[Rtk-users] Blurred piece-wise reconstruction

vincent vl at xris.eu
Thu Feb 13 10:56:14 EST 2020


Well, it worked this time....

V.

On 13.02.20 15:13, vincent wrote:
>
> 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
>>>>>
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>>>>>
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