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convertExodusToMatlab.py
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# import vtk and numpy
import vtk, numpy
def CreateVTKImage(imageDimensions,imageSpacing,imageOrigin):
# imports raw data and stores it.
dataImporter = vtk.vtkImageImport()
# array is converted to a string of chars and imported.
# numpy array stored as ROW MAJOR
# MUST write out in COLUMN MAJOR format to be the same as VTK
data_string = numpy.zeros(imageDimensions,dtype=numpy.float,order='F').tostring(order='F')
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
# The type of the newly imported data is set to unsigned char (uint8)
dataImporter.SetDataScalarTypeToDouble()
# Because the data that is imported only contains an intensity value (it isnt RGB-coded or someting similar), the importer
# must be told this is the case.
dataImporter.SetNumberOfScalarComponents(1)
# The following two functions describe how the data is stored and the dimensions of the array it is stored in. For this
# simple case, all axes are of length 75 and begins with the first element. For other data, this is probably not the case.
# I have to admit however, that I honestly dont know the difference between SetDataExtent() and SetWholeExtent() although
# VTK complains if not both are used.
dataImporter.SetDataExtent( 0, imageDimensions[0]-1, 0, imageDimensions[1]-1, 0, imageDimensions[2]-1)
dataImporter.SetWholeExtent(0, imageDimensions[0]-1, 0, imageDimensions[1]-1, 0, imageDimensions[2]-1)
dataImporter.SetDataSpacing( imageSpacing )
dataImporter.SetDataOrigin( imageOrigin )
dataImporter.SetScalarArrayName( "scalars" )
dataImporter.Update()
return dataImporter.GetOutput()
####################################################################
def ProjectImagingMesh(ini_file):
import vtk.util.numpy_support as vtkNumPy
import ConfigParser
import scipy.io as scipyio
# echo vtk version info
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
# read config file
config = ConfigParser.ConfigParser()
config.add_section("imaging")
config.add_section("fem")
config.set("imaging","listoffset","[0]")
config.read(ini_file)
# get work directory
work_dir = config.get('fem','work_dir')
# FIXME notice that order of operations is IMPORTANT
# FIXME translation followed by rotation will give different results
# FIXME than rotation followed by translation
# FIXME Translate -> RotateZ -> RotateY -> RotateX -> Scale seems to be the order of paraview
RotateX = float(config.get('fem','rotatex'))
RotateY = float(config.get('fem','rotatey'))
RotateZ = float(config.get('fem','rotatez'))
Translate = eval(config.get('fem','translate'))
Scale = eval(config.get('fem','scale'))
print "rotate", RotateX , RotateY , RotateZ ,"translate", Translate, "scale", Scale
# read imaging data geometry that will be used to project FEM data onto
dimensions = eval(config.get('imaging','dimensions'))
spacing = eval(config.get('imaging','spacing'))
origin = eval(config.get('imaging','origin'))
print spacing, origin, dimensions
templateImage = CreateVTKImage(dimensions,spacing,origin)
# write template image for position verification
vtkTemplateWriter = vtk.vtkDataSetWriter()
vtkTemplateWriter.SetFileName( "%s/imageTemplate.vtk" % work_dir )
vtkTemplateWriter.SetInput( templateImage )
vtkTemplateWriter.Update()
#setup to interpolate at 5 points across axial dimension
TransformList = []
listoffset = eval(config.get('imaging','listoffset'))
naverage = len(listoffset)
try:
subdistance = spacing[2] / (naverage-1)
except ZeroDivisionError:
subdistance = 0.0 # default is not to offset
print "listoffset",listoffset, "subspacing distance = ", subdistance
for idtransform in listoffset:
AffineTransform = vtk.vtkTransform()
AffineTransform.Translate( Translate[0],Translate[1],
Translate[2] + subdistance*idtransform )
AffineTransform.RotateZ( RotateZ )
AffineTransform.RotateY( RotateY )
AffineTransform.RotateX( RotateX )
AffineTransform.Scale( Scale )
TransformList.append( AffineTransform )
#laserTip = AffineTransform.TransformPoint( laserTip )
#laserOrientation = AffineTransform.TransformVector( laserOrientation )
# Interpolate FEM onto imaging data structures
vtkExodusIIReader = vtk.vtkExodusIIReader()
#vtkExodusIIReader.SetFileName( "%s/fem_stats.e" % work_dir )
#vtkExodusIIReader.SetPointResultArrayStatus("Mean0",1)
#vtkExodusIIReader.SetPointResultArrayStatus("StdDev0",1)
#Timesteps = 120
meshFileList = eval(config.get('fem','mesh_files'))
print meshFileList
for mesh_filename in meshFileList:
vtkExodusIIReader.SetFileName( "%s/%s" % (work_dir,mesh_filename) )
#vtkExodusIIReader.SetPointResultArrayStatus("Vard0Mean",1)
#vtkExodusIIReader.SetPointResultArrayStatus("Vard0Kurt",1)
vtkExodusIIReader.Update()
numberofresultarrays = vtkExodusIIReader.GetNumberOfPointResultArrays()
print numberofresultarrays
for resultarrayindex in range(numberofresultarrays):
resultarrayname = vtkExodusIIReader.GetPointResultArrayName(resultarrayindex)
vtkExodusIIReader.SetPointResultArrayStatus( "%s" % (resultarrayname),1)
print resultarrayname
vtkExodusIIReader.Update()
ntime = vtkExodusIIReader.GetNumberOfTimeSteps()
#print ntime
#for timeID in range(69,70):
for timeID in range(ntime):
vtkExodusIIReader.SetTimeStep(timeID)
vtkExodusIIReader.Update()
# reflect
vtkReflectX = vtk.vtkReflectionFilter()
vtkReflectX.SetPlaneToXMin()
vtkReflectX.SetInput( vtkExodusIIReader.GetOutput() )
vtkReflectX.Update()
# reflect
vtkReflectY = vtk.vtkReflectionFilter()
vtkReflectY.SetPlaneToYMax()
vtkReflectY.SetInput( vtkReflectX.GetOutput() )
vtkReflectY.Update()
# apply the average of the transform
mean_array = numpy.zeros(dimensions[0]*dimensions[1]*dimensions[2])
std_array = numpy.zeros(dimensions[0]*dimensions[1]*dimensions[2])
for affineFEMTranform in TransformList:
# get homogenius 4x4 matrix of the form
# A | b
# matrix = -----
# 0 | 1
#
matrix = affineFEMTranform.GetConcatenatedTransform(0).GetMatrix()
#print matrix
RotationMatrix = [[matrix.GetElement(0,0),matrix.GetElement(0,1),matrix.GetElement(0,2)],
[matrix.GetElement(1,0),matrix.GetElement(1,1),matrix.GetElement(1,2)],
[matrix.GetElement(2,0),matrix.GetElement(2,1),matrix.GetElement(2,2)]]
Translation = [matrix.GetElement(0,3),matrix.GetElement(1,3),matrix.GetElement(2,3)]
#print RotationMatrix
print Translation
TransformedFEMMesh = None
if vtkReflectY.GetOutput().IsA("vtkMultiBlockDataSet"):
AppendBlocks = vtk.vtkAppendFilter()
iter = vtkReflectY.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
# loop over blocks...
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
vtkTransformFEMMesh = vtk.vtkTransformFilter()
vtkTransformFEMMesh.SetTransform( affineFEMTranform )
vtkTransformFEMMesh.SetInput( curInput )
vtkTransformFEMMesh.Update()
AppendBlocks.AddInput( vtkTransformFEMMesh.GetOutput() )
AppendBlocks.Update( )
iter.GoToNextItem();
TransformedFEMMesh = AppendBlocks.GetOutput()
else:
vtkTransformFEMMesh = vtk.vtkTransformFilter()
vtkTransformFEMMesh.SetTransform( affineFEMTranform )
vtkTransformFEMMesh.SetInput( vtkReflectY.GetOutput() )
vtkTransformFEMMesh.Update()
TransformedFEMMesh = vtkTransformFEMMesh.GetOutput()
# reuse ShiftScale Geometry
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput( templateImage )
vtkResample.SetSource( TransformedFEMMesh )
vtkResample.Update()
fem_point_data= vtkResample.GetOutput().GetPointData()
#meantmp = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('Vard0Mean'))
#print meantmp.max()
#mean_array = mean_array + vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('Vard0Mean'))
#std_array = std_array + vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('Vard0Kurt'))
#print fem_array
#print type(fem_array )
# average
#mean_array = mean_array/naverage
#print mean_array.max()
#std_array = std_array /naverage
# write numpy to disk in matlab
#scipyio.savemat("%s/modelstats.navg%d.%04d.mat" % (work_dir,naverage,timeID), {'spacing':spacing, 'origin':origin,'Vard0Mean':mean_array,'Vard0Kurt':std_array })
# write output
print "writing ", timeID, mesh_filename, work_dir
vtkStatsWriter = vtk.vtkDataSetWriter()
vtkStatsWriter.SetFileTypeToBinary()
vtkStatsWriter.SetFileName("%s/modelstats.navg%d.%s.%04d.vtk"%(work_dir,naverage,mesh_filename,timeID))
vtkStatsWriter.SetInput(vtkResample.GetOutput())
vtkStatsWriter.Update()
# setup command line parser to control execution
from optparse import OptionParser
parser = OptionParser()
parser.add_option( "--ini_file",
action="store", dest="ini_file", default=None,
help="parse ini file to convert exodus FILE to matlab/imaging", metavar = "FILE")
(options, args) = parser.parse_args()
if (options.ini_file):
ProjectImagingMesh(options.ini_file)
else:
parser.print_help()
print options