def read(filenames, timestep=None):
'''Reads an unstructured mesh with added data.
:param filenames: The files to read from.
:type filenames: str
:param timestep: Time step to read from, in case of an Exodus input mesh.
:type timestep: int, optional
:returns mesh{2,3}d: The mesh data.
:returns point_data: Point data read from file.
:type point_data: dict
:returns field_data: Field data read from file.
:type field_data: dict
'''
if isinstance(filenames, (list, tuple)) and len(filenames)==1:
filenames = filenames[0]
if isinstance(filenames, basestring):
filename = filenames
# serial files
extension = os.path.splitext(filename)[1]
import re
# setup the reader
# TODO Most readers have CanReadFile() -- use that.
if extension == '.vtu':
from vtk import vtkXMLUnstructuredGridReader
reader = vtkXMLUnstructuredGridReader()
vtk_mesh = _read_vtk_mesh(reader, filename)
elif extension == '.vtk':
from vtk import vtkUnstructuredGridReader
reader = vtkUnstructuredGridReader()
vtk_mesh = _read_vtk_mesh(reader, filename)
elif extension == '.xmf':
from vtk import vtkXdmfReader
reader = vtkXdmfReader()
vtk_mesh = _read_vtk_mesh(reader, filename)
elif extension in [ '.ex2', '.exo', '.e' ]:
from vtk import vtkExodusIIReader
reader = vtkExodusIIReader()
reader.SetFileName( filename )
vtk_mesh = _read_exodusii_mesh(reader, timestep=timestep)
elif re.match('[^\.]*\.e\.\d+\.\d+', filename):
# Parallel Exodus files.
# TODO handle with vtkPExodusIIReader
from vtk import vtkExodusIIReader
reader = vtkExodusIIReader()
reader.SetFileName( filenames[0] )
vtk_mesh = _read_exodusii_mesh(reader, timestep=timestep)
else:
raise RuntimeError( 'Unknown file type \'%s\'.' % filename )
else:
# Parallel files.
# Assume Exodus format as we don't know anything else yet.
from vtk import vtkPExodusIIReader
# TODO Guess the file pattern or whatever.
reader = vtkPExodusIIReader()
reader.SetFileNames( filenames )
vtk_mesh = _read_exodusii_mesh(reader, filename, timestep=timestep)
return vtk_mesh
def read_exodus(filename,
animate_mode_shapes=True,
apply_displacements=True,
displacement_magnitude=1.0,
enabled_sidesets=None):
"""Read an ExodusII file (``'.e'`` or ``'.exo'``)."""
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
reader.UpdateInformation()
reader.SetAnimateModeShapes(animate_mode_shapes)
reader.SetApplyDisplacements(apply_displacements)
reader.SetDisplacementMagnitude(displacement_magnitude)
if enabled_sidesets is None:
enabled_sidesets = list(range(reader.GetNumberOfSideSetArrays()))
for sideset in enabled_sidesets:
if isinstance(sideset, int):
name = reader.GetSideSetArrayName(sideset)
elif isinstance(sideset, str):
name = sideset
else:
raise ValueError(
'Could not parse sideset ID/name: {}'.format(sideset))
reader.SetSideSetArrayStatus(name, 1)
reader.Update()
return pyvista.wrap(reader.GetOutput())
def GetMeshNodes(file_name):
"""
return the number of DOF for a exodus file
"""
import vtk
vtkExodusIIReader = vtk.vtkExodusIIReader()
vtkExodusIIReader.SetFileName(file_name)
#vtkExodusIIReader.SetPointResultArrayStatus("u0",1)
vtkExodusIIReader.Update()
# multi block
if vtkExodusIIReader.GetOutput().IsA("vtkMultiBlockDataSet"):
iter = vtkExodusIIReader.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
# initialize list for storage
NumberOfNodes = 0
# loop over blocks...
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
NumberOfNodes = NumberOfNodes + curInput.GetNumberOfPoints()
iter.GoToNextItem();
# return total number of nodes
return NumberOfNodes
# single block
else:
return vtkExodusIIReader.GetNumberOfNodes()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExodusIIReader(), 'Reading vtkExodusII.',
(), ('vtkExodusII',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, mesh_item_data, file_name):
MeshInfo.__init__(self, mesh_item_data)
self.file_name = file_name
import vtk
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_name)
reader.UpdateInformation()
num_nodesets = reader.GetNumberOfNodeSetArrays()
num_sidesets = reader.GetNumberOfSideSetArrays()
num_blocks = reader.GetNumberOfElementBlockArrays()
self.nodesets = set()
for i in xrange(num_nodesets):
self.nodesets.add(reader.GetObjectId(vtk.vtkExodusIIReader.NODE_SET,i))
if 'Unnamed' not in reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,i).split(' '):
self.nodesets.add(reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,i).split(' ')[0])
self.sidesets = set()
for i in xrange(num_sidesets):
self.sidesets.add(reader.GetObjectId(vtk.vtkExodusIIReader.SIDE_SET,i))
if 'Unnamed' not in reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,i).split(' '):
self.sidesets.add(reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,i).split(' ')[0])
self.blocks = set()
for i in xrange(num_blocks):
self.blocks.add(reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK,i))
if 'Unnamed' not in reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' '):
self.blocks.add(reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' ')[0])
def read(filetype, filename):
if filetype == 'vtk':
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'exodus':
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
else:
raise RuntimeError('Unknown file type \'%s\'.' % filename)
# Explicitly extract points, cells, point data, field data
points = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetPoints().GetData())
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
cell_data = _read_data(vtk_mesh.GetCellData())
field_data = _read_data(vtk_mesh.GetFieldData())
return points, cells, point_data, cell_data, field_data
def __init__(self, exodusFileName, structuredGrid):
'''
Initialize with path to exodus file and the structured grid you wish
to resample over
'''
self.eReader = vtk.vtkExodusIIReader()
self.eReader.SetFileName(exodusFileName)
self.grid = structuredGrid
def average_fields(names, var):
""" given list of filenames and var, generate average field """
# open each file, and add the field data
# to our averaged array
for name in names:
d = vtk.vtkExodusIIReader()
d.SetFileName(name)
d.UpdateInformation()
d.SetPointResultArrayStatus(var,1)
d.Update()
blocks = d.GetOutput().GetNumberOfBlocks()
data = d.GetOutput()
#
# range to integrate over
#
height = 0.842820346355
thresh = 0.004
# open text file
f = open('slices/'+var+'/'+name+'.txt', 'w')
for j in xrange(blocks):
blk = data.GetBlock(0).GetBlock(j)
try:
pts = blk.GetNumberOfPoints()
except:
ss='no data in this block'
else:
pt_data = blk.GetPointData().GetArray(var)
if pt_data is None:
print 'Nada!'
print 'I cannot find the variable field: ', var
print 'Exiting...'
sys.exit(1)
for i in xrange(pts):
# gather x,y,z location
#z,y,x = blk.GetPoint(i)
x,y,z = blk.GetPoint(i)
if(abs(z-height)<thresh):
# gather point scalar value
u = pt_data.GetValue(i)
f.write(str(x)+' , '+str(y)+' , '+str(u)+'\n')
# close file
f.close()
#
# steady as she goes
#
return 0
def main():
colors = vtk.vtkNamedColors()
# Input file and variable
filename, nodal_var = get_program_parameters()
# Read Exodus Data
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
reader.UpdateInformation()
reader.SetTimeStep(10)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL,
1) # enables all NODAL variables
reader.Update()
# print(reader) # uncomment this to show the file information
# Create Geometry
geometry = vtk.vtkCompositeDataGeometryFilter()
geometry.SetInputConnection(0, reader.GetOutputPort(0))
geometry.Update()
# Mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(geometry.GetOutputPort())
mapper.SelectColorArray(nodal_var)
mapper.SetScalarModeToUsePointFieldData()
mapper.InterpolateScalarsBeforeMappingOn()
# Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Renderer
renderer = vtk.vtkRenderer()
renderer.AddViewProp(actor)
renderer.SetBackground(colors.GetColor3d('DimGray'))
renderer.GetActiveCamera().SetPosition(9.0, 9.0, 7.0)
renderer.GetActiveCamera().SetFocalPoint(0, 0, 0)
renderer.GetActiveCamera().SetViewUp(0.2, -0.7, 0.7)
renderer.GetActiveCamera().SetDistance(14.5)
# Window and Interactor
window = vtk.vtkRenderWindow()
window.AddRenderer(renderer)
window.SetSize(600, 600)
window.SetWindowName('ReadExodusData')
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(window)
interactor.Initialize()
# Show the result
window.Render()
interactor.Start()
def integrate(name, var):
""" given filename and var, generate profile """
d = vtk.vtkExodusIIReader()
d.SetFileName(name)
d.UpdateInformation()
print var
d.SetPointResultArrayStatus(var,1)
d.Update()
blocks = d.GetOutput().GetNumberOfBlocks()
data = d.GetOutput()
#
# range to integrate over
#
height = 0.804380714893
thresh = 0.004
rmin = 0.0
rmax = 1.0
nr = 10
dr = (rmax-rmin)/nr
#
# print data.GetBlock(0).GetBlock(0).GetPointData().GetArray(var).GetValue(0)
#
for j in xrange(blocks):
blk = data.GetBlock(0).GetBlock(j)
try:
pts = blk.GetNumberOfPoints()
except:
ss='no data in this block'
else:
# grabbing vtkDataArray
pt_data = blk.GetPointData().GetArray(var)
pt_data2 = blk.GetPointData().GetArray(var)
if pt_data is None:
print 'Nada!'
print 'I cannot find the variable field: ', var
print 'Exiting...'
sys.exit(1)
for i in xrange(pts):
# gather x,y,z location
z,y,x = blk.GetPoint(i)
# gather point scalar value
#print dir(pt_data)
u = pt_data.GetValue(i)
print u
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self,
module_manager,
vtk.vtkExodusIIReader(),
"Reading vtkExodusII.",
(),
("vtkExodusII",),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None,
)
def testAll(self):
reader = vtk.vtkExodusIIReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/disk_out_ref.ex2")
reader.SetPointResultArrayStatus("Temp", 1)
reader.SetPointResultArrayStatus("Pres", 1)
reader.Update()
input = reader.GetOutput().GetBlock(0).GetBlock(0)
cf = vtk.vtkContourFilter()
cf.SetInputData(input)
cf.SetValue(0, 400)
cf.SetInputArrayToProcess(0, 0, 0, 0, "Temp")
cf.GenerateTrianglesOff()
cf.Update()
self.assertEqual(cf.GetOutput().GetNumberOfPoints(), 1047)
self.assertEqual(cf.GetOutput().GetNumberOfCells(), 1028)
cf.GenerateTrianglesOn()
cf.Update()
self.assertEqual(cf.GetOutput().GetNumberOfPoints(), 1047)
self.assertEqual(cf.GetOutput().GetNumberOfCells(), 2056)
# Check that expected arrays are in the output
# The active scalars in the input shouldn't effect the
# scalars in the output
availableScalars = ["Temp", "Pres"]
for scalar in availableScalars:
input.GetPointData().SetActiveScalars(scalar)
cf.ComputeScalarsOn()
cf.Update()
pd = cf.GetOutput().GetPointData()
self.assertNotEqual(pd.GetArray("Temp"), None)
self.assertNotEqual(pd.GetArray("Pres"), None)
cf.ComputeScalarsOff() # "Temp" array should not be in output
cf.Update()
pd = cf.GetOutput().GetPointData()
self.assertEqual(pd.GetArray("Temp"), None)
self.assertNotEqual(pd.GetArray("Pres"), None)
def testAll(self):
reader = vtk.vtkExodusIIReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/disk_out_ref.ex2")
reader.SetPointResultArrayStatus("Temp", 1);
reader.SetPointResultArrayStatus("Pres", 1);
reader.Update();
input = reader.GetOutput().GetBlock(0).GetBlock(0);
cf = vtk.vtkContourFilter()
cf.SetInputData(input)
cf.SetValue(0,400)
cf.SetInputArrayToProcess(0, 0, 0, 0, "Temp");
cf.GenerateTrianglesOff()
cf.Update()
self.assertEqual(cf.GetOutput().GetNumberOfPoints(), 1047)
self.assertEqual(cf.GetOutput().GetNumberOfCells(), 1028)
cf.GenerateTrianglesOn()
cf.Update()
self.assertEqual(cf.GetOutput().GetNumberOfPoints(), 1047)
self.assertEqual(cf.GetOutput().GetNumberOfCells(), 2056)
# Check that expected arrays are in the output
# The active scalars in the input shouldn't effect the
# scalars in the output
availableScalars = ["Temp", "Pres"]
for scalar in availableScalars:
input.GetPointData().SetActiveScalars(scalar)
cf.ComputeScalarsOn()
cf.Update()
pd = cf.GetOutput().GetPointData()
self.assertNotEqual(pd.GetArray("Temp"), None)
self.assertNotEqual(pd.GetArray("Pres"), None)
cf.ComputeScalarsOff() # "Temp" array should not be in output
cf.Update()
pd = cf.GetOutput().GetPointData()
self.assertEqual(pd.GetArray("Temp"), None)
self.assertNotEqual(pd.GetArray("Pres"), None)
def __init__(self, filename, **kwargs):
super(ExodusReader, self).__init__(**kwargs)
# Set the filename for the reader.
self.__filename = filename
if not os.path.isfile(self.__filename):
raise IOError("The file {} is not a valid filename.".format(
self.__filename))
self.__vtkreader = vtk.vtkExodusIIReader()
self.__active = None # see utils.get_active_filenames
self.__current = None # current TimeData object
self.__timedata = [] # all the TimeData objects
self.__fileinfo = collections.OrderedDict(
) # sorted FileInformation objects
self.__blockinfo = dict() # BlockInformation objects
self.__variableinfo = collections.OrderedDict(
) # VariableInformation objects
def integrate(name, var):
""" given filename and var, generate profile """
d = vtk.vtkExodusIIReader()
d.SetFileName(name)
d.UpdateInformation()
d.SetPointResultArrayStatus(var,1)
d.Update()
blocks = d.GetOutput().GetNumberOfBlocks()
data = d.GetOutput()
# range to integrate at
height = 0.804380714893
thresh = 0.004
rmin = 0.0
rmax = 1.0
nr = 10
dr = (rmax-rmin)/nr
rint = np.zeros(nr)
rn = np.ones(nr)
for j in xrange(blocks):
blk = data.GetBlock(0).GetBlock(j)
pts = blk.GetNumberOfPoints()
pt_data = blk.GetPointData().GetArray(var)
for i in xrange(pts):
# gather x,y,z location
z,y,x = blk.GetPoint(i)
# gather point scalar value
u = pt_data.GetValue(i)
# now, find all values near the target height
# (convert to cylindrical)
if(abs(z - height) < thresh):
r = np.sqrt((x)**2 + (y)**2)
fr = np.floor(r/dr)
rint[fr] += u
rn [fr] += 1
return rint/rn
def __init__(self, filename, **kwargs):
super(ExodusReader, self).__init__(**kwargs)
# Set the filename for the reader.
self.__filename = filename
if not os.path.isfile(self.__filename):
raise IOError("The file {} is not a valid filename.".format(self.__filename))
self.__vtkreader = vtk.vtkExodusIIReader()
self.__active = None # see utils.get_active_filenames
self.__current = None # current TimeData object
self.__timedata = [] # all the TimeData objects
self.__fileinfo = collections.OrderedDict() # sorted FileInformation objects
self.__blockinfo = dict() # BlockInformation objects
self.__variableinfo = collections.OrderedDict() # VariableInformation objects
# Error handling
self._error_observer = ExodusReaderErrorObserver()
self.__vtkreader.AddObserver('ErrorEvent', self._error_observer)
def testAll(self):
reader = vtk.vtkExodusIIReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/disk_out_ref.ex2")
reader.SetPointResultArrayStatus("Temp",1);
reader.Update ();
input = reader.GetOutput().GetBlock(0).GetBlock(0);
cf = vtk.vtkContourFilter()
cf.SetInputData(input)
cf.SetValue(0,400)
cf.SetInputArrayToProcess(0, 0, 0, 0, "Temp");
cf.GenerateTrianglesOff()
cf.Update()
self.failUnlessEqual(cf.GetOutput().GetNumberOfPoints(),1047)
self.failUnlessEqual(cf.GetOutput().GetNumberOfCells(),1028)
cf.GenerateTrianglesOn()
cf.Update()
self.failUnlessEqual(cf.GetOutput().GetNumberOfPoints(),1047)
self.failUnlessEqual(cf.GetOutput().GetNumberOfCells(),2056)
def load(self):
self._reader = vtk.vtkExodusIIReader()
with common.lock_file(self._file_name):
self._readTimeInfo()
self._reader.SetFileName(self._file_name)
if self._times is not None:
self._reader.SetTimeStep(self._time_steps[-1])
self._reader.UpdateInformation()
self._reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
self._reader.SetAllArrayStatus(vtk.vtkExodusIIReader.ELEM_BLOCK, 1)
self._reader.SetAllArrayStatus(vtk.vtkExodusIIReader.GLOBAL, 1)
self._reader.Update()
self._readBlockInfo()
for obj_type, data in self._block_info.items():
for info in data.values():
self._reader.SetObjectStatus(info.object_type,
info.object_index, 1)
self._readVariableInfo()
def testAll(self):
reader = vtk.vtkExodusIIReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/disk_out_ref.ex2")
reader.SetPointResultArrayStatus("Temp",1);
reader.Update ();
input = reader.GetOutput().GetBlock(0).GetBlock(0);
cf = vtk.vtkContourFilter()
cf.SetInputData(input)
cf.SetValue(0,400)
cf.SetInputArrayToProcess(0, 0, 0, 0, "Temp");
cf.GenerateTrianglesOff()
cf.Update()
self.failUnlessEqual(cf.GetOutput().GetNumberOfPoints(),1047)
self.failUnlessEqual(cf.GetOutput().GetNumberOfCells(),1028)
cf.GenerateTrianglesOn()
cf.Update()
self.failUnlessEqual(cf.GetOutput().GetNumberOfPoints(),1047)
self.failUnlessEqual(cf.GetOutput().GetNumberOfCells(),2056)
def ExtractSolutionFromExodus(inputExodusFile,variableID,timeID,fileID):
"""
extract data as a vector from exodus file
"""
import vtk
import vtk.util.numpy_support as vtkNumPy
import numpy
vtkExodusIIReader = vtk.vtkExodusIIReader()
print "opening %s " % inputExodusFile
vtkExodusIIReader.SetFileName( inputExodusFile )
vtkExodusIIReader.Update()
ntime = vtkExodusIIReader.GetNumberOfTimeSteps()
print "ntime %d varID %s time %d " % (ntime,variableID,timeID)
vtkExodusIIReader.SetTimeStep(timeID)
vtkExodusIIReader.SetPointResultArrayStatus(variableID,1)
vtkExodusIIReader.Update()
# multi block
if vtkExodusIIReader.GetOutput().IsA("vtkMultiBlockDataSet"):
iter = vtkExodusIIReader.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
# initialize list for storage
Soln = []
# loop over blocks...
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
fem_point_data= curInput.GetPointData()
Soln.append( vtkNumPy.vtk_to_numpy(fem_point_data.GetArray(variableID)) )
iter.GoToNextItem();
# concatenate blocks
numpy.savetxt( ("data/"+SolnOutputTemplate+".%d") % (variableID,timeID,fileID),numpy.concatenate(Soln))
# single block
else:
curInput = vtkExodusIIReader.GetOutput()
fem_point_data= curInput.GetPointData()
Soln = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray(variableID))
numpy.savetxt( ("data/"+SolnOutputTemplate+".%d") % (variableID,timeID,fileID),Soln)
def read(filetype, filename):
import vtk
from vtk.util import numpy_support
def _read_data(data):
"""Extract numpy arrays from a VTK data set.
"""
# Go through all arrays, fetch data.
out = {}
for k in range(data.GetNumberOfArrays()):
array = data.GetArray(k)
if array:
array_name = array.GetName()
out[array_name] = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(array))
return out
def _read_cells(vtk_mesh):
data = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(vtk_mesh.GetCells().GetData()))
offsets = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellLocationsArray()))
types = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(vtk_mesh.GetCellTypesArray()))
# `data` is a one-dimensional vector with
# (num_points0, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
# Translate it into the cells dictionary.
cells = {}
for vtk_type, meshio_type in vtk_to_meshio_type.items():
# Get all offsets for vtk_type
os = offsets[numpy.argwhere(types == vtk_type).transpose()[0]]
num_cells = len(os)
if num_cells > 0:
if meshio_type == "polygon":
for idx_cell in range(num_cells):
num_pts = data[os[idx_cell]]
cell = data[os[idx_cell] + 1:os[idx_cell] + 1 +
num_pts]
key = meshio_type + str(num_pts)
if key in cells:
cells[key] = numpy.vstack([cells[key], cell])
else:
cells[key] = cell
else:
num_pts = data[os[0]]
# instantiate the array
arr = numpy.empty((num_cells, num_pts), dtype=int)
# store the num_pts entries after the offsets into the columns
# of arr
for k in range(num_pts):
arr[:, k] = data[os + k + 1]
cells[meshio_type] = arr
return cells
if filetype in ["vtk", "vtk-ascii", "vtk-binary"]:
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ["vtu", "vtu-ascii", "vtu-binary"]:
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ["xdmf", "xdmf2"]:
reader = vtk.vtkXdmfReader()
reader.SetFileName(filename)
reader.SetReadAllColorScalars(1)
reader.SetReadAllFields(1)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTCoords(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
elif filetype == "xdmf3":
reader = vtk.vtkXdmf3Reader()
reader.SetFileName(filename)
reader.SetReadAllColorScalars(1)
reader.SetReadAllFields(1)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTCoords(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
else:
assert filetype == "exodus", "Unknown file type '{}'.".format(filename)
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
# Explicitly extract points, cells, point data, field data
points = numpy.copy(
numpy_support.vtk_to_numpy(vtk_mesh.GetPoints().GetData()))
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
field_data = _read_data(vtk_mesh.GetFieldData())
cell_data = _read_data(vtk_mesh.GetCellData())
# split cell_data by the cell type
cd = {}
index = 0
for cell_type in cells:
num_cells = len(cells[cell_type])
cd[cell_type] = {}
for name, array in cell_data.items():
cd[cell_type][name] = array[index:index + num_cells]
index += num_cells
cell_data = cd
return Mesh(points,
cells,
point_data=point_data,
cell_data=cell_data,
field_data=field_data)
def ProjectImagingMesh(fem_mesh_file):
import vtk
import vtk.util.numpy_support as vtkNumPy
import scipy.io as scipyio
# echo vtk version info
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
# 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
AffineTransform = vtk.vtkTransform()
# should be in meters
AffineTransform.Translate(.0000001,.0000001,.0000001)
AffineTransform.RotateZ( 0 )
AffineTransform.RotateY( 0 )
AffineTransform.RotateX( 0 )
AffineTransform.Scale([1.,1.,1.])
# get homogenius 4x4 matrix of the form
# A | b
# matrix = -----
# 0 | 1
#
matrix = AffineTransform.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 ,Translation
#laserTip = AffineTransform.TransformPoint( laserTip )
#laserOrientation = AffineTransform.TransformVector( laserOrientation )
# read imaging data geometry that will be used to project FEM data onto
#vtkReader = vtk.vtkXMLImageDataReader()
vtkReader = vtk.vtkDataSetReader()
#vtkReader.SetFileName('/data/cjmaclellan/mdacc/nano/spio/spioVTK/67_11/tmap_67_11.0000.vtk' )
vtkReader.SetFileName('/data/cjmaclellan/mdacc/deltap_phantom_oct10/VTKtmaps/S695/S695.0000.vtk' )
#vtkReader.SetFileName('/data/cjmaclellan/mdacc/nano/nrtmapsVTK/R695/R695.0000.vtk' )
vtkReader.Update()
templateImage = vtkReader.GetOutput()
dimensions = templateImage.GetDimensions()
spacing = templateImage.GetSpacing()
origin = templateImage.GetOrigin()
print spacing, origin, dimensions
#fem.SetImagingDimensions( dimensions ,origin,spacing)
## project imaging onto fem mesh
#if (vtk != None):
# vtkImageReader = vtk.vtkDataSetReader()
# vtkImageReader.SetFileName('/data/fuentes/mdacc/uqModelStudy/dog1_980/temperature.%04d.vtk' % timeID )
# vtkImageReader.Update()
# image_cells = vtkImageReader.GetOutput().GetPointData()
# data_array = vtkNumPy.vtk_to_numpy(image_cells.GetArray('scalars'))
# v1 = PETSc.Vec().createWithArray(data_array, comm=PETSc.COMM_SELF)
# fem.ProjectImagingToFEMMesh("MRTI", v1)
# fem.StoreSystemTimeStep("MRTI",timeID )
#
# # extract voi for QOI
# vtkVOIExtract = vtk.vtkExtractVOI()
# vtkVOIExtract.SetInput( vtkImageReader.GetOutput() )
# VOI = [10,100,100,150,0,0]
# vtkVOIExtract.SetVOI( VOI )
# vtkVOIExtract.Update()
# mrti_point_data= vtkVOIExtract.GetOutput().GetPointData()
# mrti_array = vtkNumPy.vtk_to_numpy(mrti_point_data.GetArray('scalars'))
# #print mrti_array
# #print type(mrti_array)
# Interpolate FEM onto imaging data structures
vtkExodusIIReader = vtk.vtkExodusIIReader()
vtkExodusIIReader.SetFileName( fem_mesh_file )
vtkExodusIIReader.SetPointResultArrayStatus("u0",1)
vtkExodusIIReader.SetPointResultArrayStatus("u0*",1)
vtkExodusIIReader.SetPointResultArrayStatus("u1",1)
matsize = int(dimensions[1])#get matrix size
#preallocate size of arrays
u0_array_1 = scipy.zeros((matsize,matsize))
u0_array_2 = scipy.zeros((matsize,matsize,ntime*nsubstep))
u1_array_1 = scipy.zeros((matsize,matsize))
u1_array_2 = scipy.zeros((matsize,matsize,ntime*nsubstep))
u0star_array_1 = scipy.zeros((matsize,matsize))
u0star_array_2 = scipy.zeros((matsize,matsize,ntime*nsubstep))
#for timeID in range(1,2):
for timeID in range(1,ntime*nsubstep):
vtkExodusIIReader.SetTimeStep(timeID-1)
vtkExodusIIReader.Update()
# apply the transform
TransformedFEMMesh = None
if vtkExodusIIReader.GetOutput().IsA("vtkMultiBlockDataSet"):
AppendBlocks = vtk.vtkAppendFilter()
iter = vtkExodusIIReader.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
# loop over blocks...
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
vtkTransformFEMMesh = vtk.vtkTransformFilter()
vtkTransformFEMMesh.SetTransform( AffineTransform )
vtkTransformFEMMesh.SetInput( curInput )
vtkTransformFEMMesh.Update()
AppendBlocks.AddInput( vtkTransformFEMMesh.GetOutput() )
AppendBlocks.Update( )
iter.GoToNextItem();
TransformedFEMMesh = AppendBlocks.GetOutput()
else:
vtkTransformFEMMesh = vtk.vtkTransformFilter()
vtkTransformFEMMesh.SetTransform( AffineTransform )
vtkTransformFEMMesh.SetInput( vtkExodusIIReader.GetOutput() )
vtkTransformFEMMesh.Update()
TransformedFEMMesh = vtkTransformFEMMesh.GetOutput()
# reflect
#vtkReflectX = vtk.vtkReflectionFilter()
#vtkReflectX.SetPlaneToXMin()
#vtkReflectX.SetInput( TransformedFEMMesh )
#vtkReflectX.Update()
# reflect
#vtkReflectZ = vtk.vtkReflectionFilter()
#vtkReflectZ.SetPlaneToZMax()
#vtkReflectZ.SetInput( vtkReflectX.GetOutput() )
#vtkReflectZ.Update()
# reuse ShiftScale Geometry
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput( templateImage )
vtkResample.SetSource( TransformedFEMMesh )
#vtkResample.SetSource( vtkReflectZ.GetOutput() )
vtkResample.Update()
fem_point_data= vtkResample.GetOutput().GetPointData()
u0_array = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('u0'))
u0star_array = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('u0*'))
u1_array = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('u1'))
#go from 1x256^2 array to 256X256 array for each timestep
for nn in range(0,matsize):
u0_array_1[nn,:]=u0_array[nn*matsize:(nn+1)*matsize]
u0star_array_1[nn,:]=u0star_array[nn*matsize:(nn+1)*matsize]
u1_array_1[nn,:]=u1_array[nn*matsize:(nn+1)*matsize]
#apply proper rotations/reflections and combine 2D arrays into 3D array
u0_array_2[:,:,timeID-1]=numpy.fliplr(numpy.rot90(u0_array_1,k=3))
u0star_array_2[:,:,timeID-1]=numpy.fliplr(numpy.rot90(u0star_array_1,k=3))
u1_array_2[:,:,timeID-1]=numpy.fliplr(numpy.rot90(u1_array_1,k=3))
# write numpy to disk in matlab
#scipyio.savemat("MS795.%04d.mat" % (timeID), {'u0':u1_array,'MRTI0':MRTI0_array })
# write output
print "writing ", timeID
vtkStatsWriter = vtk.vtkDataSetWriter()
vtkStatsWriter.SetFileTypeToBinary()
vtkStatsWriter.SetFileName("test.%04d.vtk" % timeID )
vtkStatsWriter.SetInput(vtkResample.GetOutput())
vtkStatsWriter.Update()
scipyio.savemat("S695.mat",{'ModelFluence':u1_array_2,'MRTI':u0star_array_2,'ModelTemp':u0_array_2})
def setFileName(self, file_name):
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_name)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.EDGE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.SIDE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL, 1)
reader.UpdateInformation()
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, 0, 1)
num_sidesets = reader.GetNumberOfSideSetArrays()
num_nodesets = reader.GetNumberOfNodeSetArrays()
num_blocks = reader.GetNumberOfElementBlockArrays()
self.sidesets = []
self.sideset_id_to_exodus_block = {}
for i in xrange(num_sidesets):
sideset_id = reader.GetObjectId(vtk.vtkExodusIIReader.SIDE_SET,i)
self.sidesets.append(sideset_id)
self.sideset_id_to_exodus_block[sideset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.SIDE_SET, i, 1)
self.nodesets = []
self.nodeset_id_to_exodus_block = {}
for i in xrange(num_nodesets):
nodeset_id = reader.GetObjectId(vtk.vtkExodusIIReader.NODE_SET,i)
self.nodesets.append(nodeset_id)
self.nodeset_id_to_exodus_block[nodeset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, i, 1)
self.blocks = []
self.block_id_to_exodus_block = {}
for i in xrange(num_blocks):
block_id = reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK,i)
self.blocks.append(block_id)
self.block_id_to_exodus_block[block_id] = i
reader.SetTimeStep(1)
reader.Update()
self.data = reader.GetOutput()
self.all_actors = []
self.sideset_actors = {}
self.clipped_sideset_actors = {}
self.current_sideset_actors = self.sideset_actors
for i in xrange(num_sidesets):
actor = ExodusActor(self.renderer, self.data, ExodusMap.sideset_vtk_block, i)
actor.setColor(red)
self.sideset_actors[str(self.sidesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_sideset_actors[str(self.sidesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,i).split(' ')
if 'Unnamed' not in name:
self.sideset_actors[name[0]] = actor
self.clipped_sideset_actors[name[0]] = clipped_actor
self.nodeset_actors = {}
self.clipped_nodeset_actors = {}
self.current_nodeset_actors = self.nodeset_actors
for i in xrange(num_nodesets):
actor = ExodusActor(self.renderer, self.data, ExodusMap.nodeset_vtk_block, i)
actor.setColor(red)
self.nodeset_actors[str(self.nodesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_nodeset_actors[str(self.nodesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,i).split(' ')
if 'Unnamed' not in name:
self.nodeset_actors[name[0]] = actor
self.clipped_nodeset_actors[name[0]] = clipped_actor
self.block_actors = {}
self.clipped_block_actors = {}
self.current_block_actors = self.block_actors
for i in xrange(num_blocks):
actor = ExodusActor(self.renderer, self.data, ExodusMap.element_vtk_block, i)
self.block_actors[str(self.blocks[i])] = actor
self.all_actors.append(actor)
actor.show()
actor.showEdges()
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_block_actors[str(self.blocks[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' ')
if 'Unnamed' not in name:
self.block_actors[name[0]] = actor
self.clipped_block_actors[name[0]] = clipped_actor
self.setBounds()
# Avoid z-buffer fighting
vtk.vtkPolyDataMapper().SetResolveCoincidentTopologyToPolygonOffset()
self.renderer.ResetCamera()
self.vtkwidget.updateGL()
def pennesModeling(**kwargs):
"""
treatment planning model
"""
# import needed modules
import petsc4py, numpy, sys
PetscOptions = sys.argv
PetscOptions.append("-ksp_monitor")
PetscOptions.append("-ksp_rtol")
PetscOptions.append("1.0e-15")
#PetscOptions.append("-idb")
petsc4py.init(PetscOptions)
from petsc4py import PETSc
# break processors into separate communicators
petscRank = PETSc.COMM_WORLD.getRank()
petscSize = PETSc.COMM_WORLD.Get_size()
sys.stdout.write("petsc rank %d petsc nproc %d\n" % (petscRank, petscSize))
# set shell context
import femLibrary
# initialize libMesh data structures
libMeshInit = femLibrary.PyLibMeshInit(PetscOptions, PETSc.COMM_WORLD)
# the original configuration ini file should be stored
config = kwargs['config_parser']
# store control variables
getpot = femLibrary.PylibMeshGetPot(PetscOptions)
# copy all values from the input file
for section in config.sections():
for name, value in config.items(section):
#print "%s/%s" % (section,name) , value
getpot.SetIniValue("%s/%s" % (section, name), value)
# nodeset 1 will be treated as dirichlet
dirichletID = 1
getpot.SetIniValue("bc/u_dirichlet", '%d' % dirichletID)
# set tissue lookup tables
k_0Table = {
"default": config.getfloat("thermal_conductivity", "k_0_healthy"),
"vessel": config.getfloat("thermal_conductivity", "k_0_healthy"),
"grey": config.getfloat("thermal_conductivity", "k_0_grey"),
"white": config.getfloat("thermal_conductivity", "k_0_white"),
"csf": config.getfloat("thermal_conductivity", "k_0_csf"),
"tumor": config.getfloat("thermal_conductivity", "k_0_tumor")
}
w_0Table = {
"default": config.getfloat("perfusion", "w_0_healthy"),
"vessel": config.getfloat("perfusion", "w_0_healthy"),
"grey": config.getfloat("perfusion", "w_0_grey"),
"white": config.getfloat("perfusion", "w_0_white"),
"csf": config.getfloat("perfusion", "w_0_csf"),
"tumor": config.getfloat("perfusion", "w_0_tumor")
}
mu_aTable = {
"default": config.getfloat("optical", "mu_a_healthy"),
"vessel": config.getfloat("optical", "mu_a_healthy"),
"grey": config.getfloat("optical", "mu_a_grey"),
"white": config.getfloat("optical", "mu_a_white"),
"csf": config.getfloat("optical", "mu_a_csf"),
"tumor": config.getfloat("optical", "mu_a_tumor")
}
mu_sTable = {
"default": config.getfloat("optical", "mu_s_healthy"),
"vessel": config.getfloat("optical", "mu_s_healthy"),
"grey": config.getfloat("optical", "mu_s_grey"),
"white": config.getfloat("optical", "mu_s_white"),
"csf": config.getfloat("optical", "mu_s_csf"),
"tumor": config.getfloat("optical", "mu_s_tumor")
}
labelTable = {
config.get("labels", "greymatter"): "grey",
config.get("labels", "whitematter"): "white",
config.get("labels", "csf"): "csf",
config.get("labels", "tumor"): "tumor",
config.get("labels", "vessel"): "vessel"
}
labelCount = {
"default": 0,
"grey": 0,
"white": 0,
"csf": 0,
"tumor": 0,
"vessel": 0
}
# imaging params
import vtk
import vtk.util.numpy_support as vtkNumPy
SegmentFile = config.get("exec", "segment_file")
# set the default reader based on extension
if (SegmentFile.split(".").pop() == "vtk"):
vtkImageReader = vtk.vtkDataSetReader
elif (SegmentFile.split(".").pop() == "vti"):
vtkImageReader = vtk.vtkXMLImageDataReader
else:
raise RuntimeError("uknown file")
# get dimension info from header
vtkSetupReader = vtkImageReader()
vtkSetupReader.SetFileName(SegmentFile)
vtkSetupReader.Update()
vtkImageMask = vtkSetupReader.GetOutput()
dimensions = vtkSetupReader.GetOutput().GetDimensions()
numberPointsImage = vtkSetupReader.GetOutput().GetNumberOfPoints()
spacing_mm = vtkSetupReader.GetOutput().GetSpacing()
origin_mm = vtkSetupReader.GetOutput().GetOrigin()
# convert to meters
spacing = [dx * .001 for dx in spacing_mm]
origin = [x0 * .001 for x0 in origin_mm]
# pass pointer to c++
image_cells = vtkImageMask.GetPointData()
data_array = vtkNumPy.vtk_to_numpy(image_cells.GetArray(0))
# need to pass numpy array's w/ Fortran storage... ie painful to debug
imageDataVec = PETSc.Vec().createWithArray(numpy.ravel(data_array,
order='F'),
comm=PETSc.COMM_SELF)
# FIXME - center around quadrature in out-of-plane direction
# FIXME - need better out of plane cooling model
quadratureOffset = 1. / numpy.sqrt(3.0) * spacing[2] / 2.0
# expecting roi and subsample of the form:
# roi = [(40,210),(30,220),(6,78)]
# subsample = [3,3,2]
ROI = eval(config.get('exec', 'roi'))
subsample = eval(config.get('exec', 'subsample'))
nelemROI = [(pixel[1] - pixel[0] - 1) / sub
for pixel, sub in zip(ROI, subsample)]
xbounds = [
origin[0] + spacing[0] * (ROI[0][0] + 0.5),
origin[0] + spacing[0] * (ROI[0][1] + 0.5)
]
ybounds = [
origin[1] + spacing[1] * (ROI[1][0] + 0.5),
origin[1] + spacing[1] * (ROI[1][1] + 0.5)
]
zbounds = [
origin[2] + spacing[2] * (ROI[2][0] + 0.5),
origin[2] + spacing[2] * (ROI[2][1] + 0.5)
]
if (petscRank == 0):
print "#points", numberPointsImage, "dimensions ", dimensions, "spacing ", spacing, "origin ", origin
print "ROI", ROI, "nelemROI ", nelemROI, "bounds", xbounds, ybounds, zbounds
#set to steady state solve
getpot.SetIniValue("steadystate/domain_0", "true")
# initialize FEM Mesh
femMesh = femLibrary.PylibMeshMesh()
#femMesh.SetupUnStructuredGrid(kwargs['mesh_file'],0,RotationMatrix, Translation )
#femMesh.ReadFile(kwargs['mesh_file'])
femMesh.SetupStructuredGrid(nelemROI, xbounds, ybounds, zbounds,
[2, 2, 2, 2, 2, 2])
# get output file name else set default name
try:
MeshOutputFile = config.get("exec", "exodus_file")
except ConfigParser.NoOptionError:
MeshOutputFile = "fem.e"
# add the data structures for the Background System Solve
# set deltat, number of time steps, power profile, and add system
eqnSystems = femLibrary.PylibMeshEquationSystems(femMesh, getpot)
#getpot.SetIniPower(1,[[19,119],[90.0,100.0]] )
getpot.SetIniPower(1, kwargs['powerHistory'])
# AddPennesSDASystem
# AddPennesRFSystem
# AddPennesDeltaPSystem
pennesSystem = eval("eqnSystems.%s('StateSystem',kwargs['deltat'])" %
kwargs['physics'])
pennesSystem.AddStorageVectors(kwargs['ntime'] + 1)
# add system for labels
# FIXME: need both nodal, for dirichlet bc, and element version, for parameter masks
maskElemSystem = eqnSystems.AddExplicitSystem("ElemImageMask")
maskElemSystem.AddConstantMonomialVariable("maskElem")
# initialize libMesh data structures
eqnSystems.init()
# print info
eqnSystems.PrintSelf()
# setup imaging to interpolate onto FEM mesh
femImaging = femLibrary.PytttkImaging(getpot, dimensions, origin, spacing)
# Project imaging onto libMesh data structures
femImaging.ProjectImagingToFEMMesh("ElemImageMask", 0.0, imageDataVec,
eqnSystems)
femImaging.ProjectImagingToFEMMesh("StateSystem", 0.0, imageDataVec,
eqnSystems)
# create dirichlet nodes from this mask
numNodes = pennesSystem.PetscFEMSystemCreateNodeSetFromMask(
config.getfloat("labels", "vessel"), dirichletID)
print "# of dirichlet nodes %d" % numNodes
# get image label as numpy array
imageLabel = maskElemSystem.GetSolutionVector()[...]
#imageLabel = numpy.floor(10.0*imageLabel.copy())+1
k_0Label = imageLabel.copy()
w_0Label = imageLabel.copy()
mu_aLabel = imageLabel.copy()
mu_sLabel = imageLabel.copy()
for (idpos, label) in enumerate(imageLabel):
try:
tissueType = labelTable["%d" % int(label)]
except KeyError:
tissueType = "default"
labelCount[tissueType] = labelCount[tissueType] + 1
k_0Label[idpos] = k_0Table[tissueType]
w_0Label[idpos] = w_0Table[tissueType]
mu_aLabel[idpos] = mu_aTable[tissueType]
mu_sLabel[idpos] = mu_sTable[tissueType]
# create array of imaging data as petsc vec
k_0Vec = PETSc.Vec().createWithArray(k_0Label, comm=PETSc.COMM_SELF)
w_0Vec = PETSc.Vec().createWithArray(w_0Label, comm=PETSc.COMM_SELF)
mu_aVec = PETSc.Vec().createWithArray(mu_aLabel, comm=PETSc.COMM_SELF)
mu_sVec = PETSc.Vec().createWithArray(mu_sLabel, comm=PETSc.COMM_SELF)
# copy material properties to the system
eqnSystems.GetSystem("k_0").SetSolutionVector(k_0Vec)
eqnSystems.GetSystem("w_0").SetSolutionVector(w_0Vec)
eqnSystems.GetSystem("mu_a").SetSolutionVector(mu_aVec)
eqnSystems.GetSystem("mu_s").SetSolutionVector(mu_sVec)
# write IC
exodusII_IO = femLibrary.PylibMeshExodusII_IO(femMesh)
exodusII_IO.WriteTimeStep(MeshOutputFile, eqnSystems, 1, 0.0)
exodusII_IO.WriteParameterSystems(eqnSystems)
# setup IC
pennesSystem.PetscFEMSystemSetupInitialConditions()
# create list of laser positions
laserPositionList = [((.015, .015, 2 * spacing[2] + quadratureOffset),
(.018, .018, 2 * spacing[2] + quadratureOffset)),
((.015, .015, 2 * spacing[2] + quadratureOffset),
(.016, .018, 2 * spacing[2] + quadratureOffset)),
((.015, .015, 1 * spacing[2] + quadratureOffset),
(.014, .014, 1 * spacing[2] + quadratureOffset)),
((.015, .015, 1 * spacing[2] + quadratureOffset),
(.015, .018, 3 * spacing[2] + quadratureOffset))]
# time stamp
import pickle, time
timeStamp = 0
# set power id to turn laser on
pennesSystem.PetscFEMSystemUpdateTimeStep(1)
# loop over laser position and solve steady state equations for each position
#for (idpos,(pos0,pos1)) in enumerate(laserPositionList):
# loop and read new laser parameters
while (True):
if (os.path.getmtime(fem_params['ini_filename']) > timeStamp):
timeStamp = os.path.getmtime(fem_params['ini_filename'])
newIni = ConfigParser.SafeConfigParser({})
newIni.read(fem_params['ini_filename'])
laserParams = {}
laserParams['position1'] = [
newIni.getfloat("probe", varID)
for varID in ["x_0", "y_0", "z_0"]
]
laserParams['position2'] = [
newIni.getfloat("probe", varID)
for varID in ["x_1", "y_1", "z_1"]
]
print "laser position = ", newIni.getfloat("timestep",
"power"), laserParams
pennesSystem.PennesSDASystemUpdateLaserPower(
newIni.getfloat("timestep", "power"), 1)
pennesSystem.PennesSDASystemUpdateLaserPosition(
laserParams['position1'], laserParams['position2'])
pennesSystem.SystemSolve()
#fem.StoreTransientSystemTimeStep("StateSystem",timeID )
#exodusII_IO.WriteTimeStep(MeshOutputFile ,eqnSystems, idpos+2, idpos*kwargs['deltat'])
exodusII_IO.WriteTimeStep(MeshOutputFile, eqnSystems, 2, 1.0)
exodusII_IO.WriteParameterSystems(eqnSystems)
# write to txt file
if (petscRank == 0):
time.sleep(1)
vtkExodusIIReader = vtk.vtkExodusIIReader()
print "opening %s " % MeshOutputFile
vtkExodusIIReader.SetFileName(MeshOutputFile)
vtkExodusIIReader.Update()
ntime = vtkExodusIIReader.GetNumberOfTimeSteps()
variableID = "u0"
print "ntime %d %s " % (ntime, variableID)
vtkExodusIIReader.SetTimeStep(1)
vtkExodusIIReader.SetPointResultArrayStatus(variableID, 1)
vtkExodusIIReader.Update()
curInput = None
# multi block
if vtkExodusIIReader.GetOutput().IsA("vtkMultiBlockDataSet"):
iter = vtkExodusIIReader.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
curInput = iter.GetCurrentDataObject()
else:
curInput = vtkExodusIIReader.GetOutput()
#fem_point_data= curInput.GetPointData().GetArray('u0')
#Soln=vtkNumPy.vtk_to_numpy(fem_point_data)
#numpy.savetxt( "temperature.txt" ,Soln)
# 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
# scale back to millimeter
# TODO verify that the data sets are registered in the native slicer coordinate system
# TODO segmented data MUST be read in with:
# TODO add data -> volume -> show options -> ignore orientation
# TODO add data -> volume -> show options -> ignore orientation
# TODO add data -> volume -> show options -> ignore orientation
AffineTransform = vtk.vtkTransform()
AffineTransform.Translate([0.0, 0.0, 0.0])
AffineTransform.RotateZ(0.0)
AffineTransform.RotateY(0.0)
AffineTransform.RotateX(0.0)
AffineTransform.Scale([1000., 1000., 1000.])
# scale to millimeter
transformFilter = vtk.vtkTransformFilter()
transformFilter.SetInput(curInput)
transformFilter.SetTransform(AffineTransform)
transformFilter.Update()
# setup contour filter
vtkContour = vtk.vtkContourFilter()
vtkContour.SetInput(transformFilter.GetOutput())
# TODO: not sure why this works...
# set the array to process at the temperature == u0
vtkContour.SetInputArrayToProcess(0, 0, 0, 0, 'u0')
contourValuesList = eval(newIni.get('exec', 'contours'))
vtkContour.SetNumberOfContours(len(contourValuesList))
print "plotting array:", vtkContour.GetArrayComponent()
for idContour, contourValue in enumerate(contourValuesList):
print "plotting contour:", idContour, contourValue
vtkContour.SetValue(idContour, contourValue)
vtkContour.Update()
# setup threshold filter
vtkThreshold = vtk.vtkThreshold()
vtkThreshold.SetInput(transformFilter.GetOutput())
vtkThreshold.ThresholdByLower(contourValuesList[0])
#vtkThreshold.SetSelectedComponent( 0 )
vtkThreshold.SetComponentModeToUseAny()
vtkThreshold.Update()
# resample onto image
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput(vtkImageMask)
vtkResample.SetSource(vtkThreshold.GetOutput())
vtkResample.Update()
# write output
print "writing fem.vtk "
vtkImageWriter = vtk.vtkDataSetWriter()
vtkImageWriter.SetFileTypeToBinary()
vtkImageWriter.SetFileName("fem.vtk")
vtkImageWriter.SetInput(vtkResample.GetOutput())
vtkImageWriter.Update()
# write stl file
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetInput(vtkContour.GetOutput())
stlWriter.SetFileName("fem.stl")
stlWriter.SetFileTypeToBinary()
stlWriter.Write()
# write support file to signal full stl file is written
# Slicer module will wait for this file to be written
# before trying to open stl file to avoid incomplete reads
with open('./fem.finish', 'w') as signalFile:
signalFile.write("the stl file has been written\n")
else:
print "waiting on user input.."
# echo lookup table
if (petscRank == 0):
print "lookup tables"
print "labeled %d voxels" % len(imageLabel)
print "labels", labelTable
print "counts", labelCount
print "conductivity", k_0Table
print "perfusion", w_0Table
print "absorption", mu_aTable
print "scattering", mu_sTable
time.sleep(2)
# import vtk module
import vtk
import vtk.util.numpy_support as vtkNumPy
# load FEM data
vtkExodusIIReader = vtk.vtkExodusIIReader()
vtkExodusIIReader.SetFileName("fem_data.e")
vtkExodusIIReader.Update()
ntime = vtkExodusIIReader.GetNumberOfTimeSteps()
femData = vtkExodusIIReader.GetOutput()
# get the bounding box
femBounds = None
if femData.IsA("vtkMultiBlockDataSet"):
iter = femData.NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
bounds = curInput.GetBounds()
if femBounds == None:
femBounds = bounds
else:
femBounds = (
min(femBounds[0], bounds[0]),
max(femBounds[1], bounds[1]),
min(femBounds[2], bounds[2]),
max(femBounds[3], bounds[3]),
min(femBounds[4], bounds[4]),
max(femBounds[5], bounds[5]),
)
def setFileName(self, file_name):
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_name)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.EDGE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.SIDE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL, 1)
reader.UpdateInformation()
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, 0, 1)
num_sidesets = reader.GetNumberOfSideSetArrays()
num_nodesets = reader.GetNumberOfNodeSetArrays()
num_blocks = reader.GetNumberOfElementBlockArrays()
self.sidesets = []
self.sideset_id_to_exodus_block = {}
for i in xrange(num_sidesets):
sideset_id = reader.GetObjectId(vtk.vtkExodusIIReader.SIDE_SET, i)
self.sidesets.append(sideset_id)
self.sideset_id_to_exodus_block[sideset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.SIDE_SET, i, 1)
self.nodesets = []
self.nodeset_id_to_exodus_block = {}
for i in xrange(num_nodesets):
nodeset_id = reader.GetObjectId(vtk.vtkExodusIIReader.NODE_SET, i)
self.nodesets.append(nodeset_id)
self.nodeset_id_to_exodus_block[nodeset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, i, 1)
self.blocks = []
self.block_id_to_exodus_block = {}
for i in xrange(num_blocks):
block_id = reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK, i)
self.blocks.append(block_id)
self.block_id_to_exodus_block[block_id] = i
reader.SetTimeStep(1)
reader.Update()
self.data = reader.GetOutput()
self.all_actors = []
self.sideset_actors = {}
self.clipped_sideset_actors = {}
self.current_sideset_actors = self.sideset_actors
for i in xrange(num_sidesets):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.sideset_vtk_block, i)
actor.setColor(red)
self.sideset_actors[str(self.sidesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_sideset_actors[str(self.sidesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,
i).split(' ')
if 'Unnamed' not in name:
self.sideset_actors[name[0]] = actor
self.clipped_sideset_actors[name[0]] = clipped_actor
self.nodeset_actors = {}
self.clipped_nodeset_actors = {}
self.current_nodeset_actors = self.nodeset_actors
for i in xrange(num_nodesets):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.nodeset_vtk_block, i)
actor.setColor(red)
self.nodeset_actors[str(self.nodesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_nodeset_actors[str(self.nodesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,
i).split(' ')
if 'Unnamed' not in name:
self.nodeset_actors[name[0]] = actor
self.clipped_nodeset_actors[name[0]] = clipped_actor
self.block_actors = {}
self.clipped_block_actors = {}
self.current_block_actors = self.block_actors
for i in xrange(num_blocks):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.element_vtk_block, i)
self.block_actors[str(self.blocks[i])] = actor
self.all_actors.append(actor)
actor.show()
actor.showEdges()
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_block_actors[str(self.blocks[i])] = clipped_actor
self.all_actors.append(clipped_actor)
name = reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,
i).split(' ')
if 'Unnamed' not in name:
self.block_actors[name[0]] = actor
self.clipped_block_actors[name[0]] = clipped_actor
self.setBounds()
# Avoid z-buffer fighting
vtk.vtkPolyDataMapper().SetResolveCoincidentTopologyToPolygonOffset()
self.renderer.ResetCamera()
self.vtkwidget.updateGL()
def go(self):
print "Mapping",self.cfdData,"to",self.feaMesh
# identify inner wall points
"""
reader = vtk.vtkSTLReader()
reader.SetFileName(self.feaMesh)
reader.ScalarTagsOn()
reader.Update()
feadata = reader.GetOutput()
"""
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.feaMesh)
reader.UpdateInformation()
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1) # enables all NODAL variables
reader.GenerateGlobalNodeIdArrayOn()
reader.GenerateGlobalElementIdArrayOn()
reader.ExodusModelMetadataOn()
reader.Update()
feadata = vtk.vtkCompositeDataGeometryFilter()
feadata.SetInputConnection(0, reader.GetOutputPort(0))
feadata.Update()
transform = vtk.vtkTransform()
transform.Scale(1000, 1000, 1000)
test = vtk.vtkTransformPolyDataFilter()
test.SetTransform(transform)
test.SetInput(feadata.GetOutput())
test.Update()
feadata = test.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInput(feadata)
normals.ComputeCellNormalsOn()
normals.ComputePointNormalsOn()
normals.ConsistencyOn()
normals.AutoOrientNormalsOn()
normals.SplittingOn()
normals.Update()
feabody = normals.GetOutput()
norms = feabody.GetPointData().GetArray('Normals')
norms_n = numpy_support.vtk_to_numpy(norms)
#print (norms_n)
feapnts = feabody.GetPoints().GetData()
feapnts_n = numpy_support.vtk_to_numpy(feapnts)
#print (feapnts_n)
reader = vtk.vtkPolyDataReader()
reader.SetFileName(self.cfdData)
reader.ReadAllVectorsOn()
reader.ReadAllScalarsOn()
reader.Update()
cfddata = reader.GetOutput()
transform = vtk.vtkTransform()
transform.Scale(1000, 1000, 1000)
test = vtk.vtkTransformPolyDataFilter()
test.SetTransform(transform)
test.SetInputConnection(reader.GetOutputPort())
test.Update()
cfddata = test.GetOutput()
"""
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName("volume.vtk")
reader.ReadAllVectorsOn()
reader.ReadAllScalarsOn()
reader.Update()
cfdvol = reader.GetOutput()
"""
cfdpnts = cfddata.GetPoints().GetData()
cfdpnts_n = numpy_support.vtk_to_numpy(cfdpnts)
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(feabody)
pointLocator.BuildLocator()
innerIds = []
for cfdpnt in cfdpnts_n:
id = pointLocator.FindClosestPoint(cfdpnt)
innerIds.append(id)
innerIds = np.unique(innerIds)
# foreach fea innerpoint
# find the intersection point to cfddata
# probe field cfddata using intersection point
# append the field data to feabody
caster = pycaster.rayCaster(cfddata)
interPoints={}
interPointsSave = vtk.vtkPoints()
ptcount=0
for id in innerIds:
feainpnt = feapnts_n[id]
feainnorm = norms_n[id]
sourcePnt = feainpnt
targetPnt = feainpnt+(feainnorm*100)
pointsIntersection = caster.castRay(sourcePnt, targetPnt)
if len(pointsIntersection)!=0:
interPointsSave.InsertPoint(ptcount, pointsIntersection[0]+(feainnorm*0))
interPoints[id]=ptcount
ptcount+=1
else:
targetPnt = feainpnt-(feainnorm*100)
pointsIntersection = caster.castRay(sourcePnt, targetPnt)
if len(pointsIntersection)!=0:
interPointsSave.InsertPoint(ptcount, pointsIntersection[0]-(feainnorm*0))
interPoints[id]=ptcount
ptcount+=1
# for each interPoint, probe cfddata fields
innerPointData = vtk.vtkPolyData()
innerPointData.SetPoints(interPointsSave)
"""
# IF LOADING FROM VOLUME
transform = vtk.vtkTransform()
transform.Scale(0.001,0.001,0.001)
test = vtk.vtkTransformPolyDataFilter()
test.SetTransform(transform)
test.SetInput(innerPointData)
test.Update()
innerPointData = test.GetOutput()
"""
probe = vtk.vtkProbeFilter()
probe.SetInput(innerPointData)
probe.SetSource(cfddata)
pd = vtk.vtkAppendPolyData()
pd.AddInputConnection(probe.GetOutputPort())
pd.Update()
probeData=pd.GetOutput()
# detect all fields
#fields=[]
#for f in range(0,probeData.GetPointData().GetNumberOfArrays()):
# fields.append(probeData.GetPointData().GetArrayName(f))
globalNodeIds=numpy_support.vtk_to_numpy(feabody.GetPointData().GetArray('PedigreeNodeId'))
fieldData={}
for f in self.fields:
fieldData[f]=numpy_support.vtk_to_numpy(probeData.GetPointData().GetArray(f))
for f in self.fields:
ff = open("bc/"+f+"/"+f+"_"+self.cfdData.split("_")[1].replace(".vtk",".inp"),'w')
if (f == "T"):
ff.write("*BOUNDARY\n")
elif (f == "p"):
ff.write("*CLOAD\n")
for id in innerIds:
try:
#print ",".join([str(globalNodeIds[id]),'11','11',str(fieldData[f][interPoints[id]])])
if fieldData[f][interPoints[id]] != 0:
if (f == "T"):
ff.write(",".join([str(globalNodeIds[id]),'11','11',str(fieldData[f][interPoints[id]])])+"\n")
elif (f == "p"):
ff.write(",".join([str(globalNodeIds[id]),'3',str(fieldData[f][interPoints[id]])])+"\n")
except:
pass
ff.close()
#writer = vtk.vtkDataSetWriter()
#writer.SetFileName('probe.vtk')
#writer.SetInput(probe.GetOutput())
#writer.Write()
"""
# WRITE INTERSECTION POINTS TO FILE
interPointsSave = vtk.vtkPoints()
ptcount=0
for pnt in interPoints:
interPointsSave.InsertPoint(ptcount, pnt)
ptcount+=1
innerPointData = vtk.vtkPolyData()
innerPointData.SetPoints(interPointsSave)
writer = vtk.vtkDataSetWriter()
writer.SetFileName('points.vtk')
writer.SetInput(innerPointData)
writer.Write()
"""
"""
def pennesModeling(**kwargs):
"""
treatment planning model
"""
# import needed modules
import petsc4py, numpy, sys
PetscOptions = sys.argv
PetscOptions.append("-ksp_monitor")
PetscOptions.append("-ksp_rtol")
PetscOptions.append("1.0e-15")
#PetscOptions.append("-idb")
petsc4py.init(PetscOptions)
from petsc4py import PETSc
# break processors into separate communicators
petscRank = PETSc.COMM_WORLD.getRank()
petscSize = PETSc.COMM_WORLD.Get_size()
sys.stdout.write("petsc rank %d petsc nproc %d\n" % (petscRank, petscSize))
# set shell context
import femLibrary
# initialize libMesh data structures
libMeshInit = femLibrary.PyLibMeshInit(PetscOptions,PETSc.COMM_WORLD)
# the original configuration ini file should be stored
config = kwargs['config_parser']
# store control variables
getpot = femLibrary.PylibMeshGetPot(PetscOptions)
# copy all values from the input file
for section in config.sections():
for name,value in config.items(section):
#print "%s/%s" % (section,name) , value
getpot.SetIniValue( "%s/%s" % (section,name) , value )
# nodeset 1 will be treated as dirichlet
dirichletID = 1
getpot.SetIniValue( "bc/u_dirichlet" , '%d' % dirichletID )
# set tissue lookup tables
k_0Table = {"default":config.getfloat("thermal_conductivity","k_0_healthy") ,
"vessel" :config.getfloat("thermal_conductivity","k_0_healthy") ,
"grey" :config.getfloat("thermal_conductivity","k_0_grey" ) ,
"white" :config.getfloat("thermal_conductivity","k_0_white" ) ,
"csf" :config.getfloat("thermal_conductivity","k_0_csf" ) ,
"tumor" :config.getfloat("thermal_conductivity","k_0_tumor" ) }
w_0Table = {"default":config.getfloat("perfusion","w_0_healthy") ,
"vessel" :config.getfloat("perfusion","w_0_healthy") ,
"grey" :config.getfloat("perfusion","w_0_grey" ) ,
"white" :config.getfloat("perfusion","w_0_white" ) ,
"csf" :config.getfloat("perfusion","w_0_csf" ) ,
"tumor" :config.getfloat("perfusion","w_0_tumor" ) }
mu_aTable = {"default":config.getfloat("optical","mu_a_healthy") ,
"vessel" :config.getfloat("optical","mu_a_healthy") ,
"grey" :config.getfloat("optical","mu_a_grey" ) ,
"white" :config.getfloat("optical","mu_a_white" ) ,
"csf" :config.getfloat("optical","mu_a_csf" ) ,
"tumor" :config.getfloat("optical","mu_a_tumor" ) }
mu_sTable = {"default":config.getfloat("optical","mu_s_healthy") ,
"vessel" :config.getfloat("optical","mu_s_healthy") ,
"grey" :config.getfloat("optical","mu_s_grey" ) ,
"white" :config.getfloat("optical","mu_s_white" ) ,
"csf" :config.getfloat("optical","mu_s_csf" ) ,
"tumor" :config.getfloat("optical","mu_s_tumor" ) }
labelTable= {config.get("labels","greymatter" ):"grey" ,
config.get("labels","whitematter"):"white",
config.get("labels","csf" ):"csf" ,
config.get("labels","tumor" ):"tumor",
config.get("labels","vessel" ):"vessel"}
labelCount= {"default":0,
"grey" :0,
"white" :0,
"csf" :0,
"tumor" :0,
"vessel" :0}
# imaging params
import vtk
import vtk.util.numpy_support as vtkNumPy
SegmentFile=config.get("exec","segment_file")
# set the default reader based on extension
if( SegmentFile.split(".").pop() == "vtk"):
vtkImageReader = vtk.vtkDataSetReader
elif( SegmentFile.split(".").pop() == "vti"):
vtkImageReader = vtk.vtkXMLImageDataReader
else:
raise RuntimeError("uknown file")
# get dimension info from header
vtkSetupReader = vtkImageReader()
vtkSetupReader.SetFileName(SegmentFile )
vtkSetupReader.Update()
vtkImageMask = vtkSetupReader.GetOutput()
dimensions = vtkSetupReader.GetOutput().GetDimensions()
numberPointsImage = vtkSetupReader.GetOutput().GetNumberOfPoints()
spacing_mm = vtkSetupReader.GetOutput().GetSpacing()
origin_mm = vtkSetupReader.GetOutput().GetOrigin()
# convert to meters
spacing = [dx*.001 for dx in spacing_mm]
origin = [x0*.001 for x0 in origin_mm]
# pass pointer to c++
image_cells = vtkImageMask.GetPointData()
data_array = vtkNumPy.vtk_to_numpy( image_cells.GetArray(0) )
# need to pass numpy array's w/ Fortran storage... ie painful to debug
imageDataVec = PETSc.Vec().createWithArray(numpy.ravel(data_array,order='F'), comm=PETSc.COMM_SELF)
# FIXME - center around quadrature in out-of-plane direction
# FIXME - need better out of plane cooling model
quadratureOffset = 1./numpy.sqrt(3.0) * spacing[2]/2.0
# expecting roi and subsample of the form:
# roi = [(40,210),(30,220),(6,78)]
# subsample = [3,3,2]
ROI = eval(config.get('exec','roi'))
subsample = eval(config.get('exec','subsample'))
nelemROI = [ (pixel[1] - pixel[0] - 1 )/sub for pixel,sub in zip(ROI,subsample)]
xbounds = [ origin[0]+spacing[0]*(ROI[0][0]+0.5),origin[0]+spacing[0]*(ROI[0][1]+0.5) ]
ybounds = [ origin[1]+spacing[1]*(ROI[1][0]+0.5),origin[1]+spacing[1]*(ROI[1][1]+0.5) ]
zbounds = [ origin[2]+spacing[2]*(ROI[2][0]+0.5),origin[2]+spacing[2]*(ROI[2][1]+0.5) ]
if( petscRank ==0 ):
print "#points",numberPointsImage , "dimensions ",dimensions , "spacing ",spacing , "origin ",origin
print "ROI",ROI , "nelemROI ",nelemROI , "bounds", xbounds, ybounds, zbounds
#set to steady state solve
getpot.SetIniValue("steadystate/domain_0","true")
# initialize FEM Mesh
femMesh = femLibrary.PylibMeshMesh()
#femMesh.SetupUnStructuredGrid(kwargs['mesh_file'],0,RotationMatrix, Translation )
#femMesh.ReadFile(kwargs['mesh_file'])
femMesh.SetupStructuredGrid(nelemROI,xbounds,ybounds,zbounds,
[2,2,2,2,2,2])
# get output file name else set default name
try:
MeshOutputFile = config.get("exec","exodus_file" )
except ConfigParser.NoOptionError:
MeshOutputFile = "fem.e"
# add the data structures for the Background System Solve
# set deltat, number of time steps, power profile, and add system
eqnSystems = femLibrary.PylibMeshEquationSystems(femMesh,getpot)
#getpot.SetIniPower(1,[[19,119],[90.0,100.0]] )
getpot.SetIniPower(1,kwargs['powerHistory'] )
# AddPennesSDASystem
# AddPennesRFSystem
# AddPennesDeltaPSystem
pennesSystem = eval("eqnSystems.%s('StateSystem',kwargs['deltat'])" % kwargs['physics'])
pennesSystem.AddStorageVectors( kwargs['ntime']+1 )
# add system for labels
# FIXME: need both nodal, for dirichlet bc, and element version, for parameter masks
maskElemSystem = eqnSystems.AddExplicitSystem( "ElemImageMask" )
maskElemSystem.AddConstantMonomialVariable( "maskElem" )
# initialize libMesh data structures
eqnSystems.init( )
# print info
eqnSystems.PrintSelf()
# setup imaging to interpolate onto FEM mesh
femImaging = femLibrary.PytttkImaging(getpot, dimensions ,origin,spacing)
# Project imaging onto libMesh data structures
femImaging.ProjectImagingToFEMMesh("ElemImageMask" ,0.0,imageDataVec,eqnSystems)
femImaging.ProjectImagingToFEMMesh("StateSystem" ,0.0,imageDataVec,eqnSystems)
# create dirichlet nodes from this mask
numNodes = pennesSystem.PetscFEMSystemCreateNodeSetFromMask(config.getfloat("labels","vessel"),dirichletID)
print "# of dirichlet nodes %d" %numNodes
# get image label as numpy array
imageLabel = maskElemSystem.GetSolutionVector()[...]
#imageLabel = numpy.floor(10.0*imageLabel.copy())+1
k_0Label = imageLabel.copy()
w_0Label = imageLabel.copy()
mu_aLabel = imageLabel.copy()
mu_sLabel = imageLabel.copy()
for (idpos,label) in enumerate(imageLabel):
try:
tissueType = labelTable["%d"%int(label)]
except KeyError:
tissueType = "default"
labelCount[tissueType] = labelCount[tissueType] + 1
k_0Label[ idpos] = k_0Table[ tissueType]
w_0Label[ idpos] = w_0Table[ tissueType]
mu_aLabel[idpos] = mu_aTable[tissueType]
mu_sLabel[idpos] = mu_sTable[tissueType]
# create array of imaging data as petsc vec
k_0Vec = PETSc.Vec().createWithArray(k_0Label , comm=PETSc.COMM_SELF)
w_0Vec = PETSc.Vec().createWithArray(w_0Label , comm=PETSc.COMM_SELF)
mu_aVec = PETSc.Vec().createWithArray(mu_aLabel, comm=PETSc.COMM_SELF)
mu_sVec = PETSc.Vec().createWithArray(mu_sLabel, comm=PETSc.COMM_SELF)
# copy material properties to the system
eqnSystems.GetSystem("k_0").SetSolutionVector( k_0Vec )
eqnSystems.GetSystem("w_0").SetSolutionVector( w_0Vec )
eqnSystems.GetSystem("mu_a").SetSolutionVector(mu_aVec)
eqnSystems.GetSystem("mu_s").SetSolutionVector(mu_sVec)
# write IC
exodusII_IO = femLibrary.PylibMeshExodusII_IO(femMesh)
exodusII_IO.WriteTimeStep(MeshOutputFile,eqnSystems, 1, 0.0 )
exodusII_IO.WriteParameterSystems(eqnSystems)
# setup IC
pennesSystem.PetscFEMSystemSetupInitialConditions( )
# create list of laser positions
laserPositionList = [ ((.015,.015,2*spacing[2]+quadratureOffset),
(.018,.018,2*spacing[2]+quadratureOffset) ),
((.015,.015,2*spacing[2]+quadratureOffset),
(.016,.018,2*spacing[2]+quadratureOffset) ),
((.015,.015,1*spacing[2]+quadratureOffset),
(.014,.014,1*spacing[2]+quadratureOffset) ),
((.015,.015,1*spacing[2]+quadratureOffset),
(.015,.018,3*spacing[2]+quadratureOffset) )]
# time stamp
import pickle,time
timeStamp =0
# set power id to turn laser on
pennesSystem.PetscFEMSystemUpdateTimeStep( 1 )
# loop over laser position and solve steady state equations for each position
#for (idpos,(pos0,pos1)) in enumerate(laserPositionList):
# loop and read new laser parameters
while(True):
if(os.path.getmtime(fem_params['ini_filename']) > timeStamp):
timeStamp = os.path.getmtime(fem_params['ini_filename'] )
newIni = ConfigParser.SafeConfigParser({})
newIni.read(fem_params['ini_filename'])
laserParams = {}
laserParams['position1'] = [newIni.getfloat("probe",varID ) for varID in ["x_0","y_0","z_0"] ]
laserParams['position2'] = [newIni.getfloat("probe",varID ) for varID in ["x_1","y_1","z_1"] ]
print "laser position = ", newIni.getfloat("timestep","power") , laserParams
pennesSystem.PennesSDASystemUpdateLaserPower(newIni.getfloat("timestep","power"),1)
pennesSystem.PennesSDASystemUpdateLaserPosition(laserParams['position1'],laserParams['position2'])
pennesSystem.SystemSolve( )
#fem.StoreTransientSystemTimeStep("StateSystem",timeID )
#exodusII_IO.WriteTimeStep(MeshOutputFile ,eqnSystems, idpos+2, idpos*kwargs['deltat'])
exodusII_IO.WriteTimeStep(MeshOutputFile ,eqnSystems, 2, 1.0)
exodusII_IO.WriteParameterSystems(eqnSystems)
# write to txt file
if( petscRank ==0 ):
time.sleep(1)
vtkExodusIIReader = vtk.vtkExodusIIReader()
print "opening %s " % MeshOutputFile
vtkExodusIIReader.SetFileName( MeshOutputFile )
vtkExodusIIReader.Update()
ntime = vtkExodusIIReader.GetNumberOfTimeSteps()
variableID = "u0"
print "ntime %d %s " % (ntime,variableID)
vtkExodusIIReader.SetTimeStep(1)
vtkExodusIIReader.SetPointResultArrayStatus(variableID,1)
vtkExodusIIReader.Update()
curInput = None
# multi block
if vtkExodusIIReader.GetOutput().IsA("vtkMultiBlockDataSet"):
iter = vtkExodusIIReader.GetOutput().NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
curInput = iter.GetCurrentDataObject()
else:
curInput = vtkExodusIIReader.GetOutput()
#fem_point_data= curInput.GetPointData().GetArray('u0')
#Soln=vtkNumPy.vtk_to_numpy(fem_point_data)
#numpy.savetxt( "temperature.txt" ,Soln)
# 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
# scale back to millimeter
# TODO verify that the data sets are registered in the native slicer coordinate system
# TODO segmented data MUST be read in with:
# TODO add data -> volume -> show options -> ignore orientation
# TODO add data -> volume -> show options -> ignore orientation
# TODO add data -> volume -> show options -> ignore orientation
AffineTransform = vtk.vtkTransform()
AffineTransform.Translate([ 0.0,0.0,0.0])
AffineTransform.RotateZ( 0.0 )
AffineTransform.RotateY( 0.0 )
AffineTransform.RotateX( 0.0 )
AffineTransform.Scale([1000.,1000.,1000.])
# scale to millimeter
transformFilter = vtk.vtkTransformFilter()
transformFilter.SetInput(curInput)
transformFilter.SetTransform(AffineTransform)
transformFilter.Update()
# setup contour filter
vtkContour = vtk.vtkContourFilter()
vtkContour.SetInput( transformFilter.GetOutput() )
# TODO: not sure why this works...
# set the array to process at the temperature == u0
vtkContour.SetInputArrayToProcess(0,0,0,0,'u0')
contourValuesList = eval(newIni.get('exec','contours'))
vtkContour.SetNumberOfContours( len(contourValuesList ) )
print "plotting array:", vtkContour.GetArrayComponent( )
for idContour,contourValue in enumerate(contourValuesList):
print "plotting contour:",idContour,contourValue
vtkContour.SetValue( idContour,contourValue )
vtkContour.Update( )
# setup threshold filter
vtkThreshold = vtk.vtkThreshold()
vtkThreshold.SetInput( transformFilter.GetOutput() )
vtkThreshold.ThresholdByLower( contourValuesList[0] )
#vtkThreshold.SetSelectedComponent( 0 )
vtkThreshold.SetComponentModeToUseAny( )
vtkThreshold.Update()
# resample onto image
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput( vtkImageMask )
vtkResample.SetSource( vtkThreshold.GetOutput() )
vtkResample.Update()
# write output
print "writing fem.vtk "
vtkImageWriter = vtk.vtkDataSetWriter()
vtkImageWriter.SetFileTypeToBinary()
vtkImageWriter.SetFileName("fem.vtk")
vtkImageWriter.SetInput(vtkResample.GetOutput())
vtkImageWriter.Update()
# write stl file
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetInput(vtkContour.GetOutput( ))
stlWriter.SetFileName("fem.stl")
stlWriter.SetFileTypeToBinary()
stlWriter.Write()
# write support file to signal full stl file is written
# Slicer module will wait for this file to be written
# before trying to open stl file to avoid incomplete reads
with open('./fem.finish', 'w') as signalFile:
signalFile.write("the stl file has been written\n")
else:
print "waiting on user input.."
# echo lookup table
if( petscRank ==0 ):
print "lookup tables"
print "labeled %d voxels" % len(imageLabel)
print "labels" , labelTable
print "counts" , labelCount
print "conductivity", k_0Table
print "perfusion" , w_0Table
print "absorption" , mu_aTable
print "scattering" , mu_sTable
time.sleep(2)
def buildActors(self, file_name):
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_name)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.EDGE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.SIDE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL, 1)
reader.UpdateInformation()
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, 0, 1)
num_sidesets = reader.GetNumberOfSideSetArrays()
num_nodesets = reader.GetNumberOfNodeSetArrays()
num_blocks = reader.GetNumberOfElementBlockArrays()
self.sidesets = []
self.sideset_id_to_exodus_block = {}
self.sideset_id_to_name = {}
self.name_to_sideset_id = {}
for i in xrange(num_sidesets):
sideset_id = reader.GetObjectId(vtk.vtkExodusIIReader.SIDE_SET,i)
self.sidesets.append(sideset_id)
self.sideset_id_to_exodus_block[sideset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.SIDE_SET, i, 1)
name = reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,i).split(' ')
if 'Unnamed' not in name:
self.sideset_id_to_name[sideset_id] = name[0]
self.name_to_sideset_id[name[0]] = sideset_id
self.nodesets = []
self.nodeset_id_to_exodus_block = {}
self.nodeset_id_to_name = {}
self.name_to_nodeset_id = {}
for i in xrange(num_nodesets):
nodeset_id = reader.GetObjectId(vtk.vtkExodusIIReader.NODE_SET,i)
self.nodesets.append(nodeset_id)
self.nodeset_id_to_exodus_block[nodeset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, i, 1)
name = reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,i).split(' ')
if 'Unnamed' not in name:
self.nodeset_id_to_name[nodeset_id] = name[0]
self.name_to_nodeset_id[name[0]] = nodeset_id
self.blocks = []
self.block_id_to_exodus_block = {}
self.block_id_to_name = {}
self.name_to_block_id = {}
for i in xrange(num_blocks):
block_id = reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK,i)
self.blocks.append(block_id)
self.block_id_to_exodus_block[block_id] = i
name = reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' ')
if 'Unnamed' not in name:
self.block_id_to_name[block_id] = name[0]
self.name_to_block_id[name[0]] = block_id
reader.SetTimeStep(1)
reader.Update()
self.data = reader.GetOutput()
for i in xrange(num_sidesets):
actor = ExodusActor(self.renderer, self.data, ExodusMap.sideset_vtk_block, i)
self.sideset_actors[str(self.sidesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_sideset_actors[str(self.sidesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
for i in xrange(num_nodesets):
actor = ExodusActor(self.renderer, self.data, ExodusMap.nodeset_vtk_block, i)
self.nodeset_actors[str(self.nodesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_nodeset_actors[str(self.nodesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
for i in xrange(num_blocks):
actor = ExodusActor(self.renderer, self.data, ExodusMap.element_vtk_block, i)
self.block_actors[str(self.blocks[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_block_actors[str(self.blocks[i])] = clipped_actor
self.all_actors.append(clipped_actor)
def convertExodusII2MSH(fname):
import vtk
import numpy
import struct
from ctypes import c_int, c_double
useBinaryFormat = True
def write_in_binary_format(fname):
file = open(fname, 'wb')
file.writelines(("$MeshFormat\n", "2.1 1 8\n"))
file.write(struct.pack("i", 1))
file.write("\n".encode("utf-8"))
file.writelines(
("$EndMeshFormat\n", "$Nodes\n", "%d\n" % len(node_dict)))
rnode_dict = numpy.zeros((len(node_dict), 3), dtype=float)
for k, v in node_dict.items():
rnode_dict[v - 1][0] = k[0]
rnode_dict[v - 1][1] = k[1]
rnode_dict[v - 1][2] = k[2]
dtype = [("index", c_int), ("x", c_double, (3, ))]
tmp = numpy.empty(len(node_dict), dtype=dtype)
tmp["index"] = 1 + numpy.arange(len(node_dict))
tmp["x"] = numpy.asarray(rnode_dict)
file.write(tmp.tostring())
file.write("\n".encode("utf-8"))
file.write("$EndNodes\n")
file.write("$Elements\n")
file.write("%d\n" % (len(ele_face_dict) + len(ele_vol_dict)))
# header
file.write(struct.pack("i", 2))
file.write(struct.pack(
"i", len(ele_face_dict))) # or maybe +len(ele_face_dict)
file.write(struct.pack("i", 2))
for k, ele in enumerate(ele_face_dict):
file.write(
struct.pack("iiiiii", k + 1, ele[0], ele[0], ele[1], ele[2],
ele[3]))
file.write(struct.pack("i", 4))
file.write(struct.pack(
"i", len(ele_vol_dict))) # or maybe +len(ele_face_dict)
file.write(struct.pack("i", 2))
for k, ele in enumerate(ele_vol_dict):
file.write(
struct.pack("iiiiiii", k + 1 + len(ele_face_dict), ele[0],
ele[0], ele[1], ele[2], ele[3], ele[4]))
file.write("\n".encode("utf-8"))
file.write("$EndElements\n")
file.close()
def write_in_ASCII_format(fname):
file = open(fname, 'w')
file.writelines(("$MeshFormat\n", "2.2 0 8\n", "$EndMeshFormat\n",
"$Nodes\n", "%d\n" % len(node_dict)))
for k in range(len(node_dict)):
p = rnode_dict[k + 1]
file.write("%d %f %f %f\n" % (k + 1, p[0], p[1], p[2]))
file.write("$EndNodes\n")
file.write("$Elements\n")
file.write("%d\n" % (len(ele_face_dict) + len(ele_vol_dict)))
for k, ele in enumerate(ele_face_dict):
file.write("%d 2 2 %d %d %d %d %d\n" %
(k + 1, ele[0], ele[0], ele[1], ele[2], ele[3]))
for k, ele in enumerate(ele_vol_dict):
file.write("%d 4 2 %d %d %d %d %d %d\n" %
(k + 1, ele[0], ele[0], ele[1], ele[2], ele[3], ele[4]))
file.write("$EndElements\n")
file.close()
r = vtk.vtkExodusIIReader()
if (fname[-2:] == '-h'):
print 'This script converts a general exodus ii file into ASCII .msh file format. It requires the vtk python library to be installed on the system.'
print 'The input should be the name of the file, and the output is that same name .msh. Example: python exodus2msh.py test.e'
print 'To convert to .msh binary format use the option /geometry/create_binary_msh in Diamond.'
exit()
elif (fname[-2:] != '.e'):
fname += '.e'
print 'Converting the input exodus ii file into .msh format...'
r.SetFileName(fname)
r.UpdateInformation()
r.GenerateGlobalNodeIdArrayOn()
r.GenerateGlobalElementIdArrayOn()
r.GenerateObjectIdCellArrayOn()
#r.ExodusModelMetadataOn()
#r.PackExodusModelOntoOutputOn()
for i in range(r.GetNumberOfSideSetArrays()):
name = r.GetSideSetArrayName(i)
r.SetSideSetArrayStatus(name, 1)
r.Update()
data = r.GetOutput()
node_dict = {}
ele_face_dict = []
ele_vol_dict = []
n = 1
def f():
global n
a = n
n = n + 1
return a
for j in range(data.GetBlock(4).GetNumberOfBlocks()):
ug = data.GetBlock(4).GetBlock(j)
sidesetID = r.GetObjectId(3, j)
for k in range(ug.GetNumberOfPoints()):
lnodes = {}
p = ug.GetPoint(k)
N = node_dict.get(p)
if N == None:
node_dict[p] = n
n += 1
lnodes[k] = node_dict.get(p)
for k in range(ug.GetNumberOfCells()):
cp = ug.GetCell(k).GetPoints()
ele_face_dict.append(
(sidesetID, node_dict[cp.GetPoint(0)],
node_dict[cp.GetPoint(1)], node_dict[cp.GetPoint(2)]))
for j in range(data.GetBlock(0).GetNumberOfBlocks()):
ug = data.GetBlock(0).GetBlock(j)
blockID = r.GetObjectId(1, j)
for k in range(ug.GetNumberOfPoints()):
lnodes = {}
p = ug.GetPoint(k)
N = node_dict.get(p)
if N == None:
node_dict[p] = n
n += 1
lnodes[k] = node_dict.get(p)
for k in range(ug.GetNumberOfCells()):
cp = ug.GetCell(k).GetPoints()
ele_vol_dict.append(
(blockID, node_dict[cp.GetPoint(0)], node_dict[cp.GetPoint(1)],
node_dict[cp.GetPoint(2)], node_dict[cp.GetPoint(3)]))
fname = fname[:-2] + '.msh'
if useBinaryFormat:
write_in_binary_format(fname)
else:
write_in_ASCII_format(fname)
print '...file created => ' + fname
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()
def ProjectImagingMesh(work_dir,data_set):
import vtk
import vtk.util.numpy_support as vtkNumPy
import numpy
import scipy.io as scipyio
# echo vtk version info
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
# 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
vtkReader = vtk.vtkDataSetReader()
# offset averaging +/- in both directions about center
listoffset = [-2,-1,0,1,2]
if (data_set == "dog1"):
# should be in meters
#AffineTransform.Translate(0.206,0.289,-0.0215)
#AffineTransform.RotateZ( 0.0 )
#AffineTransform.RotateY( 0.0 )
#AffineTransform.RotateX( 90.0 )
Translate = (0.293,0.0634,0.12345)
RotateZ = -90.0
RotateY = 0.0
RotateX = 90.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/FUS4/data2/BioTex/Brain_PhaseII/060626_BrainDog1_Treat/ProcessedTMAPData/BioTexCanines/dog1dtmap.0000.vtk'
elif (data_set == "dog2"):
# should be in meters
Translate = (0.2335,0.235,-0.0335)
RotateZ = 6.0
RotateY = 0.0
RotateX = 90.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/data/sjfahrenholtz/mdacc/Dog/dog2_98000/mrivis/temperature.0000.vtk'
ImageFileTemplate = '/FUS4/data2/BioTex/Brain_PhaseII/060626_BrainDog1_Treat/ProcessedTMAPData/BioTexCanines/dog2dtmap.0000.vtk'
elif (data_set == "dog3"):
# should be in meters
Translate = (0.209,0.2625,-0.0247)
RotateZ = -8.0
RotateY = 0.0
RotateX = 90.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/data/sjfahrenholtz/mdacc/Dog/dog3_98000/mrivis/temperature.0000.vtk'
ImageFileTemplate = '/FUS4/data2/BioTex/Brain_PhaseII/060626_BrainDog1_Treat/ProcessedTMAPData/BioTexCanines/dog3dtmap.0000.vtk'
elif (data_set == "dog4"):
# should be in meters
Translate = (0.195,0.245,-0.0715)
RotateZ = -15.0
RotateY = 0.0
RotateX = 90.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/FUS4/data2/BioTex/Brain_PhaseII/060626_BrainDog1_Treat/ProcessedTMAPData/BioTexCanines/dog4dtmap.0000.vtk'
elif (data_set == "human0"):
# should be in meters
vtkReader = vtk.vtkXMLImageDataReader()
Translate = (0.051,0.080,0.0509)
RotateZ = 29.0
RotateY = 86.0
RotateX = 0.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/data/fuentes/biotex/090318_751642_treat/Processed/imaging/temperature.0000.vti'
elif (data_set == "agar0"):
# should be in meters
Translate = (0.0,0.13,-0.095)
RotateZ = 0.0
RotateY = 180.0
RotateX = 0.0
Scale = [1.,1.,1.]
ImageFileTemplate = '/data/jyung/MotionCorrection/motion_phantom_sept11/tmap.0000.vtk'
else:
raise RuntimeError("\n\n unknown case... ")
# read imaging data geometry that will be used to project FEM data onto
vtkReader.SetFileName( ImageFileTemplate )
vtkReader.Update()
templateImage = vtkReader.GetOutput()
dimensions = templateImage.GetDimensions()
spacing = templateImage.GetSpacing()
origin = templateImage.GetOrigin()
print spacing, origin, dimensions
#fem.SetImagingDimensions( dimensions ,origin,spacing)
#setup to interpolate at 5 points across axial dimension
TransformList = []
naverage = len(listoffset)
subdistance = spacing[2] / (naverage-1)
print "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
for ii in range(0,120):
vtkExodusIIReader.SetFileName( "%s/fem_stats.%04d.e" % (work_dir,ii) )
#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()
#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, ii, work_dir
vtkStatsWriter = vtk.vtkDataSetWriter()
vtkStatsWriter.SetFileTypeToBinary()
vtkStatsWriter.SetFileName("%s/modelstats.navg%d.%04d.vtk" % ( work_dir,naverage,ii ))
vtkStatsWriter.SetInput(vtkResample.GetOutput())
vtkStatsWriter.Update()
def AssembleStatistics(data_dir):
"""
collect all statistics into one exodus file
"""
# post process stats on FEM mesh
# import petsc and numpy
import vtk, numpy
import vtk.util.numpy_support as vtkNumPy
# initialize FEM Mesh
pkl_file = open('%s/CaseInfo.pkl' % ".", 'rb')
fem_params = pickle.load(pkl_file)
pkl_file.close()
vtkExodusIIReader = vtk.vtkExodusIIReader()
print "opening %s " % fem_params['mesh_file']
vtkExodusIIReader.SetFileName( fem_params['mesh_file'] )
#vtkExodusIIReader.SetFileName( "/data/fuentes/utsa/vasculature_july10/vessel_0/realization.1//fem_data.0001.e")
vtkExodusIIReader.ExodusModelMetadataOn ()
vtkExodusIIReader.Update()
exodusObject = vtkExodusIIReader.GetOutput()
responseLevelVarList = fem_params['responseLevelVarList']
probabilityLevelList = fem_params['probabilityLevelList']
reliabilityLevelList = fem_params['reliabilityLevelList']
# loop over time steps and import data
# vtkTemporalDataSet = vtk.vtkTemporalDataSet()
# multiBlockData = {}
#for timeID in [69]:
#TODO how can we assemble all time steps at once ?
#for timeID in range(0,fem_params['ntime']+1):
for timeID in [int(data_dir.split(".").pop())]:
for variable,responseList in responseLevelVarList:
#(variable,responseList) = responseLevelVarList[0]
basePath = "%s/%s" % (data_dir,variable)
# mean
meanFile=open("%s/meanFile.txt" % (basePath) ,"r")
meandataList = [float(line.strip()) for line in meanFile]
meanFile.close()
# std dev
stdFile=open("%s/stddFile.txt" % (basePath),"r")
stdddataList = [float(line.strip()) for line in stdFile]
stdFile.close()
# skewness
skewFile=open("%s/skewFile.txt" % (basePath),"r")
skewdataList = [float(line.strip()) for line in skewFile]
skewFile.close()
# kurtosis
kurtFile=open("%s/kurtFile.txt" % (basePath),"r")
kurtdataList = [float(line.strip()) for line in kurtFile]
kurtFile.close()
# response data
responsedataList = []
for iii,response in enumerate(responseList):
responseFile=open("%s/response.%d.txt" %(basePath,iii),"r")
singleresponseList = [float(line.strip()) for line in responseFile]
responseFile.close()
responsedataList.append(singleresponseList)
# probability data
probabilitydataList = []
for iii,probability in enumerate(probabilityLevelList):
probFile=open("%s/probability.%d.txt" %(basePath,iii),"r")
probList = [float(line.strip()) for line in probFile]
probFile.close()
probabilitydataList.append(probList)
# reliability data
reliabilitydataList = []
for iii,reliability in enumerate(reliabilityLevelList):
reliabFile=open("%s/reliability.%d.txt" %(basePath,iii),"r")
reliabList = [float(line.strip()) for line in reliabFile]
reliabFile.close()
reliabilitydataList.append(reliabList)
# multi block
if exodusObject.IsA("vtkMultiBlockDataSet"):
iter = exodusObject.NewIterator()
iter.UnRegister(None)
iter.InitTraversal()
# iter.GoToNextItem();
# iter.GoToNextItem();
metadata = exodusObject.GetMetaData(iter)
# initialize list for storage
listSliceInit = 0
# loop over blocks...
while not iter.IsDoneWithTraversal():
curInput = iter.GetCurrentDataObject()
curNumberPoints = curInput.GetNumberOfPoints()
fem_point_data= curInput.GetPointData()
DeepCopy = 1
#print timeID,listSliceInit,curNumberPoints
vtkMean= vtkNumPy.numpy_to_vtk( meandataList[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkStdD= vtkNumPy.numpy_to_vtk( stdddataList[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkSkew= vtkNumPy.numpy_to_vtk( skewdataList[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkKurt= vtkNumPy.numpy_to_vtk( kurtdataList[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkMean.SetName( "Var%sMean" % variable )
vtkStdD.SetName( "Var%sStdDev" % variable )
vtkSkew.SetName( "Var%sSkew" % variable )
vtkKurt.SetName( "Var%sKurt" % variable )
fem_point_data.AddArray( vtkMean )
fem_point_data.AddArray( vtkStdD )
fem_point_data.AddArray( vtkSkew )
fem_point_data.AddArray( vtkKurt )
fem_point_data.Update()
for iii,response in enumerate(responsedataList):
vtkResponse= vtkNumPy.numpy_to_vtk( response[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkResponse.SetName( "Var%sresponse%d" %(variable,iii) )
fem_point_data.AddArray( vtkResponse )
fem_point_data.Update()
for iii,probability in enumerate(probabilitydataList):
vtkProb= vtkNumPy.numpy_to_vtk( probability[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkProb.SetName( "Var%sprobability%d" %(variable,iii) )
fem_point_data.AddArray( vtkProb )
fem_point_data.Update()
for iii,reliability in enumerate(reliabilitydataList):
vtkReliab= vtkNumPy.numpy_to_vtk( reliability[listSliceInit:listSliceInit+curNumberPoints ] , DeepCopy)
vtkReliab.SetName( "Var%sreliability%d" %(variable,iii) )
fem_point_data.AddArray( vtkReliab )
fem_point_data.Update()
#vtkSoln = vtkNumPy.numpy_to_vtk( listSliceInit * numpy.ones(curNumberPoints ), DeepCopy )
#vtkSoln.SetName("%d" % listSliceInit)
curInput.Update()
# multiBlockData['%d' % timeID] = vtk.vtkUnstructuredGrid()
# multiBlockData['%d' % timeID].DeepCopy( curInput )
listSliceInit = listSliceInit + curNumberPoints
iter.GoToNextItem();
# single block
else:
raise RuntimeError("not implemented yet... " )
vtkExodusIIWriter = vtk.vtkExodusIIWriter()
vtkExodusIIWriter.SetFileName( '%s/fem_stats.%04d.e' % (".",timeID) )
vtkExodusIIWriter.SetInput( exodusObject)
vtkExodusIIWriter.Update()
def read(filetype, filename):
import vtk
from vtk.util import numpy_support
def _read_data(data):
'''Extract numpy arrays from a VTK data set.
'''
# Go through all arrays, fetch data.
out = {}
for k in range(data.GetNumberOfArrays()):
array = data.GetArray(k)
if array:
array_name = array.GetName()
out[array_name] = vtk.util.numpy_support.vtk_to_numpy(array)
return out
def _read_cells(vtk_mesh):
data = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCells().GetData()
)
offsets = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellLocationsArray()
)
types = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellTypesArray()
)
vtk_to_meshio_type = {
vtk.VTK_VERTEX: 'vertex',
vtk.VTK_LINE: 'line',
vtk.VTK_TRIANGLE: 'triangle',
vtk.VTK_QUAD: 'quad',
vtk.VTK_TETRA: 'tetra',
vtk.VTK_HEXAHEDRON: 'hexahedron',
vtk.VTK_WEDGE: 'wedge',
vtk.VTK_PYRAMID: 'pyramid'
}
# `data` is a one-dimensional vector with
# (num_points0, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
# Translate it into the cells dictionary.
cells = {}
for vtk_type, meshio_type in vtk_to_meshio_type.items():
# Get all offsets for vtk_type
os = offsets[numpy.argwhere(types == vtk_type).transpose()[0]]
num_cells = len(os)
if num_cells > 0:
num_pts = data[os[0]]
# instantiate the array
arr = numpy.empty((num_cells, num_pts), dtype=int)
# sort the num_pts entries after the offsets into the columns
# of arr
for k in range(num_pts):
arr[:, k] = data[os+k+1]
cells[meshio_type] = arr
return cells
if filetype == 'vtk':
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'xdmf':
reader = vtk.vtkXdmfReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
elif filetype == 'exodus':
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
else:
raise RuntimeError('Unknown file type \'%s\'.' % filename)
# Explicitly extract points, cells, point data, field data
points = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetPoints().GetData()
)
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
cell_data = _read_data(vtk_mesh.GetCellData())
field_data = _read_data(vtk_mesh.GetFieldData())
return points, cells, point_data, cell_data, field_data
def read(filetype, filename):
import vtk
from vtk.util import numpy_support
def _read_data(data):
'''Extract numpy arrays from a VTK data set.
'''
# Go through all arrays, fetch data.
out = {}
for k in range(data.GetNumberOfArrays()):
array = data.GetArray(k)
if array:
array_name = array.GetName()
out[array_name] = vtk.util.numpy_support.vtk_to_numpy(array)
return out
def _read_cells(vtk_mesh):
data = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCells().GetData())
offsets = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellLocationsArray())
types = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellTypesArray())
vtk_to_meshio_type = {
vtk.VTK_VERTEX: 'vertex',
vtk.VTK_LINE: 'line',
vtk.VTK_TRIANGLE: 'triangle',
vtk.VTK_QUAD: 'quad',
vtk.VTK_TETRA: 'tetra',
vtk.VTK_HEXAHEDRON: 'hexahedron',
vtk.VTK_WEDGE: 'wedge',
vtk.VTK_PYRAMID: 'pyramid'
}
# `data` is a one-dimensional vector with
# (num_points0, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
# Translate it into the cells dictionary.
cells = {}
for vtk_type, meshio_type in vtk_to_meshio_type.items():
# Get all offsets for vtk_type
os = offsets[numpy.argwhere(types == vtk_type).transpose()[0]]
num_cells = len(os)
if num_cells > 0:
num_pts = data[os[0]]
# instantiate the array
arr = numpy.empty((num_cells, num_pts), dtype=int)
# sort the num_pts entries after the offsets into the columns
# of arr
for k in range(num_pts):
arr[:, k] = data[os + k + 1]
cells[meshio_type] = arr
return cells
if filetype == 'vtk':
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype == 'xdmf':
reader = vtk.vtkXdmfReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
elif filetype == 'exodus':
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
else:
raise RuntimeError('Unknown file type \'%s\'.' % filename)
# Explicitly extract points, cells, point data, field data
points = vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetPoints().GetData())
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
cell_data = _read_data(vtk_mesh.GetCellData())
field_data = _read_data(vtk_mesh.GetFieldData())
return points, cells, point_data, cell_data, field_data
templateImage = vtkReader.GetOutput()
dimensions = templateImage.GetDimensions()
spacing = templateImage.GetSpacing()
origin = templateImage.GetOrigin()
# loop over time steps and solve
for timeID in range(1, ntime):
print "time step = ", timeID
fem.UpdateTransientSystemTimeStep("StateSystem", timeID)
fem.SystemSolve("StateSystem")
#fem.StoreTransientSystemTimeStep("StateSystem",timeID )
fem.WriteTimeStep("fem_data.e", timeID + 1, timeID * deltat)
# Interpolate FEM onto imaging data structures
if (petscRank == -1):
vtkExodusIIReader = vtk.vtkExodusIIReader()
vtkExodusIIReader.SetFileName("fem_data.e")
vtkExodusIIReader.SetPointResultArrayStatus("u0", 1)
vtkExodusIIReader.SetTimeStep(timeID - 1)
vtkExodusIIReader.Update()
# reuse ShiftScale Geometry
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput(templateImage)
vtkResample.SetSource(vtkExodusIIReader.GetOutput())
vtkResample.Update()
# FIXME this is prob the longest round about way possible...
# FIXME convert to binary first then read back in a single component
# For VTK to be able to use the data, it must be stored as a VTK-image. This can be done by the vtkImageImport-class which
# imports raw data and stores it.
def deltapModeling(**kwargs):
"""
treatment planning model
"""
# import petsc and numpy
import petsc4py, numpy
# init petsc
PetscOptions = sys.argv
PetscOptions.append("-ksp_monitor")
PetscOptions.append("-ksp_rtol")
PetscOptions.append("1.0e-15")
#PetscOptions.append("-help")
#PetscOptions.append("-idb")
petsc4py.init(PetscOptions)
#
# break processors into separate communicators
from petsc4py import PETSc
petscRank = PETSc.COMM_WORLD.getRank()
petscSize = PETSc.COMM_WORLD.Get_size()
sys.stdout.write("petsc rank %d petsc nproc %d\n" % (petscRank, petscSize))
# set shell context
# TODO import vtk should be called after femLibrary ????
# FIXME WHY IS THIS????
import femLibrary
# initialize libMesh data structures
libMeshInit = femLibrary.PyLibMeshInit(PetscOptions,PETSc.COMM_WORLD)
# store control variables
getpot = femLibrary.PylibMeshGetPot(PetscOptions)
# from Duck table 2.11 pig dermis
getpot.SetIniValue( "material/specific_heat","3280.0" )
# set ambient temperature
getpot.SetIniValue( "initial_condition/u_init","0.0" )
# from Duck 2.7 Rat tumor measured in vivo
getpot.SetIniValue( "thermal_conductivity/k_0_tumor","0.32" )
getpot.SetIniValue( "thermal_conductivity/k_0_healthy",kwargs['cv']['k_0_healthy'] )
# water properties at http://www.d-a-instruments.com/light_absorption.html
getpot.SetIniValue( "optical/mu_a_healthy", kwargs['cv']['mu_a_healthy'] )
# FIXME large mu_s (> 30) in agar causing negative fluence to satisfy BC
getpot.SetIniValue( "optical/mu_s_healthy",
kwargs['cv']['mu_s_healthy'] )
# from AE paper
#http://scitation.aip.org/journals/doc/MPHYA6-ft/vol_36/iss_4/1351_1.html#F3
#For SPIOs
#getpot.SetIniValue( "optical/guass_radius","0.0035" )
#For NR/NS
getpot.SetIniValue( "optical/guass_radius",".003" )
# cauchy BC
getpot.SetIniValue( "bc/u_infty","0.0" )
getpot.SetIniValue( "bc/newton_coeff","1.0e5" )
# 1-300
getpot.SetIniValue( "optical/mu_a_tumor",
kwargs['cv']['mu_a_tumor'] )
# 1-300
getpot.SetIniValue( "optical/mu_s_tumor",
kwargs['cv']['mu_s_tumor'] )
#getpot.SetIniValue( "optical/mu_a_tumor","71.0" )
#getpot.SetIniValue( "optical/mu_s_tumor","89.0" )
# .9 - .99
getpot.SetIniValue( "optical/anfact",kwargs['cv']['anfact'] )
#agar length
#for SPIOs
#getpot.SetIniValue( "optical/agar_length","0.0206" )
#for NR/NS
getpot.SetIniValue( "optical/agar_length","0.023" )
getpot.SetIniValue("optical/refractive_index","1.0")
#
# given the original orientation as two points along the centerline z = x2 -x1
# the transformed orienteation would be \hat{z} = A x2 + b - A x1 - b = A z
# ie transformation w/o translation which is exactly w/ vtk has implemented w/ TransformVector
# TransformVector = TransformPoint - the transation
#Setup Affine Transformation for registration
RotationMatrix = [[1.,0.,0.],
[0.,1.,0.],
[0.,0.,1.]]
Translation = [0.,0.,0.]
# original coordinate system laser input
# For SPIOs 67_11
#laserTip = [0.,-.000625,.035]
# For SPIOs 67_10
#laserTip = [0.,-.0001562,.035]
# For SPIOs 335_11
#laserTip = [0.,-.0014062,.035]
# For NR
#laserTip = [0.,.0002,.035]
# For NS
laserTip = [0.00001,.000001,.000001]
laserOrientation = [0.0,0.,-1.0]
import vtk
import vtk.util.numpy_support as vtkNumPy
# echo vtk version info
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
# 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
AffineTransform = vtk.vtkTransform()
# should be in meters
# For NS
#AffineTransform.Translate([ .01320,-.0037,0.00000010])
#AffineTransform.Translate([ .005,-.0035,0.0])
AffineTransform.Translate([-.006,-.0022,0.0])
AffineTransform.RotateZ( 0.0 )
AffineTransform.RotateY( -90.0 )
AffineTransform.RotateX( 0.0 )
AffineTransform.Scale([1.,1.,1.])
# get homogenius 4x4 matrix of the form
# A | b
# matrix = -----
# 0 | 1
#
matrix = AffineTransform.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 ,Translation
laserTip = AffineTransform.TransformPoint( laserTip )
laserOrientation = AffineTransform.TransformVector( laserOrientation )
# set laser orientation values
getpot.SetIniValue( "probe/x_0","%f" % laserTip[0])
getpot.SetIniValue( "probe/y_0","%f" % laserTip[1])
getpot.SetIniValue( "probe/z_0","%f" % laserTip[2])
getpot.SetIniValue( "probe/x_orientation","%f" % laserOrientation[0] )
getpot.SetIniValue( "probe/y_orientation","%f" % laserOrientation[1] )
getpot.SetIniValue( "probe/z_orientation","%f" % laserOrientation[2] )
# initialize FEM Mesh
femMesh = femLibrary.PylibMeshMesh()
# must setup Ini File first
#For SPIOs
#femMesh.SetupUnStructuredGrid( "/work/01741/cmaclell/data/mdacc/deltap_phantom_oct10/phantomMeshFullTess.e",0,RotationMatrix, Translation )
#For NS/NR
RotationMatrix = [[1,0,0],
[0,1,0],
[0,0,1]]
Translation = [.0000001,.00000001,.000001]
#
femMesh.SetupUnStructuredGrid( "./sphereMesh.e",0,RotationMatrix, Translation )
#femMesh.SetupUnStructuredGrid( "phantomMesh.e",0,RotationMatrix, Translation )
MeshOutputFile = "fem_data.%04d.e" % kwargs['fileID']
#femMes.SetupStructuredGrid( (10,10,4) ,[0.0,1.0],[0.0,2.0],[0.0,1.0])
# add the data structures for the background system solve
# set deltat, number of time steps, power profile, and add system
nsubstep = 1
#for SPIOs
#acquisitionTime = 4.9305
#for NS/NR
acquisitionTime = 5.09
deltat = acquisitionTime / nsubstep
ntime = 60
eqnSystems = femLibrary.PylibMeshEquationSystems(femMesh,getpot)
#For SPIOs
#getpot.SetIniPower(nsubstep, [ [1,6,30,ntime],[1.0,0.0,4.5,0.0] ])
#For NS/NR
getpot.SetIniPower(nsubstep, [ [1,6,42,ntime],[1.0,0.0,1.13,0.0] ])
deltapSystem = eqnSystems.AddPennesDeltaPSystem("StateSystem",deltat)
deltapSystem.AddStorageVectors(ntime)
# hold imaging
mrtiSystem = eqnSystems.AddExplicitSystem( "MRTI" )
mrtiSystem.AddFirstLagrangeVariable( "u0*" )
mrtiSystem.AddStorageVectors(ntime)
maskSystem = eqnSystems.AddExplicitSystem( "ImageMask" )
maskSystem.AddFirstLagrangeVariable( "mask" )
# initialize libMesh data structures
eqnSystems.init( )
# print info
eqnSystems.PrintSelf()
# write IC
exodusII_IO = femLibrary.PylibMeshExodusII_IO(femMesh)
exodusII_IO.WriteTimeStep(MeshOutputFile,eqnSystems, 1, 0.0 )
# read imaging data geometry that will be used to project FEM data onto
#For 67_11
#vtkReader.SetFileName('/work/01741/cmaclell/data/mdacc/deltap_phantom_oct10/spio/spioVTK/67_11/tmap_67_11.0000.vtk')
#For 67_10
#vtkReader.SetFileName('/work/01741/cmaclell/data/mdacc/deltap_phantom_oct10/spio/spioVTK/67_10/tmap_67_10.0000.vtk')
#For 335_11
#vtkReader.SetFileName('/work/01741/cmaclell/data/mdacc/deltap_phantom_oct10/spio/spioVTK/335_11/tmap_335_11.0000.vtk')
#For NS
#vtkReader.SetFileName('/work/01741/cmaclell/data/mdacc/deltap_phantom_oct10/nrtmapsVTK/S695/S695.0000.vtk')
#For NR
imageFileNameTemplate = '/work/01741/cmaclell/data/mdacc/NanoMouseJune12/matlab_VTK/control_1_tmap.%04d.vtk'
imageFileNameTemplate = '/FUS4/data2/CJM/SPIO_mice/matlab_VTK/control_1_tmap.%04d.vtk'
#imageFileNameTemplate = "/share/work/fuentes/deltap_phantom_oct10/nrtmapsVTK/R695/R695.%04d.vtk"
#imageFileNameTemplate = "/data/fuentes/mdacc/deltap_phantom_oct10/nrtmapsVTK/R695/R695.%04d.vtk"
#vtkReader = vtk.vtkXMLImageDataReader()
vtkReader = vtk.vtkDataSetReader()
vtkReader.SetFileName( imageFileNameTemplate % 0 )
vtkReader.Update()
templateImage = vtkReader.GetOutput()
dimensions = templateImage.GetDimensions()
spacing = templateImage.GetSpacing()
origin = templateImage.GetOrigin()
print spacing, origin, dimensions
femImaging = femLibrary.PytttkImaging(getpot, dimensions ,origin,spacing)
ObjectiveFunction = 0.0
# loop over time steps and solve
for timeID in range(1,ntime*nsubstep):
#for timeID in range(1,10):
# project imaging onto fem mesh
vtkImageReader = vtk.vtkDataSetReader()
vtkImageReader.SetFileName( imageFileNameTemplate % timeID )
vtkImageReader.Update()
image_cells = vtkImageReader.GetOutput().GetPointData()
data_array = vtkNumPy.vtk_to_numpy(image_cells.GetArray('scalars'))
v1 = PETSc.Vec().createWithArray(data_array, comm=PETSc.COMM_SELF)
femImaging.ProjectImagingToFEMMesh("MRTI",0.0,v1,eqnSystems)
mrtiSystem.StoreSystemTimeStep(timeID )
# create image mask
# The = operator for numpy arrays just copies by reference
# .copy() provides a deep copy (ie physical memory copy)
image_mask = data_array.copy().reshape(dimensions,order='F')
# Set all image pixels to large value
largeValue = 1.e6
image_mask[:,:] = 1
# RMS error will be computed within this ROI/VOI imagemask[xcoords/column,ycoords/row]
#image_mask[93:153,52:112] = 1.0
#image_mask[98:158,46:106] = 1.0
v2 = PETSc.Vec().createWithArray(image_mask, comm=PETSc.COMM_SELF)
femImaging.ProjectImagingToFEMMesh("ImageMask",largeValue,v2,eqnSystems)
#print mrti_array
#print type(mrti_array)
print "time step = " ,timeID
eqnSystems.UpdatePetscFEMSystemTimeStep("StateSystem",timeID )
deltapSystem.SystemSolve()
#eqnSystems.StoreTransientSystemTimeStep("StateSystem",timeID )
# accumulate objective function
#
# qoi = ( (FEM - MRTI) / ImageMask)^2
#
qoi = femLibrary.WeightedL2Norm( deltapSystem,"u0",
mrtiSystem,"u0*",
maskSystem,"mask" )
ObjectiveFunction =( ObjectiveFunction + qoi)
# control write output
writeControl = True
if ( timeID%nsubstep == 0 and writeControl ):
# write exodus file
exodusII_IO.WriteTimeStep(MeshOutputFile,eqnSystems, timeID+1, timeID*deltat )
# Interpolate FEM onto imaging data structures
if (vtk != None):
vtkExodusIIReader = vtk.vtkExodusIIReader()
vtkExodusIIReader.SetFileName(MeshOutputFile )
vtkExodusIIReader.SetPointResultArrayStatus("u0",1)
vtkExodusIIReader.SetTimeStep(timeID-1)
vtkExodusIIReader.Update()
# reflect
vtkReflect = vtk.vtkReflectionFilter()
vtkReflect.SetPlaneToYMax()
vtkReflect.SetInput( vtkExodusIIReader.GetOutput() )
vtkReflect.Update()
# reuse ShiftScale Geometry
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetInput( vtkImageReader.GetOutput() )
vtkResample.SetSource( vtkReflect.GetOutput() )
vtkResample.Update()
fem_point_data= vtkResample.GetOutput().GetPointData()
fem_array = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('u0'))
#print fem_array
#print type(fem_array )
# only rank 0 should write
#if ( petscRank == 0 ):
# print "writing ", timeID
# vtkTemperatureWriter = vtk.vtkDataSetWriter()
# vtkTemperatureWriter.SetFileTypeToBinary()
# vtkTemperatureWriter.SetFileName("invspio_67_11.%04d.vtk" % timeID )
# vtkTemperatureWriter.SetInput(vtkResample.GetOutput())
# vtkTemperatureWriter.Update()
print 'Objective Fn'
print ObjectiveFunction
retval = dict([])
retval['fns'] = [ObjectiveFunction *10000000.]
retval['rank'] = petscRank
return(retval)
def buildActors(self, file_name):
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_name)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.EDGE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.SIDE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODE_SET, 1)
reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL, 1)
reader.UpdateInformation()
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, 0, 1)
num_sidesets = reader.GetNumberOfSideSetArrays()
num_nodesets = reader.GetNumberOfNodeSetArrays()
num_blocks = reader.GetNumberOfElementBlockArrays()
self.sidesets = []
self.sideset_id_to_exodus_block = {}
self.sideset_id_to_name = {}
self.name_to_sideset_id = {}
for i in xrange(num_sidesets):
sideset_id = reader.GetObjectId(vtk.vtkExodusIIReader.SIDE_SET, i)
self.sidesets.append(sideset_id)
self.sideset_id_to_exodus_block[sideset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.SIDE_SET, i, 1)
name = reader.GetObjectName(vtk.vtkExodusIIReader.SIDE_SET,
i).split(' ')
if 'Unnamed' not in name:
self.sideset_id_to_name[sideset_id] = name[0]
self.name_to_sideset_id[name[0]] = sideset_id
self.nodesets = []
self.nodeset_id_to_exodus_block = {}
self.nodeset_id_to_name = {}
self.name_to_nodeset_id = {}
for i in xrange(num_nodesets):
nodeset_id = reader.GetObjectId(vtk.vtkExodusIIReader.NODE_SET, i)
self.nodesets.append(nodeset_id)
self.nodeset_id_to_exodus_block[nodeset_id] = i
reader.SetObjectStatus(vtk.vtkExodusIIReader.NODE_SET, i, 1)
name = reader.GetObjectName(vtk.vtkExodusIIReader.NODE_SET,
i).split(' ')
if 'Unnamed' not in name:
self.nodeset_id_to_name[nodeset_id] = name[0]
self.name_to_nodeset_id[name[0]] = nodeset_id
self.blocks = []
self.block_id_to_exodus_block = {}
self.block_id_to_name = {}
self.name_to_block_id = {}
for i in xrange(num_blocks):
block_id = reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK, i)
self.blocks.append(block_id)
self.block_id_to_exodus_block[block_id] = i
name = reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,
i).split(' ')
if 'Unnamed' not in name:
self.block_id_to_name[block_id] = name[0]
self.name_to_block_id[name[0]] = block_id
reader.SetTimeStep(1)
reader.Update()
self.data = reader.GetOutput()
for i in xrange(num_sidesets):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.sideset_vtk_block, i)
self.sideset_actors[str(self.sidesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_sideset_actors[str(self.sidesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
for i in xrange(num_nodesets):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.nodeset_vtk_block, i)
self.nodeset_actors[str(self.nodesets[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_nodeset_actors[str(self.nodesets[i])] = clipped_actor
self.all_actors.append(clipped_actor)
for i in xrange(num_blocks):
actor = ExodusActor(self.renderer, self.data,
ExodusMap.element_vtk_block, i)
self.block_actors[str(self.blocks[i])] = actor
self.all_actors.append(actor)
clipped_actor = ClippedActor(actor, self.plane)
self.clipped_block_actors[str(self.blocks[i])] = clipped_actor
self.all_actors.append(clipped_actor)
def setFileName(self, file_name, lut):
try:
self.currently_has_actor = True
self.lut = lut
self.file_name = file_name
self.reader = vtk.vtkExodusIIReader()
self.reader.SetFileName(self.file_name)
self.reader.UpdateInformation()
self.current_dim = self.reader.GetDimensionality()
self.min_timestep = 0
self.max_timestep = 0
range = self.reader.GetTimeStepRange()
self.min_timestep = range[0]
self.max_timestep = range[1]
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.ELEM_BLOCK, 1)
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL, 1)
self.reader.SetTimeStep(self.max_timestep)
self.reader.Update()
self.current_variable_point_data = {}
self.current_nodal_variables = []
self.current_elemental_variables = []
self.current_nodal_components = {}
self.current_elemental_components = {}
self.component_index = -1
num_blocks = self.reader.GetNumberOfElementBlockArrays()
self.blocks = set()
self.block_to_name = {}
for i in xrange(num_blocks):
block_num = self.reader.GetObjectId(vtk.vtkExodusIIReader.ELEM_BLOCK,i)
self.blocks.add(block_num)
if 'Unnamed' not in self.reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' '):
self.block_to_name[block_num] = self.reader.GetObjectName(vtk.vtkExodusIIReader.ELEM_BLOCK,i).split(' ')[0]
cdp = vtk.vtkCompositeDataPipeline()
vtk.vtkAlgorithm.SetDefaultExecutivePrototype(cdp)
self.output = self.reader.GetOutput()
self.geom = vtk.vtkCompositeDataGeometryFilter()
self.geom.SetInputConnection(0,self.reader.GetOutputPort(0))
self.geom.Update()
self.data = self.geom.GetOutput()
num_nodal_variables = self.data.GetPointData().GetNumberOfArrays()
for var_num in xrange(num_nodal_variables):
var_name = self.data.GetPointData().GetArrayName(var_num)
self.current_nodal_variables.append(var_name)
components = self.data.GetPointData().GetVectors(var_name).GetNumberOfComponents()
self.current_nodal_components[var_name] = components
# self.data.GetPointData().GetVectors(value_string).GetComponentName(0)
num_elemental_variables = self.data.GetCellData().GetNumberOfArrays()
for var_num in xrange(num_elemental_variables):
var_name = self.data.GetCellData().GetArrayName(var_num)
self.current_elemental_variables.append(var_name)
components = self.data.GetCellData().GetVectors(var_name).GetNumberOfComponents()
self.current_elemental_components[var_name] = components
self.application_filter = self.render_widget.application.filterResult(self.geom)
self.mapper = vtk.vtkPolyDataMapper()
# self.mapper.SetInputConnection(self.tf.GetOutputPort())
self.mapper.SetInputConnection(self.application_filter.GetOutputPort())
self.mapper.ScalarVisibilityOn()
self.mapper.SetLookupTable(lut)
self.mapper.SetColorModeToMapScalars()
self.mapper.InterpolateScalarsBeforeMappingOn()
self.actor = vtk.vtkActor()
self.current_actors.append(self.actor)
self.actor.SetMapper(self.mapper)
self.current_actor = self.actor
self.clipper = vtk.vtkTableBasedClipDataSet()
if vtk.VTK_MAJOR_VERSION <= 5:
self.clipper.SetInput(self.output)
else:
self.clipper.SetInputData(self.output)
self.clipper.SetClipFunction(self.plane)
self.clipper.Update()
self.clip_geom = vtk.vtkCompositeDataGeometryFilter()
self.clip_geom.SetInputConnection(0,self.clipper.GetOutputPort(0))
self.clip_geom.Update()
self.clip_data = self.clip_geom.GetOutput()
self.clip_application_filter = self.render_widget.application.filterResult(self.clip_geom)
self.clip_mapper = vtk.vtkPolyDataMapper()
self.clip_mapper.SetInputConnection(self.clip_application_filter.GetOutputPort())
self.clip_mapper.ScalarVisibilityOn()
self.clip_mapper.SetLookupTable(lut)
self.clip_actor = vtk.vtkActor()
self.clip_actor.SetMapper(self.clip_mapper)
self.current_actors.append(self.clip_actor)
self.scalar_bar = vtk.vtkScalarBarActor()
self.current_actors.append(self.scalar_bar)
self.scalar_bar.SetLookupTable(self.mapper.GetLookupTable())
self.scalar_bar.SetNumberOfLabels(4)
self.current_bounds = self.actor.GetBounds()
except:
pass
def setFileName(self, file_name, lut):
try:
self.currently_has_actor = True
self.lut = lut
self.file_name = file_name
self.reader = vtk.vtkExodusIIReader()
self.reader.SetFileName(self.file_name)
self.reader.UpdateInformation()
self.current_dim = self.reader.GetDimensionality()
self.min_timestep = 0
self.max_timestep = 0
range = self.reader.GetTimeStepRange()
self.min_timestep = range[0]
self.max_timestep = range[1]
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.ELEM_BLOCK, 1)
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL, 1)
self.reader.SetAllArrayStatus(vtk.vtkExodusIIReader.NODAL_TEMPORAL,
1)
self.reader.SetTimeStep(self.max_timestep)
self.reader.Update()
self.current_variable_point_data = {}
self.current_nodal_variables = []
self.current_elemental_variables = []
self.current_nodal_components = {}
self.current_elemental_components = {}
self.component_index = -1
num_blocks = self.reader.GetNumberOfElementBlockArrays()
self.blocks = set()
self.block_to_name = {}
for i in xrange(num_blocks):
block_num = self.reader.GetObjectId(
vtk.vtkExodusIIReader.ELEM_BLOCK, i)
self.blocks.add(block_num)
if 'Unnamed' not in self.reader.GetObjectName(
vtk.vtkExodusIIReader.ELEM_BLOCK, i).split(' '):
self.block_to_name[block_num] = self.reader.GetObjectName(
vtk.vtkExodusIIReader.ELEM_BLOCK, i).split(' ')[0]
cdp = vtk.vtkCompositeDataPipeline()
vtk.vtkAlgorithm.SetDefaultExecutivePrototype(cdp)
self.output = self.reader.GetOutput()
self.geom = vtk.vtkCompositeDataGeometryFilter()
self.geom.SetInputConnection(0, self.reader.GetOutputPort(0))
self.geom.Update()
self.data = self.geom.GetOutput()
num_nodal_variables = self.data.GetPointData().GetNumberOfArrays()
for var_num in xrange(num_nodal_variables):
var_name = self.data.GetPointData().GetArrayName(var_num)
self.current_nodal_variables.append(var_name)
components = self.data.GetPointData().GetVectors(
var_name).GetNumberOfComponents()
self.current_nodal_components[var_name] = components
# self.data.GetPointData().GetVectors(value_string).GetComponentName(0)
num_elemental_variables = self.data.GetCellData(
).GetNumberOfArrays()
for var_num in xrange(num_elemental_variables):
var_name = self.data.GetCellData().GetArrayName(var_num)
self.current_elemental_variables.append(var_name)
components = self.data.GetCellData().GetVectors(
var_name).GetNumberOfComponents()
self.current_elemental_components[var_name] = components
self.application_filter = self.render_widget.application.filterResult(
self.geom)
self.mapper = vtk.vtkPolyDataMapper()
# self.mapper.SetInputConnection(self.tf.GetOutputPort())
self.mapper.SetInputConnection(
self.application_filter.GetOutputPort())
self.mapper.ScalarVisibilityOn()
self.mapper.SetLookupTable(lut)
self.mapper.SetColorModeToMapScalars()
self.mapper.InterpolateScalarsBeforeMappingOn()
self.actor = vtk.vtkActor()
self.current_actors.append(self.actor)
self.actor.SetMapper(self.mapper)
self.current_actor = self.actor
self.clipper = vtk.vtkTableBasedClipDataSet()
if vtk.VTK_MAJOR_VERSION <= 5:
self.clipper.SetInput(self.output)
else:
self.clipper.SetInputData(self.output)
self.clipper.SetClipFunction(self.plane)
self.clipper.Update()
self.clip_geom = vtk.vtkCompositeDataGeometryFilter()
self.clip_geom.SetInputConnection(0, self.clipper.GetOutputPort(0))
self.clip_geom.Update()
self.clip_data = self.clip_geom.GetOutput()
self.clip_application_filter = self.render_widget.application.filterResult(
self.clip_geom)
self.clip_mapper = vtk.vtkPolyDataMapper()
self.clip_mapper.SetInputConnection(
self.clip_application_filter.GetOutputPort())
self.clip_mapper.ScalarVisibilityOn()
self.clip_mapper.SetLookupTable(lut)
self.clip_actor = vtk.vtkActor()
self.clip_actor.SetMapper(self.clip_mapper)
self.current_actors.append(self.clip_actor)
self.scalar_bar = vtk.vtkScalarBarActor()
self.current_actors.append(self.scalar_bar)
self.scalar_bar.SetLookupTable(self.mapper.GetLookupTable())
self.scalar_bar.SetNumberOfLabels(4)
self.current_bounds = self.actor.GetBounds()
except:
pass
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()
