Hi, Thanks a lot! It's been merged after minor modifications but would you have one projection to share for creating a small test? You seemed to be unsure of the offsets sign, I think that a wrong sign would show up on the reconstructions. I would suggest to test it if you have time. Simon
On Fri, Nov 25, 2016 at 4:25 PM, Andreas Gravgaard Andersen <[email protected]> wrote: > Dear Simon, > > I have created a pull-request with the XIM file reader. > I'm sorry for being late with the promised pull-request (there were a lot of > merge conflicts, so it got postponed). > > I have cleaned it up, but it is still not flawless as mentioned in the > pull-request-message. > I have tried to keep the RTK coding-style by creating it as a modified HND > file reader, but I have only a year of experience with C++, so I apologize > if I've left some ugly code in there.. > > Best regards > Andreas > > > __________________________________ > > Andreas Gravgaard Andersen > > Department of Oncology, > > Aarhus University Hospital > > Nørrebrogade 44, > > 8000, Aarhus C > > Mail: [email protected] > > Cell: +45 3165 8140 > > > > 2016-11-23 18:44 GMT+01:00 Simon Rit <[email protected]>: >> >> Dear Andreas, >> Today we had the RTK training and some users were looking for a XIM file >> reader. I pointed to your contributions but any chance to have it put in RTK >> soon? >> Thanks in advance, >> Simon >> >> On Mon, Sep 19, 2016 at 9:26 AM, Simon Rit >> <[email protected]> wrote: >>> >>> Hi, >>> Thanks for sharing. There still seems to be some streak artefacts, do you >>> see the same in the Varian reconstruction? >>> I'm looking forward to the pull-request, I think we should try to make >>> the bzip2 optional. >>> Simon >>> >>> On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen >>> <[email protected]> wrote: >>>> >>>> Thanks for the fast response Simon! >>>> >>>> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were >>>> right all along! >>>> I just didn't get why it makes a difference. I think I do now, as the >>>> resulting image was flipped upside down and not left/right as I expected. >>>> [attached] >>>> >>>> The reconstruction is significantly better, I'll look into what should >>>> be included in the reader and what I should keep in my program to keep >>>> conformity with the other readers. Then I'll create a pull request. >>>> >>>> Just for the purpose of others hitting the same or a similar bug, I also >>>> attempted: >>>> I did the SART reconstruction with 10 iterations, lambda=0.3, and >>>> Joseph back/forward projection, but with no significant improvement >>>> [attached] >>>> >>>> And: >>>> If you want you can download the data set from: [Dropbox link to 460MB >>>> zip (I'll keep it up as long as Dropbox allows me)] Only the >>>> Acquisitions/subfolder is used along with the Scan.xml (Calibrations folder >>>> may be used in the future in my program, but I'm not sure if you can rely >>>> on >>>> the existence of the content). >>>> >>>> A MatLab XimReader is available: link (also available from Varian >>>> bitbucket along a with a python version and a C#->matlab plugin). Otherwise >>>> my fork with the RTK-style reader is available from the same repository (I >>>> have also added Hnc support, thanks to the Geoff Hugo fork, so bzip2 is a >>>> new dependancy). >>>> >>>> Best regards >>>> Andreas >>>> >>>> >>>> __________________________________ >>>> >>>> Andreas Gravgaard Andersen >>>> >>>> Department of Oncology, >>>> >>>> Aarhus University Hospital >>>> >>>> Nørrebrogade 44, >>>> >>>> 8000, Aarhus C >>>> >>>> Mail: [email protected] >>>> >>>> Cell: +45 3165 8140 >>>> >>>> >>>> >>>> 2016-09-16 16:13 GMT+02:00 Simon Rit <[email protected]>: >>>>> >>>>> Hi, >>>>> You can try any iterative reconstruction, they can also handle short >>>>> scans. Start with a few iterations of rtksart or rtkconjugategradient. >>>>> However, the nature of the artifacts indicate more a problem in the >>>>> geometry >>>>> in my opinion. I have seen such errors when, for example, rotating in the >>>>> wrong direction. I can have a look if you share the dataset. >>>>> Cheers, >>>>> Simon >>>>> >>>>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen >>>>> <[email protected]> wrote: >>>>>> >>>>>> Thanks for the suggestions, Simon and Cyril! >>>>>> >>>>>> I have been carefully looking though the geometry and from what I >>>>>> understand of the transformations matrices, the geometry looks >>>>>> correct/(as >>>>>> expected). >>>>>> >>>>>> HOWEVER: I found out that the reason for the Hnd to behave differently >>>>>> were because had used half-fan scans (full-arc). >>>>>> When I used a full-fan (half-arc) scan of Hnd projections the same >>>>>> artifacts occurs! >>>>>> >>>>>> Are there other (built-in) means of improving half-arc scans, than the >>>>>> parker short scan filter? >>>>>> >>>>>> Parker short scan does a decent job, but the result is still far from >>>>>> the quality of the Varian software reconstruction at least for the >>>>>> CatPhan. >>>>>> >>>>>> Best regards >>>>>> Andreas >>>>>> >>>>>> >>>>>> __________________________________ >>>>>> >>>>>> Andreas Gravgaard Andersen >>>>>> >>>>>> Department of Oncology, >>>>>> >>>>>> Aarhus University Hospital >>>>>> >>>>>> Nørrebrogade 44, >>>>>> >>>>>> 8000, Aarhus C >>>>>> >>>>>> Mail: [email protected] >>>>>> >>>>>> Cell: +45 3165 8140 >>>>>> >>>>>> >>>>>> >>>>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory >>>>>> <[email protected]>: >>>>>>> >>>>>>> One suggestion since it works with the Hnd projections: >>>>>>> You can run rtkprojections twice (with the Hnd projections, then with >>>>>>> Xim projections) and output two projection stack files and two geometry >>>>>>> files, then compare the projection stack files by subtracting one to the >>>>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If >>>>>>> they >>>>>>> are identical, then I do not see any reason why the reconstructions >>>>>>> should >>>>>>> be different, so my guess is that you will find differences. >>>>>>> >>>>>>> >>>>>>> On 09/13/2016 10:18 PM, Simon Rit wrote: >>>>>>>> >>>>>>>> Hi, >>>>>>>> I have almost never worked with Varian data but it looks like a >>>>>>>> geometry problem. Maybe the problem comes from a bad ordering of the >>>>>>>> projections which results in assigning a bad geometry to each >>>>>>>> projection. How did you name your projections? Maybe check that the >>>>>>>> order matches that of the RTK geometry file. Otherwise, there might >>>>>>>> be >>>>>>>> an issue in the creation of the geometry file itself. >>>>>>>> All this sounds good, happy bug hunt and don't hesitate to share >>>>>>>> your >>>>>>>> code when you feel it's ready. >>>>>>>> Simon >>>>>>>> >>>>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen >>>>>>>> <[email protected]> wrote: >>>>>>>>> >>>>>>>>> Dear RTK experts, >>>>>>>>> >>>>>>>>> I am reconstructing Varian ProBeam projections of the Xim image >>>>>>>>> format. I >>>>>>>>> have written the reader myself - very similar to the Hnd one >>>>>>>>> already >>>>>>>>> available with RTK. >>>>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader] >>>>>>>>> >>>>>>>>> The reader apparently works (Images and angles displays as expected >>>>>>>>> in UI), >>>>>>>>> however when reconstructing with a regular FDK I get a >>>>>>>>> reconstructed image >>>>>>>>> that is smeared out around the high and low density areas [see >>>>>>>>> attached >>>>>>>>> image] >>>>>>>>> >>>>>>>>> I'm using half arc, full fan images with no bow-tie filter from >>>>>>>>> Scripps >>>>>>>>> (~520 projections). Fixed detector and source (offset=0) with >>>>>>>>> SID=2m, >>>>>>>>> SDD=3m. >>>>>>>>> >>>>>>>>> For the Hnd projections the reconstruction works perfectly (Same >>>>>>>>> algorithm). >>>>>>>>> The reconstruction of the Xim projections performed on Varian >>>>>>>>> software works >>>>>>>>> perfectly. >>>>>>>>> >>>>>>>>> Without the Parker Short Scan Filter the first and last projections >>>>>>>>> creates >>>>>>>>> streaks across the reconstruction as if they were way too bright. >>>>>>>>> If the first few projections are excluded, the following projection >>>>>>>>> will act >>>>>>>>> the same way. >>>>>>>>> >>>>>>>>> The projections are corrected for beam hardening and all the >>>>>>>>> projections >>>>>>>>> have the expected attenuation. >>>>>>>>> No "smearing" filters (like median) is used, and iterative >>>>>>>>> reconstruction >>>>>>>>> makes the same artifacts. >>>>>>>>> >>>>>>>>> Setting the value of the first and last projection to zero has the >>>>>>>>> same >>>>>>>>> effect as excluding. Changing the ramp filter only changes noise, >>>>>>>>> not the >>>>>>>>> artifacts. >>>>>>>>> >>>>>>>>> Have any of you had a similar problem? Am I missing something? >>>>>>>>> Any suggestions are welcome I'm running out of ideas. >>>>>>>>> >>>>>>>>> Best regards >>>>>>>>> Andreas >>>>>>>>> >>>>>>>>> __________________________________ >>>>>>>>> >>>>>>>>> Andreas Gravgaard Andersen >>>>>>>>> >>>>>>>>> Department of Oncology, >>>>>>>>> >>>>>>>>> Aarhus University Hospital >>>>>>>>> >>>>>>>>> Nørrebrogade 44, >>>>>>>>> >>>>>>>>> 8000, Aarhus C >>>>>>>>> >>>>>>>>> Mail: [email protected] >>>>>>>>> >>>>>>>>> Cell: +45 3165 8140 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> [email protected] >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Rtk-users mailing list >>>>>>>> [email protected] >>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ Rtk-users mailing list [email protected] http://public.kitware.com/mailman/listinfo/rtk-users
