[Rtk-users] Streaming filter in ProjectionsReader

[Chao Wu]

Great suggestions. I'll play with them tomorrow. Thanks.

Regards, Chao
Sent from Samsung Galaxy Note 3
2015年6月12日 12:32 AM于 "Simon Rit" <simon.rit at creatis.insa-lyon.fr>写道：

> The problem of an extract filter is that you need to set the extract
> region, I don't think that the requested region is the default. I would
> simply use an addimagefilter with a 0 constant or a multiplyimagefilter
> with a 1 constant...
>
> On Thu, Jun 11, 2015 at 11:56 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>
>> This is exactly my problem.
>>
>> There is also a parker short scan filter after the dd filter. If I move
>> the ddf then pssf shall also be moved. This may be too much change.
>>
>> If I use the CPU version of ddf, I guess the same issue will occur at
>> pssf, then I shall use CPU version of pssf as well. Sounds also a
>> suboptimal solution.
>>
>> Maybe adding an extract filter between reader and ddf is still the most
>> straightforward way? Then I guess the later extract filter in the fdk will
>> be inplace and do nothing?
>>
>> Regards, Chao
>> Sent from Samsung Galaxy Note 3
>> 2015年6月11日 11:35 PM于 "Simon Rit" <simon.rit at creatis.insa-lyon.fr>写道：
>>
>>> Sorry, I see what I missed: the whole stack projection is loaded by the
>>> displaced detector filter. I think the best would be to move the displaced
>>> detector filter in the FDKConeBeamReconstructionFilter, between the extract
>>> and the FDKWeightProjectionFilter or to roll back to the CPU displaced
>>> detector imagefilter.
>>>
>>> On Thu, Jun 11, 2015 at 11:31 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Interesting problem. First a comment: normally with mhd files, it only
>>>> reads from disk what is requested, not the whole projection. I have
>>>> implemented FDK so that it only request the lines that are necessary for
>>>> the piece of the volume that is being computed. However, the full
>>>> projection is read with some input formats that did not implement streaming
>>>> or if you use the --hannY option or the scatter glare correction. Another
>>>> comment that crosses my mind: once it's been read from disk once, if you
>>>> have enough ram, it will be cached and the second time it reads it should
>>>> be much faster, as if it were in RAM.
>>>> For your solution, I would say that it's already what it does. The
>>>> reader, the preprocessing and the streaming are encapsulated in the
>>>> rtk::ProjectionsReader so if you request the full stack from the
>>>> projections reader, i.e., without
>>>>  the --lowmem option, it will compute the whole stack but it will do it
>>>> one projection at a time since there is a streaming filter encapsulated. Is
>>>> this not what you observe? Projections will still be loaded substack per
>>>> substack to the gpu after since there is an extract filter in FDK. In
>>>> short, don't use the --lowmem option and you should be set. If not, let me
>>>> know because there is something I'm missing or not working.
>>>> Simon
>>>>
>>>> On Thu, Jun 11, 2015 at 10:52 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>>>>
>>>>> Thanks Simon, it is clear.
>>>>>
>>>>> I have an issue with rtkfdk. When using cuda, the first several
>>>>> (mini-) filters in rtkfdk look like this:
>>>>> file reader -> preprocessing filters -> streaming filter -> cuda
>>>>> displaced detector filter -> ...
>>>>> When the streaming filter is updated, all preprocessed projection data
>>>>> will be store in RAM, which is not a problem so far.
>>>>> However when executing the cuda displaced detector filter, RAM to GRAM
>>>>> copy will be triggered. In my case the GRAM is not big enough to
>>>>> store the data.
>>>>> I know --lowmem will work but when it combines with --division the
>>>>> projection files will be re-read several times from harddisk, which is
>>>>> quite inefficient and slow.
>>>>>
>>>>> My previous temporary solution is to use the streaming filter as a
>>>>> sort of isolator:
>>>>> Instead of updating the streaming filter in the first step, I only
>>>>> update the last preprocessing filter.
>>>>> This way, when updating the remaining part of the pipeline, the
>>>>> buffered region of the input of the streaming filter will be the full stack
>>>>> of projections, but the buffered region of the output of the streaming
>>>>> filter will just be the requested region by the cuda displaced detector
>>>>> filter (#subsetsize projections). Then there is no problem to copy this
>>>>> small amount of projections from RAM to GRAM during execution of the cuda
>>>>> displaced detector filter.
>>>>> Nevertheless looking at your explanations about the purpose of the
>>>>> streaming filter, I found this is not an optimal solution.
>>>>>
>>>>> Now I am thinking to add a simple filter between the streaming filter
>>>>> and the cuda displace detector filter for isolation, so that its input will
>>>>> buffer the full stack of projections after updating the streaming filter,
>>>>> but its output only buffers the requested region (#subsetsize
>>>>> projections). How do you think about this solution? Any better
>>>>> opinions?
>>>>>
>>>>> Regards,
>>>>> Chao
>>>>>
>>>>>
>>>>> 2015-06-11 19:19 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>>>>>
>>>>>> Not stupid at all. We have recently introduced the possibility to
>>>>>> automatically compute the I0 (pixel value without object). This is the
>>>>>> filter I0EstimationProjectionFilter in the ProjectionsReader, see graph in
>>>>>> doc
>>>>>> <http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html>.
>>>>>> In many scanners, the exposure varies from frame-to-frame and we wanted
>>>>>> this to be projection-specific which is why we did this. We also think that
>>>>>> all the preprocessing is more efficient per projection but this is pure
>>>>>> conjecture.
>>>>>> There were only pros in our opinion but do you see cons to this
>>>>>> solution?
>>>>>> Simon
>>>>>>
>>>>>> On Thu, Jun 11, 2015 at 7:06 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> Maybe a stupid question... what is the purpose of the streaming
>>>>>>> filter at the end of the mini-filter pipeline inside the ProjectionsReader?
>>>>>>> Thanks.
>>>>>>>
>>>>>>> Regards, Chao
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rtk-users mailing list
>>>>>>> Rtk-users at public.kitware.com
>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>
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