[vtkusers] Copy image data into vtkImageData from a textfile
kenichiro yoshimi
rccm.kyoshimi at gmail.com
Fri Jul 27 16:37:22 EDT 2018
Hi,
Thank you for sharing your code. At first glance, the parameters of
imageData have to be set according to your own data.
---
imageData.SetDimensions(512, 512, 192)
imageData.SetOrigin(0.0, 0.0, 0.0)
imageData.SetSpacing(1, 1, 1)
---
And would you try to use vtkSmartVolumeMapper, instead of
vtkVolumeRaycastMapper?
Thanks
2018年7月28日(土) 4:03 Lizeth Castellanos <castellanoslizan at gmail.com>:
>
> 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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>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> >
>> >> >
>> >
>> >
>> >
>> >
>> > --
>> >
>> >
>> >
>
>
>
>
> --
> Lizeth Castellanos.
> PhD Student
> Federal University of Rio Grande do Sul (UFRGS)
>
>
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