[Insight-users] Memory problem
Melanie Uks
meluks2010 at googlemail.com
Wed Apr 13 10:24:32 EDT 2011
Thanks for your replies.
Neil, I splitted the image and repeated the process (see the code at the end
of my e-mail). The strange thing I totally don't understand is why the
processing is working when I run just this processing in a separate programm
and not when I include the processing as a "function" in my acutal
program.In the separate program it is just working when I split the image in
4 parts.
Gerald, I used now for every filter: filter->SetReleaseDataFlag(true);
There was no difference... unfortunately :-(
2011/4/13 Lodron, Gerald <Gerald.Lodron at joanneum.at>
> itk uses pipelining which means that there is one image in memory after
> each filtering. So when you have
>
> ->image->filter1->filter2->filter3
>
> you get the memory of the image 4 times. If you want to release the memory
> after each filter step you can use the release data flag of each filter
> (SetReleaseDataFlagOn). Then you hage the memory only one time
>
> If you have an image of 300x300x512x3 with float (4 byte) you have 527 MB
> memory per image, windows 32 theoretically only allows propgramms 2GB (in my
> tests this theoretically is 1.2 GB in practice) so you only can have the
> image stored into two vairables, in the third time the allocation will fail!
>
> Another solution is to use the RequestedRegion instead of
> largestpossibleregion but this is not supported for all filters. here only a
> part of an image is loaded and processed...I have no experience with this
>
> best regards
>
> ------------------------------
> *Von:* insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org]
> *Im Auftrag von *Melanie Uks
> *Gesendet:* Mittwoch, 13. April 2011 15:34
> *An:* insight-users at itk.org
> *Betreff:* Re: [Insight-users] Memory problem
>
> Sorry, I don't have that much expertice: what does "individual chunks" mean
> and how to implement?
>
> 2011/4/13 Neil Panjwani <paniwani at gmail.com>
>
>> I had similar memory allocation problems when running several CT slices in
>> 32 bit. If you can, using 64-bit should solve your memory problems.
>>
>> Otherwise, I think you'd have to apply your algorithm on individual chunks
>> at a time and combine them at the end.
>>
>>
>> On Wed, Apr 13, 2011 at 9:22 AM, Melanie Uks <meluks2010 at googlemail.com>wrote:
>>
>>> I am running 32 bit.
>>>
>>>
>>> 2011/4/13 Neil Panjwani <paniwani at gmail.com>
>>>
>>>> Are you running in 32 or 64 bit?
>>>>
>>>> On Wed, Apr 13, 2011 at 4:47 AM, Melanie Uks <
>>>> meluks2010 at googlemail.com> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I tried to filter a 3D image (300x300x512) with the CannyEdgeFilter. I
>>>>> had the problem that I could not allocate the memory for the filtering.
>>>>> Anyway I don't like the CannyEdgeFilter Implementation as one has to guess
>>>>> which values to take for the thresholding before the gradientmagnitude image
>>>>> exists... Therefore I wanted to write my own edge detection routine.
>>>>>
>>>>> The steps:
>>>>> I generate a image (size: 300x300x512)
>>>>> I generate a vector image (size: 300x300x512, vector dimension:3)
>>>>> a) I split the image, process the imagepart with
>>>>> GradientRecursiveGaussianImageFilter
>>>>> b) I paste the processed imagepart in the vector image with the
>>>>> PasteImageFilter
>>>>> I repeat a) and b) until the whole image is processed
>>>>>
>>>>> Now the first question: Why can't I process the complete image. I have
>>>>> to split the image and get a result... This is the error I get:
>>>>> *itk::ExceptionObject (0151C728)
>>>>> Location: "class itk::CovariantVector<float,3> *__thiscall
>>>>> itk::ImportImageConta
>>>>> iner<unsigned long,class itk::CovariantVector<float,3>
>>>>> >::AllocateElements(unsig
>>>>> ned long) const"
>>>>> File:
>>>>> h:\itk\insighttoolkit-3.16.0\code\common\itkImportImageContainer.txx
>>>>> Line: 188
>>>>> Description: Failed to allocate memory for image.*
>>>>>
>>>>> Ok, if I accept that I have to split the image, I have a second
>>>>> question: I was able to run my example programm (code at the end of this
>>>>> mail). Then I copied the code into my actual program. It is a programm with
>>>>> several itk functions and Qt GUI. The only difference is that the image is
>>>>> saved as global variable. I was not able to run the processing. I always had
>>>>> the memory error. Why???
>>>>>
>>>>> Here now the code for the example processing:
>>>>>
>>>>> edgetest.cxx
>>>>>
>>>>> #include "conio.h"
>>>>>
>>>>> #include "itkImageFileWriter.h"
>>>>> #include "itkImageFileReader.h"
>>>>> #include "itkRegionOfInterestImageFilter.h"
>>>>> #include "itkGradientRecursiveGaussianImageFilter.h"
>>>>> #include "itkGradientToMagnitudeImageFilter.h"
>>>>> #include "itkPasteImageFilter.h"
>>>>> #include "itkImage.h"
>>>>>
>>>>> int main(int argc, char* argv[])
>>>>> {
>>>>> // Verify number of parameters in command line
>>>>> // if( argc < 3 )
>>>>> // {
>>>>> // std::cerr << "Usage: " << std::endl;
>>>>> // std::cerr << argv[0] << " inputImageFile outputVectorImageFile
>>>>> " << std::endl;
>>>>> // return EXIT_FAILURE;
>>>>> // }
>>>>> typedef float PixelType;
>>>>> typedef float ComponentType;
>>>>> static const unsigned int Dimension = 3;
>>>>> typedef itk::Image< PixelType, Dimension > ImageType;
>>>>> typedef itk::CovariantVector< ComponentType,
>>>>> Dimension > OutputPixelType;
>>>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>>>>
>>>>>
>>>>> ImageType::Pointer image = ImageType::New();
>>>>>
>>>>> ImageType::IndexType start;
>>>>> for(int i = 0; i < Dimension; i++)
>>>>> start[i]=0;
>>>>>
>>>>> ImageType::SizeType size;
>>>>> size[0] = 300;
>>>>> size[1] = 300;
>>>>> size[2] = 512;
>>>>>
>>>>> ImageType::RegionType region;
>>>>> region.SetSize(size);
>>>>> region.SetIndex(start);
>>>>>
>>>>> ImageType::SpacingType spacing;
>>>>> spacing[0] = 20;
>>>>> spacing[1] = 20;
>>>>> spacing[2] = 4.00493;
>>>>>
>>>>> image->SetRegions(region);
>>>>> image->SetSpacing(spacing);
>>>>> image->Allocate();
>>>>>
>>>>> std::cout << region << std::endl;
>>>>>
>>>>> OutputImageType::Pointer vec_image = OutputImageType::New();
>>>>> OutputImageType::RegionType vecregion;
>>>>>
>>>>> OutputImageType::SizeType vecsize; //Size
>>>>> vecsize[0] = (image->GetLargestPossibleRegion().GetSize())[0];
>>>>> vecsize[1] = (image->GetLargestPossibleRegion().GetSize())[1];
>>>>> vecsize[2] = (image->GetLargestPossibleRegion().GetSize())[2];
>>>>> std::cout<<"size0: "<< vecsize[0]<< " size1: "<< vecsize[1] << "
>>>>> size2: " << vecsize[2] <<std::endl;
>>>>> vecregion.SetSize( vecsize );
>>>>>
>>>>> OutputImageType::IndexType vecstart; //Start
>>>>> vecstart[0] = (image->GetOrigin())[0];
>>>>> vecstart[1] = (image->GetOrigin())[1];
>>>>> vecstart[2] = (image->GetOrigin())[2];
>>>>> std::cout<<" start0: "<< vecstart[0]<< " start1: "<< vecstart[1] << "
>>>>> start2: " << vecstart[2] <<std::endl;
>>>>> vecregion.SetIndex( vecstart );
>>>>>
>>>>> vec_image->SetRegions(vecregion);
>>>>> vec_image->SetSpacing(image->GetSpacing());
>>>>> vec_image->Allocate();
>>>>>
>>>>> // The image buffer is initialized to a particular value
>>>>> OutputImageType::PixelType initialValue;
>>>>>
>>>>> // A vector can initialize all its components to the
>>>>> // same value by using the Fill() method.
>>>>> initialValue.Fill( 0.0 );
>>>>>
>>>>> // Now the image buffer can be initialized with this
>>>>> // vector value.
>>>>> vec_image->FillBuffer( initialValue );
>>>>> std::cout<< "Allocate" << std::endl;
>>>>>
>>>>> typedef itk::RegionOfInterestImageFilter< ImageType, ImageType >
>>>>> ROIFilterType;
>>>>> ROIFilterType::Pointer roifilter = ROIFilterType::New();
>>>>>
>>>>> // Number of Regions
>>>>> int splitcnt_x = 2;
>>>>> int splitcnt_y = 2;
>>>>> int overlap = 15;
>>>>>
>>>>> int stepcnt_x = (int) (size[0]*1.0/splitcnt_x + 0.5);
>>>>> int stepcnt_y = (int) (size[1]*1.0/splitcnt_y + 0.5);
>>>>>
>>>>>
>>>>> ImageType::IndexType roistart;
>>>>> roistart[2]=0;
>>>>> ImageType::SizeType roisize;
>>>>> roisize[2]=512;
>>>>> ImageType::RegionType roiregion;
>>>>>
>>>>>
>>>>> for (int cnt_x = 0; cnt_x < splitcnt_x; cnt_x++)
>>>>> {
>>>>> for (int cnt_y = 0; cnt_y < splitcnt_y; cnt_y++)
>>>>> {
>>>>> roistart[0]= cnt_x*stepcnt_x - overlap;
>>>>> roistart[1]= cnt_y*stepcnt_y - overlap;
>>>>> if(cnt_x == 0)
>>>>> {
>>>>> roistart[0] = 0;
>>>>> roisize[0] = stepcnt_x + overlap;
>>>>> }
>>>>> else
>>>>> {
>>>>> roisize[0] = stepcnt_x + 2*overlap;
>>>>> }
>>>>> if(roisize[0]+roistart[0] > size[0])
>>>>> {
>>>>> roisize[0] = size[0]-roistart[0];
>>>>> }
>>>>> if(cnt_y == 0)
>>>>> {
>>>>> roistart[1] = 0;
>>>>> roisize[1] = stepcnt_y + overlap;
>>>>> }
>>>>> else
>>>>> {
>>>>> roisize[1] = stepcnt_y + 2*overlap;
>>>>> }
>>>>> if(roisize[1]+roistart[1] > size[1])
>>>>> {
>>>>> roisize[1] = size[1]-roistart[1];
>>>>> }
>>>>>
>>>>>
>>>>> roiregion.SetSize(roisize);
>>>>> roiregion.SetIndex(roistart);
>>>>>
>>>>> std::cout << "cnt_x: " << cnt_x << " cnt_y: " << cnt_y <<
>>>>> std::endl;
>>>>>
>>>>> std::cout << roiregion << std::endl;
>>>>>
>>>>> std::cout << "ROI region inside image region is " <<
>>>>> region.IsInside(roiregion) << std::endl;
>>>>>
>>>>> roifilter->SetRegionOfInterest(roiregion);
>>>>> roifilter->SetInput(image);
>>>>>
>>>>> //Filter class is instantiated
>>>>> typedef itk::GradientRecursiveGaussianImageFilter<ImageType,
>>>>> OutputImageType> GradFilterType;
>>>>>
>>>>> GradFilterType::Pointer gradfilter = GradFilterType::New();
>>>>>
>>>>> //sigma is specified in millimeters
>>>>> gradfilter->SetSigma( 1.5 );
>>>>>
>>>>> // processing pipeline:
>>>>> gradfilter->SetInput(roifilter->GetOutput());
>>>>>
>>>>>
>>>>> typedef itk::PasteImageFilter <OutputImageType, OutputImageType
>>>>> > PasteImageFilterType;
>>>>> // The SetDestinationIndex() method prescribes where in the
>>>>> first
>>>>> // input to start pasting data from the second input.
>>>>> // The SetSourceRegion method prescribes the section of the
>>>>> second
>>>>> // image to paste into the first.
>>>>>
>>>>> OutputImageType::IndexType destinationIndex;
>>>>> destinationIndex[0] = cnt_x*stepcnt_x;
>>>>> destinationIndex[1] = cnt_y*stepcnt_y;
>>>>> destinationIndex[2] = 0;
>>>>>
>>>>> PasteImageFilterType::Pointer pasteFilter =
>>>>> PasteImageFilterType::New ();
>>>>> pasteFilter->SetSourceImage(gradfilter->GetOutput());
>>>>> pasteFilter->SetDestinationImage(vec_image);
>>>>>
>>>>> OutputImageType::RegionType pasteregion;
>>>>> OutputImageType::IndexType pastestart;
>>>>> pastestart[2]=0;
>>>>> OutputImageType::SizeType pastesize;
>>>>> pastesize[2]=512;
>>>>>
>>>>> pastestart[0]= overlap;
>>>>> pastestart[1]= overlap;
>>>>> pastesize[0] = stepcnt_x;
>>>>> pastesize[1] = stepcnt_y;
>>>>>
>>>>> if(cnt_x == 0)
>>>>> {
>>>>> pastestart[0] = 0;
>>>>> }
>>>>> if(cnt_y == 0)
>>>>> {
>>>>> pastestart[1] = 0;
>>>>> }
>>>>>
>>>>> pasteregion.SetIndex(pastestart);
>>>>> pasteregion.SetSize(pastesize);
>>>>>
>>>>> pasteFilter->SetSourceRegion(pasteregion);
>>>>> pasteFilter->SetDestinationIndex(destinationIndex);
>>>>>
>>>>> try
>>>>> {
>>>>> pasteFilter->Update();
>>>>> }
>>>>> catch( itk::ExceptionObject & err )
>>>>> {
>>>>> std::cerr << "ExceptionObject caught !" << std::endl;
>>>>> std::cerr << err << std::endl;
>>>>> return EXIT_SUCCESS;
>>>>> }
>>>>> }
>>>>> typedef itk::GradientToMagnitudeImageFilter< OutputImageType,
>>>>> ImageType > MagFilterType;
>>>>> MagFilterType::Pointer magfilter = MagFilterType::New();
>>>>>
>>>>> magfilter->SetInput(vec_image);
>>>>>
>>>>> try
>>>>> {
>>>>> magfilter->Update();
>>>>> image = magfilter->GetOutput();
>>>>> }
>>>>> catch( itk::ExceptionObject & err )
>>>>> {
>>>>> std::cerr << "ExceptionObject caught !" << std::endl;
>>>>> std::cerr << err << std::endl;
>>>>> return EXIT_SUCCESS;
>>>>> }
>>>>>
>>>>> }
>>>>>
>>>>> getch();
>>>>> return EXIT_SUCCESS;
>>>>> }
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.html
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
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>>
>
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