[Rtk-users] Blurred piece-wise reconstruction
Simon Rit
simon.rit at creatis.insa-lyon.fr
Thu Feb 13 06:28:17 EST 2020
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 <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> 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 <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
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> <mailto:Rtk-users at public.kitware.com>
>>> https://public.kitware.com/mailman/listinfo/rtk-users
>>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> <mailto:Rtk-users at public.kitware.com>
>> https://public.kitware.com/mailman/listinfo/rtk-users
>>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com <mailto:Rtk-users at public.kitware.com>
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20200213/3978a489/attachment.html>
More information about the Rtk-users
mailing list