[ITK] registration - memory concerns

[Luigi Riba]

Dear Dženan and Matias,

thank you very much for the help.

I'll test your suggestion and I'll post back the results for the community.

Best,

Luigi

2015-11-16 16:53 GMT+01:00 Matias Montroull <matimontg at gmail.com>:

> That was my assumption Luigi
>
> El lun., 16 de nov. de 2015 a la(s) 12:30 p. m., Dženan Zukić <
> dzenanz at gmail.com> escribió:
>
>> 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
>>>>
>>>
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>> --
> Matias
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20151116/a01e6258/attachment-0001.html>