[Castor-users] SPECT reading Interfile
Simon Stute
simon.stute at cea.fr
Tue Apr 18 17:26:33 CEST 2017
Hello,
The castor configuration folder also contains other configuration files,
so it is not only related to the scanner geometries.
However, a third possibility is to copy the whole 'config' folder (it is
light) into your working directory, put your geom files inside the
'scanner' sub-folder and then you can use the '-conf
./your_config_folder' option to overload the path of the configuration
directory at run-time.
The '-conf' option is described when calling 'castor-recon -help-misc'.
Regards
Simon
Le 18/04/2017 à 17:13, Didier Benoit a écrit :
> 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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>>
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>>
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>>
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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
> -------------------------------------------------------------------------------
>
>
> _______________________________________________
> Castor-users mailing list
> Castor-users at lists.castor-project.org
> http://lists.castor-project.org/listinfo/castor-users
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