Comments on: Getting Started with Python-InsightToolkit

By: paul

paul — Wed, 30 Nov 2011 21:15:28 +0000

@loli I am not compiling unsigned longs(UL) in these packages. It looks like the WatershedImageFilter has a hard-coded output of UL, so that is why it returns UL. Unfortunately, you would have to recompile the packages with UL turned on, so that all the other filters will also be able to use this data type.

By: loli

loli — Fri, 25 Nov 2011 15:26:59 +0000

I stumbled the problem that itk.Image.UL2/3 exist and is returned by filters such as itk.WatershedImageFilter. But practically no filter templates exist for this type. Especially frustrating is that neither itk.ImageFileWriter nor itk.RescaleIntensityImageFilter nor the most simple itk.CastImageFilter can handle the UL type.

Any suggestion how I could retrieve my data without having to write my own conversion filter?

Greetings.

By: paul

paul — Fri, 30 Sep 2011 12:57:39 +0000

@shan I don't have floats wrapped for that type, but it looks like doubles are. If you use ipython you can figure out what types are wrapped and which aren't. See my comment here.

By: shan

shan — Wed, 28 Sep 2011 01:38:51 +0000

Hi, I am wondering if itk.Mesh has a wrapper. I tried doing as follows
itk.Mesh[itk.F,3]

it say that there is no such template. Or I am not doing it correctly???

Thanks

By: Helen

Helen — Wed, 08 Jun 2011 18:31:47 +0000

Thanks, this was really useful.
Has anyone tried using image registration with python? I’m trying to convert Imageregistration7 example and getting the error:
RuntimeError: /tmp/buildd/insighttoolkit-3.18.0/Code/Numerics/itkRegularStepGradientDescentBaseOptimizer.cxx:197:
itk::ERROR: RegularStepGradientDescentOptimizer(0xad25f0e8): The size of Scales is 6, but the NumberOfParameters for the CostFunction is 4.

Does anyone know how to increase the number of parameters in python?

By: paul

paul — Mon, 06 Dec 2010 14:33:11 +0000

@gordon: Hmm, that looks like a great feature. I'll look into it.

By: gordon

gordon — Sat, 04 Dec 2010 23:15:26 +0000

@paul thanks for your work on maintaining this package! I noticed somewhere mentioned there is a optional patch to enable access by index to the structure such as itk.Size.

http://mima2.jouy.inra.fr/darcs/contrib-itk/WrapITK/patch/optional/

Is it possible to apply them to your build?

By: paul

paul — Thu, 02 Dec 2010 15:29:32 +0000

@gordon: For image direction, it is a little hairy. But you can get a scipy matrx with the following:

import scipy
scipy_matrix = scipy.matrix(scipy.zeros((3,3)))
vnl_matrix = i.GetDirection().GetVnlMatrix()
for i in range(3):
    for j in range(3):
        scipy_matrix[i,j] = vnl_matrix.get(i,j)

With the scipy matrix you can now do all sorts of matrix manipulations including vector multiplication. I would look for a scipy tutorial if you are not familiar with it.

By: gordon

gordon — Mon, 29 Nov 2010 02:41:07 +0000

how can i access to the element of matrix type(e.g. image.GetDirection())? and do multiplication with the vector.

By: Paolo

Paolo — Wed, 05 May 2010 19:55:04 +0000

@paul:
That command doesn’t work!
If I write
image_type = itk.Image[itk.F, 3]
it works, but I don’t want use float type!