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#!/bin/env python
from __future__ import print_function
from Xdmf import *
from vtk import *
from libvtkXdmfPython import *
class DataParser :
CellTypes = {
1 : 'Vertex',
2 : 'PolyVertex',
3 : 'Line',
4 : 'PolyLine',
5 : 'Triangle',
6 : 'TriangleStrip',
7 : 'Polygon',
8 : 'Pixel',
9 : 'Quadrilateral',
10 : 'Tetrahedron',
11 : 'Voxel',
12 : 'Hexahedron',
13 : 'Wedge',
14 : 'Pyramid',
99 : 'Unknown'
}
def __init__(self) :
self.DOM = XdmfDOM()
self.Root = XdmfRoot()
self.Root.SetDOM(self.DOM)
self.Root.SetVersion(2.0)
self.Root.Build()
self.Root.DebugOn()
self.Domain = XdmfDomain()
self.Root.Insert(self.Domain)
self.MainGrid = XdmfGrid()
self.MainGrid.SetName('Main Grid')
self.MainGrid.SetGridType(XDMF_GRID_TREE)
self.Domain.Insert(self.MainGrid)
self.Grids = []
self.Arrays = []
def ParseUGrid(self, UGrid) :
if UGrid.IsHomogeneous() :
print ('Homogeneous UGrid ', UGrid)
Fd = UGrid.GetFieldData()
if Fd :
NameArray = Fd.GetArray('Name')
print ('NameArray = ', NameArray)
print ('name = ', NameArray.GetValue(0))
CellArray = UGrid.GetCells()
Conns = CellArray.GetData()
print ('%d Cells' % UGrid.GetNumberOfCells())
for i in range(UGrid.GetNumberOfCells()) :
print ('(%d) %d = %s' % (i, UGrid.GetCellType(i), self.CellTypes[UGrid.GetCellType(i)]))
print ('%d Points' % UGrid.GetNumberOfPoints())
for i in range(UGrid.GetNumberOfPoints()) :
x, y, z = UGrid.GetPoint(i)
print ('(%d) %f %f %f' % (i, x, y, z))
print ('%d Connections' % CellArray.GetNumberOfConnectivityEntries())
i = 0
while i < Conns.GetNumberOfTuples() :
n = Conns.GetValue(i)
i += 1
for j in range(n) :
p = Conns.GetValue(i)
i += 1
print ('%d ' % p)
Pd = UGrid.GetPointData()
print ('# of Point Attributes = %d' % Pd.GetNumberOfArrays())
for i in range(Pd.GetNumberOfArrays()) :
Pa = Pd.GetArray(i)
print (Pd.GetArrayName(i), ' = ',Pa)
for j in range(Pa.GetNumberOfTuples()) :
print ('(%d) %f' % (j, Pa.GetValue(j)))
Cd = UGrid.GetCellData()
print ('# of Cell Attributes = %d' % Cd.GetNumberOfArrays())
# print (UGrid)
else :
print ('Heterogeneous UGrid')
def DataArrayToXdmfArray(self, da) :
# print ('Converting ', da)
print ('Data Type', da.GetDataType(), ' = ', da.GetDataTypeAsString())
Xda = XdmfArray()
Xda.SetNumberOfElements(da.GetNumberOfTuples() * da.GetNumberOfComponents())
Type = da.GetDataTypeAsString()
pntr = da.GetVoidPointer(0)
Xpntr = VoidPointerHandleToXdmfPointer(pntr)
if Type.upper() == 'FLOAT' :
# print ('Array is Float32')
Xda.SetNumberType(XDMF_FLOAT32_TYPE)
elif Type.upper() == 'INT' :
# print ('Array is Int32')
Xda.SetNumberType(XDMF_INT32_TYPE)
elif Type.upper() == 'DOUBLE' :
# print ('Array is Float64')
Xda.SetNumberType(XDMF_FLOAT64_TYPE)
elif Type.upper() == 'LONG' :
# print ('Array is Int64')
Xda.SetNumberType(XDMF_INT64_TYPE)
elif Type.upper() == 'IDTYPE' :
# print ('Array is Int64')
Xda.SetNumberType(XDMF_INT64_TYPE)
else :
print ('Illegal NumberType : ', Type)
return None
Xda.SetDataPointer(Xpntr)
print ('Values ',Xda.GetValues(0, 10))
return Xda
def WriteIGrid(self, IGrid, Group, Index) :
print ('Homogeneous Image UGrid ', IGrid.GetDimensions())
def WriteUGrid(self, UGrid, Group, Index) :
if UGrid.IsHomogeneous() :
print ('Homogeneous UGrid ')
Fd = UGrid.GetFieldData()
if Fd :
NameArray = Fd.GetArray('Name')
print ('NameArray = ', NameArray)
print ('name = ', NameArray.GetValue(0))
Xgrid = XdmfGrid()
Xgrid.SetName('Group %05d Index %05d' % (Group, Index))
self.MainGrid.Insert(Xgrid)
self.Grids.append(Xgrid)
CellArray = UGrid.GetCells()
Conns = CellArray.GetData()
XConns = self.DataArrayToXdmfArray(Conns)
print ('%d Cells' % UGrid.GetNumberOfCells())
NodesPerElement = XConns.GetValueAsInt64(0)
print ('%d NodesPerElement' % NodesPerElement)
XConns.SetShapeFromString("%d %d" % (UGrid.GetNumberOfCells(), NodesPerElement + 1))
print ('Shape ', XConns.GetShapeAsString())
Start = '0 1'
Stride = '1 1'
Count = '%d %d' % (UGrid.GetNumberOfCells(), NodesPerElement)
XConns.SelectHyperSlabFromString(Start, Stride, Count)
Xtop = Xgrid.GetTopology()
Xtop.SetTopologyTypeFromString(self.CellTypes[UGrid.GetCellType(0)])
Xtop.SetNumberOfElements(UGrid.GetNumberOfCells())
H5 = XdmfHDF()
H5.CopyType(XConns)
H5.SetShapeFromString(Count)
H5.Open('CORE:Data.h5:Group %05d/Index %05d/Conns' % (Group, Index), 'rw')
H5.Write(XConns)
JustConns = XdmfArray()
JustConns.CopyType(H5)
JustConns.CopyShape(H5)
H5.Read(JustConns)
Xtop.SetConnectivity(JustConns)
H5.Close()
self.Arrays.append(JustConns)
# for i in range(UGrid.GetNumberOfCells()) :
# print ('(%d) %d = %s' % (i, UGrid.GetCellType(i), self.CellTypes[UGrid.GetCellType(i)]))
print ('%d Points' % UGrid.GetNumberOfPoints())
pnts = UGrid.GetPoints().GetData()
# print ("Points = ", pnts)
Xpnts = self.DataArrayToXdmfArray(pnts)
Xgeo = Xgrid.GetGeometry()
Xgeo.SetGeometryType(XDMF_GEOMETRY_XYZ)
Xgeo.SetPoints(Xpnts)
self.Arrays.append(Xpnts)
# H5 = XdmfHDF()
# H5.CopyType(Xpnts)
# H5.CopyShape(Xpnts)
# H5.Open('Data.h5:Group %05d/Index %05d/XYZ' % (Group, Index), 'rw')
# H5.Write(Xpnts)
# H5.Close()
# for i in range(UGrid.GetNumberOfPoints()) :
# x, y, z = UGrid.GetPoint(i)
# print ('(%d) %f %f %f' % (i, x, y, z))
# print ('%d Connections' % CellArray.GetNumberOfConnectivityEntries())
# i = 0
# while i < Conns.GetNumberOfTuples() :
# n = Conns.GetValue(i)
# i += 1
# for j in range(n) :
# p = Conns.GetValue(i)
# i += 1
# print ('%d ' % p)
Pd = UGrid.GetPointData()
print ('# of Point Attributes = %d' % Pd.GetNumberOfArrays())
for i in range(Pd.GetNumberOfArrays()) :
Pa = Pd.GetArray(i)
Xpa = self.DataArrayToXdmfArray(Pa)
Xattr = XdmfAttribute()
Xattr.SetName("Point Attribute %d" % i)
Xattr.SetAttributeCenter(XDMF_ATTRIBUTE_CENTER_NODE)
Xattr.SetAttributeType(XDMF_ATTRIBUTE_TYPE_SCALAR)
Xattr.SetValues(Xpa)
Xgrid.Insert(Xattr)
self.Arrays.append(Xpa)
self.Arrays.append(Xattr)
# self.Arrays.append(Xpa)
# print (Pd.GetArrayName(i), ' = ',Pa)
# for j in range(Pa.GetNumberOfTuples()) :
# print ('(%d) %f' % (j, Pa.GetValue(j)))
Cd = UGrid.GetCellData()
print ('# of Cell Attributes = %d' % Cd.GetNumberOfArrays())
for i in range(Cd.GetNumberOfArrays()) :
Ca = Cd.GetArray(i)
Xca = self.DataArrayToXdmfArray(Ca)
Xattr = XdmfAttribute()
Xattr.SetName("Cell Attribute %d" % i)
Xattr.SetAttributeCenter(XDMF_ATTRIBUTE_CENTER_CELL)
Xattr.SetAttributeType(XDMF_ATTRIBUTE_TYPE_SCALAR)
Xattr.SetValues(Xca)
Xgrid.Insert(Xattr)
self.Arrays.append(Xca)
self.Arrays.append(Xattr)
# print (UGrid)
else :
print ('Heterogeneous UGrid')
def ParseMultiGroup(self, Output) :
print ('Parsing a vtkMultiGroupDataSet ')
NGroups = Output.GetNumberOfGroups()
print ('Output has %d Groups' % NGroups)
for g in range(NGroups) :
NDataSets = Output.GetNumberOfDataSets(g)
print ('Group %d has %d DataSets' % (g + 1, NDataSets))
for i in range(NDataSets) :
ds = Output.GetDataSet(g,i)
print ('Output Group %d Index %d (%s) has %d Cells' % (g + 1, i + 1, ds.GetClassName(), ds.GetNumberOfCells()))
if ds.IsA('vtkUnstructuredGrid') :
self.ParseUGrid(ds)
self.WriteUGrid(ds, g, i)
if ds.IsA('vtkImageData') :
self.WriteIGrid(ds, g, i)
else :
print ('Can not handle vtk class = ', ds.GetClassName())
def Parse(self, Output) :
if Output.IsA('vtkMultiGroupDataSet') :
self.ParseMultiGroup(Output)
else :
print ('Can not handle vtk class = ', Output.GetClassName())
if __name__ == '__main__' :
# Reader = vtkXdmfReader()
Reader = vtkXMLMultiGroupDataReader()
# Reader = vtkXMLDataReader()
# Controller = vtkMPIController()
# Reader.SetController(Controller)
# ProcId = Reader.GetController().GetLocalProcessId()
# NumProcs = Reader.GetController().GetNumberOfProcesses()
# print ('Hello from %d of %d' % (ProcId, NumProcs))
# Reader.SetFileName('Points1.xmf')
# Reader.SetFileName('VtkTest.pvd')
Reader.SetFileName('VtkMulti.vtm')
Reader.UpdateInformation()
# Reader.DisableAllGrids()
# Reader.EnableGrid(2)
# Reader.DebugOn()
# Reader.EnableAllGrids()
# Reader.EnableAllArrays()
# Reader.DisableGrid(0)
# Reader.DisableGrid(1)
Reader.Update()
p = DataParser()
print ('Reader has %d outputs' % Reader.GetNumberOfOutputPorts())
for on in range(Reader.GetNumberOfOutputPorts()) :
print ('Reading Output ', on)
Output = Reader.GetOutput(on)
p.Parse(Output)
p.Root.Build()
print (p.DOM.Serialize())
p.DOM.Write('junk.xmf')
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