def PaintVOI(self):
wholeExtent = self.Image.GetExtent()[:]
origin = self.Image.GetOrigin()
spacing = self.Image.GetSpacing()
paintedVOI = [0, 0, 0, 0, 0, 0]
paintedVOI[0] = max(
wholeExtent[0],
int(math.ceil((self.BoxBounds[0] - origin[0]) / spacing[0])))
paintedVOI[1] = min(
wholeExtent[1],
int(math.floor((self.BoxBounds[1] - origin[0]) / spacing[0])))
paintedVOI[2] = max(
wholeExtent[2],
int(math.ceil((self.BoxBounds[2] - origin[1]) / spacing[1])))
paintedVOI[3] = min(
wholeExtent[3],
int(math.floor((self.BoxBounds[3] - origin[1]) / spacing[1])))
paintedVOI[4] = max(
wholeExtent[4],
int(math.ceil((self.BoxBounds[4] - origin[2]) / spacing[2])))
paintedVOI[5] = min(
wholeExtent[5],
int(math.floor((self.BoxBounds[5] - origin[2]) / spacing[2])))
# extent trick. TODO: fix vtkvmtkImageBoxPainter
paintedVOI[0] -= wholeExtent[0]
paintedVOI[1] -= wholeExtent[0]
paintedVOI[2] -= wholeExtent[2]
paintedVOI[3] -= wholeExtent[2]
paintedVOI[4] -= wholeExtent[4]
paintedVOI[5] -= wholeExtent[4]
translate = vtk.vtkImageTranslateExtent()
translate.SetInputData(self.Image)
translate.SetTranslation(-wholeExtent[0], -wholeExtent[2],
-wholeExtent[4])
translate.Update()
imageBoxPainter = vtkvmtk.vtkvmtkImageBoxPainter()
imageBoxPainter.SetInputConnection(translate.GetOutputPort())
imageBoxPainter.SetBoxExtent(paintedVOI)
imageBoxPainter.SetBoxDefinitionToUseExtent()
imageBoxPainter.SetPaintValue(self.PaintValue)
imageBoxPainter.Update()
translate = vtk.vtkImageTranslateExtent()
translate.SetInputConnection(imageBoxPainter.GetOutputPort())
translate.SetTranslation(wholeExtent[0], wholeExtent[2],
wholeExtent[4])
translate.Update()
self.Image.ShallowCopy(translate.GetOutput())
def Execute(self):
if self.Image == None:
self.PrintError('Error: No Image.')
extent = self.Image.GetExtent()
translateExtent = vtk.vtkImageTranslateExtent()
translateExtent.SetInputData(self.Image)
translateExtent.SetTranslation(-extent[0],-extent[2],-extent[4])
translateExtent.Update()
if (self.ArrayName != ''):
translateExtent.GetOutput().GetPointData().SetActiveScalars(self.ArrayName)
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInputConnection(translateExtent.GetOutputPort())
marchingCubes.SetValue(0,self.Level)
marchingCubes.Update()
self.Surface = marchingCubes.GetOutput()
if self.Connectivity == 1:
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputData(self.Surface)
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
self.Surface = connectivityFilter.GetOutput()
def VTKImageShift(x,u,v,numret=False,interp=True,wrap=False,mirror=False,
constant=None,cubic=False):
if type(x) == type(np.arange(2)): i = NumToVTKImage(x)
else: i = x
if 0 and int(u) == u and int(v) == v:
s = vtk.vtkImageTranslateExtent()
s.SetInput(i)
s.SetTranslation(u,v,0)
o = s.GetOutput()
s.Update()
else:
s = vtk.vtkImageReslice()
s.AutoCropOutputOn()
if wrap: s.WrapOn()
else: s.WrapOff()
if mirror or constant != None: s.MirrorOn()
else: s.MirrorOff()
if interp:
s.InterpolateOn()
if cubic:
s.SetInterpolationModeToCubic()
else:
s.SetInterpolationModeToLinear()
else: s.InterpolateOff()
s.OptimizationOn()
s.SetOutputOrigin(u,v,0)
s.SetInputData(i)
o=s.GetOutput()
s.Update()
if numret: return VTKImageToNum(o)
else: return o
def Execute(self):
if self.Image == None:
self.PrintError('Error: No Image.')
extent = self.Image.GetExtent()
translateExtent = vtk.vtkImageTranslateExtent()
translateExtent.SetInputData(self.Image)
translateExtent.SetTranslation(-extent[0],-extent[2],-extent[4])
translateExtent.Update()
if (self.ArrayName != ''):
translateExtent.GetOutput().GetPointData().SetActiveScalars(self.ArrayName)
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInputConnection(translateExtent.GetOutputPort())
marchingCubes.SetValue(0,self.Level)
marchingCubes.Update()
self.Surface = marchingCubes.GetOutput()
if self.Connectivity == 1:
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputData(self.Surface)
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
self.Surface = connectivityFilter.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageTranslateExtent(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self,
module_manager,
vtk.vtkImageTranslateExtent(),
"Processing.",
("vtkImageData",),
("vtkImageData",),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None,
)
def PaintVOI(self):
wholeExtent = self.Image.GetExtent()[:]
origin = self.Image.GetOrigin()
spacing = self.Image.GetSpacing()
paintedVOI = [0,0,0,0,0,0]
paintedVOI[0] = max(wholeExtent[0],int(math.ceil((self.BoxBounds[0]-origin[0])/spacing[0])))
paintedVOI[1] = min(wholeExtent[1],int(math.floor((self.BoxBounds[1]-origin[0])/spacing[0])))
paintedVOI[2] = max(wholeExtent[2],int(math.ceil((self.BoxBounds[2]-origin[1])/spacing[1])))
paintedVOI[3] = min(wholeExtent[3],int(math.floor((self.BoxBounds[3]-origin[1])/spacing[1])))
paintedVOI[4] = max(wholeExtent[4],int(math.ceil((self.BoxBounds[4]-origin[2])/spacing[2])))
paintedVOI[5] = min(wholeExtent[5],int(math.floor((self.BoxBounds[5]-origin[2])/spacing[2])))
# extent trick. TODO: fix vtkvmtkImageBoxPainter
paintedVOI[0] -= wholeExtent[0]
paintedVOI[1] -= wholeExtent[0]
paintedVOI[2] -= wholeExtent[2]
paintedVOI[3] -= wholeExtent[2]
paintedVOI[4] -= wholeExtent[4]
paintedVOI[5] -= wholeExtent[4]
translate = vtk.vtkImageTranslateExtent()
translate.SetInputData(self.Image)
translate.SetTranslation(-wholeExtent[0],-wholeExtent[2],-wholeExtent[4])
translate.Update()
imageBoxPainter = vtkvmtk.vtkvmtkImageBoxPainter()
imageBoxPainter.SetInputConnection(translate.GetOutputPort())
imageBoxPainter.SetBoxExtent(paintedVOI)
imageBoxPainter.SetBoxDefinitionToUseExtent()
imageBoxPainter.SetPaintValue(self.PaintValue)
imageBoxPainter.Update()
translate = vtk.vtkImageTranslateExtent()
translate.SetInputConnection(imageBoxPainter.GetOutputPort())
translate.SetTranslation(wholeExtent[0],wholeExtent[2],wholeExtent[4])
translate.Update()
self.Image.ShallowCopy(translate.GetOutput())
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the stencil filter by using one image
# to stencil another
# Image pipeline
reader1 = vtk.vtkBMPReader()
reader1.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/masonry.bmp")
reader2 = vtk.vtkPNMReader()
reader2.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/B.pgm")
translate = vtk.vtkImageTranslateExtent()
translate.SetInputConnection(reader2.GetOutputPort())
translate.SetTranslation(60,60,0)
imageToStencil = vtk.vtkImageToImageStencil()
imageToStencil.SetInputConnection(translate.GetOutputPort())
imageToStencil.ThresholdBetween(0,127)
# silly stuff to increase coverage
imageToStencil.SetUpperThreshold(imageToStencil.GetUpperThreshold())
imageToStencil.SetLowerThreshold(imageToStencil.GetLowerThreshold())
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(reader1.GetOutputPort())
stencil.SetBackgroundValue(0)
stencil.ReverseStencilOn()
stencil.SetStencilConnection(imageToStencil.GetOutputPort())
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(stencil.GetOutputPort())
viewer.SetColorWindow(255.0)
viewer.SetColorLevel(127.5)
# do alpha-blending of two images, but also clip with stencil reader1 = vtk.vtkBMPReader() reader1.SetFileName(VTK_DATA_ROOT + "/Data/masonry.bmp") reader2 = vtk.vtkPNMReader() reader2.SetFileName(VTK_DATA_ROOT + "/Data/B.pgm") table = vtk.vtkLookupTable() table.SetTableRange(0, 127) table.SetValueRange(0.0, 1.0) table.SetSaturationRange(0.0, 0.0) table.SetHueRange(0.0, 0.0) table.SetAlphaRange(0.9, 0.0) table.Build() translate = vtk.vtkImageTranslateExtent() translate.SetInputConnection(reader2.GetOutputPort()) translate.SetTranslation(60, 60, 0) sphere = vtk.vtkSphere() sphere.SetCenter(121, 131, 0) sphere.SetRadius(70) functionToStencil = vtk.vtkImplicitFunctionToImageStencil() functionToStencil.SetInput(sphere) blend = vtk.vtkImageBlend() blend.SetInputConnection(reader1.GetOutputPort()) blend.AddInputConnection(translate.GetOutputPort()) # excercise the ReplaceNthInputConnection method
def execute(self, inputs, update=0, last=0):
"""
Execute the filter with given inputs and return the output
"""
if not lib.ProcessingFilter.ProcessingFilter.execute(self, inputs):
return None
maxx, maxy, maxz = self.dataUnit.getDimensions()
minx = 0
miny = 0
minz = 0
if self.parameters["UseROI"]:
minx, maxx = 99999, 0
miny, maxy = 99999, 0
roi = self.parameters["ROI"][1]
pts = roi.getCoveredPoints()
for (x, y) in pts:
if minx > x:
minx = x
if x > maxx:
maxx = x
if miny > y:
miny = y
if y > maxy:
maxy = y
minz = self.parameters["FirstSlice"]
maxz = self.parameters["LastSlice"]
minz -= 1
maxz -= 1
maxx -= 1
maxy -= 1
scripting.wantWholeDataset = 1
imagedata = self.getInput(1)
imagedata.SetUpdateExtent(imagedata.GetWholeExtent())
imagedata.Update()
# Mask original image
if self.parameters["UseROI"]:
mask = lib.ImageOperations.getMaskFromPoints(
pts, maxx + 1, maxy + 1, maxz + 1)
maskFilter = vtk.vtkImageMask()
maskFilter.SetImageInput(imagedata)
maskFilter.SetMaskInput(mask)
imagedata = maskFilter.GetOutput()
imagedata.Update()
# Extract VOI of original data
self.vtkfilter.SetInput(imagedata)
self.vtkfilter.SetVOI(minx, maxx, miny, maxy, minz, maxz)
data = self.vtkfilter.GetOutput()
translate = vtk.vtkImageTranslateExtent()
translate.SetInput(data)
#print "input data=",data
translation = [0, 0, 0]
if minz > 0:
translation[2] = -minz
if minx > 0:
translation[0] = -minx
if miny > 0:
translation[1] = -miny
newTranslation = translation[:]
#if self.translation:
# dx = self.translation[0]-minx
# dy = self.translation[1]-miny
# dz = self.translation[2]-minz
# newTranslation = [dx,dy,dz]
self.translation = newTranslation
#lib.messenger.send(None, bxdevents.TRANSLATE_DATA, tuple(self.translation))
if translation != [0, 0, 0]:
translate.SetTranslation(tuple(translation))
#translate.SetOutputOrigin(0,0,0)
data = translate.GetOutput()
data.Update()
reslice = vtk.vtkImageChangeInformation()
reslice.SetOutputOrigin(0, 0, 0)
reslice.SetInput(data)
data = reslice.GetOutput()
print "Returning data", data
return data
def execute(self, inputs, update = 0, last = 0): """ Execute the filter with given inputs and return the output """ if not lib.ProcessingFilter.ProcessingFilter.execute(self, inputs): return None maxx, maxy, maxz = self.dataUnit.getDimensions() minx = 0 miny = 0 minz = 0 if self.parameters["UseROI"]: minx, maxx = 99999, 0 miny, maxy = 99999, 0 roi = self.parameters["ROI"][1] pts = roi.getCoveredPoints() for (x, y) in pts: if minx > x: minx = x if x > maxx: maxx = x if miny > y: miny = y if y > maxy: maxy = y minz = self.parameters["FirstSlice"] maxz = self.parameters["LastSlice"] minz -= 1 maxz -= 1 maxx -= 1 maxy -= 1 scripting.wantWholeDataset=1 imagedata = self.getInput(1) imagedata.SetUpdateExtent(imagedata.GetWholeExtent()) imagedata.Update() # Mask original image if self.parameters["UseROI"]: mask = lib.ImageOperations.getMaskFromPoints(pts, maxx+1, maxy+1, maxz+1) maskFilter = vtk.vtkImageMask() maskFilter.SetImageInput(imagedata) maskFilter.SetMaskInput(mask) imagedata = maskFilter.GetOutput() imagedata.Update() # Extract VOI of original data self.vtkfilter.SetInput(imagedata) self.vtkfilter.SetVOI(minx, maxx, miny, maxy, minz, maxz) data = self.vtkfilter.GetOutput() translate = vtk.vtkImageTranslateExtent() translate.SetInput(data) #print "input data=",data translation = [0,0,0] if minz > 0: translation[2] = -minz if minx > 0: translation[0] = -minx if miny > 0: translation[1] = -miny newTranslation = translation[:] #if self.translation: # dx = self.translation[0]-minx # dy = self.translation[1]-miny # dz = self.translation[2]-minz # newTranslation = [dx,dy,dz] self.translation = newTranslation #lib.messenger.send(None, bxdevents.TRANSLATE_DATA, tuple(self.translation)) if translation != [0,0,0]: translate.SetTranslation(tuple(translation)) #translate.SetOutputOrigin(0,0,0) data = translate.GetOutput() data.Update() reslice = vtk.vtkImageChangeInformation() reslice.SetOutputOrigin(0,0,0) reslice.SetInput(data) data = reslice.GetOutput() print "Returning data",data return data
