[ITK] registration - memory concerns

[Dženan Zukić]

I believe Matias thought that your original pixel type was signed short.

So just use the images you read as unsigned short (set them as input to the
registration), and don't make another copy of the images by casting them to
float.

HTH

On Mon, Nov 16, 2015 at 10:17 AM, Luigi Riba <ribaluigi at gmail.com> wrote:

> Dear Matias,
>
> thank you very much for your quick reply.
>
> Unfortunately, I didn't have time yet to test it. Anyhow, could you please
> tell me the rationale behind it?
>
> In my code:
>
>
>    1. I read two grayscale 16 bit .mhd images. To read them I define the
>    IOPixelTyep as unsigned short;
>    2. I cast them to the "operational" type called PixelType as float
>    3. I define all the registration objects templated on float.
>
> Why should I cast my images to PixelType == signed short?
>
> Thanks in advance for the support,
> Luigi
>
>
>
>
>
> 2015-11-10 15:45 GMT+01:00 Matias Montroull <matimontg at gmail.com>:
>
>> try this:
>> typedef  signed short  PixelType;
>>
>>
>> El mar., 10 de nov. de 2015 a la(s) 11:36 a. m., Luigi Riba <
>> ribaluigi at gmail.com> escribió:
>>
>>> Dear Matt,
>>>
>>> I have tried following your suggestion but, unfortunately, it didn't
>>> work out.
>>>
>>> In particular:
>>>
>>>    1. I read a pair of uint16 images;
>>>    2. I cast them to float pixel type via the CastImageFilter;
>>>    3. I change the TInternalComputationValueType for the metric, the
>>>    optimizer, the transform and the registration doing something like:
>>>
>>> const unsigned int Dimension = 3;
>>>
>>> typedef float PixelType;
>>>
>>> typedef unsigned short IOPixelType;
>>>>
>>> typedef itk::Image<IOPixelType, Dimension> IOImageType;
>>>
>>> typedef itk::Image<PixelType, Dimension> ImageType;
>>>
>>> typedef itk::AffineTransform<float, Dimension > TransformType;
>>>
>>> typedef itk::RegularStepGradientDescentOptimizerv4<float> OptimizerType;
>>>
>>> typedef itk::MeanSquaresImageToImageMetricv4<ImageType,
>>>> ImageType,ImageType,float> MetricType;
>>>
>>> typedef itk::ImageRegistrationMethodv4<ImageType, ImageType,
>>>> TransformType> RegistrationType;
>>>
>>> typedef itk::ResampleImageFilter<IOImageType, IOImageType, float,float>
>>>> ResampleFilterType;
>>>
>>>
>>>
>>>
>>>
>>> I have put one memory probe before the registration procedure and one
>>> afterwards of it. In the "double" case and in the "float" case I've seen
>>> the same memory consumption.
>>>
>>> Am I missing something? Are there other things I should change in my
>>> code?
>>>
>>> Thanks again for the support,
>>> Luigi
>>>
>>>
>>>
>>> 2015-11-09 17:23 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>>>
>>>> Hi Luigi,
>>>>
>>>> The type of optimizer should not have too large of an impact on memory
>>>> consumption.  Using a gradient-free optimizer may help slightly, but
>>>> try changing the pixel type of the input images or, if possible, the
>>>> parameter type of the transformation, from double to float.
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>> On Mon, Nov 9, 2015 at 10:24 AM, Luigi Riba <ribaluigi at gmail.com>
>>>> wrote:
>>>> > Dear all,
>>>> >
>>>> > I am registering a couple of volumes with ITK 4 on windows 7 64 bit.
>>>> >
>>>> > I wrote a code based on the affine transformation, with the mean
>>>> square
>>>> > error metric and the RegularStepGradientDescentOptimizerv4.
>>>> Unfortunately,
>>>> > the memory usage is pretty high.
>>>> >
>>>> > I have checked memory consumption with the itkMemoryProbe and, after
>>>> looking
>>>> > around on previous mailing list messages I have decided to try with a
>>>> > gradient free optimizer like the Nelder-Mead one.
>>>> >
>>>> > So I have rewrote the code using the AmoebaOptimizerV4 and I have
>>>> continued
>>>> > monitoring the memory consumption via MemoryProbe. Unfortunately, it
>>>> seems
>>>> > that nothing has changed. Is this working as expected? If this is the
>>>> case,
>>>> > do you have any suggestion to gave me in order to reduce the memory
>>>> > consumption of the code?
>>>> >
>>>> > Thanks in advance for the help.
>>>> >
>>>> > Best,
>>>> >
>>>> > Luigi
>>>> >
>>>> > _______________________________________________
>>>> > Community mailing list
>>>> > Community at itk.org
>>>> > http://public.kitware.com/mailman/listinfo/community
>>>> >
>>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>> --
>> Matias
>>
>
>
> _______________________________________________
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>
>
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