[Rtk-users] FirstReconstruction questions

[Simon Rit]

Hi,
I think the issue is that your projection images are given in the TIFF file
format which does not contain important meta information such as the origin
and the spacing of the projections. You should use ChangeInformationFilter
<https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html>
to set these. I'm guessing that the origin is currently (0,0) and since you
do not set any offsets when using AddProjection, it comes down to having
the corner of your projection aligned with the central ray (line defined by
the source and the center of rotation).
You can share projections or a subset of them if you'd like us to give it a
try with your code.
Good luck!
Simon

On Mon, Jan 4, 2021 at 4:35 PM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:

> Hi,
>
> The code is as attached. Just for further reference, I am given images as
> attached, and there are 800 of them, with 0.45 degrees separating each
> frame. The naming of the screenshots depicts the frame that it is in.
>
> Thanks in advance for the advice and help!! I really appreciate this
> community 🙂
>
> Regards
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, December 30, 2020 9:35 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> RTK cone beam reconstruction filters expect line integrals but the
> projection that you are showing seems to have the highest value in air. RTK
> automatically processes such projections with log and normalization if the
> pixels are unsigned short. Otherwise, you need to do it yourself.
> It is not clear if the geometry is correct from the reconstruction screen
> shot. The best would be to share your code if you want us to have a look.
> Simon
>
> On Mon, Dec 28, 2020 at 8:34 AM Lai Yao Hao <yao_hao777 at hotmail.com>
> wrote:
>
> Dear Simon and the RTK community
>
> Really thank you for the answer, and really sorry for the late reply. I am
> trying to reconstruct a 3d model using 800 images, rotating an object 360
> degrees using rtk::ThreeDCircularProjectionGeometry,
> rtk::ConstantImageSource and rtk:: FDKConeBeamReconstructionFilter from the
> FirstReconstruction example as well as itk::ImageSeriesReader.
>
> However, the reconstruction created is shown above in the screenshot and
> after checking all the parameters, I have no idea on how to move forward
> from here. From reading the forums, I think that I should do one more image
> filter before applying the cone beam reconstruction? However, I am not too
> sure. Please advise on the next steps that can enable me to get the 3d
> reconstruction.
>
> Thanks so much in advance and look forward to everyone's reply!!
>
> PS: the tif file is just 1 of the 800 images I am given to reconstruct the
> object
>
> Regards
> lyh
>
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, December 9, 2020 4:23 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> constantImageSource creates a constant volume. In the example, one is used
> as input of the simulation of projections of an ellipsoid (rei) and one as
> input of the reconstruction algorithm (feldkamp). fieldofview masks out
> (i.e., set to 0) voxels which are not in the field of view.
> I don't understand your screenshot either but if you use the tiff format,
> make sure you use a viewer capable of dealing with 3D tiff images (e.g.,
> vv <http://vv.creatis.insa-lyon.fr> or ImageJ).
> Simon
>
> On Wed, Dec 9, 2020 at 8:59 AM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:
>
> Hi to all the rtk-users
>
> I am a new user of rtk, and I have some questions regarding the
> FirstReconstruction example given in github. I have generated an image as
> attached, with 4 tiny ball-like drawing hanging from the top. Can anyone
> explain to me why do I get such image and what are the implications of
> constantImageSource, rei, constantImageSource2, feldkamp and fieldofview?
>
> Your explanation will be much appreciated. Thanks in advance!
>
> Regards
> lyh
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