Hi Chao, hi Simon,
I have to admit that I heavily use the computer on multitasking mode.
I'll make sure that enough RAM is available and test again under the
same conditions.
Thank you for your help,
Vincent
On 13.02.20 15:09, Chao Wu wrote:
Ah, right, I see. itk::MemoryAllocationError.
So maybe less than 30 GB RAM is available at that moment...
Simon Rit <[email protected]
<mailto:[email protected]>> 于2020年2月13日周四
下午12:26写道：
Well, the error was a CPU memory error, not a GPU error. But that
should have fitted in RAM, I'm not sure why it didn't.
On 2/12/20 1:20 PM, Chao Wu wrote:
But streamerBP uses CPUOutputImageType so the 30Go is allocated
on RAM instead of GRAM, so shouldn't be a problem...
Regards, Chao
Simon Rit <[email protected]
<mailto:[email protected]>> 于2020年2月12日周三
上午9:28写道：
Actually, the way I have implemented the streaming, it still
allocates the 30Go complete volume and compute it piece by
piece. One thing you could try is to remove the streamerBP
object, connect directly the reconstruction to the writer
"writer->SetInput(pfeldkamp->GetOutput());" and set the
streaming in the writer
"writer->SetNumberOfStreamDivisions(args_info.divisions_arg);".
Then it never allocates the whole volume in memory. If that
works for you, I think you can open a PR on github with this
change, that makes a lot more sense in my opinion.
On Tue, Feb 11, 2020 at 8:46 PM vincent <[email protected]
<mailto:[email protected]>> wrote:
Hi Simon,
yes, I used both in my command line. I have 64 Go RAM on
the machine, so that shouldn't be the issue. For the
sake of completeness, I also tried the subset option in
combination with the divisions option, going as low as 1,
but to no avail.
I'll investigate further tomorrow.
Thank you again for your help,
Vincent
On 2020-02-11 8:08 p.m., Simon Rit wrote:
Have you tried the combination of both? To be clear,
--divisions acts on the reconstructed volume so it
should be ~7 Go with the "--divisions 4" option (instead
of 2000*2000*2000*4/1024/1024/1024=29.8 Go otherwise).
The --lowmem option acts on the projections and you have
250 Mo (instead of 2048*2048*1500*4/1024/1024/1024=23.4
Go otherwise).
The message "Failed to allocate memory for image" seems
to be a CPU memory issue. Are you sure you have about 10
Go available to run this reconstruction?
On Tue, Feb 11, 2020 at 7:31 PM vincent <[email protected]
<mailto:[email protected]>> wrote:
Hi Simon,
I am afraid I forgot to mention something in my last
email. I tried to use the lowmem option, as you
suggested a while ago in the list for the same
problem, but I am afraid I am still getting the same
error.
kind regards,
Vincent
On 11.02.20 17:36, Simon Rit wrote:
Hi Vincent,
There is a way to do such a thing in rtkfdk with
the --divisions option, see code here
<https://github.com/SimonRit/RTK/blob/master/applications/rtkfdk/rtkfdk.cxx#L190-L196>.
I also don't really understand either what's going
on in your bottom reconstruction, it seems to be a
geometric problem. Have you checked an axial slice?
Simon
On Tue, Feb 11, 2020 at 4:21 PM vincent <[email protected]
<mailto:[email protected]>> wrote:
Hello RTK community,
I am afraid that my question might not be
directly related to the
excellent implementation we are all using, but
it might still be
interesting for some of you.
I have a stack of 1500 projections of size
2048*2048. I obviously can't
reconstruct the full resolution volume on my
graphics card, as it is too
big. So my solution was to split the sinogram
into N parts, for which
each reconstructed volume would fit in my GPU
memory and then reassemble
them. I did a test with a 700*820*900
sinogram, that I cut in two parts
of 700*410(+a small overlap)*900.
While the reconstruction of the whole volume
was acceptable, I got a
weird issue with the split ones: the one
corresponding to the top of the
image is also ok, but the bottom one is very
blurry. The three images
can be found at the following links:
https://ibb.co/vLk9ZhQ
https://ibb.co/m4pm0LT
https://ibb.co/Jyf1yKM
I used the same calibration parameters for the
three reconstruction. I
visually checked the split sinograms and they
looked fine.
Any insight will be much appreciated !
Thanks in advance,
kindest regards,
Vincent
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