Hi, For the first line (rtksimulatedgeometry), it's already there I believe. For the second line, as I said, you need to use itkChangeInformationImageFilter and set the origin and spacing of the projections equal to those given by newspacing and neworigin. Simon
On Wed, Jan 13, 2021 at 9:51 AM Lai Yao Hao <yao_hao...@hotmail.com> wrote: > Hi Simon > > Thank you so much for your help; the reconstructed image is almost similar > to the image you sent (see attached file). In the previous email, for the > command lines > rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo > 278.044+372.528 | bc -l) -f 6.3 > rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 > --neworigin $(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512 > how do I get this line into the test.cxx file? If there is no way to get > these lines into the test.cxx file, then do I run these lines in the > terminal? > > Look forward for your favourable reply. > > With thanks > lyh > > > ------------------------------ > *From:* Simon Rit <simon....@creatis.insa-lyon.fr> > *Sent:* Tuesday, January 12, 2021 4:22 AM > *To:* Lai Yao Hao <yao_hao...@hotmail.com> > *Cc:* rtk-users@public.kitware.com <rtk-users@public.kitware.com> > *Subject:* Re: [Rtk-users] FirstReconstruction questions > > Hi lyh, > I had a look at what you've sent. I obtain a first result with the > following command lines: > rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo > 278.044+372.528 | bc -l) -f 6.3 > rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 > --neworigin $(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512 > The newspacing and neworigin options set the projections spacing and > origin with the ChangeInformationImageFilter. The result is not perfect, I > believe the geometry is not right yet. Maybe there is a detector offset > you're not aware of? But your text file indicate no offset so I don't know > what's wrong. Attached is a snapshot. There are also some dead pixels which > you could try to prefilter. > I hope this helps. Cheers, > Simon > > On Tue, Jan 5, 2021 at 5:35 PM Lai Yao Hao <yao_hao...@hotmail.com> wrote: > > Hi, > I cannot send the projections via email as the projections are too big in > size. Instead, I am sharing the files on Drive, with the hyperlink as > below. In the folder, there is a subset of 100 projections out of the 800 > projections, with the angle between each projection being 3.6 degrees. > There are other details on the projects as listed in report.txt file in the > folder. > > Google drive share link: > > https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing > > Regards > lyh > ------------------------------ > *From:* Simon Rit <simon....@creatis.insa-lyon.fr> > *Sent:* Tuesday, January 5, 2021 5:21 PM > *To:* Lai Yao Hao <yao_hao...@hotmail.com> > *Cc:* rtk-users@public.kitware.com <rtk-users@public.kitware.com> > *Subject:* Re: [Rtk-users] FirstReconstruction questions > > 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_hao...@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....@creatis.insa-lyon.fr> > *Sent:* Wednesday, December 30, 2020 9:35 PM > *To:* Lai Yao Hao <yao_hao...@hotmail.com> > *Cc:* rtk-users@public.kitware.com <rtk-users@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_hao...@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....@creatis.insa-lyon.fr> > *Sent:* Wednesday, December 9, 2020 4:23 PM > *To:* Lai Yao Hao <yao_hao...@hotmail.com> > *Cc:* rtk-users@public.kitware.com <rtk-users@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_hao...@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 > _______________________________________________ > Rtk-users mailing list > Rtk-users@public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > >
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