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

[Triltsch, Nicolas]

Hey Simon,

Thanks for your always very helpful answers. For your last point, I 
found out a little work around. I used an alias of the form "Gate 
[rot_angle,$(angle*i)][run_id,$i] mymacro.mac" combined with a for loop 
with parameter i. In the macro I named the files in the output folder 
"output_files{i}". I can highly recommend not to use bash scripts to 
execute the Gate commands which where created in a for loop style. 
Defining variables (especially floats, etc.) is quite handy. It's better 
to use a python script and execute the Gate macros in a so called 
subprocess.call(), multiprocessing module is required here.

Some more questions popped up my mind while I was reading your email.

- I think you didn't understood me correctly. I used 1000 photons per 
projection, not in total. I am NOT only interested in the primary image, 
but also in the images compton.mha and rayleigh.mha. Where in the 
calculation comes the NOT deterministic part? And do you have any 
experience how many photons are necessary for a trustworthy result?

Thanks in advance,

Nico

On 02/07/2017 05:37 PM, Simon Rit wrote:
> 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 <mailto: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 <tel:+49%2089%2028912591>
>
>     nicolas.triltsch at tum.de <mailto:nicolas.triltsch at tum.de>
>     www.e17.ph.tum.de <http://www.e17.ph.tum.de>
>
>
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>

-- 
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

nicolas.triltsch at tum.de
www.e17.ph.tum.de

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