[Insight-users] ImageSeriesReader memory allocation for large datasets

[Luis Ibanez]

Hi Marius,



    Could you please help us to track this problem ?



Please do the following:


Edit the file:

    Insight/Code/Common/itkImportImageContainer.txx

and in lines 182 - 196 you will find the following code:

   try
     {
     data = new TElement[size];
     }
   catch(...)
     {
     data = 0;
     }
   if(!data)
     {
     // We cannot construct an error string here because we may be out
     // of memory.  Do not use the exception macro.
     throw MemoryAllocationError(__FILE__, __LINE__,
                                 "Failed to allocate memory for image.",
                                 ITK_LOCATION);
     }



Could you please add a print out for the value of "size" in line 183,

    std::cout << "Number of pixels requested = " << size << std::endl;

and also add a printout for the sizeof(TElement), just to make sure
that we know how much a pixel is taking in memory:

    std::cout << "Bytes per pixel = " << sizeof(TElement) << std::endl;




Then attempt to load your series again....


Please let us know what numerical values you get from these two
print outs.



      Thanks


         Luis



-------------------
Marius Erdt wrote:
> Hello Luis,
> 
> I'm using a 32-Bit windows, but the process memory limit should not be a 
> problem since the data consumes just about 500 Mb in total. The data is 
> not copied or processed in advance, but just loaded using the itk image 
> series reader.
> 
> The number of pixels of my data is 573x330 in all slices. However, I 
> experience the same problem when loading big medical data sets of 
> 512x512. I don't know if it is maybe a problem with the total amount of 
> slices that can be handled by the itk image series reader or if it is 
> another issue.
> Does anyone know if the itk reader has some built in memory limit?
> 
> Regards,
> Marius
> 
> 
> Luis Ibanez wrote:
> 
>> Are you running this in a Windows 64 bits machine ?
>>
>> Otherwise, Windows 32 processes can only manage 2Gb of RAM
>> regardless whether you have more RAM available in your machine.
>>
>> BTW: you mention the number of slices, and the number of bits
>>      per pixel, but not the number of pixels per slice.
>>      Could you please clarify ?
>>
>>>
>>> I'm getting the following memory allocation error together with the 
>>> itk::ImageSeriesReader when loading series of png images:
>>>
>>> d:\itk\src\insighttoolkit-3.4.0\code\common\itkImportImageContainer.txx:188: 
>>>
>>> Failed to allocate memory for image.
>>>
>>> However, the data (about 1000 slices of 16Bit png or ~560 Mb) should 
>>> fit into main memory (4Gbyte). Since the data is just loaded, the 
>>> Windows data allocation limit for a single process should also not be 
>>> the problem.
>>>
>>> I'm experiencing this behavior not just for png images but for all 
>>> big datasets I want to load with itk. Does anyone know what exactly 
>>> the problem is or how to load such big data sets with itk?
>>>
>>> Thanks for help,
>>> Marius
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>
> 
>