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 <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (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 >>> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also >>> available from Varian bitbucket along a with a python version and a >>> C#->matlab plugin >>> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). >>> 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 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
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