[Insight-developers] Trying to minimize the memory needed by itkImageFileReader

[Luis Ibanez]

Hi Roger,

Looking at the code, there are three cases:

A) When not pixel buffer conversion is needed

B) Conversion is needed due to mismatch of
     number of components.

C) Buffering is needed because the number of
     pixels read doesn't match the number of
     expected pixels.

============================

In case A, the allocations are, in order:

a) AllocateOutputs()
b) Inside the GDCM reader.

then (b) is copied into (a).

This seems to be the common case for
a DICOM reading, and it is only allocating
two buffers.  Is this the case that gives you
the most concern ?


============================

In case B, the allocations are, in order:

a) AllocateOutputs()
b) loadBuffer
c) Inside the GDCM reader.

Then (c) is copied into (b), and
then (b) is converted/copied into (a)


============================

In case C, the allocations are, in order:

a) AllocateOutputs()
b) loadBuffer
c) Inside the GDCM reader.

Then (c) is copied into (b), and
then (b) is converted/copied into (a)


===============================
===============================

Potential options for saving memory are:


Case A:

Tell GDCM to use the ITK output buffer as
the place to read the image in the first place.

Case B & C:

Destroy the ImageIO after the Read() call,
or add an API to flush its internal memory.

=================================


    Luis



------------------------------------
On Mon, Apr 11, 2011 at 2:24 AM, Roger Bramon Feixas
<rogerbramon at gmail.com> wrote:
> Hi Luis,
> Yes, it's another issue. It's a problem of itkImageFileReader instead of
> itkImageSeriesReader.
> Let me know if it's not so well explained.
> Thanks,
> Roger
>
> On Mon, Apr 11, 2011 at 12:45 AM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Roger,
>>
>> It this different from what this patch was fixing ?:
>>
>> http://review.source.kitware.com/#change,1248
>>
>> Please let us know,
>>
>>
>>     Thanks
>>
>>
>>           Luis
>>
>>
>> ------------------------------------------
>> On Tue, Apr 5, 2011 at 3:32 AM, Roger Bramon Feixas
>> <rogerbramon at gmail.com> wrote:
>> > Hi,
>> > I'm trying to minimize the memory needed at the same time to read a
>> > DICOM
>> > file using itkImageFileReader. Basically, the problem is related with
>> > the
>> > pixel type chosen. I always use "signed short" because I actually work
>> > with
>> > CT and MR but sometimes GDCMImageIO chooses another pixel type and a
>> > conversion has to be done. It means that when GDCMImageIO is reading, 3
>> > buffers are allocated:
>> > - Buffer allocated by this->AllocateOutputs(); in
>> > ImageFileReader::GenerateData() (line 370 of itkImageFileReader.txx)
>> > - Buffer allocated by loadBuffer = new char[ sizeOfActualIORegion ]; in
>> > ImageFileReader::GenerateData() (line 414 of itkImageFileReader.txx)
>> > - Buffer allocated by reader.Read() in GDCMImageIO::Read of
>> > itkGDCMImageIO.cxx
>> > but not all of them are used at the same time. I mean, the memory needed
>> > to
>> > the outputs is allocated at the top of ImageFileReader::GenerateData()
>> > when this->AllocateOutputs() is called. However, if a conversion has to
>> > be
>> > done, this buffer is used after reading since the buffer used
>> > is loadBuffer.
>> > Could be possible to allocate the output memory after the reading (if a
>> > conversion is needed)? It would allow us to have 2 buffers instead of 3
>> > at
>> > the same time and it would be great to minimize memory problems reading
>> > huge
>> > multiframes DICOM files which are really common.
>> > I hope you understand my problem.
>> > Thanks,
>> > Roger
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