calculate_attenuation_coefficients.cxx File Reference

Calculates attenuation coefficients (as an alternative to correct_projdata). More...

#include "stir/ProjDataInterfile.h"
#include "stir/RelatedViewgrams.h"
#include "stir/VoxelsOnCartesianGrid.h"
#include "stir/Viewgram.h"
#include "stir/ArrayFunction.h"
#include "stir/recon_buildblock/ForwardProjectorByBinUsingRayTracing.h"
#include "stir/recon_buildblock/ForwardProjectorByBinUsingProjMatrixByBin.h"
#include "stir/recon_buildblock/ProjMatrixByBinUsingRayTracing.h"
#include "stir/recon_buildblock/BinNormalisationFromAttenuationImage.h"
#include "stir/DataSymmetriesForViewSegmentNumbers.h"
#include "stir/IO/read_from_file.h"
#include "stir/info.h"
#include "stir/warning.h"
#include <iostream>
#include <list>
#include <algorithm>

Namespaces
	stir
	Namespace for the STIR library (and some/most of its applications)

Functions
int	main (int argc, char *argv[])

Detailed Description

Calculates attenuation coefficients (as an alternative to correct_projdata).

Usage

   calculate_attenuation_coefficients
           [--PMRT --NOPMRT]  --AF|--ACF <output filename > <input image file name> <template_proj_data>
[forwardprojector-parfile] 

–ACF calculates the attenuation correction factors, –AF calculates the attenuation factor (i.e. the inverse of the ACFs).

The option –PMRT forces forward projection using the Probability Matrix Using Ray Tracing (stir::ProjMatrixByBinUsingRayTracing).

The option –NOPMRT forces forward projection using the (old) Ray Tracing

Optionally include a parameter file for specifying the forward projector (overrules –PMRT and –NOPMRT options)

Forward Projector parameters:=
  type := Matrix
    Forward projector Using Matrix Parameters :=
      Matrix type := Ray Tracing
       Ray tracing matrix parameters :=
       End Ray tracing matrix parameters :=
      End Forward Projector Using Matrix Parameters :=
End:=

The attenuation_image has to contain an estimate of the mu-map for the image. It will be used to estimate attenuation factors as exp(-forw_proj(*attenuation_image_ptr)).

Note

Output is non-TOF, even if a TOF template is used.

Warning

attenuation image data are supposed to be in units cm^-1. Reference: water has mu .096 cm^-1.

Author

Sanida Mustafovic

Kris Thielemans