[ITK] registration - memory concerns
Matt McCormick
matt.mccormick at kitware.com
Wed Nov 18 16:50:16 EST 2015
Hi Luigi,
It may be prudent to downsample the images using something like the
BinShrinkImageFilter. Often, the full-resolution is overkill for the
registration task.
HTH,
Matt
On Wed, Nov 18, 2015 at 1:21 PM, Matias Montroull <matimontg at gmail.com> wrote:
> Luigi, I assume you are workimg on release mode right?
> Would you be able to send the cpp file that you are compiling to test?
>
> Matias
>
> On Nov 18, 2015 7:53 AM, "Luigi Riba" <ribaluigi at gmail.com> wrote:
>>
>> 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:
>>>>>>
>>>>>> I read two grayscale 16 bit .mhd images. To read them I define the
>>>>>> IOPixelTyep as unsigned short;
>>>>>> I cast them to the "operational" type called PixelType as float
>>>>>> 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:
>>>>>>>>
>>>>>>>> I read a pair of uint16 images;
>>>>>>>> I cast them to float pixel type via the CastImageFilter;
>>>>>>>> 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
>>>
>>>
>>
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
More information about the Community
mailing list