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Merged
KrisThielemans merged 5 commits into from
Apr 19, 2023
Merged

changing SPECTUB global variables to class members #1169

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94efb22
making useful global variable class members
Mar 2, 2023
b318f26
making variable non-static;
Mar 10, 2023
2f8b9e4
Merge branch 'UCL:master' into SPECTglobal
danieldeidda Apr 18, 2023
573e4bd
remove dependence from global variable;
Apr 18, 2023
581c302
remove comments and add info to release5.3
Apr 19, 2023
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13 changes: 9 additions & 4 deletions src/include/stir/recon_buildblock/ProjMatrixByBinSPECTUB.h
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Expand Up @@ -75,7 +75,7 @@ class Bin;
End Projection Matrix By Bin SPECT UB Parameters:=
\endverbatim
*/

using namespace SPECTUB;
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class ProjMatrixByBinSPECTUB :
public RegisteredParsingObject<
ProjMatrixByBinSPECTUB,
Expand All @@ -97,7 +97,7 @@ class ProjMatrixByBinSPECTUB :
virtual void set_up(
const shared_ptr<const ProjDataInfo>& proj_data_info_ptr,
const shared_ptr<const DiscretisedDensity<3,float> >& density_info_ptr // TODO should be Info only
);
);

bool get_keep_all_views_in_cache() const;
//! Enable keeping the matrix in memory
Expand Down Expand Up @@ -146,7 +146,6 @@ class ProjMatrixByBinSPECTUB :

void
set_resolution_model(const float collimator_sigma_0_in_mm, const float collimator_slope_in_mm, const bool full_3D = true);

private:

// parameters that will be parsed
Expand All @@ -172,6 +171,9 @@ class ProjMatrixByBinSPECTUB :

bool already_setup;

static wm_da_type wm;
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static wmh_type wmh; // this could be an arry of wmh_type for each index
float * Rrad;

virtual void
calculate_proj_matrix_elems_for_one_bin(
Expand Down Expand Up @@ -206,7 +208,10 @@ class ProjMatrixByBinSPECTUB :
int maxszb;


void compute_one_subset(const int kOS) const;
void compute_one_subset(const int kOS,
wm_da_type& wm,
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wmh_type& wmh,
float * Rrad) const;
void delete_UB_SPECT_arrays();
mutable std::vector<bool> subset_already_processed;
};
Expand Down
29 changes: 17 additions & 12 deletions src/include/stir/recon_buildblock/SPECTUB_Weight3d.h
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Expand Up @@ -51,20 +51,25 @@ void wm_calculation( const int kOS,
const bool *msk_2d,
const int maxszb,
const discrf_type *const gaussdens,
const int *const NITEMS
const int *const NITEMS,
wm_da_type& wm,
wmh_type& wmh,
float * Rrad
);

void wm_size_estimation (int kOS,
const angle_type * const ang,
voxel_type vox,
bin_type bin,
const volume_type& vol,
const proj_type& prj,
const bool * const msk_3d,
const bool *const msk_2d,
const int maxszb,
const discrf_type * const gaussdens,
int *NITEMS);
const angle_type * const ang,
voxel_type vox,
bin_type bin,
const volume_type& vol,
const proj_type& prj,
const bool * const msk_3d,
const bool *const msk_2d,
const int maxszb,
const discrf_type * const gaussdens,
int *NITEMS,
wmh_type &wmh,
float *Rrad);


//... geometric component ............................................
Expand Down Expand Up @@ -96,7 +101,7 @@ void calc_psf_bin ( float center_psf, float binszcm, discrf_type const * const v

void calc_att_path ( const bin_type& bin, const voxel_type& vox, const volume_type& vol, attpth_type *attpth );

float calc_att ( const attpth_type *const attpth, const float *const attmap, int islc );
float calc_att (const attpth_type *const attpth, const float *const attmap, int islc , wmh_type &wmh);

int comp_dist ( float dx, float dy, float dz, float dlast );

Expand Down
29 changes: 18 additions & 11 deletions src/recon_buildblock/ProjMatrixByBinSPECTUB.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
Copyright (C) 2013, Institute for Bioengineering of Catalonia
Copyright (C) Biomedical Image Group (GIB), Universitat de Barcelona, Barcelona, Spain.
Copyright (C) 2013-2014, 2019, 2020 University College London
Copyright (C) 2023 National Physical Laboratory
This file is part of STIR.

SPDX-License-Identifier: Apache-2.0
Expand All @@ -17,6 +18,7 @@
\author Berta Marti Fuster
\author Carles Falcon
\author Kris Thielemans
\author Daniel Deidda
*/

//#include "stir/ProjDataInterfile.h"
Expand Down Expand Up @@ -60,14 +62,14 @@
#include "stir/recon_buildblock/SPECTUB_Weight3d.h"

/* UB-SPECT global variables */
namespace SPECTUB {
wm_da_type wm;
wmh_type wmh;
float * Rrad;
}
//namespace SPECTUB {
// wm_da_type wm;
// wmh_type wmh;
// float * Rrad;
//}

START_NAMESPACE_STIR

using namespace SPECTUB;
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const char * const
ProjMatrixByBinSPECTUB::registered_name =
Expand Down Expand Up @@ -658,7 +660,8 @@ set_up(

//... size estimations ........................................................

wm_size_estimation ( kOS, ang, vox, bin, vol, prj, msk_3d, msk_2d, maxszb, &gaussdens, NITEMS[kOS] );
wm_size_estimation ( kOS, ang, vox, bin, vol, prj, msk_3d, msk_2d, maxszb, &gaussdens, NITEMS[kOS],
wmh,Rrad );

//cout << "\nwm_SPECT. Size estimation done. time (s): " << double( clock()-ini )/CLOCKS_PER_SEC <<std::endl;

Expand Down Expand Up @@ -734,7 +737,10 @@ delete_UB_SPECT_arrays()
}
void
ProjMatrixByBinSPECTUB::
compute_one_subset(const int kOS) const
compute_one_subset(const int kOS,
wm_da_type& wm,
wmh_type& wmh,
float * Rrad) const
{
using namespace SPECTUB;

Expand Down Expand Up @@ -807,7 +813,8 @@ compute_one_subset(const int kOS) const

//... wm calculation for this subset ...........................

wm_calculation ( kOS, ang, vox, bin, vol, prj, attmap, msk_3d, msk_2d, maxszb, &gaussdens, NITEMS[kOS] );
wm_calculation ( kOS, ang, vox, bin, vol, prj, attmap, msk_3d, msk_2d, maxszb, &gaussdens, NITEMS[kOS],
wm, wmh, Rrad );
info(boost::format("Weight matrix calculation done. time %1% (s)") % timer.value(),
2);

Expand Down Expand Up @@ -868,8 +875,8 @@ calculate_proj_matrix_elems_for_one_bin(ProjMatrixElemsForOneBin& lor
subset_already_processed.assign(prj.NOS,false);
}
info(boost::format("Computing matrix elements for view %1%") % view_num,
2);
compute_one_subset(kOS);
2);// potentially pass a wm, wmh[threadh] not sure if works then in setup we need an array of wmh
compute_one_subset(kOS,wm,wmh,Rrad);
subset_already_processed[kOS]=true;
}
lor.erase();
Expand Down
35 changes: 19 additions & 16 deletions src/recon_buildblock/SPECTUB_Weight3d.cxx
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Expand Up @@ -45,18 +45,18 @@ using namespace std;
//=== wm_calculation =======================================================
//==========================================================================

void wm_calculation( const int kOS,
const angle_type *const ang,
voxel_type vox,
bin_type bin,
const volume_type& vol,
const proj_type& prj,
const float *attmap,
const bool *msk_3d,
const bool *msk_2d,
const int maxszb,
const discrf_type *const gaussdens,
const int *const NITEMS)
void wm_calculation(const int kOS,
const angle_type *const ang,
voxel_type vox,
bin_type bin,
const volume_type& vol,
const proj_type& prj,
const float *attmap,
const bool *msk_3d,
const bool *msk_2d,
const int maxszb,
const discrf_type *const gaussdens,
const int *const NITEMS, wm_da_type &wm, wmh_type &wmh, float *Rrad)
{

float weight;
Expand Down Expand Up @@ -232,7 +232,7 @@ void wm_calculation( const int kOS,
if ( !msk_3d[ vox.iv ] ) continue;
}

if ( wmh.do_att && !wmh.do_full_att ) coeff_att = calc_att( &attpth[ 0 ], attmap , vox.islc );
if ( wmh.do_att && !wmh.do_full_att ) coeff_att = calc_att( &attpth[ 0 ], attmap , vox.islc, wmh);

//... weight matrix values calculation .......................................

Expand All @@ -248,7 +248,7 @@ void wm_calculation( const int kOS,

jp = k * prj.Nbp + ks * prj.Nbin + psf.ib[ ie ];

if ( wmh.do_full_att ) coeff_att = calc_att( &attpth[ ie ], attmap, vox.islc );
if ( wmh.do_full_att ) coeff_att = calc_att( &attpth[ ie ], attmap, vox.islc, wmh );

weight = psf.val[ ie ] * eff * coeff_att ;

Expand Down Expand Up @@ -312,7 +312,9 @@ void wm_size_estimation (int kOS,
const bool *const msk_2d,
const int maxszb,
const discrf_type * const gaussdens,
int *NITEMS)
int *NITEMS,
wmh_type& wmh,
float * Rrad)
{
int jp;
float eff;
Expand Down Expand Up @@ -926,7 +928,8 @@ int comp_dist( float dx,
//=== cal_att =================================================================
//=============================================================================

float calc_att( const attpth_type *const attpth, const float *const attmap , int nsli ){
float calc_att( const attpth_type *const attpth, const float *const attmap , int nsli,
wmh_type& wmh){

float att_coef = (float)0.;
int iv;
Expand Down