[Rtk-users] Blurred piece-wise reconstruction
vincent
vl at xris.eu
Thu Feb 13 09:13:54 EST 2020
Hi Chao, hi Simon,
I have to admit that I heavily use the computer on multitasking mode.
I'll make sure that enough RAM is available and test again under the
same conditions.
Thank you for your help,
Vincent
On 13.02.20 15:09, Chao Wu wrote:
> Ah, right, I see. itk::MemoryAllocationError.
> So maybe less than 30 GB RAM is available at that moment...
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> 于2020年2月13日周四
> 下午12:26写道：
>
> 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/20200213/8f778a44/attachment.html>
More information about the Rtk-users
mailing list