[Rtk-users] About Kaiser-Bessel Filter
Simon Rit
simon.rit at creatis.insa-lyon.fr
Wed Nov 19 09:02:25 EST 2014
Yes! Try "-f CudaRayCast -b CudaVoxelBased".
Simon
On Wed, Nov 19, 2014 at 2:50 PM, Guangming Zang <guangming.zang at kaust.edu.sa
> wrote:
> Yes, thanks for your prompt reply.
> what i want is to figure out how to set -f and -b to get i fastest
> reconstruction (not -p,sorry for my mistake.). and in -b. which one is
> related to our trilinear interpolation, CudaRayCast?? thanks
> Best
>
> *Guangming Zang (Alex)*
> *King Abdullah University of Science and Technology(KAUST)*
> *University of Chinese Academy of Sciences(UCAS)*
>
>
> 2014-11-19 16:40 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> Hi,
>> I think you are looking at the code generated by gengetopt for the
>> rtksart application. In general, it's simpler to simply do "rtksart --help"
>> when you want to find out how to use a parameter. You will then find the
>> following help section
>> Projectors:
>> -f, --fp=ENUM Forward projection method (possible
>> values="Joseph", "RayCastInterpolator",
>> "CudaRayCast" default=`Joseph')
>> -b, --bp=ENUM Back projection method (possible
>> values="VoxelBasedBackProjection",
>> "Joseph",
>> "CudaVoxelBased", "NormalizedJoseph"
>> default=`VoxelBasedBackProjection')
>> That should answer your question rtksart -b CudaVoxelBased. -p is the
>> option for the path where the program will look for your projection images.
>> Simon
>>
>> On Wed, Nov 19, 2014 at 2:26 PM, Guangming Zang <
>> guangming.zang at kaust.edu.sa> wrote:
>>
>>> Hi,Simon and Chao,
>>> i want to test the cuda performance in SART algorithm.
>>> but when i looked in the parameters in forwardprojection and
>>> backprojection. i got the enum:
>>>
>>> enum enum_fp { fp__NULL = -1, fp_arg_Joseph = 0,
>>> fp_arg_RayCastInterpolator, fp_arg_CudaRayCast };
>>> enum enum_bp { bp__NULL = -1, bp_arg_VoxelBasedBackProjection = 0,
>>> bp_arg_Joseph, bp_arg_CudaVoxelBased, bp_arg_NormalizedJoseph };
>>>
>>> So if i want to use the trilinear intrtpolation forwardprojection you
>>> mentioned , how should i set the -b and -p in SART? or how to choose -b and
>>> -p that i can get a fastest reconstruction in SART in this case??
>>>
>>> thanks for your help in advance.
>>> Best
>>> Guangming
>>>
>>> *Guangming Zang (Alex)*
>>> *King Abdullah University of Science and Technology(KAUST)*
>>> *University of Chinese Academy of Sciences(UCAS)*
>>>
>>>
>>> 2014-11-18 19:47 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>>>
>>>> The trilinear version is available with CUDA:
>>>>
>>>> http://www.openrtk.org/Doxygen/classrtk_1_1CudaForwardProjectionImageFilter.html
>>>> Simon
>>>>
>>>> On Tue, Nov 18, 2014 at 5:43 PM, Guangming Zang <
>>>> guangming.zang at kaust.edu.sa> wrote:
>>>>
>>>>> Hi Chao,
>>>>> Thanks very much for your prompt and so kind reply.
>>>>> I will recheck the process of setting carefully with your suggestions
>>>>> and a short report may be given later.
>>>>> BTW, do you have any plan recently to add other interpolation
>>>>> filter(e.g.Kaiser-Bessel or Trilinear)??
>>>>> Thanks for your time.
>>>>> Regards
>>>>> Guangming
>>>>>
>>>>>
>>>>>
>>>>> 2014-11-18 19:09 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:
>>>>>
>>>>>> Hi Guangming,
>>>>>>
>>>>>> To reconstruct a volume from a series of tiff files you have to let
>>>>>> the algorithm know the geometrical relationship among the source, the
>>>>>> volume and the projections stored in the tiffs. The idea is the same: RTK
>>>>>> uses projection matrices and image coordinates to understand the
>>>>>> positioning of those projections. The projection matrices are based on a
>>>>>> lot of geometrical parameters like gantry angle, source position, detector
>>>>>> position, in-plane and out-of-plane rotation angles of the detector etc. I
>>>>>> won't go though all since most of them have no differences if you use tiff
>>>>>> files or whatever format as input. I focus on some tiff tips.
>>>>>>
>>>>>> In the simplest situation, the tiff files contain correct resolution
>>>>>> (DPI) information, then you need to do nothing on these files. You have to
>>>>>> specify the correct detector offset though, since in the tiff image
>>>>>> coordinates the origin is the first pixel (corner pixel) which is
>>>>>> apparently not the intersection of the central ray and the detector. The
>>>>>> detector offsets in x and y actually mean the position of the image origin
>>>>>> (the first pixel) in the coordinate system centred at the intersection.
>>>>>> Since the direction cosines is an identity matrix and pixel sizes are
>>>>>> positive, the detector offsets in x and y will be negative.
>>>>>>
>>>>>> If the resolution information of the tiff files is not correct, you
>>>>>> have to rewrite this information. You can of course perform a
>>>>>> pre-processing to change the DPI of all tiff files with a third-party
>>>>>> software, or you can alter the RTK code to allow such changes after reading
>>>>>> the images, by using a itk::ChangeInformationImageFilter filter.
>>>>>>
>>>>>> Another non-geometrical issue with tiff files is that when their
>>>>>> integer pixel values are converted into attenuation, the maximum possible
>>>>>> integer is used as the reference value. This may not be correct in
>>>>>> practice, e.g. in your 16-bit tiffs you use 62000 to represent air (no
>>>>>> attenuation) leaving the integer range from 62001 to 65535 for statistical
>>>>>> fluctuation. If for instance you only use the lower 14 bits for your data
>>>>>> then this problem is more severe. For sure you can correct this by changing
>>>>>> the code and specify the correct reference value.
>>>>>>
>>>>>> Hope these can help.
>>>>>>
>>>>>> Regards,
>>>>>> Chao
>>>>>>
>>>>>> 2014-11-18 15:09 GMT+01:00 Guangming Zang <
>>>>>> guangming.zang at kaust.edu.sa>:
>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> *Guangming Zang (Alex)*
>>>>>>> *King Abdullah University of Science and Technology(KAUST)*
>>>>>>> *University of Chinese Academy of Sciences(UCAS)*
>>>>>>>
>>>>>>>
>>>>>>> 2014-11-18 16:46 GMT+03:00 Guangming Zang <
>>>>>>> guangming.zang at kaust.edu.sa>:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>> I am using the sart reconstruction in RTK, it works well.Thanks for
>>>>>>>> your great work.
>>>>>>>> and i was wondering do you have any plan to add other filters
>>>>>>>> except Joseph, such as Kaiser-Bessel??? ( described here
>>>>>>>> http://wscg.zcu.cz/wscg2003/papers_2003/herman.pdf)
>>>>>>>> BTW, i have read the messages sent by other users(
>>>>>>>> http://public.kitware.com/pipermail/rtk-users/2014-October/000573.html
>>>>>>>> )
>>>>>>>> but i still can not make it. can u help me and explain again about
>>>>>>>> using a series of .tiff images ans sart algorithms to get the volume.
>>>>>>>> Thanks in advance
>>>>>>>> Best
>>>>>>>> *King Abdullah University of Science and Technology(KAUST)*
>>>>>>>> *University of Chinese Academy of Sciences(UCAS)*
>>>>>>>>
>>>>>>>>
>>>>>>>
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