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changing SPECTUB global variables to class members #1169

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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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14 changes: 10 additions & 4 deletions src/include/stir/recon_buildblock/ProjMatrixByBinSPECTUB.h
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ class Bin;
End Projection Matrix By Bin SPECT UB Parameters:=
\endverbatim
*/

//using namespace SPECTUB;
class ProjMatrixByBinSPECTUB :
public RegisteredParsingObject<
ProjMatrixByBinSPECTUB,
Expand All @@ -90,14 +90,17 @@ class ProjMatrixByBinSPECTUB :
//! Default constructor (calls set_defaults())
ProjMatrixByBinSPECTUB();

// disable copy-constructor as currently unsafe to copy due to bare pointers
ProjMatrixByBinSPECTUB(const ProjMatrixByBinSPECTUB&) = delete;

//! Destructor (deallocates UB SPECT memory)
~ProjMatrixByBinSPECTUB();

//! Checks all necessary geometric info
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 +149,6 @@ 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 +174,9 @@ class ProjMatrixByBinSPECTUB :

bool already_setup;

mutable SPECTUB::wm_da_type wm;
mutable SPECTUB::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 +211,8 @@ class ProjMatrixByBinSPECTUB :
int maxszb;


void compute_one_subset(const int kOS) const;
void compute_one_subset(const int kOS,
const float *Rrad) const;
void delete_UB_SPECT_arrays();
mutable std::vector<bool> subset_already_processed;
};
Expand Down
22 changes: 11 additions & 11 deletions src/include/stir/recon_buildblock/SPECTUB_Tools.h
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Expand Up @@ -319,38 +319,38 @@ typedef struct
//... functions from wmtools_SPECT.cpp .........................................


void write_wm_FC (); // to write double array weight matrix
void write_wm_FC (wm_da_type &wm); // to write double array weight matrix

void write_wm_hdr (); // to write header of a matrix
void write_wm_hdr (wm_da_type &wm, wmh_type &wmh); // to write header of a matrix

void write_wm_STIR (); // to write matrix in STIR format
void write_wm_STIR (SPECTUB::wm_da_type& wm); // to write matrix in STIR format


void index_calc ( int *indexs ); // to calculate projection index order in subsets
void index_calc (int *indexs , wmh_type &wmh); // to calculate projection index order in subsets

void read_Rrad (); // to read variable rotation radius from a text file (1 radius per line)
void read_Rrad (float *Rrad, wmh_type &wmh); // to read variable rotation radius from a text file (1 radius per line)

//
//void col_params ( collim_type *COL ); // to fill collimator structure
//
//void read_col_params ( collim_type *COL); // to read collimator parameters from a file


void fill_ang ( angle_type *ang ); // to fill angle structure
void fill_ang (angle_type *ang , wmh_type &wmh, const float *Rrad); // to fill angle structure

void generate_msk ( bool *msk_3d, bool *msk_2d, float *att, volume_type *vol); // to create a boolean mask for wm (no weights outside the msk)
void generate_msk (bool *msk_3d, bool *msk_2d, float *att, volume_type *vol, wmh_type &wmh); // to create a boolean mask for wm (no weights outside the msk)

void read_msk_file ( bool * msk ); // to read mask from a file
void read_msk_file (bool * msk , wmh_type &wmh); // to read mask from a file


void read_att_map ( float *attmap ); // to read attenuation map from a file
void read_att_map (float *attmap , wmh_type &wmh); // to read attenuation map from a file


int max_psf_szb ( angle_type *ang );
int max_psf_szb (angle_type *ang , wmh_type &wmh);

float calc_sigma_h ( voxel_type vox, collim_type COL);

float calc_sigma_v ( voxel_type vox, collim_type COL);
float calc_sigma_v (voxel_type vox, collim_type COL, wmh_type &wmh);


char *itoa ( int n, char *s); // to conver integer to ascii
Expand Down
95 changes: 47 additions & 48 deletions src/include/stir/recon_buildblock/SPECTUB_Weight3d.h
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Expand Up @@ -23,68 +23,67 @@
Berta Marti Fuster, Carles Falcon, Charalampos Tsoumpas, Lefteris Livieratos, Pablo Aguiar, Albert Cot, Domenec Ros and Kris Thielemans,
<i>Integration of advanced 3D SPECT modeling into the open-source STIR framework</i>,
Med. Phys. 40, 092502 (2013); http://dx.doi.org/10.1118/1.4816676

\todo Variables wm, wmh and Rrad are currently global variables. This means that this code would be very dangerous
in a parallel setting.
*/

namespace SPECTUB {

/* Global variables: the matrix etc TODO
Need to be defined elsewhere

A lot of the functions below modify these variables.
*/
extern wm_da_type wm; //! weight (or probability) matrix
extern wmh_type wmh; //! information to construct wm
extern float * Rrad; //! radii per view


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
);
// extern wm_da_type wm; //! weight (or probability) matrix
// extern wmh_type wmh; //! information to construct wm
// extern float * Rrad; //! radii per view


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


//... geometric component ............................................

void calc_gauss ( discrf_type *gaussdens );
void calc_gauss ( SPECTUB::discrf_type *gaussdens );

void calc_vxprj ( angle_type *ang );
void calc_vxprj ( SPECTUB::angle_type *ang );

void voxel_projection ( voxel_type *vox, float * eff, float lngcmd2 );
void voxel_projection (SPECTUB::voxel_type *vox, float * eff, float lngcmd2 , SPECTUB::wmh_type &wmh);

void fill_psf_no( psf2da_type *psf, psf1d_type *psf1d_h, const voxel_type& vox, const angle_type * const ang, float szdx );
void fill_psf_no(SPECTUB::psf2da_type *psf, SPECTUB::psf1d_type *psf1d_h, const SPECTUB::voxel_type& vox, const angle_type * const ang, float szdx , SPECTUB::wmh_type &wmh);

void fill_psf_2d( psf2da_type *psf, psf1d_type *psf1d_h, const voxel_type& vox, discrf_type const*const gaussdens, float szdx );
void fill_psf_2d( SPECTUB::psf2da_type *psf, SPECTUB::psf1d_type *psf1d_h, const SPECTUB::voxel_type& vox, SPECTUB::discrf_type const*const gaussdens, float szdx, SPECTUB::wmh_type &wmh);

void fill_psf_3d(psf2da_type *psf,
psf1d_type *psf1d_h,
psf1d_type *psf1d_v,
const voxel_type& vox, discrf_type const * const gaussdens, float szdx, float thdx, float thcmd2 );
void fill_psf_3d(SPECTUB::psf2da_type *psf,
SPECTUB::psf1d_type *psf1d_h,
SPECTUB::psf1d_type *psf1d_v,
const SPECTUB::voxel_type& vox, SPECTUB::discrf_type const * const gaussdens,
float szdx, float thdx, float thcmd2,
wmh_type &wmh);

void calc_psf_bin ( float center_psf, float binszcm, discrf_type const * const vxprj, psf1d_type *psf );
void calc_psf_bin (float center_psf, float binszcm, SPECTUB::discrf_type const * const vxprj, SPECTUB::psf1d_type *psf , SPECTUB::wmh_type &wmh);


//... attenuation...................................................
Expand All @@ -94,9 +93,9 @@ void calc_psf_bin ( float center_psf, float binszcm, discrf_type const * const v

//void size_attpth_full( psf2da_type *psf, voxel_type vox, volume_type vol, float *att, angle_type *ang );

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

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

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

Expand Down
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