def ExtractVOI(self):
wholeExtent = self.Image.GetExtent()
origin = self.Image.GetOrigin()
spacing = self.Image.GetSpacing()
newVOI = [0, 0, 0, 0, 0, 0]
newVOI[0] = max(
wholeExtent[0],
int(math.ceil((self.BoxBounds[0] - origin[0]) / spacing[0])))
newVOI[1] = min(
wholeExtent[1],
int(math.floor((self.BoxBounds[1] - origin[0]) / spacing[0])))
newVOI[2] = max(
wholeExtent[2],
int(math.ceil((self.BoxBounds[2] - origin[1]) / spacing[1])))
newVOI[3] = min(
wholeExtent[3],
int(math.floor((self.BoxBounds[3] - origin[1]) / spacing[1])))
newVOI[4] = max(
wholeExtent[4],
int(math.ceil((self.BoxBounds[4] - origin[2]) / spacing[2])))
newVOI[5] = min(
wholeExtent[5],
int(math.floor((self.BoxBounds[5] - origin[2]) / spacing[2])))
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInputData(self.CroppedImage)
extractVOI.SetVOI(newVOI)
extractVOI.Update()
self.CroppedImage.DeepCopy(extractVOI.GetOutput())
def __init__(self, parent=None):
self.nameSize = 24
self.CrosshairNode = None
self.CrosshairNodeObserverTag = None
self.frame = qt.QFrame(parent)
self.frame.setLayout(qt.QVBoxLayout())
modulePath = slicer.modules.dataprobe.path.replace("DataProbe.py","")
self.iconsDIR = modulePath + '/Resources/Icons'
self.showImage = False
# Used in _createMagnifiedPixmap()
self.imageCrop = vtk.vtkExtractVOI()
self.painter = qt.QPainter()
self.pen = qt.QPen()
self._createSmall()
#Helper class to calculate and display tensor scalars
self.calculateTensorScalars = CalculateTensorScalars()
# Observe the crosshair node to get the current cursor position
self.CrosshairNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLCrosshairNode')
if self.CrosshairNode:
self.CrosshairNodeObserverTag = self.CrosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, self.processEvent)
def CreatePlanes(func, actor, numberOfPlanes):
#
# Extract planes from implicit function.
#
append = vtk.vtkAppendFilter()
dims = func.GetSampleDimensions()
sliceIncr = (dims[2] - 1) // (numberOfPlanes + 1)
sliceNum = -4
for i in range(0, numberOfPlanes):
extract = vtk.vtkExtractVOI()
extract.SetInputConnection(func.GetOutputPort())
extract.SetVOI(0, dims[0] - 1,
0, dims[1] - 1,
sliceNum + sliceIncr, sliceNum + sliceIncr)
append.AddInputConnection(extract.GetOutputPort())
sliceNum += sliceIncr
append.Update()
# Map planes
planesMapper = vtk.vtkDataSetMapper()
planesMapper.SetInputConnection(append.GetOutputPort())
planesMapper.SetScalarRange(0, 7)
actor.SetMapper(planesMapper)
actor.GetProperty().SetAmbient(1.)
return
def _handlerVoiSaveButton(self, event):
input_data = self.getPrimaryInput()
filename = self.controlFrame.voiFilenameText.GetValue()
if input_data and self._voi_widget.GetEnabled() and filename:
# see if we need to reset to zero origin
zor = self.controlFrame.voiResetToOriginCheck.GetValue()
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInput(input_data)
extractVOI.SetVOI(self._currentVOI)
writer = vtk.vtkXMLImageDataWriter()
writer.SetDataModeToBinary()
writer.SetFileName(filename)
if zor:
ici = vtk.vtkImageChangeInformation()
ici.SetOutputExtentStart(0,0,0)
ici.SetInput(extractVOI.GetOutput())
writer.SetInput(ici.GetOutput())
else:
writer.SetInput(extractVOI.GetOutput())
writer.Write()
def ipl_open(image_in, open):
ipl_open_settings(open)
extent = image_in.GetExtent()
clip = vtk.vtkImageReslice()
clip.SetInput(image_in)
clip.SetOutputExtent(extent[0] - open - 2, extent[1] + open + 2,
extent[2] - open - 2, extent[3] + open + 2,
extent[4] - open - 2, extent[5] + open + 2)
clip.MirrorOn()
clip.Update()
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(clip.GetOutputPort())
erode.SetKernelSize(2 * open + 1, 2 * open + 1, 2 * open + 1)
erode.Update()
#Kernel size is twice the dilation distance plus one for the center voxel
dilate = vtk.vtkImageContinuousDilate3D()
dilate.SetInputConnection(erode.GetOutputPort())
dilate.SetKernelSize(2 * open + 1, 2 * open + 1, 2 * open + 1)
dilate.Update()
voi = vtk.vtkExtractVOI()
voi.SetInput(dilate.GetOutput())
voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4],
extent[5])
voi.Update()
image_out = voi.GetOutput()
return image_out
def crop(self, top=None, bottom=None, right=None, left=None, pixels=False):
"""Crop picture.
:param float top: fraction to crop from the top margin
:param float bottom: fraction to crop from the bottom margin
:param float left: fraction to crop from the left margin
:param float right: fraction to crop from the right margin
:param bool pixels: units are pixels
"""
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInputData(self._data)
extractVOI.IncludeBoundaryOn()
d = self.GetInput().GetDimensions()
if pixels:
extractVOI.SetVOI(right, d[0]-left, bottom, d[1]-top, 0, 0)
else:
bx0, bx1, by0, by1 = 0, d[0]-1, 0, d[1]-1
if left is not None: bx0 = int((d[0]-1)*left)
if right is not None: bx1 = int((d[0]-1)*(1-right))
if bottom is not None: by0 = int((d[1]-1)*bottom)
if top is not None: by1 = int((d[1]-1)*(1-top))
extractVOI.SetVOI(bx0, bx1, by0, by1, 0, 0)
extractVOI.Update()
return self._update(extractVOI.GetOutput())
def ipl_maskaimpeel(image_in1, image_in2, peel_iter):
ipl_maskaimpeel_settings(peel_iter)
extent = image_in1.GetExtent()
voi = vtk.vtkExtractVOI()
voi.SetInput(image_in1)
voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4],
extent[5])
voi.Update()
shift = vtk.vtkImageShiftScale()
shift.SetInputConnection(voi.GetOutputPort())
shift.SetOutputScalarTypeToUnsignedChar()
shift.Update()
mask = vtk.vtkImageMask()
mask.SetImageInput(image_in2)
mask.SetMaskInput(shift.GetOutput())
mask.SetMaskedOutputValue(0)
mask.Update()
if peel_iter != 0:
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(mask.GetOutputPort())
erode.SetKernelSize(peel_iter + 1, peel_iter + 1, peel_iter + 1)
erode.Update()
mask = erode
image_out = mask.GetOutput()
return image_out
def getIsoActor(fname, colour, opacity, value):
isoreader = vtk.vtkStructuredPointsReader()
isoreader.SetFileName(fname)
isoreader.Update()
extractiso = vtk.vtkExtractVOI()
if (options.xmax > -1 or options.ymax > -1 or options.zmax > -1):
extractiso.SetVOI(options.zmin,options.zmax, options.ymin,options.ymax, options.xmin,options.xmax)
extractiso.SetInput(isoreader.GetOutput())
iso = vtk.vtkMarchingCubes()
iso.SetInput(extractiso.GetOutput())
iso.SetValue(0,value)
polymap = vtk.vtkPolyDataMapper()
polymap.SetInput(iso.GetOutput())
polymap.ScalarVisibilityOff()
isoactor = vtk.vtkActor()
isoactor.SetMapper(polymap)
isoactor.GetProperty().SetColor(colour)
isoactor.GetProperty().SetOpacity(opacity)
return (isoreader, isoactor)
def create_planes(func: vtk.vtkSampleFunction,
number_of_planes: int) -> vtk.vtkActor:
"""
Creates a number of planes that show a slice of the data at that slice.
Adapted from
https://lorensen.github.io/VTKExamples/site/Python/Visualization/QuadricVisualization/
:param func: a vtkSampleFunction
:param number_of_planes: the number of planes to add to the actor.
:return: the actor to which the planes will be added.
"""
actor = vtk.vtkActor()
append = vtk.vtkAppendFilter()
dimensions = func.GetSampleDimensions()
slice_increment = (dimensions[2] - 1) // (number_of_planes + 1)
slice_num = -4
for i in range(0, number_of_planes):
extract = vtk.vtkExtractVOI()
extract.SetInputConnection(func.GetOutputPort())
extract.SetVOI(0, dimensions[0] - 1, 0, dimensions[1] - 1,
slice_num + slice_increment,
slice_num + slice_increment)
append.AddInputConnection(extract.GetOutputPort())
slice_num += slice_increment
append.Update()
planes_mapper = vtk.vtkDataSetMapper()
planes_mapper.SetInputConnection(append.GetOutputPort())
planes_mapper.SetScalarRange(0, 7)
actor.SetMapper(planes_mapper)
actor.GetProperty().SetAmbient(1.)
return actor
def avgProjectionsVtk(self, filenames , extent):
'''Returns the average of the input images
Input is passed as filenames pointing to 2D TIFF
Output is a vtkImageData
gives the same result as avgProjections within machine precision.
'''
num = len(filenames)
readers = [vtk.vtkTIFFReader() for i in range(num)]
scalers = [vtk.vtkImageShiftScale() for i in range(num)]
vois = [vtk.vtkExtractVOI() for i in range(num)]
avger = vtk.vtkImageWeightedSum()
counter = 0
for reader, voi, scaler, filename in zip(readers, vois , scalers ,filenames):
reader.SetFileName(filename)
reader.Update()
print ("reading {0}".format(filename))
voi.SetInputData(reader.GetOutput())
voi.SetVOI(extent)
voi.Update()
print ("extracting VOI")
scaler.SetInputData(voi.GetOutput())
scaler.SetOutputScalarTypeToDouble()
scaler.SetScale(1)
scaler.SetShift(0)
scaler.Update()
avger.AddInputData(scaler.GetOutput())
avger.SetWeight(counter , 1/float(num))
counter = counter + 1
print ("adding input connection {0}".format(counter))
avger.Update()
return avger.GetOutput()
def getPlane(self, data, plane, xCoordinate, yCoordinate, zCoordinate, applyZScaling = 0): """ Get a plane from given the volume """ xAxis, yAxis, zAxis = 0, 1, 2 dataWidth, dataHeight, dataDepth = data.GetDimensions() if not self.voi: self.voi = vtk.vtkExtractVOI() else: self.voi.RemoveAllInputs() if not self.permute: self.permute = vtk.vtkImagePermute() else: self.permute.RemoveAllInputs() self.permute.SetInputConnection(data.GetProducerPort()) spacing = data.GetSpacing() xscale = 1 yscale = 1 if plane == "zy": data.SetUpdateExtent(xCoordinate, xCoordinate, 0, dataHeight - 1, 0, dataDepth - 1) self.permute.SetFilteredAxes(zAxis, yAxis, xAxis) self.permute.Update() data = self.permute.GetOutput() self.voi.SetInput(data) self.voi.SetVOI(0, dataDepth - 1, 0, dataHeight - 1, xCoordinate, xCoordinate) xdim = dataDepth ydim = dataHeight if applyZScaling: xdim *= spacing[2] xscale = spacing[2] elif plane == "xz": data.SetUpdateExtent(0, dataWidth - 1, yCoordinate, yCoordinate, 0, dataDepth - 1) self.permute.SetFilteredAxes(xAxis, zAxis, yAxis) self.permute.Update() data = self.permute.GetOutput() self.voi.SetInput(data) self.voi.SetVOI(0, dataWidth - 1, 0, dataDepth - 1, yCoordinate, yCoordinate) xdim = dataWidth ydim = dataDepth if applyZScaling: ydim *= spacing[2] yscale = 1 self.voi.Update() if applyZScaling: self.voi.Update() return lib.ImageOperations.scaleImage(self.voi.GetOutput(), interpolation = 2, xfactor = xscale, yfactor = yscale) self.voi.Update() return self.voi.GetOutput()
def vtkVOIdata(self, volum = 'GAUSSIAN'):
""" Modification du volume d'interet """
#-----------------------------------------
# Creation de la VOI
#-----------------------------------------
self.vtkVolum = vtk.vtkExtractVOI()
self.vtkVolum.SetInput(self.vtkVolumAll.GetOutput())
self.vtkVolum.SetVOI(self.VOI_pt1[0], self.VOI_pt2[0], \
self.VOI_pt1[1], self.VOI_pt2[1], \
self.VOI_pt1[2], self.VOI_pt2[2])
self.vtkVolumBlur = vtk.vtkImageGaussianSmooth()
#-----------------------------------------
# Creation du volume sur volume filtre gaussien
#-----------------------------------------
if volum == 'GAUSSIAN':
self.vtkVolumBlur.SetInputConnection(self.vtkVolum.GetOutputPort())
#-----------------------------------------
# Creation du volume sur volume filtre gradient + gaussien
#-----------------------------------------
if volum == 'GRADIENT':
self.vtkVolumGrad = vtk.vtkImageGradientMagnitude()
self.vtkVolumGrad.SetDimensionality(3)
self.vtkVolumGrad.HandleBoundariesOn()
self.vtkVolumGrad.SetInputConnection(self.vtkVolum.GetOutputPort())
self.vtkVolumBlur.SetInputConnection(self.vtkVolumGrad.GetOutputPort())
self.vtkVolumBlur.SetStandardDeviation(self.valGaussianFilter)
self.vtkVolumBlur.Update()
self.vtkVolumRange = self.vtkVolumBlur.GetOutput().GetScalarRange()
print " Range from Volume Of Interest : ", self.vtkVolumRange
def test_dither_boat(self):
self.print_param.fill_pattern.value = 1
self.print_param.skin_offset.value = 1.0
self.print_param.infill.value = 0.5
slicer = VoxelSlicer()
slicer.set_settings(self.printer_setting,
self.printhead_setting, self.print_param)
slicer.SetInputDataObject(self.part)
slicer.Update()
slice_stack = slicer.GetOutputDataObject(0)
img_dim = slice_stack.GetDimensions()
self.assertTrue(img_dim[2] > 0)
(x_min, x_max, y_min, y_max, _, _) = slice_stack.GetExtent()
mid_point = int(img_dim[2]/2)
single_im = vtk.vtkExtractVOI()
single_im.SetVOI(x_min, x_max, y_min, y_max, mid_point, mid_point)
single_im.SetSampleRate(1, 1, 1)
single_im.SetInputData(slice_stack)
single_im.Update()
writer = vtk.vtkBMPWriter()
writer.SetInputData(single_im.GetOutput())
writer.SetFileName(os.path.join(self.out_dir, 'test_d.bmp'))
writer.Update()
writer.Write()
writer_3d = vtk.vtkXMLImageDataWriter()
writer_3d.SetFileName(os.path.join(self.out_dir, 'test_d.vti'))
writer_3d.SetInputData(slice_stack)
writer_3d.Update()
writer_3d.Write()
def crop(self,
left=None, right=None,
back=None, front=None,
bottom=None, top=None,
VOI=()
):
"""Crop a ``Volume`` object.
:param float left: fraction to crop from the left plane (negative x)
:param float right: fraction to crop from the right plane (positive x)
:param float back: fraction to crop from the back plane (negative y)
:param float front: fraction to crop from the front plane (positive y)
:param float bottom: fraction to crop from the bottom plane (negative z)
:param float top: fraction to crop from the top plane (positive z)
:param list VOI: extract Volume Of Interest expressed in voxel numbers
Eg.: vol.crop(VOI=(xmin, xmax, ymin, ymax, zmin, zmax)) # all integers nrs
"""
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInputData(self.imagedata())
if len(VOI):
extractVOI.SetVOI(VOI)
else:
d = self.imagedata().GetDimensions()
bx0, bx1, by0, by1, bz0, bz1 = 0, d[0]-1, 0, d[1]-1, 0, d[2]-1
if left is not None: bx0 = int((d[0]-1)*left)
if right is not None: bx1 = int((d[0]-1)*(1-right))
if back is not None: by0 = int((d[1]-1)*back)
if front is not None: by1 = int((d[1]-1)*(1-front))
if bottom is not None: bz0 = int((d[2]-1)*bottom)
if top is not None: bz1 = int((d[2]-1)*(1-top))
extractVOI.SetVOI(bx0, bx1, by0, by1, bz0, bz1)
extractVOI.Update()
return self._update(extractVOI.GetOutput())
def extractVOI(image, b0, b1, b2, b3, b4, b5):
min_voxel_ijk = [int()] * 3
max_voxel_ijk = [int()] * 3
pcoords = [float()] * 3
image.ComputeStructuredCoordinates([b0, b2, b4], min_voxel_ijk, pcoords)
image.ComputeStructuredCoordinates([b1, b3, b5], max_voxel_ijk, pcoords)
def ifZero(value):
if value == 0:
return value
else:
return value + 1
start_voxel_ijk = map(ifZero, min_voxel_ijk)
extents_ijk = list(
reduce(lambda i, j: i + j, zip(start_voxel_ijk, max_voxel_ijk)))
extract_voi = vtk.vtkExtractVOI()
if vtk.vtkVersion.GetVTKMajorVersion() < 6:
extract_voi.SetInput(image)
else:
extract_voi.SetInputData(image)
extract_voi.SetVOI(*extents_ijk)
extract_voi.Update()
return extract_voi.GetOutput()
def ipl_erosion(image_in, erode_distance):
ipl_erosion_settings(erode_distance)
extent = image_in.GetExtent()
#Actual distance of pixel erosion
distance = erode_distance + 1
pad = vtk.vtkImageReslice()
pad.SetInput(image_in)
pad.SetOutputExtent(extent[0], extent[1], extent[2], extent[3], extent[4],
extent[5])
pad.Update()
#Kernel size is twice the dilation distance plus one for the center voxel
erode = vtk.vtkImageContinuousErode3D()
erode.SetInputConnection(pad.GetOutputPort())
erode.SetKernelSize(2 * distance + 1, 2 * distance + 1, 2 * distance + 1)
erode.Update()
voi = vtk.vtkExtractVOI()
voi.SetInput(erode.GetOutput())
voi.SetVOI(extent[0] + distance, extent[1] - distance,
extent[2] + distance, extent[3] - distance,
extent[4] + distance, extent[5] - distance)
voi.Update()
image_out = voi.GetOutput()
return image_out
def _handlerVoiSaveButton(self, event):
input_data = self.getPrimaryInput()
filename = self.controlFrame.voiFilenameText.GetValue()
if input_data and self._voi_widget.GetEnabled() and filename:
# see if we need to reset to zero origin
zor = self.controlFrame.voiResetToOriginCheck.GetValue()
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInput(input_data)
extractVOI.SetVOI(self._currentVOI)
writer = vtk.vtkXMLImageDataWriter()
writer.SetDataModeToBinary()
writer.SetFileName(filename)
if zor:
ici = vtk.vtkImageChangeInformation()
ici.SetOutputExtentStart(0, 0, 0)
ici.SetInput(extractVOI.GetOutput())
writer.SetInput(ici.GetOutput())
else:
writer.SetInput(extractVOI.GetOutput())
writer.Write()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkExtractVOI(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
self.initialOrigin = self.input.GetOrigin()
self.initialExtent = self.input.GetExtent()
self.initialSpacing = self.input.GetSpacing()
self.initialAoi = self.getUnscaledWorldExtent( self.initialExtent, self.initialSpacing )
self.currentAoi = list( self.initialAoi )
self.clip = vtk.vtkExtractVOI()
self.inputModule.inputToAlgorithm( self.clip )
self.pad = vtk.vtkImageMagnify()
self.pad.InterpolateOn()
self.pad.SetInputConnection( self.clip.GetOutputPort() )
self.imageInfo = vtk.vtkImageChangeInformation()
self.imageInfo.SetInputConnection( self.pad.GetOutputPort() )
self.imageInfo.SetOutputOrigin( self.initialOrigin[0], self.initialOrigin[1], self.initialOrigin[2] )
self.imageInfo.SetOutputExtentStart( self.initialExtent[0], self.initialExtent[2], self.initialExtent[4] )
self.imageInfo.SetOutputSpacing( self.initialSpacing[0], self.initialSpacing[1], self.initialSpacing[2] )
self.setExtent( self.initialExtent )
self.set3DOutput( port=self.imageInfo.GetOutputPort() )
def visQuadFunc():
""" vtk sample scene with iso contours """
# VTK supports implicit functions of the form f(x,y,z)=constant. These
# functions can represent things spheres, cones, etc. Here we use a
# general form for a quadric to create an elliptical data field.
quadric = vtk.vtkQuadric()
quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
# vtkSampleFunction samples an implicit function over the x-y-z range
# specified (here it defaults to -1,1 in the x,y,z directions).
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(30, 30, 30)
sample.SetImplicitFunction(quadric)
# Create five surfaces F(x,y,z) = constant between range specified. The
# GenerateValues() method creates n isocontour values between the range
# specified.
contours = vtk.vtkContourFilter()
contours.SetInputConnection(sample.GetOutputPort())
contours.GenerateValues(8, 0.0, 1.2)
contMapper = vtk.vtkPolyDataMapper()
contMapper.SetInputConnection(contours.GetOutputPort())
contMapper.SetScalarRange(0.0, 1.2)
contActor = vtk.vtkActor()
contActor.SetMapper(contMapper)
# We'll put a simple outline around the data.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(sample.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(1, 0.5, 0)
# extract data from the volume
extract = vtk.vtkExtractVOI()
extract.SetInputConnection(sample.GetOutputPort())
extract.SetVOI(0, 29, 0, 29, 15, 15)
extract.SetSampleRate(1, 2, 3)
contours2 = vtk.vtkContourFilter()
contours2.SetInputConnection(extract.GetOutputPort())
contours2.GenerateValues(8, 0.0, 1.2)
contMapper2 = vtk.vtkPolyDataMapper()
contMapper2.SetInputConnection(contours2.GetOutputPort())
contMapper2.SetScalarRange(0.0, 1.2)
contActor2 = vtk.vtkActor()
contActor2.SetMapper(contMapper2)
return contActor, contActor2, outlineActor, contours, contours2
def visQuadFunc():
""" vtk sample scene with iso contours """
# VTK supports implicit functions of the form f(x,y,z)=constant. These
# functions can represent things spheres, cones, etc. Here we use a
# general form for a quadric to create an elliptical data field.
quadric = vtk.vtkQuadric()
quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
# vtkSampleFunction samples an implicit function over the x-y-z range
# specified (here it defaults to -1,1 in the x,y,z directions).
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(30, 30, 30)
sample.SetImplicitFunction(quadric)
# Create five surfaces F(x,y,z) = constant between range specified. The
# GenerateValues() method creates n isocontour values between the range
# specified.
contours = vtk.vtkContourFilter()
contours.SetInputConnection(sample.GetOutputPort())
contours.GenerateValues(8, 0.0, 1.2)
contMapper = vtk.vtkPolyDataMapper()
contMapper.SetInputConnection(contours.GetOutputPort())
contMapper.SetScalarRange(0.0, 1.2)
contActor = vtk.vtkActor()
contActor.SetMapper(contMapper)
# We'll put a simple outline around the data.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(sample.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(1, 0.5, 0)
# extract data from the volume
extract = vtk.vtkExtractVOI()
extract.SetInputConnection(sample.GetOutputPort())
extract.SetVOI(0, 29, 0, 29, 15, 15)
extract.SetSampleRate(1, 2, 3)
contours2 = vtk.vtkContourFilter()
contours2.SetInputConnection(extract.GetOutputPort())
contours2.GenerateValues(8, 0.0, 1.2)
contMapper2 = vtk.vtkPolyDataMapper()
contMapper2.SetInputConnection(contours2.GetOutputPort())
contMapper2.SetScalarRange(0.0, 1.2)
contActor2 = vtk.vtkActor()
contActor2.SetMapper(contMapper2)
return contActor, contActor2, outlineActor, contours, contours2
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkExtractVOI(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def initialize (self):
debug ("In ExtractGrid::__init__ ()")
self.fil = vtk.vtkExtractVOI()
self.dim = [0,0,0]
self._set_input()
self.fil.UpdateWholeExtent()
self.fil.Update ()
self.voi_slider = []
self.sr_slider = []
def _MakeXYActors(self, reduce=1):
# get a texture-mapped actor
extent = self._ImageReslice.GetOutputExtent()
origin = self._ImageReslice.GetOutputOrigin()
spacing = self._ImageReslice.GetOutputSpacing()
bounds = [
origin[0] + spacing[0] * (extent[0] - 0.5),
origin[0] + spacing[0] * (extent[1] + 0.5),
origin[1] + spacing[1] * (extent[2] - 0.5),
origin[1] + spacing[1] * (extent[3] + 0.5),
origin[2] + spacing[2] * (extent[4] - 0.5),
origin[2] + spacing[2] * (extent[5] + 0.5)
]
for sliceNumber in range(extent[4], old_div((extent[5] + 1), reduce)):
# the z position of the slice
z = origin[2] + reduce * sliceNumber * spacing[2]
plane = vtk.vtkPlaneSource()
plane.SetXResolution(1)
plane.SetYResolution(1)
plane.SetOrigin(bounds[0], bounds[2], z)
plane.SetPoint1(bounds[1], bounds[2], z)
plane.SetPoint2(bounds[0], bounds[3], z)
imageClip = vtk.vtkExtractVOI()
imageClip.SetInput(self._ImageToStructuredPoints.GetOutput())
imageClip.SetVOI(extent[0], extent[1], extent[2], extent[3],
reduce * sliceNumber, reduce * sliceNumber)
imageClip.ReleaseDataFlagOn()
texture = vtk.vtkTexture()
texture.SetQualityTo32Bit()
texture.SetInput(imageClip.GetOutput())
texture.RepeatOff()
texture.InterpolateOn()
texture.MapColorScalarsThroughLookupTableOff()
for i in range(3):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(plane.GetOutput())
mapper.SetClippingPlanes(self._ClippingPlanes[i])
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.SetTexture(texture)
actor.PickableOff()
actor.SetProperty(self._PropertyXY)
self._PlanesXY.append(plane)
self._ImageClipsXY.append(imageClip)
self._ActorsXY.append(actor)
numberOfPlanes = (extent[5] - extent[4] + 1) / reduce * 3
return self._ActorsXY[-numberOfPlanes:]
def _MakeXYActors(self, reduce=1):
# get a texture-mapped actor
extent = self._ImageReslice.GetOutputExtent()
origin = self._ImageReslice.GetOutputOrigin()
spacing = self._ImageReslice.GetOutputSpacing()
bounds = [origin[0] + spacing[0] * (extent[0] - 0.5),
origin[0] + spacing[0] * (extent[1] + 0.5),
origin[1] + spacing[1] * (extent[2] - 0.5),
origin[1] + spacing[1] * (extent[3] + 0.5),
origin[2] + spacing[2] * (extent[4] - 0.5),
origin[2] + spacing[2] * (extent[5] + 0.5)]
for sliceNumber in range(extent[4], old_div((extent[5] + 1), reduce)):
# the z position of the slice
z = origin[2] + reduce * sliceNumber * spacing[2]
plane = vtk.vtkPlaneSource()
plane.SetXResolution(1)
plane.SetYResolution(1)
plane.SetOrigin(bounds[0], bounds[2], z)
plane.SetPoint1(bounds[1], bounds[2], z)
plane.SetPoint2(bounds[0], bounds[3], z)
imageClip = vtk.vtkExtractVOI()
imageClip.SetInput(self._ImageToStructuredPoints.GetOutput())
imageClip.SetVOI(extent[0], extent[1],
extent[2], extent[3],
reduce * sliceNumber, reduce * sliceNumber)
imageClip.ReleaseDataFlagOn()
texture = vtk.vtkTexture()
texture.SetQualityTo32Bit()
texture.SetInput(imageClip.GetOutput())
texture.RepeatOff()
texture.InterpolateOn()
texture.MapColorScalarsThroughLookupTableOff()
for i in range(3):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(plane.GetOutput())
mapper.SetClippingPlanes(self._ClippingPlanes[i])
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.SetTexture(texture)
actor.PickableOff()
actor.SetProperty(self._PropertyXY)
self._PlanesXY.append(plane)
self._ImageClipsXY.append(imageClip)
self._ActorsXY.append(actor)
numberOfPlanes = (extent[5] - extent[4] + 1) / reduce * 3
return self._ActorsXY[-numberOfPlanes:]
def ipl_add_aims(image_in1, image_in2):
ipl_add_aims_settings()
extent1 = image_in1.GetExtent()
voi1 = vtk.vtkExtractVOI()
voi1.SetInput(image_in1)
voi1.SetVOI(extent1[0], extent1[1], extent1[2], extent1[3], extent1[4],
extent1[5])
extent2 = image_in2.GetExtent()
voi2 = vtk.vtkExtractVOI()
voi2.SetInput(image_in2)
voi2.SetVOI(extent2[0], extent2[1], extent2[2], extent2[3], extent2[4],
extent2[5])
shift1 = vtk.vtkImageShiftScale()
shift1.SetInputConnection(voi1.GetOutputPort())
shift1.SetOutputScalarTypeToChar()
shift1.Update()
shift2 = vtk.vtkImageShiftScale()
shift2.SetInputConnection(voi2.GetOutputPort())
shift2.SetOutputScalarTypeToChar()
shift2.Update()
add = vtk.vtkImageMathematics()
add.SetInput1(shift1.GetOutput())
add.SetInput2(shift2.GetOutput())
add.SetOperationToAdd()
add.Update()
temp = vtk.vtkImageMathematics()
temp.SetInput1(add.GetOutput())
temp.SetConstantC(-2)
temp.SetConstantK(127)
temp.SetOperationToReplaceCByK()
temp.Update()
image_out = temp.GetOutput()
return image_out
def ExtractVOI(imagedata, xi, xf, yi, yf, zi, zf):
"""
Cropping the vtkImagedata according
with values.
"""
voi = vtk.vtkExtractVOI()
voi.SetVOI(xi, xf, yi, yf, zi, zf)
voi.SetInput(imagedata)
voi.SetSampleRate(1, 1, 1)
voi.Update()
return voi.GetOutput()
def ExtractVOI(imagedata,xi,xf,yi,yf,zi,zf):
"""
Cropping the vtkImagedata according
with values.
"""
voi = vtk.vtkExtractVOI()
voi.SetVOI(xi,xf,yi,yf,zi,zf)
voi.SetInputData(imagedata)
voi.SetSampleRate(1, 1, 1)
voi.Update()
return voi.GetOutput()
def updateRendering(self):
"""
Update the Rendering of this module
"""
data = self.getInput(1)
x, y, z = self.dataUnit.getDimensions()
data = optimize.optimize(image=data,
updateExtent=(0, x - 1, 0, y - 1, 0, z - 1))
if data.GetNumberOfScalarComponents() > 3:
extract = vtk.vtkImageExtractComponents()
extract.SetInput(data)
extract.SetComponents(1, 1, 1)
data = extract.GetOutput()
if data.GetNumberOfScalarComponents() > 1:
self.luminance.SetInput(data)
data = self.luminance.GetOutput()
z = self.parameters["Slice"]
ext = (0, x - 1, 0, y - 1, z, z)
voi = vtk.vtkExtractVOI()
voi.SetVOI(ext)
voi.SetInput(data)
slice = voi.GetOutput()
self.geometry.SetInput(slice)
self.warp.SetInput(self.geometry.GetOutput())
self.warp.SetScaleFactor(self.parameters["Scale"])
self.merge.SetGeometry(self.warp.GetOutput())
if slice.GetNumberOfScalarComponents() == 1:
maptocol = vtk.vtkImageMapToColors()
ctf = self.getInputDataUnit(1).getColorTransferFunction()
maptocol.SetInput(slice)
maptocol.SetLookupTable(ctf)
maptocol.Update()
scalars = maptocol.GetOutput()
else:
scalars = slice
self.merge.SetScalars(scalars)
data = self.merge.GetOutput()
if self.parameters["Normals"]:
self.normals.SetInput(data)
self.normals.SetFeatureAngle(self.parameters["FeatureAngle"])
print "Feature angle=", self.parameters["FeatureAngle"]
data = self.normals.GetOutput()
self.mapper.SetInput(data)
self.mapper.Update()
VisualizationModule.updateRendering(self)
self.parent.Render()
def initialize_pipeline(self):
""" Set up the necessary VTK classes for the pipeline, and the color of the contours"""
for i in range(self.nr_doseplans):
self.extracts_axial["c{0}".format(i)] = vtk.vtkExtractVOI()
self.contours_axial["c{0}".format(i)] = vtk.vtkContourFilter()
self.contour_mappers_axial["c{0}".format(
i)] = vtk.vtkPolyDataMapper()
self.contour_actors_axial["c{0}".format(i)] = vtk.vtkActor()
self.contour_actors_axial["c{0}".format(i)].GetProperty().SetColor(
0, 1, 0)
self.contour_actors_axial["c{0}".format(
i)].GetProperty().SetLineWidth(2)
self.extracts_sagittal["c{0}".format(i)] = vtk.vtkExtractVOI()
self.contours_sagittal["c{0}".format(i)] = vtk.vtkContourFilter()
self.contour_mappers_sagittal["c{0}".format(
i)] = vtk.vtkPolyDataMapper()
self.contour_actors_sagittal["c{0}".format(i)] = vtk.vtkActor()
self.contour_actors_sagittal["c{0}".format(
i)].GetProperty().SetColor(0, 1, 0)
self.contour_actors_sagittal["c{0}".format(
i)].GetProperty().SetLineWidth(2)
self.extracts_coronal["c{0}".format(i)] = vtk.vtkExtractVOI()
self.contours_coronal["c{0}".format(i)] = vtk.vtkContourFilter()
self.contour_mappers_coronal["c{0}".format(
i)] = vtk.vtkPolyDataMapper()
self.contour_actors_coronal["c{0}".format(i)] = vtk.vtkActor()
self.contour_actors_coronal["c{0}".format(
i)].GetProperty().SetColor(0, 1, 0)
self.contour_actors_coronal["c{0}".format(
i)].GetProperty().SetLineWidth(2)
self.extracts_axial["c{0}".format(i)].SetInput(
self.doseplans["p{0}".format(i)])
self.extracts_coronal["c{0}".format(i)].SetInput(
self.doseplans["p{0}".format(i)])
self.extracts_sagittal["c{0}".format(i)].SetInput(
self.doseplans["p{0}".format(i)])
def updateRendering(self): """ Update the Rendering of this module """ data = self.getInput(1) x,y,z = self.dataUnit.getDimensions() data = optimize.optimize(image = data, updateExtent = (0, x-1, 0, y-1, 0, z-1)) if data.GetNumberOfScalarComponents() > 3: extract = vtk.vtkImageExtractComponents() extract.SetInput(data) extract.SetComponents(1, 1, 1) data = extract.GetOutput() if data.GetNumberOfScalarComponents() > 1: self.luminance.SetInput(data) data = self.luminance.GetOutput() z = self.parameters["Slice"] ext = (0, x - 1, 0, y - 1, z, z) voi = vtk.vtkExtractVOI() voi.SetVOI(ext) voi.SetInput(data) slice = voi.GetOutput() self.geometry.SetInput(slice) self.warp.SetInput(self.geometry.GetOutput()) self.warp.SetScaleFactor(self.parameters["Scale"]) self.merge.SetGeometry(self.warp.GetOutput()) if slice.GetNumberOfScalarComponents() == 1: maptocol = vtk.vtkImageMapToColors() ctf = self.getInputDataUnit(1).getColorTransferFunction() maptocol.SetInput(slice) maptocol.SetLookupTable(ctf) maptocol.Update() scalars = maptocol.GetOutput() else: scalars = slice self.merge.SetScalars(scalars) data = self.merge.GetOutput() if self.parameters["Normals"]: self.normals.SetInput(data) self.normals.SetFeatureAngle(self.parameters["FeatureAngle"]) print "Feature angle=", self.parameters["FeatureAngle"] data = self.normals.GetOutput() self.mapper.SetInput(data) self.mapper.Update() VisualizationModule.updateRendering(self) self.parent.Render()
def ImageCropper(Image,X1, X2,Y1,Y2, Z1,Z2):
CroppedImage = vtk.vtkExtractVOI()
CroppedImage.SetInputData(Image)
CroppedImage.SetVOI(X1, X2,Y1,Y2, Z1,Z2)
CroppedImage.Update()
writer=vtk.vtkNIFTIImageWriter()
writer.SetInputConnection(CroppedImage.GetOutputPort())
writer.SetFileName("CroppedImageout.nii")
writer.Write()
reader=vtk.vtkNIFTIImageReader()
reader.SetFileName("CroppedImageout.nii")
reader.Update()
image=reader.GetOutput()
return(image)
def extract1Slice(image, slice=30, dir=2):
voi = vtk.vtkExtractVOI()
voi.SetInput(image)
extent = image.GetExtent()
if dir == 0:
voi.SetVOI(slice,slice,extent[2],extent[3],extent[4],extent[5])
if dir == 1:
voi.SetVOI(extent[0],extent[1],slice,slice,extent[4],extent[5])
if dir == 2:
voi.SetVOI(extent[0],extent[1],extent[2],extent[3],slice,slice)
voi.Update()
imagedata = voi.GetOutput()
imagedata.SetOrigin(image.GetOrigin())
imagedata.Update()
return imagedata
def __init__(self):
"""
Initialization
"""
lib.ProcessingFilter.ProcessingFilter.__init__(self, (1, 1))
self.reportGUI = None
self.measurements = []
self.vtkfilter = vtk.vtkExtractVOI()
self.vtkfilter.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.vtkfilter, 'ProgressEvent', self.updateProgress)
self.translation = []
self.descs = {"UseROI": "Use Region of Interest to define resulting region", \
"ROI": "Region of Interest Used in Cutting", \
"FirstSlice": "First Slice in Resulting Stack", \
"LastSlice": "Last Slice in Resulting Stack"}
self.filterDesc = "Extracts a subset from a dataset by removing slices from the top and/or bottom and/or by using a ROI to specify the subset in X and Y.\nInput: Any image\nOutput: Extracted image"
def ipl_write(image_in, output):
ipl_write_settings(image_in, output)
print "Writing: ", output
extent = image_in.GetExtent()
voi = vtk.vtkExtractVOI()
voi.SetInput(image_in)
voi.SetVOI(extent[0], extent[1], extent[2], extent[3], extent[4],
extent[5])
writer = vtkn88.vtkn88AIMWriter()
writer.SetInputConnection(voi.GetOutputPort())
writer.SetFileName(output)
writer.Update()
print "Done"
def __init__(self):
"""
Initialization
"""
lib.ProcessingFilter.ProcessingFilter.__init__(self, (1, 1))
self.reportGUI = None
self.measurements = []
self.vtkfilter = vtk.vtkExtractVOI()
self.vtkfilter.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.vtkfilter, 'ProgressEvent',
self.updateProgress)
self.translation = []
self.descs = {"UseROI": "Use Region of Interest to define resulting region", \
"ROI": "Region of Interest Used in Cutting", \
"FirstSlice": "First Slice in Resulting Stack", \
"LastSlice": "Last Slice in Resulting Stack"}
self.filterDesc = "Extracts a subset from a dataset by removing slices from the top and/or bottom and/or by using a ROI to specify the subset in X and Y.\nInput: Any image\nOutput: Extracted image"
def getSlice(volume, zslice, startpos=None, endpos=None):
"""
Extract a given slice from a volume
"""
voi = vtk.vtkExtractVOI()
voi.SetInputConnection(volume.GetProducerPort())
if startpos:
startx, starty = startpos
endx, endy = endpos
else:
# startx, starty = 0, 0
# endx, endy = volume.GetDimensions()[0:2]
startx, endx, starty, endy, a, b = volume.GetExtent()
voi.SetVOI((int(startx), int(endx), int(starty), int(endy), int(zslice), int(zslice)))
voi.Update()
data = voi.GetOutput()
return data
def ipl_median_filter(image_in, support):
ipl_median_filter_settings(support)
extent = image_in.GetExtent()
voi = vtk.vtkExtractVOI()
voi.SetInput(image_in)
voi.SetVOI(extent[0] + support, extent[1] - support, extent[2] + support,
extent[3] - support, extent[4] + support, extent[5] - support)
voi.Update()
median = vtk.vtkImageMedian3D()
median.SetKernelSize(support, support, support)
median.SetInputConnection(voi.GetOutputPort())
median.Update()
image_out = median.GetOutput()
return image_out
def getTimepoint(self, n, onlyDims=0):
"""
Return the nth timepoint
"""
if not self.readers:
self.getReadersFromFilenames()
if self.is3DImage():
if not self.readers:
raise Logging.GUIError(
"Attempt to read bad timepoint",
"Timepoint %d is not defined by the given filenames" % n)
self.reader = self.readers[0]
minZ = n * self.slicesPerTimepoint
maxZ = (n + 1) * self.slicesPerTimepoint - 1
extract = vtk.vtkExtractVOI()
extract.SetInput(self.reader.GetOutput())
extract.SetVOI(0, self.x - 1, 0, self.y - 1, minZ, maxZ)
changeInfo = vtk.vtkImageChangeInformation()
changeInfo.SetInput(extract.GetOutput())
changeInfo.SetOutputOrigin(0, 0, 0)
changeInfo.SetExtentTranslation((0, 0, -minZ))
data = changeInfo.GetOutput()
else:
if n >= len(self.readers):
n = 0
raise Logging.GUIError(
"Attempt to read bad timepoint",
"Timepoint %d is not defined by the given filenames" % n)
self.reader = self.readers[n]
data = self.reader.GetOutput()
if not self.voxelsize:
size = data.GetSpacing()
x, y, z = [size.GetElement(x) for x in range(0, 3)]
self.voxelsize = (x, y, z)
print "Read voxel size", self.voxelsize
if onlyDims:
return
return data
def getSlice(volume, zslice, startpos=None, endpos=None):
"""
Extract a given slice from a volume
"""
voi = vtk.vtkExtractVOI()
voi.SetInputConnection(volume.GetProducerPort())
if startpos:
startx, starty = startpos
endx, endy = endpos
else:
#startx, starty = 0, 0
#endx, endy = volume.GetDimensions()[0:2]
startx, endx, starty, endy, a, b = volume.GetExtent()
voi.SetVOI((int(startx), int(endx), int(starty), int(endy), int(zslice),
int(zslice)))
voi.Update()
data = voi.GetOutput()
return data
def _set_input (self):
""" This function tries its best to use an appropriate filter
for the given input data."""
debug ("In ExtractGrid::_set_input ()")
out = self.prev_fil.GetOutput ()
dim = out.GetDimensions ()
self.dim = [dim[0] -1, dim[1] -1, dim[2] -1]
if out.IsA ('vtkStructuredGrid'):
f = vtk.vtkExtractGrid()
elif out.IsA ('vtkRectilinearGrid'):
f = vtk.vtkExtractRectilinearGrid()
elif out.IsA ('vtkStructuredPoints') or out.IsA('vtkImageData'):
f = vtk.vtkExtractVOI()
else:
msg = "This module does not support the given "\
"output - %s "%(out.GetClassName ())
raise Base.Objects.ModuleException, msg
if f.GetClassName() != self.fil.GetClassName():
self.fil = f
self.fil.SetInput (out)
def ExtractVOI(self):
wholeExtent = self.Image.GetExtent()
origin = self.Image.GetOrigin()
spacing = self.Image.GetSpacing()
newVOI = [0,0,0,0,0,0]
newVOI[0] = max(wholeExtent[0],int(math.ceil((self.BoxBounds[0]-origin[0])/spacing[0])))
newVOI[1] = min(wholeExtent[1],int(math.floor((self.BoxBounds[1]-origin[0])/spacing[0])))
newVOI[2] = max(wholeExtent[2],int(math.ceil((self.BoxBounds[2]-origin[1])/spacing[1])))
newVOI[3] = min(wholeExtent[3],int(math.floor((self.BoxBounds[3]-origin[1])/spacing[1])))
newVOI[4] = max(wholeExtent[4],int(math.ceil((self.BoxBounds[4]-origin[2])/spacing[2])))
newVOI[5] = min(wholeExtent[5],int(math.floor((self.BoxBounds[5]-origin[2])/spacing[2])))
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInputData(self.CroppedImage)
extractVOI.SetVOI(newVOI)
extractVOI.Update()
self.CroppedImage.DeepCopy(extractVOI.GetOutput())
def getTimepoint(self, n, onlyDims = 0):
"""
Return the nth timepoint
"""
if not self.readers:
self.getReadersFromFilenames()
if self.is3DImage():
if not self.readers:
raise Logging.GUIError("Attempt to read bad timepoint", "Timepoint %d is not defined by the given filenames" % n)
self.reader = self.readers[0]
minZ = n * self.slicesPerTimepoint
maxZ = (n+1) * self.slicesPerTimepoint - 1
extract = vtk.vtkExtractVOI()
extract.SetInput(self.reader.GetOutput())
extract.SetVOI(0, self.x - 1, 0, self.y - 1, minZ, maxZ)
changeInfo = vtk.vtkImageChangeInformation()
changeInfo.SetInput(extract.GetOutput())
changeInfo.SetOutputOrigin(0, 0, 0)
changeInfo.SetExtentTranslation((0,0,-minZ))
data = changeInfo.GetOutput()
else:
if n >= len(self.readers):
n = 0
raise Logging.GUIError("Attempt to read bad timepoint", "Timepoint %d is not defined by the given filenames" % n)
self.reader = self.readers[n]
data = self.reader.GetOutput()
if not self.voxelsize:
size = data.GetSpacing()
x, y, z = [size.GetElement(x) for x in range(0, 3)]
self.voxelsize = (x, y, z)
print "Read voxel size", self.voxelsize
if onlyDims:
return
return data
def __init__(self, parent=None,type='small'):
self.type = type
self.nameSize = 24
# the currentLayoutName is tag on the slice node that corresponds
# view which should currently be shown in the DataProbe window.
# Keeping track of this allows us to respond to non-interactor updates
# to the slice (like from an external tracker) but only in the view where
# the mouse has most recently entered.
self.currentLayoutName = None
self.CrosshairNode = None
self.CrosshairNodeObserverTag = None
self.frame = qt.QFrame(parent)
self.frame.setLayout(qt.QVBoxLayout())
modulePath = slicer.modules.dataprobe.path.replace("DataProbe.py","")
self.iconsDIR = modulePath + '/Resources/Icons'
self.imageCrop = vtk.vtkExtractVOI()
self.imageZoom = 10
self.showImage = False
self.painter = qt.QPainter()
self.pen = qt.QPen()
if type == 'small':
self.createSmall()
#Helper class to calculate and display tensor scalars
self.calculateTensorScalars = CalculateTensorScalars()
# Observe the crosshair node to get the current cursor position
self.CrosshairNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLCrosshairNode')
if self.CrosshairNode:
self.CrosshairNodeObserverTag = self.CrosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, self.processEvent)
# coefficients to the equations are set. quadric = vtk.vtkQuadric() quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0) # The vtkSampleFunction uses the quadric function and evaluates function # value over a regular lattice (i.e., a volume). sample = vtk.vtkSampleFunction() sample.SetSampleDimensions(30, 30, 30) sample.SetImplicitFunction(quadric) sample.ComputeNormalsOff() sample.Update() # Here a single slice (i.e., image) is extracted from the volume. (Note: in # actuality the VOI request causes the sample function to operate on just the # slice.) extract = vtk.vtkExtractVOI() extract.SetInputConnection(sample.GetOutputPort()) extract.SetVOI(0, 29, 0, 29, 15, 15) extract.SetSampleRate(1, 2, 3) # The image is contoured to produce contour lines. Thirteen contour values # ranging from (0,1.2) inclusive are produced. contours = vtk.vtkContourFilter() contours.SetInputConnection(extract.GetOutputPort()) contours.GenerateValues(13, 0.0, 1.2) # The contour lines are mapped to the graphics library. contMapper = vtk.vtkPolyDataMapper() contMapper.SetInputConnection(contours.GetOutputPort()) contMapper.SetScalarRange(0.0, 1.2)
# to mark the origin sphere = vtk.vtkSphereSource() sphere.SetRadius(2.0) sphereMapper = vtk.vtkPolyDataMapper() sphereMapper.SetInputConnection(sphere.GetOutputPort()) sphereMapper.ImmediateModeRenderingOn() sphereActor = vtk.vtkActor() sphereActor.SetMapper(sphereMapper) rt = vtk.vtkRTAnalyticSource() rt.SetWholeExtent(-50, 50, -50, 50, 0, 0) voi = vtk.vtkExtractVOI() voi.SetInputConnection(rt.GetOutputPort()) voi.SetVOI(-11, 39, 5, 45, 0, 0) voi.SetSampleRate(5, 5, 1) # Get rid of ambiguous triagulation issues. surf = vtk.vtkDataSetSurfaceFilter() surf.SetInputConnection(voi.GetOutputPort()) tris = vtk.vtkTriangleFilter() tris.SetInputConnection(surf.GetOutputPort()) mapper = vtk.vtkPolyDataMapper() mapper.SetInputConnection(tris.GetOutputPort()) mapper.ImmediateModeRenderingOn() mapper.SetScalarRange(130, 280)
def init_cell_field_actors_borderless(self, actor_specs, drawing_params=None):
hex_flag = False
lattice_type_str = self.get_lattice_type_str()
if lattice_type_str.lower() == 'hexagonal':
hex_flag = True
# todo 5 - check if this should be called earlier
# self.extractCellFieldData() # initializes self.usedCellTypesList
field_dim = self.currentDrawingParameters.bsd.fieldDim
cell_type_image_data = vtk.vtkImageData()
cell_type_image_data.SetDimensions(field_dim.x + 2, field_dim.y + 2,
field_dim.z + 2) # adding 1 pixel border around the lattice to make rendering smooth at lattice borders
cell_type_image_data.GetPointData().SetScalars(self.cell_type_array)
voi = vtk.vtkExtractVOI()
if VTK_MAJOR_VERSION >= 6:
voi.SetInputData(cell_type_image_data)
else:
voi.SetInput(cell_type_image_data)
# voi.SetVOI(1,self.dim[0]-1, 1,self.dim[1]-1, 1,self.dim[2]-1 ) # crop out the artificial boundary layer that we created
voi.SetVOI(0, 249, 0, 189, 0, 170)
# # todo 5- check if it is possible to call it once
# self.usedCellTypesList = self.extractCellFieldData()
number_of_actors = len(self.used_cell_types_list)
# creating and initializing filters, smoothers and mappers - one for each cell type
filterList = [vtk.vtkDiscreteMarchingCubes() for i in xrange(number_of_actors)]
smootherList = [vtk.vtkSmoothPolyDataFilter() for i in xrange(number_of_actors)]
normalsList = [vtk.vtkPolyDataNormals() for i in xrange(number_of_actors)]
mapperList = [vtk.vtkPolyDataMapper() for i in xrange(number_of_actors)]
# actorCounter=0
# for i in usedCellTypesList:
for actorCounter, actor_number in enumerate(self.used_cell_types_list):
# for actorCounter in xrange(len(self.usedCellTypesList)):
if VTK_MAJOR_VERSION >= 6:
filterList[actorCounter].SetInputData(cell_type_image_data)
else:
filterList[actorCounter].SetInput(cell_type_image_data)
# filterList[actorCounter].SetInputConnection(voi.GetOutputPort())
# filterList[actorCounter].SetValue(0, usedCellTypesList[actorCounter])
filterList[actorCounter].SetValue(0, self.used_cell_types_list[actorCounter])
smootherList[actorCounter].SetInputConnection(filterList[actorCounter].GetOutputPort())
# smootherList[actorCounter].SetNumberOfIterations(200)
normalsList[actorCounter].SetInputConnection(smootherList[actorCounter].GetOutputPort())
normalsList[actorCounter].SetFeatureAngle(45.0)
mapperList[actorCounter].SetInputConnection(normalsList[actorCounter].GetOutputPort())
mapperList[actorCounter].ScalarVisibilityOff()
actors_dict = actor_specs.actors_dict
cell_type_lut = self.get_type_lookup_table()
cell_type_lut_max = cell_type_lut.GetNumberOfTableValues() - 1
if actor_number in actors_dict.keys():
actor = actors_dict[actor_number]
actor.SetMapper(mapperList[actorCounter])
actor.GetProperty().SetDiffuseColor(
cell_type_lut.GetTableValue(self.used_cell_types_list[actorCounter])[0:3])
# actor.GetProperty().SetDiffuseColor(
# # self.celltypeLUT.GetTableValue(self.usedCellTypesList[actorCounter])[0:3])
# self.celltypeLUT.GetTableValue(actor_number)[0:3])
if hex_flag:
actor.SetScale(self.xScaleHex, self.yScaleHex, self.zScaleHex)
import vtk
reader = vtk.vtkDICOMImageReader()
reader.SetDirectoryName('../Data/1000_KORAALS1/20110617/00006_POLS_0_5_MM')
reader.Update()
imageData = vtk.vtkImageData()
imageData.DeepCopy(reader.GetOutput())
extractor = vtk.vtkExtractVOI()
extractor.SetInput(imageData)
extractor.SetVOI(0,300,0,300,0,300)
extractor.GetVOI()
opacityFunction = vtk.vtkPiecewiseFunction()
opacityFunction.AddPoint(1000, 0.0)
opacityFunction.AddPoint(1400, 0.4)
opacityFunction.AddPoint(1800, 0.0)
opacityFunction.AddPoint(2000, 0.1)
opacityFunction.AddPoint(2400, 0.4)
opacityFunction.AddPoint(2800, 0.0)
colorFunction = vtk.vtkColorTransferFunction()
colorFunction.AddRGBPoint(1400, 0.0, 1.0, 0.0)
colorFunction.AddRGBPoint(2000, 1.0, 0.0, 0.0)
colorFunction.AddRGBPoint(2400, 0.0, 0.0, 1.0)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunction)
volumeProperty.SetScalarOpacity(opacityFunction)
volumeProperty.SetInterpolationTypeToLinear()
# colorbar
# http://www.vtk.org/doc/release/5.8/html/c2_vtk_e_3.html#c2_vtk_e_vtkLookupTable
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetTitle("Temperature")
scalarBar.SetNumberOfLabels(4)
scalarBar.SetLookupTable(hueLut)
## # image viewer
## imageViewer.SetInput(vtkTempImage)
## imageViewer.SetSize(512,512)
## imageViewer.SetSlice(DisplaySlice)
## imageViewer.SetPosition(512,0)
## imageViewer.Render()
# extract VOI to display
extractVOI = vtk.vtkExtractVOI()
extractVOI.SetInput(vtkTempImage)
extractVOI.SetVOI([0,fileHelper.MapDimensions[0],0,fileHelper.MapDimensions[1],DisplaySlice,DisplaySlice])
extractVOI.Update()
# mapper
#mapper = vtk.vtkDataSetMapper()
mapper = vtk.vtkImageMapToColors()
mapper.SetInput(extractVOI.GetOutput())
# set echo to display
mapper.SetActiveComponent( options.speciesID )
mapper.SetLookupTable(hueLut)
# actor
actor = vtk.vtkImageActor()
actor.SetInput(mapper.GetOutput())
def return_vtk_reader(self,data):
self.reader=vtk.vtkExtractVOI()
self.reader.SetInput(data)
#self.reader.SetVOI(data.GetBounds())
self.reader.Update()
return self.reader
def ComputeObjective(self,MRTIDataDirectory,VolumeOfInterest ):
print self.SEMDataDirectory
ObjectiveFunction = 0.0
# loop over time points of interest
for idwrite,(SEMtimeID,MRTItimeID) in enumerate([(0,135),(0,136),(0,137),(0,138)]):
mrtifilename = '%s/temperature.%04d.vtk' % (MRTIDataDirectory,MRTItimeID)
if MRTItimeID in self.DataDictionary:
print "already loaded", mrtifilename
else:
print 'opening' , mrtifilename
# FIXME vtk needs to be loaded AFTER kernel is built
import vtk
import vtk.util.numpy_support as vtkNumPy
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
print "read SEM data"
vtkImageReader = vtk.vtkDataSetReader()
vtkImageReader.SetFileName(mrtifilename )
vtkImageReader.Update()
## image_cells = vtkImageReader.GetOutput().GetPointData()
## data_array = vtkNumPy.vtk_to_numpy(image_cells.GetArray('scalars'))
# extract voi for QOI
vtkVOIExtract = vtk.vtkExtractVOI()
vtkVOIExtract.SetInput( vtkImageReader.GetOutput() )
vtkVOIExtract.SetVOI( VolumeOfInterest )
vtkVOIExtract.Update()
mrti_point_data= vtkVOIExtract.GetOutput().GetPointData()
mrti_array = vtkNumPy.vtk_to_numpy(mrti_point_data.GetArray('image_data'))
#print mrti_array
#print type(mrti_array)
print "project SEM onto MRTI for comparison"
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetSource( vtkVOIExtract.GetOutput() )
vtkResample.SetInput( self.SEMRegister.GetOutput() )
vtkResample.Update()
if ( self.DebugObjective ):
roifileName = "%s/mrti.%04d.vtu" % (self.SEMDataDirectory,MRTItimeID)
print "writing ", roifileName
start = time.clock()
# setup mrti projection file
vtkTemperatureWriter = vtk.vtkXMLUnstructuredGridWriter()
vtkTemperatureWriter.SetFileName( roifileName )
vtkTemperatureWriter.SetInput(vtkResample.GetOutput())
vtkTemperatureWriter.Update()
elapsed = (time.clock() - start)
print "write output", elapsed
print " accumulate objective function"
fem_point_data= vtkResample.GetOutput().GetPointData()
self.DataDictionary[MRTItimeID] = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('image_data'))
#print fem_array
#print type(fem_array )
h_mrti = self.DataDictionary[MRTItimeID]
mf = cl.mem_flags
d_mrti = cl.Buffer(self.ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=h_mrti )
# TODO need to get cl buffer from brainNek
d_fem = cl.Buffer(self.ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=h_mrti )
# storage for output
dest_buf = cl.Buffer(self.ctx, mf.WRITE_ONLY, h_mrti.nbytes)
self.prg.diff_sq(self.queue, h_mrti.shape, None, d_mrti , d_fem , dest_buf)
mrti_minus_fem_squared = numpy.empty_like(h_mrti)
cl.enqueue_copy(self.queue, mrti_minus_fem_squared , dest_buf)
ObjectiveFunction = ObjectiveFunction + mrti_minus_fem_squared.sum()
return ObjectiveFunction
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
if self.input() == None:
print>>sys.stderr, "Must supply 'volume' port input to Voxelizer"
return
xMin, xMax, yMin, yMax, zMin, zMax = self.input().GetWholeExtent()
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
cellData = self.input().GetCellData()
pointData = self.input().GetPointData()
vectorsArray = pointData.GetVectors()
if vectorsArray == None:
print>>sys.stderr, "Must supply point vector data for 'volume' port input to Voxelizer"
return
self.setRangeBounds( list( vectorsArray.GetRange(-1) ) )
self.nComponents = vectorsArray.GetNumberOfComponents()
# for iC in range(-1,3): print "Value Range %d: %s " % ( iC, str( vectorsArray.GetRange( iC ) ) )
# for iV in range(10): print "Value[%d]: %s " % ( iV, str( vectorsArray.GetTuple3( iV ) ) )
self.initialOrigin = self.input().GetOrigin()
self.initialExtent = self.input().GetExtent()
self.initialSpacing = self.input().GetSpacing()
self.dataBounds = self.getUnscaledWorldExtent( self.initialExtent, self.initialSpacing, self.initialOrigin )
metadata = self.getMetadata()
self.resample = vtk.vtkExtractVOI()
self.resample.SetInput( self.input() )
self.resample.SetVOI( self.initialExtent )
sRate = [ int( round( self.sampleRate[0] ) ), int( round( self.sampleRate[1] ) ), int( round( self.sampleRate[2] ) ) ]
print "Sample rate: %s " % str( sRate )
self.resample.SetSampleRate( sRate[0], sRate[1], sRate[2] )
self.resampled_data = self.resample.GetOutput()
self.resampled_data.Update()
point_data = self.resampled_data.GetPointData()
input_variable_data = point_data.GetVectors()
nComp = input_variable_data.GetNumberOfComponents()
nTup = input_variable_data.GetNumberOfTuples()
print "-- Got input data points: nComp=%d, nTup=%d" % ( nComp, nTup )
for iComp in range(nComp):
cName = input_variable_data.GetComponentName( iComp )
variable_point_data = vtk.vtkFloatArray()
variable_point_data = input_variable_data
self.pointCloud = VtkPointCloud(1.0)
for iPt in range(nTup):
point = variable_point_data.GetTuple( iPt )
self.pointCloud.addPoint( point )
# self.pointCloud.setPoints( variable_point_data )
vars = metadata['vars']
xbounds = metadata[ 'valueRange-'+vars[0] ]
ybounds = metadata[ 'valueRange-'+vars[1] ]
zbounds = metadata[ 'valueRange-'+vars[2] ]
self.pointCloud.setScaling( xbounds, ybounds, zbounds )
self.pointCloud.dbgprint()
self.renderer.AddActor( self.pointCloud.vtkActor )
self.renderer.SetBackground( VTK_BACKGROUND_COLOR[0], VTK_BACKGROUND_COLOR[1], VTK_BACKGROUND_COLOR[2] )
self.set3DOutput ( wmod=self.wmod, name="pointcloud" )
def cut_data_set(self,data_reader,bounds):
self.cut_reader=vtk.vtkExtractVOI()
self.cut_reader.SetInput(data_reader.get_data_set())
self.cut_reader.SetVOI(bounds)
self.cut_reader.Update()
import Tkinter import vtk from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor # Prepare to read the file readerVolume = vtk.vtkImageReader() readerVolume.SetDataScalarType( vtk.VTK_UNSIGNED_SHORT ) readerVolume.SetFileDimensionality( 3 ) readerVolume.SetDataExtent ( 0,255, 0,255, 0,576) readerVolume.SetDataSpacing( 1,1,1 ) readerVolume.SetNumberOfScalarComponents( 1 ) readerVolume.SetDataByteOrderToBigEndian() readerVolume.SetFileName( "./Female.raw" ) # Extract the region of interest voiHead = vtk.vtkExtractVOI() voiHead.SetInput( readerVolume.GetOutput() ) voiHead.SetVOI( 0,255, 60,255, 0,100 ) voiHead.SetSampleRate( 1,1,1 ) # Generate an isosurface # UNCOMMENT THE FOLLOWING LINE FOR CONTOUR FILTER # contourBoneHead = vtk.vtkContourFilter() contourBoneHead = vtk.vtkMarchingCubes() contourBoneHead.SetInput( voiHead.GetOutput() ) contourBoneHead.ComputeNormalsOn() contourBoneHead.SetValue( 0, 1250 ) # Bone isovalue # Take the isosurface data and create geometry geoBoneMapper = vtk.vtkPolyDataMapper() geoBoneMapper.SetInput( contourBoneHead.GetOutput() )
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
self.colorInputModule = self.wmod.forceGetInputFromPort( "colors", None )
if self.input() == None:
print>>sys.stderr, "Must supply 'volume' port input to VectorCutPlane"
return
xMin, xMax, yMin, yMax, zMin, zMax = self.input().GetWholeExtent()
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
cellData = self.input().GetCellData()
pointData = self.input().GetPointData()
vectorsArray = pointData.GetVectors()
if vectorsArray == None:
print>>sys.stderr, "Must supply point vector data for 'volume' port input to VectorVolume"
return
self.setRangeBounds( list( vectorsArray.GetRange(-1) ) )
self.nComponents = vectorsArray.GetNumberOfComponents()
for iC in range(-1,3): print "Value Range %d: %s " % ( iC, str( vectorsArray.GetRange( iC ) ) )
for iV in range(10): print "Value[%d]: %s " % ( iV, str( vectorsArray.GetTuple3( iV ) ) )
self.initialOrigin = self.input().GetOrigin()
self.initialExtent = self.input().GetExtent()
self.initialSpacing = self.input().GetSpacing()
self.dataBounds = self.getUnscaledWorldExtent( self.initialExtent, self.initialSpacing, self.initialOrigin )
dataExtents = ( (self.dataBounds[1]-self.dataBounds[0])/2.0, (self.dataBounds[3]-self.dataBounds[2])/2.0, (self.dataBounds[5]-self.dataBounds[4])/2.0 )
centroid = ( (self.dataBounds[0]+self.dataBounds[1])/2.0, (self.dataBounds[2]+self.dataBounds[3])/2.0, (self.dataBounds[4]+self.dataBounds[5])/2.0 )
self.pos = [ self.initialSpacing[i]*self.initialExtent[2*i] for i in range(3) ]
if ( (self.initialOrigin[0] + self.pos[0]) < 0.0): self.pos[0] = self.pos[0] + 360.0
self.resample = vtk.vtkExtractVOI()
self.resample.SetInput( self.input() )
self.resample.SetVOI( self.initialExtent )
self.ApplyGlyphDecimationFactor()
lut = self.getLut()
if self.colorInputModule <> None:
colorInput = self.colorInputModule.getOutput()
self.color_resample = vtk.vtkExtractVOI()
self.color_resample.SetInput( colorInput )
self.color_resample.SetVOI( self.initialExtent )
self.color_resample.SetSampleRate( sampleRate, sampleRate, 1 )
# self.probeFilter = vtk.vtkProbeFilter()
# self.probeFilter.SetSourceConnection( self.resample.GetOutputPort() )
# colorInput = self.colorInputModule.getOutput()
# self.probeFilter.SetInput( colorInput )
resampledColorInput = self.color_resample.GetOutput()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetOutputScalarTypeToFloat ()
shiftScale.SetInput( resampledColorInput )
valueRange = self.getScalarRange()
shiftScale.SetShift( valueRange[0] )
shiftScale.SetScale ( (valueRange[1] - valueRange[0]) / 65535 )
colorFloatInput = shiftScale.GetOutput()
colorFloatInput.Update()
colorInput_pointData = colorFloatInput.GetPointData()
self.colorScalars = colorInput_pointData.GetScalars()
self.colorScalars.SetName('color')
lut.SetTableRange( valueRange )
self.glyph = vtk.vtkGlyph3DMapper()
# if self.colorInputModule <> None: self.glyph.SetColorModeToColorByScalar()
# else: self.glyph.SetColorModeToColorByVector()
scalarRange = self.getScalarRange()
self.glyph.SetScaleModeToScaleByMagnitude()
self.glyph.SetColorModeToMapScalars()
self.glyph.SetUseLookupTableScalarRange(1)
self.glyph.SetOrient( 1 )
# self.glyph.ClampingOn()
self.glyph.SetRange( scalarRange[0:2] )
self.glyph.SetInputConnection( self.resample.GetOutputPort() )
self.arrow = vtk.vtkArrowSource()
self.glyph.SetSourceConnection( self.arrow.GetOutputPort() )
self.glyph.SetLookupTable( lut )
self.glyphActor = vtk.vtkActor()
self.glyphActor.SetMapper( self.glyph )
self.renderer.AddActor( self.glyphActor )
self.renderer.SetBackground( VTK_BACKGROUND_COLOR[0], VTK_BACKGROUND_COLOR[1], VTK_BACKGROUND_COLOR[2] )
self.set3DOutput(wmod=self.wmod)
def ComputeObjective(SEMDataDirectory,MRTIDirectory):
import vtk
import vtk.util.numpy_support as vtkNumPy
print "using vtk version", vtk.vtkVersion.GetVTKVersion()
ObjectiveFunction = 0.0
# loop over time points of interest
for (SEMtimeID,MRTItimeID) in [(1,58)]:
# read SEM data
vtkSEMReader = vtk.vtkXMLUnstructuredGridReader()
vtufileName = "%s/%d.vtu" % (SEMDataDirectory,SEMtimeID)
vtkSEMReader.SetFileName( vtufileName )
vtkSEMReader.SetPointArrayStatus("Temperature",1)
vtkSEMReader.Update()
# get registration parameters
variableDictionary = kwargs['cv']
# register the SEM data to MRTI
AffineTransform = vtk.vtkTransform()
AffineTransform.Translate([
variableDictionary['x_displace'],variableDictionary['y_displace'],variableDictionary['z_displace']
])
# 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.RotateZ(variableDictionary['z_rotate' ] )
AffineTransform.RotateY(variableDictionary['y_rotate' ] )
AffineTransform.RotateX(variableDictionary['x_rotate' ] )
AffineTransform.Scale([1.e3,1.e3,1.e3])
SEMRegister = vtk.vtkTransformFilter()
SEMRegister.SetInput(vtkSEMReader.GetOutput())
SEMRegister.SetTransform(AffineTransform)
SEMRegister.Update()
# write output
DebugObjective = True
if ( DebugObjective ):
vtkSEMWriter = vtk.vtkDataSetWriter()
vtkSEMWriter.SetFileTypeToBinary()
semfileName = "%s/semtransform%04d.vtk" % (SEMDataDirectory,SEMtimeID)
print "writing ", semfileName
vtkSEMWriter.SetFileName( semfileName )
vtkSEMWriter.SetInput(SEMRegister.GetOutput())
vtkSEMWriter.Update()
# load image
vtkImageReader = vtk.vtkDataSetReader()
vtkImageReader.SetFileName('%s/temperature.%04d.vtk' % (MRTIDirectory, MRTItimeID) )
vtkImageReader.Update()
## image_cells = vtkImageReader.GetOutput().GetPointData()
## data_array = vtkNumPy.vtk_to_numpy(image_cells.GetArray('scalars'))
# extract voi for QOI
vtkVOIExtract = vtk.vtkExtractVOI()
vtkVOIExtract.SetInput( vtkImageReader.GetOutput() )
VOI = [110,170,70,120,0,0]
vtkVOIExtract.SetVOI( VOI )
vtkVOIExtract.Update()
mrti_point_data= vtkVOIExtract.GetOutput().GetPointData()
mrti_array = vtkNumPy.vtk_to_numpy(mrti_point_data.GetArray('image_data'))
#print mrti_array
#print type(mrti_array)
# project SEM onto MRTI for comparison
vtkResample = vtk.vtkCompositeDataProbeFilter()
vtkResample.SetSource( SEMRegister.GetOutput() )
vtkResample.SetInput( vtkVOIExtract.GetOutput() )
vtkResample.Update()
# write output
if ( DebugObjective ):
vtkTemperatureWriter = vtk.vtkDataSetWriter()
vtkTemperatureWriter.SetFileTypeToBinary()
roifileName = "%s/roi%04d.vtk" % (SEMDataDirectory,SEMtimeID)
print "writing ", roifileName
vtkTemperatureWriter.SetFileName( roifileName )
vtkTemperatureWriter.SetInput(vtkResample.GetOutput())
vtkTemperatureWriter.Update()
fem_point_data= vtkResample.GetOutput().GetPointData()
fem_array = vtkNumPy.vtk_to_numpy(fem_point_data.GetArray('Temperature'))
#print fem_array
#print type(fem_array )
# accumulate objective function
diff = mrti_array-fem_array
diffsq = diff**2
ObjectiveFunction = ObjectiveFunction + diffsq.sum()
return ObjectiveFunction
def Render(self, volumeReader):
"""
This method attempts to tesselate the image data.
:@type volumeReader: data.imageIO.base.VolumeImageReader
:@param volumeReader: This object handles opening image data and
passing it to the appropriate VTK image container
:@rtype: 2-tuple
:@return: The vtkActor created from tesselated image data and a
vtkLocator for improving picking operations.
"""
if self.imageSetID is None: return
self.volumeReader = volumeReader
self.vtkReader = volumeReader.LoadVTKReader(self.dataSpacing)
# Gaussian Smoothing
self.gaussFilter = vtk.vtkImageGaussianSmooth()
self.gaussFilter.SetDimensionality(3)
self.gaussFilter.SetStandardDeviation(1)
self.gaussFilter.SetRadiusFactors(1, 1, 1)
self.gaussFilter.SetInput(self.vtkReader.GetOutput())
# VOI Extractor
self.voi = vtk.vtkExtractVOI()
self.voi.SetInputConnection(self.gaussFilter.GetOutputPort())
# self.voi.SetInputConnection(self.vtkReader.GetOutputPort())
self.voi.SetVOI(self.volumeReader.VolumeExtents)
# Surface rendering
self.bactExtractor = vtk.vtkMarchingCubes()
self.bactExtractor.GenerateValues(1, self.isocontourLevel)
self.bactExtractor.ComputeNormalsOff()
self.bactExtractor.SetInputConnection(self.voi.GetOutputPort())
# surface rendering with dividing cubes
# self.bactExtractor = vtk.vtkRecursiveDividingCubes()
# self.bactExtractor.SetInputConnection(self.voi.GetOutputPort())
# self.bactExtractor.SetValue(self.isocontourLevel[0])
# self.bactExtractor.SetDistance(0.5)
# self.bactExtractor.SetIncrement(2)
# Smooth the mesh
relaxedMesh = vtk.vtkSmoothPolyDataFilter()
relaxedMesh.SetNumberOfIterations(50)
relaxedMesh.SetInput(self.bactExtractor.GetOutput())
# Calculate normals
meshNormals = vtk.vtkPolyDataNormals()
meshNormals.SetFeatureAngle(60.0)
meshNormals.SetInput(relaxedMesh.GetOutput())
# Restrip mesh after normal computation
restrippedMesh = vtk.vtkStripper()
restrippedMesh.SetInput(meshNormals.GetOutput())
# Convert mesh to graphics primitives
self.meshMapper = vtk.vtkPolyDataMapper()
self.meshMapper.ScalarVisibilityOff()
self.meshMapper.SetInput(restrippedMesh.GetOutput())
# Finally create a renderable object "Actor"
# that can be passed to the render window
self.ibcActor = vtk.vtkActor()
self.ibcActor.SetMapper(self.meshMapper)
ibcColor = DataStore.GetImageSet(self.imageSetID).color
self.ibcActor.GetProperty().SetDiffuseColor(ibcColor.r, ibcColor.g, ibcColor.b)
self.ibcActor.GetProperty().SetSpecular(.1)
self.ibcActor.GetProperty().SetSpecularPower(5)
self.ibcActor.GetProperty().SetOpacity(1)
self.ibcActor.SetVisibility(boolInt(self.visible))
self.renderer.AddActor(self.ibcActor)
# Optional Locator to help the ray traced picker
self.bactLocator = vtk.vtkCellLocator()
self.bactLocator.SetDataSet(restrippedMesh.GetOutput())
self.bactLocator.LazyEvaluationOn()
return self.bactLocator
def init_concentration_field_actors(self, actor_specs, drawing_params=None):
"""
initializes concentration field actors
:param actor_specs:
:param drawing_params:
:return: None
"""
actors_dict = actor_specs.actors_dict
field_dim = self.currentDrawingParameters.bsd.fieldDim
# dim_order = self.dimOrder(self.currentDrawingParameters.plane)
# dim = self.planeMapper(dim_order, (field_dim.x, field_dim.y, field_dim.z))# [fieldDim.x, fieldDim.y, fieldDim.z]
dim = [field_dim.x, field_dim.y, field_dim.z]
field_name = drawing_params.fieldName
scene_metadata = drawing_params.screenshot_data.metadata
mdata = MetadataHandler(mdata=scene_metadata)
try:
isovalues = mdata.get('ScalarIsoValues',default=[])
isovalues = list(map(lambda x: float(x), isovalues))
except:
print('Could not process isovalue list ')
isovalues = []
try:
numIsos = mdata.get('NumberOfContourLines',default=3)
except:
print('could not process NumberOfContourLines setting')
numIsos = 0
hex_flag = False
lattice_type_str = self.get_lattice_type_str()
if lattice_type_str.lower() == 'hexagonal':
hex_flag = True
import PlayerPython
types_invisible = PlayerPython.vectorint()
for type_label in drawing_params.screenshot_data.invisible_types:
types_invisible.append(int(type_label))
# self.isovalStr = Configuration.getSetting("ScalarIsoValues", field_name)
# if type(self.isovalStr) == QVariant:
# self.isovalStr = str(self.isovalStr.toString())
# else:
# self.isovalStr = str(self.isovalStr)
con_array = vtk.vtkDoubleArray()
con_array.SetName("concentration")
con_array_int_addr = extract_address_int_from_vtk_object(field_extractor=self.field_extractor, vtkObj=con_array)
cell_type_con = vtk.vtkIntArray()
cell_type_con.SetName("concelltype")
cell_type_con_int_addr = extract_address_int_from_vtk_object(field_extractor=self.field_extractor,
vtkObj=cell_type_con)
field_type = drawing_params.fieldType.lower()
if field_type == 'confield':
fill_successful = self.field_extractor.fillConFieldData3D(con_array_int_addr, cell_type_con_int_addr,
field_name, types_invisible)
elif field_type == 'scalarfield':
fill_successful = self.field_extractor.fillScalarFieldData3D(con_array_int_addr, cell_type_con_int_addr,
field_name, types_invisible)
elif field_type == 'scalarfieldcelllevel':
fill_successful = self.field_extractor.fillScalarFieldCellLevelData3D(con_array_int_addr,
cell_type_con_int_addr, field_name,
types_invisible)
if not fill_successful:
return
range_array = con_array.GetRange()
min_con = range_array[0]
max_con = range_array[1]
field_max = range_array[1]
# print MODULENAME, ' initScalarFieldDataActors(): min,maxCon=',self.minCon,self.maxCon
min_max_dict = self.get_min_max_metadata(scene_metadata=scene_metadata, field_name=field_name)
min_range_fixed = min_max_dict['MinRangeFixed']
max_range_fixed = min_max_dict['MaxRangeFixed']
min_range = min_max_dict['MinRange']
max_range = min_max_dict['MaxRange']
# Note! should really avoid doing a getSetting with each step to speed up the rendering;
# only update when changed in Prefs
if min_range_fixed:
min_con = min_range
if max_range_fixed:
max_con = max_range
uGrid = vtk.vtkStructuredPoints()
uGrid.SetDimensions(dim[0] + 2, dim[1] + 2, dim[
2] + 2) # only add 2 if we're filling in an extra boundary (rf. FieldExtractor.cpp)
# uGrid.SetDimensions(self.dim[0],self.dim[1],self.dim[2])
# uGrid.GetPointData().SetScalars(self.cellTypeCon) # cellType scalar field
uGrid.GetPointData().SetScalars(con_array)
# uGrid.GetPointData().AddArray(self.conArray) # additional scalar field
voi = vtk.vtkExtractVOI()
## voi.SetInputConnection(uGrid.GetOutputPort())
# voi.SetInput(uGrid.GetOutput())
if VTK_MAJOR_VERSION >= 6:
voi.SetInputData(uGrid)
else:
voi.SetInput(uGrid)
voi.SetVOI(1, dim[0] - 1, 1, dim[1] - 1, 1,
dim[2] - 1) # crop out the artificial boundary layer that we created
isoContour = vtk.vtkContourFilter()
# skinExtractorColor = vtk.vtkDiscreteMarchingCubes()
# skinExtractorColor = vtk.vtkMarchingCubes()
# isoContour.SetInput(uGrid)
isoContour.SetInputConnection(voi.GetOutputPort())
isoNum = 0
for isoNum, isoVal in enumerate(isovalues):
try:
isoContour.SetValue(isoNum, isoVal)
except:
print MODULENAME, ' initScalarFieldDataActors(): cannot convert to float: ', self.isovalStr[idx]
if isoNum > 0:
isoNum += 1
delIso = (max_con - min_con) / (numIsos + 1) # exclude the min,max for isovalues
isoVal = min_con + delIso
for idx in xrange(numIsos):
isoContour.SetValue(isoNum, isoVal)
isoNum += 1
isoVal += delIso
# UGLY hack to NOT display anything since our attempt to RemoveActor (below) don't seem to work
if isoNum == 0:
isoVal = field_max + 1.0 # go just outside valid range
isoContour.SetValue(isoNum, isoVal)
# concLut = vtk.vtkLookupTable()
# concLut.SetTableRange(conc_vol.GetScalarRange())
# concLut.SetTableRange([self.minCon,self.maxCon])
self.scalarLUT.SetTableRange([min_con, max_con])
# concLut.SetNumberOfColors(256)
# concLut.Build()
# concLut.SetTableValue(39,0,0,0,0)
# skinColorMapper = vtk.vtkPolyDataMapper()
# skinColorMapper.SetInputConnection(skinNormals.GetOutputPort())
# self.conMapper.SetInputConnection(skinExtractorColor.GetOutputPort())
self.conMapper.SetInputConnection(isoContour.GetOutputPort())
self.conMapper.ScalarVisibilityOn()
self.conMapper.SetLookupTable(self.scalarLUT)
# # # print " this is conc_vol.GetScalarRange()=",conc_vol.GetScalarRange()
# self.conMapper.SetScalarRange(conc_vol.GetScalarRange())
self.conMapper.SetScalarRange([min_con, max_con])
# self.conMapper.SetScalarRange(0,1500)
# rwh - what does this do?
# self.conMapper.SetScalarModeToUsePointFieldData()
# self.conMapper.ColorByArrayComponent("concentration",0)
# print MODULENAME,"initScalarFieldDataActors(): Plotting 3D Scalar field"
# self.conMapper = vtk.vtkPolyDataMapper()
# self.conActor = vtk.vtkActor()
concentration_actor = actors_dict['concentration_actor']
concentration_actor.SetMapper(self.conMapper)
self.init_min_max_actor(min_max_actor=actors_dict['min_max_text_actor'], range_array=range_array)
if hex_flag:
concentration_actor.SetScale(self.xScaleHex, self.yScaleHex, self.zScaleHex)
if actor_specs.metadata is None:
actor_specs.metadata = {'mapper': self.conMapper}
else:
actor_specs.metadata['mapper'] = self.conMapper
if mdata.get('LegendEnable',default=False):
print 'Enabling legend'
self.init_legend_actors(actor_specs=actor_specs, drawing_params=drawing_params)
