[Castor-users] [Castor-devel] Fwd: Re: TR: SPECT reading Interfile

COMTAT Claude claude.comtat at cea.fr
Wed Apr 26 14:02:35 CEST 2017


Let’s N =  mtxsizI*mtxsizJ*AllAngles and S be the number of subsets where AllAngles is a multiple of S

 

Your data are considered in CASToR as a 1D vector of size N (Data(1:N)) and not as a 3D matrix (Mat(1:mtxsizI,1:mtxsizJ,1:AllAngles)). This is the confusing part.

 

When looping on the “histogram events”, CASToR will read the following events for the first subset: Data(1),Data(S+1),Data(2*S+1),Data(3*S+1), …,Data(N-S+1) 

and the following events for the second subset: Data(2),Data(S+2),Data(2*S+2),Data(3*S+2), …, Data(N-S+2).

 

If the data are written as:

 

iEvent = 1

Do J=1,mtxsizJ

  Do I=1,mtxsizI

    Do K=1,AllAngles

      I1=I

      J1=J

      K1=K

      Data(iEvent) = Mat(I1,I1,K1)

      Angle(iEvent) = K1-1

      Bin(iEvent) = MtxsizI*(J1-1)+(I1-1)   

      Write(ITime, Data(iEvent), Angle(iEvent), Bin(iEvent))   

      iEvent = iEvent + 1  

    EndDo

  EndDo

EndDo

 

 

then, Data(1) = Mat(1,1,1), Data(S+1) = Mat(1,1,S+1), Data(2*S+1) = Mat(1,1,2*S+1), Data(3*S+1)=Mat(1,1,3*S+1), … , Data(N-S+1) = Mat(mtxsizI,mtxSizJ,AllAngles-S+1)  

and Data(2) = Mat(1,1,2), Data(S+2) = Mat(1,1,S+2), Data(2*S+2) = Mat(1,1,2*S+2), Data(3*S+2)=Mat(1,1,3*S+2), …  , Data(N-S+2)= Mat(mtxsizI,mtxSizJ,AllAngles-S+2). 

 

Hope this helps,

 

Claude

 

De : Michael Ljungberg [mailto:michael.ljungberg at med.lu.se] 
Envoyé : mercredi 26 avril 2017 12:44
À : COMTAT Claude; castor-users at lists.castor-project.org
Objet : Re: [Castor-users] [Castor-devel] Fwd: Re: TR: SPECT reading Interfile

 

OK but then it does not match what you suggested previously

 

Then, first subset will contain Mat(i=0,j=0,k=0), Mat(i=0,j=0,k=N), Mat(i=0,j=0,k=2*N), … and the resulting subsets will be better balanced.

 

Hälsningar / Best regards

Michael

 

From: Castor-users <castor-users-bounces at lists.castor-project.org> on behalf of COMTAT Claude <claude.comtat at cea.fr>
Date: Wednesday, 26 April 2017 at 12:05
To: "castor-users at lists.castor-project.org" <castor-users at lists.castor-project.org>
Subject: Re: [Castor-users] [Castor-devel] Fwd: Re: TR: SPECT reading Interfile

 

Remove the loop on the subsets, and try again:

 

 

         Do J=1,mtxsizJ

          Do I=1,mtxsizI

           Do K=1,AllAngles

 

           I1=I

           J1=J

           K1=(K-1)

        

           Write(1) ITime,Mat(i1,j1,k1),

     *     (K1-1),MtxsizI*(J1-1)+(I1-1)

     

           EndDo

          EndDo

         EndDo

 

 

 

De : Castor-devel [mailto:castor-devel-bounces at lists.castor-project.org] De la part de Carlier Thomas
Envoyé : mercredi 26 avril 2017 11:02
À : castor-devel at lists.castor-project.org
Objet : [Castor-devel] Fwd: Re: [Castor-users] TR: SPECT reading Interfile

 

Je regarde quand j'aurai le temps... Si certains veulent se lancer avant => pas de soucis !

 

Thomas



-------- Message transféré -------- 


Sujet : 

Re: [Castor-users] TR: SPECT reading Interfile


Date : 

Wed, 26 Apr 2017 08:59:17 +0000


De : 

Michael Ljungberg  <mailto:michael.ljungberg at med.lu.se> <michael.ljungberg at med.lu.se>


Pour : 

Carlier Thomas  <mailto:thomas.carlier at chu-nantes.fr> <thomas.carlier at chu-nantes.fr>






Note that I have written a conversion program from SPECT interfiles too castor format. According to our discussions I create the *.cdf file from the fortran loop

 

        Do M=1,Subsets        

         Do J=1,mtxsizJ

          Do I=1,mtxsizI

           Do K=1,IAngles

 

           I1=I

           J1=J

           K1=(K-1)*Subsets+M

        

           Write(1) ITime,Mat(i1,j1,k1),

     *     (K1-1),MtxsizI*(J1-1)+(I1-1)

     

           EndDo

          EndDo

         EndDo

        EndDo

 

I hope this is write. Here is a zip file with the projections and the reconstructed images (three iterations and data organised in 16 subsets)

 

https://www.dropbox.com/s/bjvtvs7sy17skmv/castor.zip?dl=0

 

 

Hälsningar / Best regards

Michael

 

From: Castor-users  <mailto:castor-users-bounces at lists.castor-project.org> <castor-users-bounces at lists.castor-project.org> on behalf of Carlier Thomas  <mailto:thomas.carlier at chu-nantes.fr> <thomas.carlier at chu-nantes.fr>
Date: Wednesday, 26 April 2017 at 10:26
To:  <mailto:castor-users at lists.castor-project.org> "castor-users at lists.castor-project.org"  <mailto:castor-users at lists.castor-project.org> <castor-users at lists.castor-project.org>
Subject: Re: [Castor-users] TR: SPECT reading Interfile

 

Dear Michael,

 

Would it be possible to send us your projections and your log file for this reconstruction?

We will investigate the problem with your data because we did not experience such artifacts.

Thanks

 

Thomas

 

Le 26/04/2017 à 07:57, Michael Ljungberg a écrit :

Hi Claude and others

 

I finally got it working for osem. Thank you for all help. I have noticed that when using a relatively low angles/subset there appear artefacts in the images that is constant in position though out the number of slices. The example is for 8 angles/subsets.  I will investigate effect this a little bit more. Is there any one that has seen this before?

 

Hälsningar / Best regards

Michael

 







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