[vtkusers] Extract Data from vtkImageReslice to numpy array

[Peter Bloomfield]

Hi,

I just tried the following,

I read my flat image data (I assume)
	reader = vtk.vtkImageReader2()
	reader.SetFileName("MyImage.img")
	reader.SetDataExtent(0, 255, 0, 255, 0, 206)
	reader.SetDataSpacing(1.218750, 1.218750, 1.218750)
	reader.SetDataOrigin(0.0, 0.0, 0.0)
	reader.SetDataScalarTypeToFloat()
	reader.SetFileDimensionality(3)
	reader.Update()

and then tried the following
	image_cells = reader.GetOutput().GetCellData()
	print image_cells
	vtkCellData (0x833e630)
	  Debug: Off
	  Modified Time: 211
	  Reference Count: 2
	  Registered Events: (none)
	  Number Of Arrays: 0
	  Number Of Components: 0
	  Number Of Tuples: 0
	  Copy Tuple Flags: ( 1 1 1 1 1 0 1 )
	  Interpolate Flags: ( 1 1 1 1 1 0 0 )
	  Pass Through Flags: ( 1 1 1 1 1 1 1 )
	  Scalars: (none)
	  Vectors: (none)
	  Normals: (none)
	  TCoords: (none)
	  Tensors: (none)
	  GlobalIds: (none)
	  PedigreeIds: (none)

So have i actually loaded the image data and is image_cells empty?

Thanks for your help

Peter


On Tuesday 30 June 2009 10:35:53 am Eric E. Monson wrote:
> Hey Peter,
>
> There is a handy set of utilities for converting between vtkDataArray
> (e.g. vtkDoubleArray, vtkIntArray) and numpy arrays called
> numpy_support that may help you. Try something like this:
>
> import vtk
> import vtk.util.numpy_support as VN
>
> reader = vtk.vtkXMLImageDataReader()
> reader.SetFileName('chombo3d_1.vti')
> reader.Update()
> image_cells = reader.GetOutput().GetCellData()
> phi_array = VN.vtk_to_numpy(image_cells.GetArray('phi'))
>
> Note that numpy_to_vtk() is also in there. There may be other nice
> tricks, but I find this module very useful.
>
> Good luck,
> -Eric
>
> ------------------------------------------------------
> Eric E Monson
> Duke Visualization Technology Group
>
> On Jun 30, 2009, at 9:54 AM, Peter Bloomfield wrote:
> > Hello,
> >
> > I am new to VTK, so if this has been asked before I apologise.
> >
> > I am trying to use VTK from within Python. I successfully downloaded
> > and
> > compiled VTK V5.4.2 including the python wrappings/bindings, and
> > issuing
> > 'import vtk' from within python works good.
> >
> > Initially I want to do is take a volume of data (float), re-slice it
> > in an
> > arbitrary orientation and then extract the re-sliced plane from vtk
> > and return
> > it to a numpy array.
> >
> > I am using vtk.vtkImageReslice(), but do not know how to get the
> > data out from
> > here.
> >
> > Does anyone have any suggestions of how I can achieve this? I have
> > tried
> > looking at vtkImageExportToArray but have no idea how to use this
> > from within
> > python.
> >
> > Many thanks
> >
> >
> > Peter
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