[Insight-users] SimpleITK Images to Numpy & reciprocally

[Matt McCormick]

Hi Jeff,

We are discussing this issue in this thread.

  http://review.source.kitware.com/#/c/6568/

Your thoughts would be appreciated there.

Thanks,
Matt

On Fri, Aug 3, 2012 at 11:02 AM, jeff witz <witzjean at gmail.com> wrote:
> Hello,
>
> I try to experiment Simple ITK and python.
>
> I want to make several task :
>
> 1) Reading ITK,VTK (mhd,vtk) 2D images with 2 or more
> NumberOfComponentsPerPixel,
> 2) Writing ITK,VTK (mhd,vtk) 2D images with 2 or more
> NumberOfComponentsPerPixel,
> 3) Transform from an to an numarray, ITK,VTK (mhd,vtk) 2D images with
> 2 or more NumberOfComponentsPerPixel,
>
> For now I succeed in 1) and Have bug with 2) & 3).
>
> I can easily pass from an ITK buffer to a numpy array, but the
> ordering is not the good one.
> The shape is  : (NumberOfComponentsPerPixel,Xdim,Ydim)
> So this problem can be sovled using :
> tmp = sitk.GetArrayFromImage( image )
> this work for any number of component.
>
> So if i try to do the reverse operation
> image=sitk.GetImageFromArray(tmp)
> it doesn't work, indeed, if I ask for the NumberOfComponentsPerPixel,
> I get 1. So I create a 3D image, THIS IS NOT WHAT I NEED.
>
> So in order to solve this bug I made my own system for exporting and
> importing itk image / numpy array
>
> import SimpleITK as sitk
> import numpy as np
>
> dataDir='./'
> image = sitk.ReadImage ( dataDir + "capt0242.tif" )
> z = sitk.GetArrayFromImage( image )
> image2 = sitk.Image( (z.shape[2], z.shape[1]),
> image.GetPixelIDValue(), z.shape[0] );
> sitk._SimpleITK._SetImageFromArray( z.tostring(), image2 ) # work for
> image color
> # Output, set ITK for valid output formats
> sitk.WriteImage ( image2, "./Example.mhd" )
> print time.clock()-tic
> os.system("paraview --data=./Example.mhd")
>
> if one wants to operate on data using python, If you try to
> imshow(z[0,::,::]) in order to see one component you will see a
>
> the picture as to be reshaped (it would be very simple to correct in
> SimpleITK directly) using :
> z=(a.reshape(N[0]*N[1]*N[2],1)).reshape(N[1],N[2],N[0])
>
>
> the third dimension is then the number of component as it is in matplotlib.
>
> Note that the jpeg import is not working on my PC.
>
>
>
>
> --
> Jean-François WITZ
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