[vtkusers] Copy image data into vtkImageData from a textfile
Lizeth Castellanos
castellanoslizan at gmail.com
Fri Jul 27 15:02:20 EDT 2018
Hi!
Thanks for your reply.
My doubt was about how to pass the 'Field 3' to the probe filter. I made
some adjust based in your help. However, the output shows two solid cube
instead of the points from my segmented dataset.
I am sending the code and the screenshot of the output. Thanks again :-)
reader = vtk.vtkDelimitedTextReader()
reader.SetFieldDelimiterCharacters(' ')
reader.DetectNumericColumnsOn()
reader.SetFileName('sample.csv')
reader.MergeConsecutiveDelimitersOn()
reader.Update()
tableToPoints = vtk.vtkTableToPolyData()
tableToPoints.SetInputConnection(reader.GetOutputPort())
tableToPoints.SetXColumn('Field 0')
tableToPoints.SetYColumn('Field 1')
tableToPoints.SetZColumn('Field 2')
tableToPoints.Update()
imageData = vtk.vtkImageData()
imageData.SetDimensions(3, 3, 3)
imageData.SetOrigin(0.0, 0.0, 0.0)
imageData.SetSpacing(1.0, 1.0, 1.0)
imageData.Update()
probeFilter = vtk.vtkProbeFilter()
probeFilter.SetSourceConnection(tableToPoints.GetOutputPort())
probeFilter.SetInput(imageData)
probeFilter.Update()
probeFilter.GetOutput().GetPointData().SetActiveScalars('Field 3')
scalarRange =
probeFilter.GetOutput().GetPointData().GetScalars().GetRange()
writer = vtk.vtkXMLImageDataWriter()
writer.SetInput(probeFilter.GetOutput())
writer.SetFileName('out.vti')
writer.Write()
# Create transfer mapping scalar value to opacity.
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(scalarRange[0], 0.0)
opacityTransferFunction.AddPoint(scalarRange[1], 0.5)
# Create transfer mapping scalar value to color.
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(scalarRange[0], 0.0, 0.0, 1.0)
colorTransferFunction.AddRGBPoint((scalarRange[0]+scalarRange[1])*0.5, 0.0,
1.0, 0.0)
colorTransferFunction.AddRGBPoint(scalarRange[1], 1.0, 0.0, 0.0)
# The property describes how the data will look.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetScalarOpacityUnitDistance(1.73205080757)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
# vtkVolumeRayCastMapper need data of type unsigned char or unsigned short
cast = vtk.vtkImageCast()
cast.SetInputConnection(probeFilter.GetOutputPort())
cast.SetOutputScalarTypeToUnsignedChar()
cast.Update()
## The mapper / ray cast function know how to render the data
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
volumeMapper = vtk.vtkVolumeRayCastMapper()
volumeMapper.SetVolumeRayCastFunction(compositeFunction)
volumeMapper.SetInputConnection(cast.GetOutputPort())
#The volume holds the mapper and the property.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
#Create the standard renderer, render window and interactor
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
ren.AddVolume(volume)
ren.SetBackground(1, 1, 1)
renWin.SetSize(600, 600)
renWin.Render()
iren.Initialize()
renWin.Render()
iren.Start()
On Thu, Jul 26, 2018 at 9:35 PM, kenichiro yoshimi <rccm.kyoshimi at gmail.com>
wrote:
> Hi,
>
> Your question is not clear enough. If you possible, can you post your
> code? I don't have a problem with volume rendering in my code.
>
> ----
> import vtk
>
>
> def main():
>
> reader = vtk.vtkDelimitedTextReader()
> reader.SetFileName('sample.csv')
> reader.DetectNumericColumnsOn()
> reader.SetFieldDelimiterCharacters(' ')
> reader.MergeConsecutiveDelimitersOn()
>
> tableToPoints = vtk.vtkTableToPolyData()
> tableToPoints.SetInputConnection(reader.GetOutputPort())
> tableToPoints.SetXColumn('Field 0')
> tableToPoints.SetYColumn('Field 1')
> tableToPoints.SetZColumn('Field 2')
>
> imageData = vtk.vtkImageData()
> imageData.SetDimensions(3, 3, 3)
> imageData.SetOrigin(0.0, 0.0, 0.0)
> imageData.SetSpacing(1.0, 1.0, 1.0)
>
> probeFilter = vtk.vtkProbeFilter()
> probeFilter.SetSourceConnection(tableToPoints.GetOutputPort())
> probeFilter.SetInputData(imageData)
> probeFilter.Update()
>
> writer = vtk.vtkXMLImageDataWriter()
> writer.SetInputData(probeFilter.GetOutput())
> writer.SetFileName('out.vti')
> writer.Write()
>
> probeFilter.GetOutput().GetPointData().SetActiveScalars('Field 3')
> range = probeFilter.GetOutput().GetPointData().GetScalars().GetRange()
>
> colors = vtk.vtkNamedColors()
>
> # Create the standard renderer, render window
> # and interactor.
> ren = vtk.vtkRenderer()
>
> renWin = vtk.vtkRenderWindow()
> renWin.AddRenderer(ren)
>
> iren = vtk.vtkRenderWindowInteractor()
> iren.SetRenderWindow(renWin)
>
> # Create transfer mapping scalar value to opacity.
> opacityTransferFunction = vtk.vtkPiecewiseFunction()
> opacityTransferFunction.AddPoint(range[0], 0.0)
> opacityTransferFunction.AddPoint(range[1], 1.0)
>
> # Create transfer mapping scalar value to color.
> colorTransferFunction = vtk.vtkColorTransferFunction()
> colorTransferFunction.AddRGBPoint(range[0], 0.0, 0.0, 1.0)
> colorTransferFunction.AddRGBPoint((range[0]+range[1])*0.5, 0.0, 1.0,
> 0.0)
> colorTransferFunction.AddRGBPoint(range[1], 1.0, 0.0, 0.0)
>
> # The property describes how the data will look.
> volumeProperty = vtk.vtkVolumeProperty()
> volumeProperty.SetColor(colorTransferFunction)
> volumeProperty.SetScalarOpacity(opacityTransferFunction)
> volumeProperty.SetScalarOpacityUnitDistance(1.73205080757)
> volumeProperty.SetInterpolationTypeToLinear()
>
> # The mapper / ray cast function know how to render the data.
> volumeMapper = vtk.vtkSmartVolumeMapper()
> volumeMapper.SetInputConnection(probeFilter.GetOutputPort())
> volumeMapper.SetBlendModeToComposite()
>
> # The volume holds the mapper and the property and
> # can be used to position/orient the volume.
> volume = vtk.vtkVolume()
> volume.SetMapper(volumeMapper)
> volume.SetProperty(volumeProperty)
>
> ren.AddVolume(volume)
>
> ren.SetBackground(colors.GetColor3d("White"))
> ren.GetActiveCamera().ParallelProjectionOn()
> ren.ResetCameraClippingRange()
> ren.ResetCamera()
>
> renWin.SetSize(600, 600)
> renWin.Render()
>
> iren.Start()
>
>
> if __name__ == '__main__':
> main()
> ----
>
> Regards
> 2018年7月26日(木) 0:15 Lizeth Castellanos <castellanoslizan at gmail.com>:
> >
> > Thanks for your answers!
> >
> > For the case 2) I have one more question: How can I add the scalar
> values from the intensity ('Field 3') to the data?
> >
> > I have added those two lines to your code:
> >
> > scalar = probeFilter.GetOutput().GetPointData().GetArray('Field 3')
> > probeFilter.GetOutput().GetPointData().SetScalars(scalar)
> >
> > But when I render the volume, nothing is displayed in the render window.
> >
> > Thanks
> >
> > Lizeth
> >
> >
> >
> >
> >
> > On Tue, Jul 24, 2018 at 11:29 PM, kenichiro yoshimi <
> rccm.kyoshimi at gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> 1) You need to specify PYTHON_INCLUDE_DIR and PYTHON_LIBRARY to suit
> >> your own system in the 'advanced options' in cmake.
> >>
> >> PYTHON_INCLUDE_DIR will be the name of the directory containing the
> Python.h:
> >> e.g. /usr/include/python2.7
> >> PYTHON_LIBRARY will be the full path to libpython2.7.so (or.a):
> >> e.g. /usr/lib64/libpython2.7.so
> >>
> >> 2) For example, if you apply vtkProbeFilter to sample.csv in the
> >> previous my post, script is something like below.
> >>
> >> ---
> >> import vtk
> >>
> >>
> >> def main():
> >>
> >> reader = vtk.vtkDelimitedTextReader()
> >> reader.SetFileName('sample.csv')
> >> reader.DetectNumericColumnsOn()
> >> reader.SetFieldDelimiterCharacters(' ')
> >> reader.MergeConsecutiveDelimitersOn()
> >>
> >> tableToPoints = vtk.vtkTableToPolyData()
> >> tableToPoints.SetInputConnection(reader.GetOutputPort())
> >> tableToPoints.SetXColumn('Field 0')
> >> tableToPoints.SetYColumn('Field 1')
> >> tableToPoints.SetZColumn('Field 2')
> >>
> >> imageData = vtk.vtkImageData()
> >> imageData.SetDimensions(3, 3, 3)
> >> imageData.SetOrigin(0.0, 0.0, 0.0)
> >> imageData.SetSpacing(1.0, 1.0, 1.0)
> >>
> >> probeFilter = vtk.vtkProbeFilter()
> >> probeFilter.SetSourceConnection(tableToPoints.GetOutputPort())
> >> probeFilter.SetInputData(imageData)
> >> probeFilter.Update()
> >>
> >> writer = vtk.vtkXMLImageDataWriter()
> >> writer.SetInputData(probeFilter.GetOutput())
> >> writer.SetFileName('out.vti')
> >> writer.Write()
> >>
> >>
> >> if __name__ == '__main__':
> >> main()
> >> ---
> >>
> >> For your reference.
> >> 2018年7月25日(水) 4:10 Lizeth Castellanos <castellanoslizan at gmail.com>:
> >> >
> >> > Thanks for your help Kenichiro Yoshimi
> >> >
> >> > I was able to reproduce some part of your code. However, I
> encountered new issues.
> >> >
> >> > 1)I have all my project under VTK 5.10.1 with python 2.7.12 in linux.
> I got this error: 'module' object has no attribute 'vtkResampleToImage'.
> >> > So I guess that the vtkResampleToImage class is not avaliable for my
> VTK version.
> >> > I tried to build a newer VTK version but I didn't get success. I
> tried with VTK 7.1.1 and I got errors related to the python libs Could NOT
> find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS).
> >> >
> >> > 2) I read that vtkResampleToImage samples a dataset on a uniform
> grid and it internally uses vtkProbeFilter to do the probing. So, Is there
> any way to use vtkProbeFilter instead of vtkResampleToImage?
> >> > I have tested some examples from vtkProbeFilter but I am confused
> about how use it in my specific problem.
> >> >
> >> > Thanks,
> >> >
> >> > Lizeth
> >> >
> >> > On Thu, Jul 19, 2018 at 12:38 AM, kenichiro yoshimi <
> rccm.kyoshimi at gmail.com> wrote:
> >> >>
> >> >> Hi Lizeth,
> >> >>
> >> >> Because vtkDelimitedTextReader outputs a vtkTable, you firstly need
> to
> >> >> convert it to a vtkPolyData using vtkTableToPolyData. And then you
> can
> >> >> use vtkResampleToImage to map the polyData to vtkImageData.
> >> >>
> >> >> ---sample.csv---
> >> >> 0 0 0 60.7635
> >> >> 1 0 0 107.555
> >> >> 2 0 0 80.5241
> >> >> 0 1 0 85.9694
> >> >> 1 1 0 156.706
> >> >> 2 1 0 105.73
> >> >> 0 2 0 37.3531
> >> >> 1 2 0 84.1445
> >> >> 2 2 0 57.1137
> >> >> 0 0 1 100.634
> >> >> 1 0 1 171.37
> >> >> 2 0 1 120.395
> >> >> 0 1 1 149.785
> >> >> 1 1 1 260
> >> >> 2 1 1 169.546
> >> >> 0 2 1 77.2238
> >> >> 1 2 1 147.96
> >> >> 2 2 1 96.9844
> >> >> 0 0 2 60.7635
> >> >> 1 0 2 107.555
> >> >> 2 0 2 80.5241
> >> >> 0 1 2 85.9694
> >> >> 1 1 2 156.706
> >> >> 2 1 2 105.73
> >> >> 0 2 2 37.3531
> >> >> 1 2 2 84.1445
> >> >> 2 2 2 57.1137
> >> >>
> >> >> ---
> >> >> import vtk
> >> >>
> >> >>
> >> >> def main():
> >> >> colors = vtk.vtkNamedColors()
> >> >>
> >> >> reader = vtk.vtkDelimitedTextReader()
> >> >> reader.SetFileName('sample.csv')
> >> >> reader.DetectNumericColumnsOn()
> >> >> reader.SetFieldDelimiterCharacters(' ')
> >> >> reader.MergeConsecutiveDelimitersOn()
> >> >>
> >> >> tableToPoints = vtk.vtkTableToPolyData()
> >> >> tableToPoints.SetInputConnection(reader.GetOutputPort())
> >> >> tableToPoints.SetXColumn('Field 0')
> >> >> tableToPoints.SetYColumn('Field 1')
> >> >> tableToPoints.SetZColumn('Field 2')
> >> >>
> >> >> resample = vtk.vtkResampleToImage()
> >> >> resample.SetInputConnection(tableToPoints.GetOutputPort())
> >> >> resample.SetSamplingDimensions(3, 3, 3)
> >> >> resample.Update()
> >> >>
> >> >> scalar = resample.GetOutput().GetPointData().GetArray('Field 3')
> >> >> resample.GetOutput().GetPointData().SetScalars(scalar)
> >> >>
> >> >> writer = vtk.vtkMetaImageWriter()
> >> >> writer.SetInputData(resample.GetOutput())
> >> >> writer.SetFileName('out.mha')
> >> >> writer.SetCompression(True)
> >> >> writer.Write()
> >> >>
> >> >>
> >> >> if __name__ == '__main__':
> >> >> main()
> >> >> ---
> >> >>
> >> >> Best
> >> >> 2018年7月19日(木) 3:43 Lizeth Castellanos <castellanoslizan at gmail.com>:
> >> >> >
> >> >> > Hi!
> >> >> >
> >> >> > I'd like to copy image data from a textfile (csv) into
> vtkImageData.
> >> >> > The textfile have voxel values for x,y,z and image intensity. I
> already have read the textfile into VTK with the vtkDelimitedTextReader
> class:
> >> >> >
> >> >> > Table loaded from CSV file:
> >> >> > +-----------+-----------+-----------+------------+
> >> >> > | Field 0 | Field 1 | Field 2 | Field 3 |
> >> >> > +-----------+-----------+-----------+------------+
> >> >> > | 510 | 291 | 0 | 32 |
> >> >> > | 511 | 291 | 0 | 128 |
> >> >> > | 510 | 292 | 0 | 104 |
> >> >> > | 511 | 292 | 0 | 104 |
> >> >> > | 510 | 293 | 0 | 40 |
> >> >> > | 511 | 293 | 0 | 240 |
> >> >> > | 510 | 294 | 0 | 104 |
> >> >> > | 511 | 294 | 0 | 96 |
> >> >> > | 506 | 295 | 0 | 64 |
> >> >> > | 507 | 295 | 0 | 16 |
> >> >> > .....
> >> >> > .....
> >> >> > The file is an exported segmented dataset.
> >> >> >
> >> >> > I am following the tips from this similar question
> http://vtk.1045678.n5.nabble.com/importing-image-data-into-
> VTK-from-textfile-mimics-td1243332.html
> >> >> > I have created an appropriate vtkimagedata (volume):
> >> >> >
> >> >> > imageData = vtk.vtkImageData()
> >> >> > imageData.SetDimensions(512, 512, 192)
> >> >> > imageData.SetOrigin(0.0, 0.0, 0.0)
> >> >> > imageData.SetSpacing(1, 1, 1)
> >> >> > imageData.SetNumberOfScalarComponents(1)
> >> >> > imageData.Update()
> >> >> >
> >> >> > However I don't know how to copy the data loaded from
> vtkDelimitedTextReader into vtkImageData. How do I copy the x,y,z voxel
> values into vtkImageData? How do I copy the intensity valuesVtkImageData?
> >> >> >
> >> >> > Any help provided for this would be greatly appreciated!
> >> >> >
> >> >> > Lizeth
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > Powered by www.kitware.com
> >> >> >
> >> >> > Visit other Kitware open-source projects at
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> >> >> >
> >> >> > Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
> >> >> >
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> >> >> >
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> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> >
> >> >
> >
> >
> >
> >
> > --
> >
> >
> >
>
--
Lizeth Castellanos.
PhD Student
Federal University of Rio Grande do Sul (UFRGS)
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