[vtkusers] Copy image data into vtkImageData from a textfile

[Lizeth Castellanos]

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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