[ITK] Obtaining Hessian matrix values

[Nicolas Cedilnik]

Hello,

I am very new to ITK and looking for help.
I am trying to obtain hessian matrix values, in order to extract 
information about the detected vessels orientation. I'd be fine directly 
obtaining eigenvalues and eigenvectors.
I have compiled ITK with python wrappers and the BridgeNumpy module.

What I've managed to do so far:

# read my image
pixelType = itk.F
imageType = itk.Image[pixelType, 3]
readerType = itk.ImageFileReader[imageType]
reader = readerType.New()
reader.SetFileName("/path/to/my/image.mha")
# compute Hessian matrix
hessian_filter = itk.HessianRecursiveGaussianImageFilter[imageType].New()
hessian_filter.SetInput(reader.GetOutput())
# compute vesselness image
vesselness_filter = itk.Hessian3DToVesselnessMeasureImageFilter[itk.F].New()
vesselness_filter.SetInput(hessian_filter.GetOutput())
vesselness_filter.Update()
# convert vesselness image to numpy array
itk_py_converter = itk.PyBuffer[imageType]
vesselness_ndarray = itk_py_converter.GetArrayFromImage(vesselness_filter.GetOutput())
# output: x,y,z numpy array corresponding to my input image, which is a good start

Unfortunately, if I try to convert the Hessian matrix the same way:

buf = itk.PyBuffer[itk.Image.SSRTD33]
hess_matrix_ndarray = buf.GetArrayFromImage(hessian_filter.GetOutput())

I run into this error:

(...)
KeyError: "itkTemplate : No template [<class 'itkImagePython.itkImageSSRTD33'>] for the itk::PyBuffer class"

*Is this because I did not compile/install properly or because this type 
of pixel (itkImageSSRTD33) is not implemented in the PyBuffer module?*

Anyway I tried a different approach to obtain hessian matrix values:

hessian_filter.GetOutput().GetPixel([x,y,z]).GetNthComponent(n)

which works but I don't know *in what order are****the 6 components* and 
didn't even find out *how to extract the image boundaries as python 
standard types?*

In: hessian_filter.GetOutput().GetBufferedRegion()
Out: itkImageRegion3([0, 0, 0], [480, 384, 255])  # this looks OK but...
In: hessian_filter.GetOutput().GetBufferedRegion()[1]
Out: TypeError: 'itkImageRegion3' object does not support indexing  # DAMN!

As the vesselness filter performs eigenanalysis of the hessian 
matrix,*is there a way to extract the eigenvectors from there*?

If you've read this far, thanks a lot. Please point me the right 
direction... I used SimpleITK before and was less confused but 
unfortunately it is my understanding that it is not possible to use 
hessian filters in SimpleITK at the moment.

Regards,

-- 
Nicolas
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