[Rtk-users] Blurred piece-wise reconstruction

[vincent]

Hi Simon,

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.

Many thanks for your help and suggestions !

Kindest regards,

Vincent

On 12.02.20 09:27, Simon Rit wrote:
> 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 
> <mailto: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
>>     <mailto: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
>>>         <mailto: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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