[vtkusers] Copy image data into vtkImageData from a textfile

Tue Jul 24 22:29:00 EDT 2018

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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>
>
>
> --
>
>
>