[vtkusers] Passing data between VTK and NumPy.

[David Gobbi]

In VTK 3.2 there were two python classes that would convert NumPy
arrays back and forth to vtkImageData taking data types and dimensions
into account.  They were for 2D and 3D data only, but 5D data must be
reduced to 3D before it can be seen with VTK anyway.

See http://public.kitware.com/cgi-bin/cvsweb.cgi/vtk/python/?cvsroot=vtk
and grab the classes vtkImageExportToArray.py and vtkImageImportFromArray.py

These classes might not work anymore, but if anyone wants to
upgrade them to VTK 4 it would be great to have them as part
of the VTK 4 VTK/Python package.

 - David

-- 
  David Gobbi, MSc                dgobbi at imaging.robarts.ca
  Advanced Imaging Research Group
  Robarts Research Institute, University of Western Ontario

On Thu, 19 Sep 2002, Robb Brown wrote:

> This is done very nicely with vtkImageImport (Numpy to vtkImage) and
> vtkImageExport (vtkImage to Numpy).
>
> Here's a Python function to take a vtkStructuredPoints (same as
> vtkImage) and convert it to a Numpy array (preserving the shape):
>
> def VTKtoNumpy(vol):
> 	exporter = vtkImageExport()
> 	exporter.SetInput(vol)
> 	dims = exporter.GetDataDimensions()
> 	if (exporter.GetDataScalarType() == 3):
> 		type = UnsignedInt8
> 	if (exporter.GetDataScalarType() == 5):
> 		type = Int16
> 	a = zeros(reduce(multiply,dims),type)
> 	s = a.tostring()
> 	exporter.SetExportVoidPointer(s)
> 	exporter.Export()
> 	a = reshape(fromstring(s,type),(dims[2],dims[0],dims[1]))
> 	return a
>
> Note that you have to translate the VTK scalar type into a Numeric
> type.  Inserting data into a vtkStructuredPoints is pretty much the
> same except using vtkImageImport.  This approach takes advantage of
> the fact that a Python string can substitute for a C void array.
>
> For your application it sounds like you want to start with a Numpy
> array, slice out a 3D volume, use vtkImageImport to put that into a
> VTK data type and render it.  To change the slice just do another
> import and render again.
>
>
> >Dear all,
> >I'm using VTK to visualize 5D-data.
> >However, VTK cannot handle 5D-data. I thought I had a solution but
> >there are still some things that I don't know how to solve.
> >I can put all the data of the 5D-data and the dimensions into a long
> >1D vtkStructuredPoints.
> >Later on I can reconstruct the 5D-dataset by using these dimensions.
> >This 1D vtkStructuredPoints can be used as input in an instance of
> >vtkProgrammableFilter.
> >Using the SetExecuteMethod I want to implement a method to select
> >some '3D-slices' of the 5D-dataset.
> >The wat I want to implement the slicing is by using NumPy(A fast
> >Numerical Extension of python).
> >The problem is that I don't know how to get the data from the
> >SetExecuteMethod into NumPy.
> >Afaik know NumPy can read from strings and files.
> >
> >Do I need to convert the data into a string?
> >Is there a way to 'say' to NumPy where in memory the 5D-dataset starts?
> >Does someone has experience in using NumPy in combination with VTK?
> >
> >
> >
> >
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