[Rtk-users] Blurred piece-wise reconstruction

[Simon Rit]

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 <vl at xris.eu> 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 <vl at xris.eu> 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 <vl at xris.eu> 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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