[Insight-users] A memory issue

Ali Mouizina ali.mouizina at gmail.com
Fri Jan 20 09:36:58 EST 2012 

To Dzenan :

Thank you, I increased the virtual memory but I still can't allocate 
memory for my vectors.

To alex :

Here is a part of my code :

Weights.h

typedef unsigned char PixelType;
const unsigned int Dimension3=3;
const unsigned int Dimension4=4;
typedef itk::Image<PixelType, Dimension3> ImageType;
typedef itk::Image<PixelType, Dimension4> Weightimage;

class Weights{
public:
     Weights(ImageType::Pointer image, int patch_size, int region_size, 
double var, int ln, int col, int nb_slices);

     int get_hw2() {return hw2;}

     Weightimage::Pointer get_weight() {return weight2;}


private:
     int hw1; // Half-width (patch)
     int hw2; // half-width (region)
     double h2; //std of image noise
     int nb_ln; // nb of rows
     int nb_col; // nb of columns
     int nb_slice; // nb of slices
     ImageType::Pointer read;
     Weightimage::Pointer weight2;

     ImageType::Pointer imshift(int x, int y, int z);
};

Weights . cpp

Weights::Weights(ImageType::Pointer reader, int patch_size, int 
region_size, double var, int ln, int col,int nb_slices)
     : read(reader), hw1(patch_size), hw2(region_size), h2(var), 
nb_ln(ln), nb_col(col),nb_slice(nb_slices)
{
     weight2 = Weightimage::New();

     Weightimage::IndexType start;
     start[0]=0;
     start[1]=0;
     start[2]=0;
     start[3]=0;

     Weightimage::SizeType size;
     size[0]=nb_col;
     size[1]=nb_ln;
     size[2]=nb_slice;
     size[3]=125;


     Weightimage::RegionType region;
     region.SetSize(size);
     region.SetIndex(start);

     weight2->SetRegions(region);
     weight2->Allocate(); //-> This is where it crashes
     weight2->FillBuffer(0);
}

main.cpp

ImageType::IndexType pixelIndex;

     typedef itk::ImageFileReader< ImageType > ReaderType;
     ReaderType::Pointer reader = ReaderType::New(),reader2 = 
ReaderType::New();

     const char *inputFilename="3DGado_1_brain";
     const char *inputFilename2="3DGado_2_1";
     reader->SetFileName(inputFilename);
     reader->Update();

     reader2->SetFileName(inputFilename2);
     reader2->Update();

     ImageType::Pointer image=reader->GetOutput(), 
image2=reader2->GetOutput();

     Weights w1(image,1,2,10,512,512,22); //-> I can instantiate only 
this one
     Weights w2(image2,1,2,10,512,512,22); //-> For this one it crashes 
at Weight.cpp :: weight2->Allocate();

Normally I should have enough memory for w1 and w2 (with unsigned char 
used as the pixeltype).

Regards,

Ali

Le 20/01/2012 13:59, alex Dowson a écrit :
> Hi
>
>
> Can you show your code that we can understand little what you trying 
> to do ?
>
>
>
> Alex
>
>
> -----Original Message----- From: Ali Mouizina
> Sent: Friday, January 20, 2012 6:21 PM
> To: insight-users at itk.org
> Subject: Re: [Insight-users] A memory issue
>
> To Dzenan :
>
> How can I do this ?
>
> To Kevin :
>
> All my values are within 0 and 1 but I think I can quantisize those
> values between 0 and 255. I tried your suggestion on a smaller image
> (and hence  a smaller vector 512*512*22*125 <=> 671 MB with unsigned
> char) but it crashes when I instantiate 2 vectors (it works with 1). By
> the way I have a 8 GB of RAM and windows 7 64 bits. How can I fix this ?
>
> Thank you very much for your help !
>
> Regards,
>
> Ali
>
> Le 20/01/2012 13:09, Kevin Keraudren a écrit :
>> Also, changing PixelType and using a smaller type would save memory. Of
>> course, not all algorithms can live with unsigned char.
>>
>> unsigned char: 512*512*156*125/1024/1024/1024 ~ 4.8 GB
>> double:        512*512*156*125*8/1024/1024/1024 ~ 38.1 GB
>>
>>
>> On 20/01/12 11:26, Dženan Zukić wrote:
>>> Have you tried increasing virtual memory/swap file size? That should do
>>> it, I think. But it would be slower, of course.
>>>
>>> On Fri, Jan 20, 2012 at 11:31, Ali Mouizina<ali.mouizina at gmail.com
>>> <mailto:ali.mouizina at gmail.com>>  wrote:
>>>
>>>      Hi all,
>>>
>>>      I'm currently trying to allocate a 4-D vector whose size is
>>>      512*512*156*125 to store the results of  some computations i do 
>>> on a
>>>      3D image. As expected, I don't have enough memory, is there any
>>>      trick to get round this problem ?
>>>
>>>      The results I get at each iteration of the computation process is
>>>      stored into a slice of the 4D vector, so I thought I can process
>>>      each slice separately. Any suggestions on how to do that or any
>>>      other ideas ?
>>>
>>>      Regards,
>>>
>>>      Ali
>>>
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-- 
Ali Mouizina
Diplômé en Traitement Numérique du Signal
Elève-Ingénieur en Traitement d'images
Mastère Spécialisé Telecom ParisTech : Signal, Images et Reconnaissance de formes
Paris - FRANCE

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Ali Mouizina
Graduated in Digital Signal Processing
Currently studying Image Processing
Advanced Masters at Telecom ParisTech : Signal, Images and Pattern Recognition
Paris - FRANCE

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