[Castor-users] SPECT reading Interfile
Didier Benoit
didier.benoit at inserm.fr
Tue Apr 18 17:13:41 CEST 2017
In our software, we didn't plan to read the .geom files in 2 or more
folders. I think you have 2 solutions :
1- You can copy all your .geom files for each different kind of scanners
in the CASTOR_CONFIG folder
2- Or creating a "castor_test" folder, where you write all your .geom
files (and the .geom files provided by CASToR) and set CASTOR_CONFIG to
the location of "castor_test" during the installation.
Kind regards,
Didier
On 04/18/2017 04:36 PM, Michael Ljungberg wrote:
>
> Sorry Didier
>
> I meant the CASTOR_CONFIG folder. That was my question - if it would
> be possible for your software to search first in the local directory
> for a scanner name before looking in the CASTOR_CONFIG folder.
> Sometimes one do simulations as function of different camera
> geometries and I can then imagine I would need one .geom file for each
> of them. If the search for the scanner name is first made in the local
> directory and then in the CASTOR_CONFIG folder then these local .geom
> files could be isolated from the more permanent scanner system files,
> stored in the CASTOR_CONFIG folder.
>
> Hälsningar / Best regards
>
> Michael
>
> *From: *Didier Benoit <didier.benoit at inserm.fr>
> *Date: *Tuesday, 18 April 2017 at 16:07
> *To: *Michael Ljungberg <michael.ljungberg at med.lu.se>,
> "castor-users at lists.castor-project.org"
> <castor-users at lists.castor-project.org>
> *Subject: *Re: [Castor-users] SPECT reading Interfile
>
> With a time value set to 0, the SPECT reconstruction should work.
>
> In your second question, what do you exactly mean by "SYSTEM location"
> ? I'm not sure to understand. Is it your scanner system location
> defined by "CASTOR_CONFIG" during the compilation ? If it's the case
> you can't add a path in the Cdf file for the tag " Scanner name". If
> you want to create a custom scanner file you have to save it in the
> "CASTOR_CONFIG" directory.
>
> Kind Regards,
> Didier
>
>
> On 04/18/2017 03:26 PM, Michael Ljungberg wrote:
>
> Dear Didier
>
> Thank you for your explanation. I think it will not be a major
> problem to implement. For SPECT reconstructions, does the Time
> value be clearly defined?
>
> Another related question regards the files for the system. I
> wonder if it would be possible to allow castor-recon program to
> first look in the local folder for a geometry file before looking
> in the standard SYSTEM location? If I implement direct writing to
> the caster format in the simind program, I can foresee that the
> SYSTEM folder can be quickly filled with files. Alternatively, is
> it possible to add a path to the system name in the cdh file?
>
> Hälsningar / Best regards
>
> Michael
>
> *From: *Castor-users
> <castor-users-bounces at lists.castor-project.org>
> <mailto:castor-users-bounces at lists.castor-project.org> on behalf
> of Didier Benoit <didier.benoit at inserm.fr>
> <mailto:didier.benoit at inserm.fr>
> *Date: *Tuesday, 18 April 2017 at 14:52
> *To: *"castor-users at lists.castor-project.org"
> <mailto:castor-users at lists.castor-project.org>
> <castor-users at lists.castor-project.org>
> <mailto:castor-users at lists.castor-project.org>
> *Subject: *Re: [Castor-users] SPECT reading Interfile
>
> Dear Michael,
>
> Thanks for your interest. Interfile format is only used as
> input/output format for image (not projection data). As you have
> seen, input data for SPECT (and also for PET) is composed of 2
> files: a header file (*.Cdh) and a binary file (*.Cdf) storing the
> data from a machine or a Monte Carlo simulation. Here is some
> information about this Cdf file. This file is not a pure histogram
> (a successive number of counts by bin). The Data should (must) be
> arrange as described in the “CASToR general documentation” page 30.
>
> For instance, in the case of a 64x64 float matrix for 64 angles
> (and I consider you don't have both normalization and scatter
> informations), your Cdf file should contain 262 144 events
> (64x64x64) with the following format:
>
> EVENT 0:
> time: 0 (uint32_t)
> data: 32 (float/double) it's your data for a specific bin
> projection ID: 0 (uint32_t) it's the angle ID between 0 and 63 in
> this example
> binID: 0 (uint32_t) it's the bin ID between 0 and (64x64 – 1) in
> this example
>
> We don't provide a SPECT/PET data converter, but the easiest way
> to create a correct Cdf file (I consider you are using C/C++) is
> to create a struct like this:
>
> struct SPECT_CASTOR_EVENT_FORMAT {
> uint32_t time;
> float data;
> uint32_t projectionID;
> uint32_t binID;
> };
>
> and store each bin from your data in the CASToR event format.
>
> Kind Regards,
> Didier Benoit
>
>
> On 04/14/2017 05:34 PM, Michael Ljungberg wrote:
>
> Dear Castor developers
>
> I ran into this release a week ago and it is really a nice
> contribution you have made. I have been working with Monte
> Carlo simulations for many years developing the program simind
> and often I get this question of supplying reconstruction
> software since simind only produce projections. So being able
> to direct to your webpage would be natural.
>
> However, I dont understand how to read data into castor-recon.
> I also use Interfile and float values so when reading in the
> manual at you are using interfile for both input data and
> output gave me confidence for a smooth connection. But I dont
> see how to actual do this. I checked the spect benchmark file
> but the cdh format is different. So my question is how I can
> read in for example a 64x64 float matrices for 64 angles
> stored in a data file and with an associated interfile header
> file.
>
> Hälsningar / Best regards
>
> Michael Ljungberg
>
> Lund University
>
> Sweden
>
>
>
>
>
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>
> --
>
> -------------------------------------------------------------------------------
>
> Didier BENOIT, PhD,
>
> Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
>
> CHRU Morvan, bâtiment 1, étage 1
>
> 5 Avenue Foch
>
> 29609 Brest
>
> FRANCE
>
>
>
> E-mail:
>
> didier.benoit at univ-brest.fr <mailto:didier.benoit at univ-brest.fr>
>
> didier.benoit at inserm.fr <mailto:didier.benoit at inserm.fr>
>
>
>
> Tél: +33 (0)2 98 01 81 96
>
> -------------------------------------------------------------------------------
>
>
>
> --
> -------------------------------------------------------------------------------
> Didier BENOIT, PhD,
> Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
> CHRU Morvan, bâtiment 1, étage 1
> 5 Avenue Foch
> 29609 Brest
> FRANCE
> E-mail:
> didier.benoit at univ-brest.fr <mailto:didier.benoit at univ-brest.fr>
> didier.benoit at inserm.fr <mailto:didier.benoit at inserm.fr>
> Tél: +33 (0)2 98 01 81 96
> -------------------------------------------------------------------------------
--
-------------------------------------------------------------------------------
Didier BENOIT, PhD,
Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
CHRU Morvan, bâtiment 1, étage 1
5 Avenue Foch
29609 Brest
FRANCE
E-mail:
didier.benoit at univ-brest.fr
didier.benoit at inserm.fr
Tél: +33 (0)2 98 01 81 96
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