[Gate-users] CT simulation, save multiple outputs, parallelization

[Simon Rit]

Hi Nicolas,
Good to see that ffda is used. To answer your questions:
- yes, there is an "intrinsic parallelization". The number of threads is
set by the environment variable ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS. If
you haven't set it, it will use all your cores. The Monte Carlo part is
still single-threaded, but the ray casting is multi-threaded using RTK
(based on ITK).
- you use 1000 photons. I guess you're only interested in the primary
image? In this case, 1 photon per projection is enough since the primary
part is deterministic.
- you can use the printf format to set the run id in the file primary name
(see line 842 of GateFixedForcedDetectionActor.cc
<https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateFixedForcedDetectionActor.cc#L842>
):
/gate/actor/ffda/primaryFilename    output/primary%0d.mha
- for further parallelization, I would suggest to run Gate on several
machines, each machine starting at a different angle and over an angle
range which would be limited. This requires some specific dev and careful
handling of all the outputs (they all start with a runid of 0, so you will
need to rename the outputs).
I hope this helps.
Simon


On Tue, Feb 7, 2017 at 10:58 AM, Triltsch, Nicolas <nicolas.triltsch at tum.de>
wrote:

> Hello Gate community,
>
> I am using the fixed forced detection actor (ffda) and I try to run a full
> CT simulation with 1201 projections. My first question aims to the
> possibilities of parallelization. I noticed that if I run a single
> projection, all 4 cores of my local computer are running at almost 100%. Is
> there already some intrinsic parallelization step when using the ffda and
> what further parallelization steps are possible to speed up the simulation
> for 1 projection? If it helps I use a voxelized phantom, cone beam setup, a
> xray spectrum histogram, integrating detector and 1000 Photons.
>
> My second question is how to save several .mha images in the output folder
> when simulating all 1201 projections. Still, I am using the ffda actor and
> with the command "*/gate/actor/ffda/primaryFilename
> output/primary.mha" *the primary image gets overwritten for each
> projection. How can I save different primary images for each projection?
>
> Any help is appreciated!
>
> Nico
>
> --
> B.Sc. Nicolas Triltsch
> Masterand
>
> Technische Universität München
> Physik-Department
> Lehrstuhl für Biomedizinische Physik E17
>
> James-Franck-Straße 1
> 85748 Garching b. München
>
> Tel: +49 89 289 12591 <+49%2089%2028912591>
> nicolas.triltsch at tum.dewww.e17.ph.tum.de
>
>
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