[Insight-developers] Trying to avoid an extra copy reading files using itkImageSeriesReader

[Luis Ibanez]

Hi Roger,

Thanks for pointing this out.

The ImageFileReader could indeed be told to load the image
buffer directly into a subset of the larger output image that
is going to be produced by the ImageSeriesReader.

This is done with code along the lines of:

reader->GetOutput()->GetPixelContainer()->SetImportPointer(
                    pixelData,
                    totalNumberOfPixels,
                    filterWillDeleteTheInputBuffer );


However, this will only work if the block of data that is
being loaded with the ImageFileReader corresponds to a
contiguous block of memory in the output image of the
ImageSeriesReader.

This will be the case int the common scenario of a 3D
image being loaded by reading a collection of 2D slices.

But, will not work if the mapping from files in the series
does not satisfy this requirement in the memory of the
output image. I'm suspecting that some scenarios of
streaming may break this assumption.

One option that comes to mind is that we could
analyze the relationship between:

  ImageRegionType requestedRegion = output->GetRequestedRegion();

in line 269 of itkImageSeriesReader.txx

and the region:

    sliceRegionToRequest

as it is computed in line 285 of the same file.

looking at the computation of lines 284 and 285
it would seem that the output region will always
be contiguous.

An initial patch for removing the copying
is now available in Gerrit:

http://review.source.kitware.com/#change,1248

It probably needs more testing before we merge it...

If you have some time available, it will be great
if you try that modified file in your test case, and
let us know if it addressed the concern for speed.


    Thanks


         Luis


-------------------------------------------------
On Wed, Mar 23, 2011 at 8:27 AM, Roger Bramon Feixas
<rogerbramon at gmail.com> wrote:
> Hi,
> I'm developing with ITK 3.20 + GDCM 2.0.17 + VTK 5.6 and I've noticed
> itkImageSeriesReader is ~2x slower than vtkGDCMImageReader (from GDCM2). I
> compared both codes and I think the difference is the extra copy which
> itkImageSeriesReader makes from ImageFileReader's output to its own output
> (ImageSeriesReader::GenerateData() line 393). I've commented it just to test
> the time needed without making the copy and now both readers take more or
> less the same time.
> Is there a way to avoid the copy? I mean, could ImageFileReader write into
> the itkImageSeriesReader's output allocated memory directly? It's quite
> dramatic for huge series.
> I've also attached a test program if someone want to test it.
> Thanks for your attention,
> Roger
>
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