def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImagePermute(), 'Processing.',
('vtkImageData', 'vtkImageStencilData'), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
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 permuteAxes(self, x, y, z):
"""Reorder the axes of the Volume by specifying
the input axes which are supposed to become the new X, Y, and Z."""
imp = vtk.vtkImagePermute()
imp.SetFilteredAxes(x, y, z)
imp.SetInputData(self.imagedata())
imp.Update()
return self._update(imp.GetOutput())
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple viewer for images.
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
permute = vtk.vtkImagePermute()
permute.SetInputConnection(reader.GetOutputPort())
permute.SetFilteredAxes(1,2,0)
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(permute.GetOutputPort())
viewer.SetZSlice(32)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
#viewer DebugOn
#viewer Render
#make interface
viewer.Render()
# --- end of script --
def imageDataFromNumpy(npArr, spacing, origin, shape, dims=1, outputFilename = None):
ds, o, p = shape, origin, spacing
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr\tinitializing volume..."
d = vtk.vtkImageData()
d.SetDimensions(*ds)
d.SetOrigin(o[2],o[1],o[0])
d.SetSpacing(p[2],p[1],p[0])
d.SetNumberOfScalarComponents(dims)
if dims==3:
d.SetScalarTypeToUnsignedChar()
else:
d.SetScalarTypeToUnsignedInt()
d.AllocateScalars()
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: origin: " + str(d.GetOrigin())
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: spacing: " + str(d.GetSpacing())
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: data type: " + str(d.GetScalarTypeAsString())
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: components no.: " + str(d.GetNumberOfScalarComponents())
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: points no.: " + str(d.GetNumberOfPoints())
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: setting image data..."
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: iteration sequence: %d %d %d" % (ds[2], ds[1], ds[0])
dScalars = d.GetPointData().GetScalars()
dComputePointId = d.ComputePointId
if dims==3:
for i in range(ds[2]):
for j in range(ds[1]):
for k in range(ds[0]):
id = d.ComputePointId((k,j,i))
dScalars.SetTuple3(id, *map(float,npArr[k,j,i]))
if dims==1:
for i in range(ds[2]):
for j in range(ds[1]):
for k in range(ds[0]):
id = d.ComputePointId((k,j,i))
dScalars.SetTuple1(id, int(npArr[k,j,i]))
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: applying vtkImagePermute()"
permute = vtk.vtkImagePermute()
permute.SetFilteredAxes(2,1,0)
permute.SetInput(d)
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: applying vtk.vtkImageCast()"
cast = vtk.vtkImageCast()
cast.SetInput(permute.GetOutput())
cast.SetOutputScalarTypeToFloat()
cast.Update()
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: applying vtk.vtkImageCast()"
cast2 = vtk.vtkImageCast()
cast2.SetInput(cast.GetOutput())
cast2.SetOutputScalarTypeToUnsignedInt()
cast2.Update()
print >>sys.stderr, cast2.GetOutput()
if outputFilename:
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: writing to: %s" % outputFilename
w = vtk.vtkStructuredPointsWriter()
w.SetInput(cast2.GetOutput())
w.SetFileName(outputFilename)
w.Update()
print >>sys.stderr, "\timageDataFrom3dRGBNumpyArr: done."
return cast2.GetOutput()
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple viewer for images.
# Image pipeline
reader = vtk.vtkImageReader()
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
permute = vtk.vtkImagePermute()
permute.SetInputConnection(reader.GetOutputPort())
permute.SetFilteredAxes(1, 2, 0)
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(permute.GetOutputPort())
viewer.SetZSlice(32)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
#viewer DebugOn
#viewer Render
#make interface
viewer.Render()
# --- end of script --
def permute(image,ax0,ax1,ax2):
permute = vtk.vtkImagePermute()
permute.SetInput(image)
permute.SetFilteredAxes(ax0,ax1,ax2)
return permute.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()
