometryOffset == None:
geomOffs.append(root['NumberOfPoints'].shape[0])
geomOffs.append(1)
geomOffs.append(root['Points'].shape[0])
for connect in connectivities:
geomOffs.append(root[connect + '/Offsets'].shape[0] - geomOffs[0])
for connect in connectivities:
geomOffs.append(root[connect + '/Connectivity'].shape[0])
else:
geomOffs.append(steps['PartOffsets'][geometryOffset])
geomOffs.append(1)
geomOffs.append(steps['PointOffsets'][geometryOffset])
for iC in range(len(connectivities)):
geomOffs.append(steps['CellOffsets'][geometryOffset, iC])
for connect in connectivities:
geomOffs.append(steps['ConnectivityIdOffsets'][geometryOffset, iC])
append_dataset(steps['PartOffsets'], np.array([geomOffs[0]]))
append_dataset(steps['NumberOfParts'], np.array([geomOffs[1]]))
append_dataset(steps['PointOffsets'], np.array([geomOffs[2]]))
append_dataset(steps['CellOffsets'], np.array(geomOffs[3:3+len(connectivities)]).reshape(1, len(connectivities)))
append_dataset(steps['ConnectivityIdOffsets'], np.array(geomOffs[3+len(connectivities):3+2*len(connectivities)]).reshape(1, len(connectivities)))
append_dataset(steps['PointDataOffsets/Warping'], np.array([root['PointData/Warping'].shape[0]]))
append_dataset(steps['PointDataOffsets/Normals'], np.array([root['PointData/Normals'].shape[0]]))
append_dataset(steps['CellDataOffsets/Materials'], np.array([root['CellData/Materials'].shape[0]]))
else:
steps = root['Steps']
steps['NumberOfParts'][-1] += 1
if geometryOffset == None:
append_dataset(root['NumberOfPoints'], np.array([poly_data.GetNumberOfPoints()]))
append_dataset(root['Points'], poly_data.Points)
cellArrays = [poly_data.GetVerts(), poly_data.GetLines(), poly_data.GetPolys(), poly_data.GetStrips()]
for name, connect in zip(connectivities, cellArrays):
ca = vtknp(connect.GetConnectivityArray())
append_dataset(root[name]['NumberOfConnectivityIds'], np.array([ca.shape[0]]))
append_dataset(root[name]['Connectivity'], ca)
oa = vtknp(connect.GetOffsetsArray())
append_dataset(root[name]['NumberOfCells'], np.array([oa.shape[0]-1]))
append_dataset(root[name]['Offsets'], oa)
append_dataset(root['PointData']['Warping'], poly_data.PointData['Warping'])
append_dataset(root['PointData']['Normals'], poly_data.PointData['Normals'])
append_dataset(root['CellData']['Materials'], poly_data.CellData['Materials'])
# -----------------------------------------------------------------
def append_dataset(dset, array):
origLen = dset.shape[0]
dset.resize(origLen + array.shape[0], axis=0)
dset[origLen:] = array
# -----------------------------------------------------------------
def generate_static_spheres():
sphereSrc0 = vtkSphereSource()
sphereSrc0.Update()
sphere0 = dsa.WrapDataObject(sphereSrc0.GetOutput())
sphereSrc1 = vtkSphereSource()
sphereSrc1.SetCenter(2.0, 2.0, 2.0)
sphereSrc1.SetThetaResolution(20)
sphereSrc1.SetPhiResolution(20)
sphereSrc1.Update()
sphere1 = dsa.WrapDataObject(sphereSrc1.GetOutput())
warping0 = npvtk(np.cross(sphere0.Points, [0, 0, 1]).astype(fType))
warping0.SetName('Warping')
sphere0.GetPointData().AddArray(warping0)
warping1 = npvtk(np.cross(sphere1.Points - [2, 2, 2], [0, 0, 1]).astype(fType))
warping1.SetName('Warping')
sphere1.GetPointData().AddArray(warping1)
mats0 = npvtk(np.full((sphere0.GetNumberOfCells(),), 0, dtype=idType))
mats0.SetName('Materials')
sphere0.GetCellData().AddArray(mats0)
mats1 = npvtk(np.full((sphere1.GetNumberOfCells(),), 1, dtype=idType))
mats1.SetName('Materials')
sphere1.GetCellData().AddArray(mats1)
return [sphere0]
# -----------------------------------------------------------------
def generate_morphing_spheres(t, morphGeometry=False):
pds = generate_static_spheres()
for pd in pds:
mod = (np.sin(pd.Points[:, 0]) + np.sin(pd.Points[:,1])+1)*np.cos(np.pi*t)/2.0
if morphGeometry:
pd.Points = pd.Points * mod
warped = npvtk(pd.PointData['Warping'] * mod)
warped.SetName('Warping')
pd.GetPointData().AddArray(warped)
return pds
# -----------------------------------------------------------------
def write_vtp(filepath, pds):
appender = vtkAppendFilter()
for iPD, pd in enumerate(pds):
appender.AddInputData(pd.VTKObject)
appender.Update()
surface = vtkGeometryFilter()
surface.SetInputConnection(appender.GetOutputPort())
surface.Update()
writer = vtkXMLPolyDataWriter()
writer.SetFileName(filepath)
writer.SetInputConnection(surface.GetOutputPort())
writer.Update()
# -----------------------------------------------------------------
def generate_data(root):
generate_geometry_structure(root)
generate_step_structure(root)
# ts = np.linspace(0.0, 0.5, 6)
# for iT, t in enumerate(ts):
# pds = generate_morphing_spheres(t)
# append_data(root, pds[0], newStep=t, geometryOffset=(None if t == 0.0 else 0))
# write_vtp('hdf_transient_poly_data_' + str(iT).zfill(3) + '.vtp', pds)
ts = np.linspace(0.6, 0.9, 4)
for iT, t in enumerate(ts):
pds = generate_morphing_spheres(t, True)
append_data(root, pds[0], newStep=t, geometryOffset=None)
# write_vtp('hdf_transient_poly_data_' + str(iT + 6).zfill(3) + '.vtp', pds)
# -----------------------------------------------------------------
if __name__ == "__main__":
f = h5.File('polydata_transient.vtkhdf', 'w')
root = f.create_group('VTKHDF')
generate_data(root)
f.close()
Where I commented out some code to generate the individual files etc. these are not of interest for me, only the combined final one is.
I downloaded VTKData-9.3.0.tar.gz but after untaring it crated an empty folder called VTKData-9.3.0
Where is the test_poly_data.hdf5?