[Insight-users] Computing Hessian Matrix of Large Image

[Jianxu Chen]

Hello Kevin,

Really appreciate your suggestion. I found that  "SetNumberOfStreamDivisions"
is really powerful when handling large data.

For the Hessian Matrix Filter, I noticed that this problem had already been
discussed via the maillist in 2008.


http://www.itk.org/pipermail/insight-users/2008-June/026328.html

Some tests were conducted there. It showed that it might fail to allocate
memory for the Hessian matrix even when there should be enough space
theoretically.

Anyway, your suggestion of using SetNumberOfStreamDivisions is very useful.
My problem can be solved.

Thanks again for your help.
Jianxu Chen

On Tue, Nov 6, 2012 at 9:26 AM, Kevin H. Hobbs <hobbsk at ohio.edu> wrote:

> On 11/04/2012 03:50 PM, Jianxu Chen wrote:
> > Hello,
> >
> > I encountered a weird problem when computing the Hessian Matrix of a 3D
> > image stack.
> >
> > I used HessianRecursiveGaussianImageFilter to compte the Hessian matrix.
> > However, this filter only works well when the image is very very small.
> >
> > My data is a 1024*1024*30 image stack. When calling
> > HessianRecursiveGaussianImageFilter to calculate the Hessian matrix, the
> > system cannot allocate the memory space for it. Thus, I cut my data into
> > a 350*350*30 image stack. The program works well. My computer has a 8GB
> > RAM and is a 64-bit machine. I am wondering why the system fails to
> > allocate the memory for the filter. There should be enough usable RAM in
> > the machine.
>
> If your data are unsigned char : 1024*1024*100 / 2^20 = 100 MiB.
> If your data are floats : 1024*1024*100 * 4 / 2^20 = 400 MiB.
> If your data are doubles : 1024*1024*100 * 8 / 2^20 = 800 MiB.
>
> The Hessian matrix is symmetric so only 6 values are required :
>         1024*1024*100 * 8 * 6 / 2^30 = 4.69 GiB.
>
> If you have a long pipeline your image could be in memory in many places.
>
> >
> > My data is at least 1024*1024*30, sometimes even 1024*1024*100. And I
> > have to compute the Hessian matrix in my algorithm. What should I do in
> > this case? Could you give my some advice? Really appreciate your help.
> >
>
> Shorten your pipeline. Reader => Filter => Writer.
>
> Set the ReleaseDataFlag or GlobalReleaseDataFlag so that filters free
> their data after satisfying downstream requests.
>
> Stream your pipeline :
>         writer->SetNumberOfStreamDivisions( n );
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20121106/81acbe62/attachment.htm>