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<p>Well, it worked this time....</p>
<p>V.<br>
</p>
<div class="moz-cite-prefix">On 13.02.20 15:13, vincent wrote:<br>
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cite="mid:c537d2c4-e46b-fc68-43db-cd4212540f23@xris.eu">
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<p>Hi Chao, hi Simon,</p>
<p>I have to admit that I heavily use the computer on multitasking
mode.</p>
<p>I'll make sure that enough RAM is available and test again
under the same conditions.</p>
<p>Thank you for your help,</p>
<p>Vincent<br>
</p>
<div class="moz-cite-prefix">On 13.02.20 15:09, Chao Wu wrote:<br>
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<div dir="ltr">Ah, right, I see. itk::MemoryAllocationError.
<div>So maybe less than 30 GB RAM is available at that
moment...</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Simon Rit <<a
href="mailto:simon.rit@creatis.insa-lyon.fr"
moz-do-not-send="true">simon.rit@creatis.insa-lyon.fr</a>>
于2020年2月13日周四 下午12:26写道：<br>
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<p>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.<br>
</p>
<div>On 2/12/20 1:20 PM, Chao Wu wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">But streamerBP uses CPUOutputImageType so
the 30Go is allocated on RAM instead of GRAM, so
shouldn't be a problem...
<div><br>
</div>
<div>Regards, Chao</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Simon Rit <<a
href="mailto:simon.rit@creatis.insa-lyon.fr"
target="_blank" moz-do-not-send="true">simon.rit@creatis.insa-lyon.fr</a>>
于2020年2月12日周三 上午9:28写道：<br>
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<div dir="ltr">
<div>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.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Feb 11,
2020 at 8:46 PM vincent <<a
href="mailto:vl@xris.eu" target="_blank"
moz-do-not-send="true">vl@xris.eu</a>>
wrote:<br>
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<p>Hi Simon,</p>
<p>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.</p>
<p>I'll investigate further tomorrow.</p>
<p>Thank you again for your help,</p>
<p>Vincent<br>
</p>
<div>On 2020-02-11 8:08 p.m., Simon Rit wrote:<br>
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<blockquote type="cite">
<div dir="ltr">
<div>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).</div>
<div>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).</div>
<div>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?<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue,
Feb 11, 2020 at 7:31 PM vincent <<a
href="mailto:vl@xris.eu"
target="_blank" moz-do-not-send="true">vl@xris.eu</a>>
wrote:<br>
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<p>Hi Simon, <br>
</p>
<p>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.</p>
<p>kind regards,</p>
<p>Vincent<br>
</p>
<div>On 11.02.20 17:36, Simon Rit
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Vincent,</div>
<div>There is a way to do such a
thing in rtkfdk with the
--divisions option, see code <a
href="https://github.com/SimonRit/RTK/blob/master/applications/rtkfdk/rtkfdk.cxx#L190-L196"
target="_blank"
moz-do-not-send="true">here</a>.
<br>
</div>
<div>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?</div>
<div>Simon</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Tue, Feb 11, 2020 at 4:21 PM
vincent <<a
href="mailto:vl@xris.eu"
target="_blank"
moz-do-not-send="true">vl@xris.eu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hello
RTK community,<br>
<br>
I am afraid that my question
might not be directly related to
the <br>
excellent implementation we are
all using, but it might still be
<br>
interesting for some of you.<br>
<br>
I have a stack of 1500
projections of size 2048*2048.
I obviously can't <br>
reconstruct the full resolution
volume on my graphics card, as
it is too <br>
big. So my solution was to
split the sinogram into N parts,
for which <br>
each reconstructed volume would
fit in my GPU memory and then
reassemble <br>
them. I did a test with a
700*820*900 sinogram, that I cut
in two parts <br>
of 700*410(+a small
overlap)*900.<br>
<br>
While the reconstruction of the
whole volume was acceptable, I
got a <br>
weird issue with the split ones:
the one corresponding to the top
of the <br>
image is also ok, but the bottom
one is very blurry. The three
images <br>
can be found at the following
links:<br>
<br>
<a href="https://ibb.co/vLk9ZhQ"
rel="noreferrer"
target="_blank"
moz-do-not-send="true">https://ibb.co/vLk9ZhQ</a><br>
<a href="https://ibb.co/m4pm0LT"
rel="noreferrer"
target="_blank"
moz-do-not-send="true">https://ibb.co/m4pm0LT</a><br>
<a href="https://ibb.co/Jyf1yKM"
rel="noreferrer"
target="_blank"
moz-do-not-send="true">https://ibb.co/Jyf1yKM</a><br>
<br>
I used the same calibration
parameters for the three
reconstruction. I <br>
visually checked the split
sinograms and they looked fine.<br>
<br>
<br>
Any insight will be much
appreciated !<br>
<br>
<br>
Thanks in advance,<br>
<br>
kindest regards,<br>
<br>
Vincent<br>
<br>
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