[ITK] registration - memory concerns
Luigi Riba
ribaluigi at gmail.com
Wed Nov 18 05:53:54 EST 2015
Dear all,
I have tried your suggestions and I have simplified my code. Unfortunately,
I still have some issues:
1. I cannot read the two images as unsigned short. If I do like this,
VisualStudio compiler returns:
Error 2 error C2440: 'initializing' : cannot convert from
'itk::Concept::Detail::UniqueType_bool<false>' to
'itk::Concept::Detail::UniqueType_bool<true>'
f:\libs\itk\modules\core\common\include\itkConceptChecking.h 796 1 affine3d
2. I have decided to read the images directly in float;
3. I have set everything to float but I have noticed *no* memory usage
differences between the "dobule" and "float" code. In particular, I have
set:
> typedef float InternalComputationValueType;
> typedef itk::AffineTransform< InternalComputationValueType, Dimension>
> TransformType;
> typedef
> itk::RegularStepGradientDescentOptimizerv4<InternalComputationValueType>
> OptimizerType;
> typedef itk::MeanSquaresImageToImageMetricv4<ImageType, ImageType,
> ImageType, InternalComputationValueType> MetricType;
> typedef itk::ImageRegistrationMethodv4<ImageType, ImageType,
> TransformType> RegistrationType;
> typedef float CoordinateType;
> typedef itk::LinearInterpolateImageFunction<ImageType, CoordinateType>
> InterpolationType;
RECAP:
1. I would like to reduce the memory usage of my registration code. In
fact, I work with unsigned short, i.e. 16 bit grayscale images, ~1Gb each
and memory usage gets high pretty soon (750MB images -> ~30GB total memory
usage)
2. It has been suggested to set the algorithm to work with float instead of
double;
3. How can I accomplish point 2.?
4. Is point 2. the only viable solution in order to reduce memory usage?
5 Is there a way to have a finer monitoring of memory usage. For the
moment I am using itkMemoryProbe which just gives me the total amount of
used memory.
Thank you for your kind support,
Luigi
2015-11-16 16:55 GMT+01:00 Luigi Riba <ribaluigi at gmail.com>:
> 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
>>
>
>
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