[vtkusers] vtk image from itk

[Bradley Lowekamp]

Hello,

It looks like you are now mixing SimpleITK, WrapITK, and VTK for python. I am not sure adding WrapITK will make things any easier.

There is a complication with transitioning between SimpleITK and numpy with the order of the indexes. In the SimpleITK image buffer x is the fast axis and z is the slowest.

When you index a SimpleITK image you do:

img.GetPixel(x,y,z) or img[x,y,z]

similarly

(sizeX, sizeY, sizeZ) = img.GetSize()

Now, numpy arrays are indexed in the oppo site order:

nda = sitk.GetArrayFromImage(img)
nda[z,y,z]

and

(sizeZ, sizeY, sizeX) = nda.shape()

There is also a IPython notebook which covers this issue [1].

HTH,
Brad

[1] http://simpleitk.github.io/SimpleITK-Notebooks/01_Image_Basics.html

On Jun 15, 2015, at 1:38 PM, gregthom992 <gregthom992 at gmail.com> wrote:

> Hi David , 
> 
> Thanks for your information. I ignored the origin and it didn't fix my
> images.
> I then made another attempt at a function to convert to vtk from SimpleITK. 
> This still gave me the "mangled" image. I am seeing that my img_array.shape
> is [198 512 512] but my desired image Dimension should be [512 512 198]
> Do you think that is the problem ? I am not sure how SimpleITK
> GetArrayFromImage
> does with flipping dimensions. Any help will be appreciated. 
> Greg
> 
> 
> ##CODE:
> 
>    # image = sitk image
>    sitktype = image.GetPixelID()
>    vtktype  = pixelmap[sitktype]
> 
>    # Get ndarray from SimpleITK image
>    img_array = sitk.GetArrayFromImage(sitk.Cast(image, sitk.sitkFloat32))
> 
>    Dimension = image.GetDimension()
>    OutputPixelType = itk.F
>    OutputImageType = itk.Image[OutputPixelType, Dimension]
> 
>    #PyBuffer connector
>    pyBufferConnector = itk.PyBuffer[OutputImageType]
> 
>    # Get ITK image from ndarray
>    itkImage = pyBufferConnector.GetImageFromArray(img_array)
>    # preserve ITK image information
>    itkImage.SetSpacing(image.GetSpacing())
>    #itkImage.SetOrigin(image.GetOrigin())
>    #itkImage.SetDirection(image.GetDirection())
> 
>    itk_vtk_converter = itk.ImageToVTKImageFilter[OutputImageType].New()
>    itk_vtk_converter.SetInput(itkImage)
>    itk_vtk_converter.Update()
> 
> ##END CODE
> 
> 
> 
> 
> 
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