[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
> >> >> >
> >> >> >
> >> >> > _______________________________________________
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> >> >> >
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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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> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> >
> >> >
> >
> >
> >
> >
> > --
> >
> >
> >
>



-- 
Lizeth  Castellanos.
PhD Student
Federal University of Rio Grande do Sul (UFRGS)
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