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speed up of VTK data transformation

This commit is contained in:
chen 2016-09-08 18:05:49 -04:00
parent 59e8109ced
commit da538fbce9
2 changed files with 55 additions and 60 deletions
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72
processing/post/vtk_addPointcloudData.py
View File

@ -6,6 +6,7 @@ import damask
import numpy as np import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
from vtk.util import numpy_support
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
@ -14,10 +15,10 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption,
Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp). usage='%prog options [file[s]]',
description = """Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).""",
""", version = scriptID) version = scriptID)
parser.add_option( '--vtk', parser.add_option( '--vtk',
dest = 'vtk', dest = 'vtk',
@ -104,60 +105,57 @@ for name in filenames:
for datatype,dimension,label in [['scalar',1,options.scalar], for datatype,dimension,label in [['scalar',1,options.scalar],
['vector',3,options.vector], ['vector',3,options.vector],
['tensor',9,options.tensor], ['tensor',9,options.tensor],
['color',3,options.color], ['color' ,3,options.color],
]: ]:
for i,dim in enumerate(table.label_dimension(label)): for i,dim in enumerate(table.label_dimension(label)):
me = label[i] me = label[i]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me)) if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension)) elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else: else:
remarks.append('adding {} "{}"...'.format(datatype,me)) remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me) active[datatype].append(me)
if datatype in ['scalar','vector', 'tensor']: VTKarray[me] = vtk.vtkDoubleArray()
elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
VTKarray[me].SetNumberOfComponents(dimension)
VTKarray[me].SetName(label[i])
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:
damask.util.croak(errors) damask.util.croak(errors)
table.close(dismiss = True) table.close(dismiss = True)
continue continue
# ------------------------------------------ process data --------------------------------------- # --------------------------------------- process and add data -----------------------------------
while table.data_read(): # read next data line of ASCII table table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
for datatype,labels in active.items(): # loop over scalar,color for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items for me in labels: # loop over all requested items
theData = [float(table.data[i]) for i in table.label_indexrange(me)] # read strings VTKtype = vtk.VTK_DOUBLE
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*x),theData)) VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
elif datatype == 'scalar': VTKarray[me].InsertNextValue(theData[0])
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*theData)
elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
np.array(theData) \
.reshape(3,3).T \
.reshape(9)))
table.input_close() # close input ASCII table if datatype == 'color':
VTKtype = vtk.VTK_UNSIGNED_CHAR
VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
elif datatype == 'tensor':
VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
# ------------------------------------------ add data --------------------------------------- VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,array_type=VTKtype)
VTKarray[me].SetName(me)
for datatype,labels in active.items(): # loop over scalar,color if datatype == 'color':
if datatype == 'color': Polydata.GetPointData().SetScalars(VTKarray[me])
Polydata.GetPointData().SetScalars(VTKarray[active['color'][0]]) Polydata.GetCellData().SetScalars(VTKarray[me])
Polydata.GetCellData().SetScalars(VTKarray[active['color'][0]]) else:
for me in labels: # loop over all requested items Polydata.GetPointData().AddArray(VTKarray[me])
Polydata.GetPointData().AddArray(VTKarray[me]) Polydata.GetCellData().AddArray(VTKarray[me])
Polydata.GetCellData().AddArray(VTKarray[me])
table.input_close() # close input ASCII table
# ------------------------------------------ output result ---------------------------------------
Polydata.Modified() Polydata.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update() if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
# ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLPolyDataWriter() writer = vtk.vtkXMLPolyDataWriter()
writer.SetDataModeToBinary() writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib() writer.SetCompressorTypeToZLib()
@ -175,7 +173,7 @@ if options.render:
actor.SetMapper(mapper) actor.SetMapper(mapper)
# Create the graphics structure. The renderer renders into the # Create the graphics structure. The renderer renders into the
# render window. The render window interactor captures mouse events # render window. The render window interactively captures mouse events
# and will perform appropriate camera or actor manipulation # and will perform appropriate camera or actor manipulation
# depending on the nature of the events. # depending on the nature of the events.

43
processing/post/vtk_addRectilinearGridData.py
View File

@ -4,6 +4,7 @@
import os,vtk import os,vtk
import damask import damask
import numpy as np import numpy as np
from vtk.util import numpy_support
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
@ -102,22 +103,16 @@ for name in filenames:
for datatype,dimension,label in [['scalar',1,options.scalar], for datatype,dimension,label in [['scalar',1,options.scalar],
['vector',3,options.vector], ['vector',3,options.vector],
['tensor',9,options.tensor], ['tensor',9,options.tensor],
['color',3,options.color], ['color' ,3,options.color],
]: ]:
for i,dim in enumerate(table.label_dimension(label)): for i,dim in enumerate(table.label_dimension(label)):
me = label[i] me = label[i]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me)) if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension)) elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else: else:
remarks.append('adding {} "{}"...'.format(datatype,me)) remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me) active[datatype].append(me)
if datatype in ['scalar','vector','tensor']: VTKarray[me] = vtk.vtkDoubleArray()
elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
VTKarray[me].SetNumberOfComponents(dimension)
VTKarray[me].SetName(label[i])
if remarks != []: damask.util.croak(remarks) if remarks != []: damask.util.croak(remarks)
if errors != []: if errors != []:
damask.util.croak(errors) damask.util.croak(errors)
@ -126,28 +121,30 @@ for name in filenames:
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
datacount = 0 table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
while table.data_read(): # read next data line of ASCII table for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items
VTKtype = vtk.VTK_DOUBLE
VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
datacount += 1 # count data lines if datatype == 'color':
for datatype,labels in active.items(): # loop over scalar,color VTKtype = vtk.VTK_UNSIGNED_CHAR
for me in labels: # loop over all requested items VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings elif datatype == 'tensor':
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0])) VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData)) VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
np.array(theData) \ VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,array_type=VTKtype)
.reshape(3,3).T \ VTKarray[me].SetName(me)
.reshape(9)))
table.close() # close input ASCII table table.close() # close input ASCII table
# ------------------------------------------ add data --------------------------------------- # ------------------------------------------ add data ---------------------------------------
if datacount == Npoints: mode = 'point' if len(table.data) == Npoints: mode = 'point'
elif datacount == Ncells: mode = 'cell' elif len(table.data) == Ncells: mode = 'cell'
else: else:
damask.util.croak('Data count is incompatible with grid...') damask.util.croak('Data count is incompatible with grid...')
continue continue