[Insight-users] Performance issues for single slices

[Nils Hanssen]

Hi Luis,

thanks for the detailed answer. Sounds very plausible :)

I changed the pipeline to use 2D-images and the calculation time for the
gradient magnitude reduced to 29 sec (before: 39 sec) for the 1984x1024
float image.

Is that the typical computation time for images of that size?


Regards,
Nils




> Hi Nils,
>
> It is actually surprising that the pipeline
> ran at all  :-)
>
> When you configure a 3D pipeline and feed it
> with a degenerate volume ( a single sliced
> volume), you risk to have trouble with any/all
> of the filters requiring neighborhood information.
> Since these filters look for data in the neighbor
> slices (which happen not to exist in your case).
>
> ITK filters based on the neighborhood iterator
> will be able to manage the degenerate volume but
> at the price of spending most of the computing
> time checking for boundary conditions.
>
> It is unlikely that LevelSet filters will be able
> to process correctly a degenerate volume. These
> filters solve a PDE using finite differences and
> should be attempting to look for data in the
> (again, unexisting) neighbor slices.
>
> In order to get a reasonable speed in 2D,
> and a consistent processing of your data,
> you better instantiate a native 2D pipeline.
>
> If you really want to factorize your programming
> efforts and have a 2D and a 3D  pipeline, the
> simple way to go is to create a class holding
> your entire pipeline, and template this class
> over the image dimension. Then, in your application,
> you instantiate this class for both 2D and 3D, and
> at load time you switch from one pipeline to another.
>
>
>
> Regards,
>
>
>
>     Luis
>
>
> ----------------------------
> Nils Hanssen wrote:
> > Hi,
> >
> > I put together a small application with a level-set pipeline on
> > volumetric medical data. The scalar type of the images is float.
> > When I run the filters on a volume that consists of one
> slice only, the
> > computation time is increasing significantly. The measured times
> > (compiled in release) are:
> >
> > Volume #1 (256x256x256 voxels):
> > Gradient magnitude: 6.6 sec.
> >
> > Volume #2 (1984x1024x1 voxels):
> > Gradient magnitude: 39.9 sec.
> >
> >
> > Should I expect that the computation time is much lower if I use a
> > 2-dimensional image for the slice images? The points is
> that I want to
> > keep the application general; that is it should be able to
> load slices
> > and volumetric images transparently.
> >
> >
> > Thanks in advance,
> > Nils
> >
> > -------------------------
> > Nils Hanssen
> > Surgical Systems Laboratory
> > research center c ae sa r
> > Ludwig-Erhard-Allee 2
> > 53175 Bonn
> > fon: +49-228-9656-197
> > fax: +49-228-9656-117
> > ___http://www . caesar . de/ssl_
> >
> >
>
>
>
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