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<p>Hi Simon,</p>
<p>I tested your suggestion and it worked fine for me. I was able
to reconstruct a volume the size of which didn't fit in memory. I
created the PR, sorry it took a little time, that was new
territory for me.</p>
<p>Many thanks for your help and suggestions !</p>
<p>Kindest regards,</p>
<p>Vincent<br>
</p>
<div class="moz-cite-prefix">On 12.02.20 09:27, Simon Rit wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAF0oig28_rkC3XMj5O=t7p2OBe3TbLkizs1WtgS+Y-k4UsYg4g@mail.gmail.com">
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<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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0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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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>
</div>
<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>
</div>
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0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
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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>
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<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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