[Rtk-users] Issue report regarding the recorder of Time elapsed
Guangming Zang
guangming.zang at kaust.edu.sa
Mon Jul 27 10:05:04 EDT 2015
Hi Simon,
it cost 1200s for SART algorithm at first, and the command are:
rtksimulatedgeometry -n 360 --arc -360 -o geometry.xml --sdd=725.9240729
--sid=500.0 --proj_iso_x="-128" --proj_iso_y="-128"
rtksart -p . -r 360pro_SL_Vol128_512.mha -g geometry.xml -o SART_SL.mha
-f Joseph -b VoxelBasedBackProjection --newspacing 0.5 --dimension
128,128,128 --spacing 1,1,1 --origin -64,-64,-64 -l 0.5 -n 1 --time 1
in which, the projections data(360pro_SL_Vol128_512.mha) is not generated
from rtkprojectshepploganphantom , but from my application. though it took
long time, but i can got a nice result,
And i just tried the command you used, i.e. generated the projections data
by rtkprojectshepploganphantom :
rtksimulatedgeometry -n 360 --arc -360 -o geo.xml --sdd=725.9240729
--sid=500.0
rtkprojectshepploganphantom -g geo.xml -o proj.mha --dimension 512
rtksart -p . -r proj.mha -g geo.xml -o SART_SLnew.mha -f Joseph -b
VoxelBasedBackProjection --newspacing 0.5 --dimension 128,128,128
--spacing 1,1,1 --origin -64,-64,-64 -l 0.5 -n 3 --time 1
yes, it takes about 56s.
but the reconstructed result is weird, the voxel values range from
[-142186, 208146] and can not see anything when visualizing it.
i believe you got the similar results, which maybe explain why it computes
much faster.
if i wanna use the projections generated by rtkprojectshepploganphantom ,
can you give me an example to get a nice results?
Best regards
Guangming
*Guangming Zang (Alex)*
*King Abdullah University of Science and Technology(KAUST)*
*University of Chinese Academy of Sciences(UCAS)*
2015-07-27 16:02 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
> No I expect forward projection to be longer than backprojection
> although with optimal implementations, it should take about the same
> time since they have the same complexity.
> I have 4 cores on my laptop. I don't see how it explains it, try to
> find out where does SART spend the time.
> Simon
>
> On Mon, Jul 27, 2015 at 2:50 PM, Guangming Zang
> <guangming.zang at kaust.edu.sa> wrote:
> > Hi Simon,
> > sorry for the mistake, not"the backprojection should take much longer
> time
> > than
> > sart algorithm" , but "the backprojection should take much longer time
> than
> > forward projection in sart algorithm".
> >
> > BTW, how many cores does your computer have?? Mine is 24 cores.
> > is it can explain the reason why it takes much longer time on my computer
> > than yours?
> > Regards
> > Guangming
> >
> > Guangming Zang (Alex)
> > King Abdullah University of Science and Technology(KAUST)
> > University of Chinese Academy of Sciences(UCAS)
> >
> >
> >
> >
> > 2015-07-27 15:28 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
> >>
> >> I can try. Forward and back projection have the same algorithmic
> >> complexity but voxel based backprojection benefits from several
> >> optimizations in terms of memory management and computations that
> >> makes it faster. The best is to look at the code for further
> >> details... although both have far from being optimal. And I did not
> >> get the sentence "the backprojection should take much longer time than
> >> sart algorithm." because SART contains a backprojection and other
> >> steps so SART is obviously longer than the bp alone.
> >> Your log is strange and I don't see what steps are not timed that
> >> would take most of the time. I did the same test on my computer and
> >> here is my result:
> >>
> >> OS-SR-466:tmp srit$ rtksimulatedgeometry -n 360 -o geo
> >> OS-SR-466:tmp srit$ rtkprojectshepploganphantom -g geo -o proj.mha
> >> --dimension 512
> >> OS-SR-466:tmp srit$ rtksart -p . -r proj.mha -g geo -o SART_SL3.mha
> >> -f Joseph -b VoxelBasedBackProjection --newspacing 0.5 --dimension
> >> 128,128,128 --spacing 1,1,1 --origin -64,-64,-64 -l 0.5 -n 3 --time
> >> 1
> >> Recording elapsed time...
> >> SARTConeBeamReconstructionFilter timing:
> >> Extraction of projection sub-stacks: 0.288571 s
> >> Multiplication by zero: 0.131672 s
> >> Forward projection: 34.3612 s
> >> Subtraction: 0.203409 s
> >> Multiplication by lambda: 0.146459 s
> >> Ray box intersection: 1.30755 s
> >> Division: 0.187294 s
> >> Multiplication by the gating weights: 0 s
> >> Displaced detector: 0.278408 s
> >> Back projection: 11.8456 s
> >> Volume update: 0 s
> >> It took... 53.2765 s
> >>
> >> Simon
> >>
> >> On Mon, Jul 27, 2015 at 10:41 AM, Guangming Zang
> >> <guangming.zang at kaust.edu.sa> wrote:
> >> > Hi Simon,
> >> > Thanks for your reply.
> >> > would you pls help and explain why backprojection is expected to take
> >> > shorter time than forward projection?? because i was thinking if no
> >> > caching
> >> > step, the backprojection should take much longer time than sart
> >> > algorithm.
> >> > yes, i run rtksart for 2 times once.it took 12xxs, similar to the
> time
> >> > consumed of 3 times's sart, which much slower than my own application.
> >> > BTW, D drive is local disk drive, and 360pro_SL_Vol128_512.mha are 360
> >> > shapp-logan projections(512*512 resolution each)
> >> > rtksart -p . -r 360pro_SL_Vol128_512.mha -g geometry.xml -o
> >> > ../Result_SL512/SART_SL3.mha -f Joseph -b VoxelBasedBackProjection
> >> > --newspacing 0.5 --dimension 128,128,128 --spacing 1,1,1 --origin
> >> > -64,-64,-64 -l 0.5 -n 3 --time 1
> >> >
> >> > and i will try reader->Update() like what you said.
> >> > Thanks
> >> > Guangming
> >> >
> >> >
> >> >
> >> > Guangming Zang (Alex)
> >> > King Abdullah University of Science and Technology(KAUST)
> >> > University of Chinese Academy of Sciences(UCAS)
> >> >
> >> >
> >> >
> >> >
> >> > 2015-07-27 8:59 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
> >> >>
> >> >> Hi Guangming,
> >> >> It's not surprising to me that the backprojection is faster than the
> >> >> forward projection, that's what I expect. If the total time is
> longer,
> >> >> that's probably that some individual steps are not included in the
> >> >> total
> >> >> time. Can you try to add
> >> >> reader->Update();
> >> >> before the line
> >> >>
> >> >> itk::TimeProbe totalTimeProbe;
> >> >>
> >> >> in rtksart.cxx? It may be that all the reading operations are done
> but
> >> >> not
> >> >> timed in the sart->Update(). Why they are so long, I don't know, is
> >> >> your D:
> >> >> drive a network drive? Do you observe the same behavior if you do
> >> >> rtksart 2
> >> >> times in a row?
> >> >>
> >> >> Simon
> >> >>
> >> >>
> >> >>
> >> >> On Mon, Jul 27, 2015 at 12:30 AM, Guangming Zang
> >> >> <guangming.zang at kaust.edu.sa> wrote:
> >> >>>
> >> >>> Hi RTK community,
> >> >>> i am using SART algorithm to reconstruct an object.
> >> >>> But in this new RTK version, the time recording seems a little
> weird:
> >> >>> the total time is 1219.12s , but adding the time cost in different
> >> >>> stages is not 1291.12 s. especially for "backprojection" part, only
> >> >>> 16.6051s
> >> >>> to reconstruct a 128^3 volume ?? even shorter than forward
> projection
> >> >>> part.
> >> >>> BTW, the -f and -b are Joseph and VoxelBasedBackProjection,
> >> >>> respectively,
> >> >>> both multi-threading i think.
> >> >>> Can anyone tell me what's going on?
> >> >>> Thanks
> >> >>> Regards
> >> >>> Guangming
> >> >>>
> >> >>>
> >> >>> Guangming Zang (Alex)
> >> >>> King Abdullah University of Science and Technology(KAUST)
> >> >>> University of Chinese Academy of Sciences(UCAS)
> >> >>>
> >> >>>
> >> >>>
> >> >>>
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