def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkReflectionFilter(), 'Processing.',
('vtkDataSet',), ('vtkUnstructuredGrid',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkReflectionFilter(),
'Processing.', ('vtkDataSet', ),
('vtkUnstructuredGrid', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def mirror(self):
"""
Called when mirrorPlane != None
The reflection plane is labeled as follows: From the vtkfiles documentation:
ReflectionPlane {
USE_X_MIN = 0, USE_Y_MIN = 1, USE_Z_MIN = 2, USE_X_MAX = 3,
USE_Y_MAX = 4, USE_Z_MAX = 5, USE_X = 6, USE_Y = 7,
USE_Z = 8
}
"""
vr=v.vtkReflectionFilter()
vr.SetInputData(self.data)
vr.SetPlane(self.mirrorPlane)
self.data=vr.GetOutput()
vr.Update()
#self.data.Update()
self.ncells = self.data.GetNumberOfCells()
def landmark_reflection(self, ref_axis='x'):
RefFilter = vtk.vtkReflectionFilter()
if ref_axis == 'x':
RefFilter.SetPlaneToX()
elif ref_axis == 'y':
RefFilter.SetPlaneToY()
elif ref_axis == 'z':
RefFilter.SetPlaneToZ()
else:
if self.warning:
print('Invalid ref_axis!')
RefFilter.CopyInputOff()
RefFilter.SetInputData(self.vtkPolyData)
RefFilter.Update()
self.vtkPolyData = RefFilter.GetOutput()
self.get_landmark_data_from_vtkPolyData()
def mirror(self):
"""
Called when mirrorPlane != None
The reflection plane is labeled as follows: From the vtk documentation:
ReflectionPlane {
USE_X_MIN = 0, USE_Y_MIN = 1, USE_Z_MIN = 2, USE_X_MAX = 3,
USE_Y_MAX = 4, USE_Z_MAX = 5, USE_X = 6, USE_Y = 7,
USE_Z = 8
}
"""
vr=v.vtkReflectionFilter()
vr.SetInput(self.data)
vr.SetPlane(self.mirrorPlane)
self.data=vr.GetOutput()
vr.Update()
self.data.Update()
self.ncells = self.data.GetNumberOfCells()
def mesh_reflection(self, ref_axis='x'):
'''
This function is only for tooth arch model,
it will flip the label (n=15 so far) as well.
input:
ref_axis: 'x'/'y'/'z'
'''
RefFilter = vtk.vtkReflectionFilter()
if ref_axis == 'x':
RefFilter.SetPlaneToX()
elif ref_axis == 'y':
RefFilter.SetPlaneToY()
elif ref_axis == 'z':
RefFilter.SetPlaneToZ()
else:
if self.warning:
print('Invalid ref_axis!')
RefFilter.CopyInputOff()
RefFilter.SetInputData(self.vtkPolyData)
RefFilter.Update()
self.vtkPolyData = RefFilter.GetOutput()
self.get_mesh_data_from_vtkPolyData()
original_cell_labels = np.copy(
self.cell_attributes['Label']) # add original cell label back
# for permanent teeth
for i in range(1, 15):
if len(original_cell_labels == i) > 0:
self.cell_attributes['Label'][
original_cell_labels ==
i] = 15 - i #1 -> 14, 2 -> 13, ..., 14 -> 1
# for primary teeth
for i in range(15, 25):
if len(original_cell_labels == i) > 0:
self.cell_attributes['Label'][
original_cell_labels ==
i] = 39 - i #15 -> 24, 16 -> 23, ..., 24 -> 15
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() cone = vtk.vtkConeSource() reflect = vtk.vtkReflectionFilter() reflect.SetInputConnection(cone.GetOutputPort()) reflect.SetPlaneToXMax() reflect2 = vtk.vtkReflectionFilter() reflect2.SetInputConnection(reflect.GetOutputPort()) reflect2.SetPlaneToYMax() reflect3 = vtk.vtkReflectionFilter() reflect3.SetInputConnection(reflect2.GetOutputPort()) reflect3.SetPlaneToZMax() mapper = vtk.vtkDataSetMapper() mapper.SetInputConnection(reflect3.GetOutputPort()) actor = vtk.vtkActor() actor.SetMapper(mapper) ren1 = vtk.vtkRenderer() ren1.AddActor(actor) renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren1) renWin.SetSize(200, 200) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) iren.Initialize() renWin.Render() # --- end of script --
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(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 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)
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() cone = vtk.vtkConeSource() reflect = vtk.vtkReflectionFilter() reflect.SetInputConnection(cone.GetOutputPort()) reflect.SetPlaneToXMax() reflect2 = vtk.vtkReflectionFilter() reflect2.SetInputConnection(reflect.GetOutputPort()) reflect2.SetPlaneToYMax() reflect3 = vtk.vtkReflectionFilter() reflect3.SetInputConnection(reflect2.GetOutputPort()) reflect3.SetPlaneToZMax() mapper = vtk.vtkDataSetMapper() mapper.SetInputConnection(reflect3.GetOutputPort()) actor = vtk.vtkActor() actor.SetMapper(mapper) ren1 = vtk.vtkRenderer() ren1.AddActor(actor) renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren1) renWin.SetSize(200,200) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) iren.Initialize() renWin.Render() # --- end of script --
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()