[ITK-users] [ITK] ITK PyBuffer get physical point coordinates

[Francois Budin]

Hello Fabio,

I was able to use this filter in Python. Here is the commands I typed:
In [14]: ImageType=itk.Image[itk.Vector[itk.F,2],2]

In [15]: source=itk.PhysicalPointImageSource[ImageType].New()

In [16]: source.SetSize([5,5])

In [17]: source.SetOrigin([0,0])

In [18]: source.SetSpacing([.5,.5])

In [19]: source.Update()

In [20]: itk.GetArrayFromImage(source)
Out[20]:
itkndarray([[[ 0. ,  0. ],
        [ 0.5,  0. ],
        [ 1. ,  0. ],
        [ 1.5,  0. ],
        [ 2. ,  0. ]],

       [[ 0. ,  0.5],
        [ 0.5,  0.5],
        [ 1. ,  0.5],
        [ 1.5,  0.5],
        [ 2. ,  0.5]],

       [[ 0. ,  1. ],
        [ 0.5,  1. ],
        [ 1. ,  1. ],
        [ 1.5,  1. ],
        [ 2. ,  1. ]],

       [[ 0. ,  1.5],
        [ 0.5,  1.5],
        [ 1. ,  1.5],
        [ 1.5,  1.5],
        [ 2. ,  1.5]],

       [[ 0. ,  2. ],
        [ 0.5,  2. ],
        [ 1. ,  2. ],
        [ 1.5,  2. ],
        [ 2. ,  2. ]]], dtype=float32)

It also worked with VectorImages:

In [22]: ImageType=itk.VectorImage[itk.F,2]

In [23]: source=itk.PhysicalPointImageSource[ImageType].New()

In [24]: source.SetOrigin([0,0])

In [25]: source.SetSize([5,5])

In [26]: source.SetSpacing([.5,.5])

In [27]: source.Update()

In [28]: itk.GetArrayFromImage(source)


To answer your questions:
1) This filter is only wrapped over image of vectors and vector images. You
can have the list of types that are available in Python with
itk.PhysicalPointImageSource.GetTypes()
2) You may have a version of ITK Python for which VectorImage is not
wrapped for PyBuffer. You can try to update your ITK Python [1]

Hope this helps,
Francois

[1] https://github.com/InsightSoftwareConsortium/ITKPythonPackage

On Fri, Apr 28, 2017 at 12:05 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Thank you for your reply.
>
>
>
> 1)     I have tried as a first step the following:
>
>
>
> DRRPhy = itk.PhysicalPointImageSource[itk.Image[itk.Point[itk.F,
> Dimension], Dimension]].New()
>
>
>
> But I get the error:
>
>
>
> KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>,
> 3) for the itk::Image class"
>
>
>
> So I guess I can’t generate an image with itk.Points as PixelType.
> Therefore I chose to use a VectorImage as ImageType in Input to the
> PhysicalPointImageSource.
>
>
>
> sourceImage = itk.PhysicalPointImageSource[itk.VectorImage[itk.F,
> Dimension]].New()
>
> sourceImage.SetSize(size)
>
> sourceImage.SetSpacing(spacing)
>
> sourceImage.SetOrigin(origin)
>
> #DRRPhy.SetIndex(start) it does not work, how to set the start index?
>
> DRRPhy.SetDirection(direction)
>
>
>
> 2)     However, using PyBuffer to get a numpy array form that does not
> work:
>
>
>
> sourceImageArray = itk.PyBuffer[ImageType].GetArrayFromImage(sourceImage)
>
>
>
> I get the error:
>
>
>
> AttributeError: 'itkPhysicalPointImageSourceVIF3' object has no attribute
> 'GetLargestPossibleRegion'
>
>
>
>
>
> Am I doing the right thing in point 1) ?
>
> How could I solve point 2) ?
>
>
>
> Thank you !
>
>
>
> Fabio.
>
>
>
> *From:* Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov]
>
> *Sent:* Donnerstag, 27. April 2017 23:16
> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK] [ITK-users] ITK PyBuffer get physical point
> coordinates
>
>
>
> Hi!
>
>
>
> You can generate an image of the physical locations of each pixel with the
> PhysicalPointImageSource filter:
>
> https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html
>
>
>
> Very recently added is the SetReferenceImage, which can be use to copy the
> meta data from one image to the parameters of this filter. If your version
> is not super recent then you can manually set the Size, Spacing, Origin,
> Direction and StartIndex.
>
>
>
> After you generate the point image you should be able to convert to with
> the same method.
>
>
>
> HTH,
>
> Brad
>
>
>
>
>
> On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
>
>
> Hallo,
>
>
>
> I know it’s possible to get a numpy array of an itk image with:
>
>
>
> itk.PyBuffer[ImageType].GetArrayFromImage(Image)
>
>
>
> Is it by any chance also possible to obtain a (flattended) numpy array of
> the physical coordinates of the image pixels too?
>
>
>
> Thank you!
>
>
>
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