[vtkusers] Copy image data into vtkImageData from a textfile
Lizeth Castellanos
castellanoslizan at gmail.com
Wed Jul 25 11:14:46 EDT 2018
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-V
> TK-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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