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

[Simon Rit]

Hi,
Python is probably easier indeed.
The stochastic part is for scatter and secondary radiations (compton,
rayleigh and fluorescence). FFD uses a low statistics Monte Carlo
simulation (therefore stochastic) and combines it with a deterministic
calculation. Useful unordered references to understand the technique:
dx.doi.org/10.1088/0031-9155/54/12/016
dx.doi.org/10.1109/TMI.2004.825600
doi.org/10.1109/TNS.2005.858223
1000 is not sufficient, I typically use 10^5 photons at least for one
projection. The best is to record the uncertainty image to have an estimate
of the precision of your Monte Carlo simulation (using the
*enableUncertaintySecondary* option). You'll probably want to limit the
number of pixels of your projection to accelerate the computation of your
scatter images. I typically use finer lattices for primary images than for
scatter images.
Simon


On Thu, Feb 9, 2017 at 1:11 PM, Triltsch, Nicolas <nicolas.triltsch at tum.de>
wrote:

> 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> 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
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>
>
> --
> 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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