[ITK] [ITK-users] error using Richard-Lucy deconvolution

Matt McCormick matt.mccormick at kitware.com
Thu Sep 29 17:47:16 EDT 2016 

Hi Francisco,

I think you found a bug -- the kernel should not require the same
Origin as the input image.  Please review this patch:

  http://review.source.kitware.com/#/c/21598/

Thanks,
Matt

On Fri, Sep 9, 2016 at 10:25 AM, Francisco Oliveira
<francisco.oliveira at fe.up.pt> wrote:
> Thanks Brad, your suggestion solved my problem.
> First we need forcing the input image to have spacing=[1, 1, 1], origin=[0, 0, 0] and the direction equals to identity matrix. Then we can apply the filter and after we set back the original spacing, origin and directions to the deconvoluted image (of course we need to save them before).
>
> Francisco
>
>
> -----Mensagem original-----
> De: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov]
> Enviada: sexta-feira, 9 de setembro de 2016 13:56
> Para: Francisco Oliveira; Cory Quammen
> Cc: Matt McCormick; ITK
> Assunto: Re: [ITK-users] error using Richard-Lucy deconvolution
>
> Hello,
>
> I was able to reproduce your problem in SimpleITK:
>
> In [1]: import SimpleITK as sitk
>
> In [2]: img = sitk.ReadImage("/scratch/blowekamp/build/itkSimpleFilters/ExternalData/test/Input/DSA.png")
>
> In [3]: img = sitk.VectorIndexSelectionCast(img, 0, sitk.sitkFloat32)
>
> In [4]: k = sitk.Image(11,11, sitk.sitkFloat32)
>
> In [5]: k[5,4]=.01; k[5,5]=1
>
> In [6]: out = sitk.RichardsonLucyDeconvolution(img,k)
>
> —————————
> NOTE: OK with both origins of 0
> —————————
>
>
> In [7]: sitk.Show(out)
>
>
> In [9]: img.SetOrigin([10,10])
>
> In [10]: out = sitk.RichardsonLucyDeconvolution(img,k)
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
> <ipython-input-10-05ff2abccb8c> in <module>()
> ----> 1 out = sitk.RichardsonLucyDeconvolution(img,k)
>
> /home/blowekamp/.virtualenvs/sitk-test/lib/python2.7/site-packages/SimpleITK/SimpleITK.pyc in RichardsonLucyDeconvolution(*args, **kwargs)
>   57544
>   57545     """
>> 57546     return _SimpleITK.RichardsonLucyDeconvolution(*args, **kwargs)
>   57547 class STAPLEImageFilter(ImageFilter_3):
>   57548     """
>
> RuntimeError: Exception thrown in SimpleITK RichardsonLucyDeconvolution: /tmp/SimpleITK-build/ITK-prefix/include/ITK-4.10/itkImageToImageFilter.hxx:250:
> itk::ERROR: DivideOrZeroOutImageFilter(0x4085740): Inputs do not occupy the same physical space!
> InputImage Origin: [1.0000000e+01, 1.0000000e+01], InputImage_1 Origin: [0.0000000e+00, 0.0000000e+00]
>         Tolerance: 1.0000000e-06
>
> In [11]: out = sitk.WienerDeconvolution(img,k)
>
> In [12]: out = sitk.TikhonovDeconvolution(img,k)
>
>
>
>
> You should be  able to set with images to the same origin to bypass this exception.
>
>
> I am not sure if this filter is suppose to require that both images have the same grids or not. If it does, the check should happen earlier on in the VerifyInputInformation method.
>
> But as other Deconvolution filters I tested in SimpleITK seem to expect different origins, I think it may be a bug in this filter.
>
> Brad
>
>> On Sep 9, 2016, at 3:42 AM, Francisco Oliveira <francisco.oliveira at fe.up.pt> wrote:
>>
>> Hi Matt,
>> I already tried that and it didn't work. Independently the kernel image I use the error is the same and the origin and spacing are always the same [0, 0, 0] and [1, 1, 1], respectively.
>>
>> Francisco
>>
>> -----Mensagem original-----
>> De: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Enviada: quinta-feira, 8 de setembro de 2016 19:22
>> Para: Francisco
>> Cc: insight-users at itk.org
>> Assunto: Re: [ITK-users] error using Richard-Lucy deconvolution
>>
>> Hi Francisco,
>>
>> As the error message indicates, the filter requires both inputs to have the same "information", i.e. Origin and Spacing, since it assumes that they occupy the same domain in physical space.
>>
>> HTH,
>> Matt
>>
>> On Thu, Sep 8, 2016 at 12:46 PM, Francisco <francisco.oliveira at fe.up.pt> wrote:
>>> Hi all,
>>> I'm trying to use itkRichardLucyDeconvolutionImageFilter but I have
>>> always the following error independently of the size, origin,
>>> spacing, ... of the input image and the kernel image. If I use other
>>> deconvolution filter (for instance
>>> itkLandweberDeconvolutionImageFilter) it works perfectly. I´m using the code example available in the ITK. I'm using itk-4.4.0 and VS2008.
>>>
>>> itk::ExceptionObject (0185E9CC)
>>> Location: "unknown"
>>> File:
>>> c:\libraries\itk-4.4.0\source\modules\core\common\include\itkImageToI
>>> m
>>> ageF
>>> ilter.hxx
>>> Line: 247
>>> Description: itk::ERROR: DivideOrZeroOutImageFilter(03631DB0): Inputs
>>> do not occupy the same physical space!
>>> InputImage Origin: [-2.8658594e+002, -2.1658594e+002,
>>> 9.9893402e+002],
>>> InputImage_1 Origin: [0.0000000e+000, 0.0000000e+000, 0.0000000e+000]
>>>        Tolerance: 4.0000000e-006
>>> InputImage Spacing: [4.0000000e+000, 4.0000000e+000, 4.0000000e+000],
>>> InputImage_1 Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000]
>>>        Tolerance: 4.0000000e-006
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://itk-insight-users.2283740.n2.nabble.com/error-using-Richard-Lu
>>> c y-deconvolution-tp7589179.html Sent from the ITK Insight Users
>>> mailing list archive at Nabble.com.
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>>
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>
> -----
> Não foram detetados vírus nesta  mensagem.
> Verificado por AVG - www.avg.com
> Versão: 2016.0.7752 / Base de dados de Vírus: 4649/12974 - Data de Lançamento: 09/08/16
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
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>
> Kitware offers ITK Training Courses, for more information visit:
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