Merge pull request #1577 from KrisThielemans/SPECTUB_clean

SPECTUB code clean-up (no change to functionality)

Author: KrisThielemans

src/include/stir/recon_buildblock/PinholeSPECTUB_Tools.h

@@ -4,8 +4,7 @@
     Copyright (C) 2014, 2021, University College London
     This file is part of STIR.
 
-    This software is distributed WITHOUT ANY WARRANTY;
-    without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+    SPDX-License-Identifier: Apache-2.0
 
     See STIR/LICENSE.txt for details
 
@@ -16,7 +15,7 @@
 #ifndef _WM_SPECT_mph_H
 #define _WM_SPECT_mph_H
 
-#include <iostream>
+#include <string>
 #include <vector>
 
 namespace SPECTUB_mph
@@ -382,39 +381,21 @@ typedef struct
 
 //... functions from wmtools_SPECT.cpp .........................................
 
-void wm_alloc(int* Nitems, wm_da_type& wm, wmh_mph_type& wmh); // allocate wm
-
-// void free_wm () ;                                      // delete wm
-
-// void write_wm_FC_mph ();                               // write double array weight matrix
-
-// void write_wm_hdr_mph ();                              // write header of a matrix
-
-// void write_wm_STIR_mph ();                             // write matrix in STIR format
+void wm_alloc(const int* Nitems, wm_da_type& wm, const wmh_mph_type& wmh); // allocate wm
 
 void read_prj_params_mph(wmh_mph_type& wmh); // read ring parameters from a file
 
 void read_coll_params_mph(wmh_mph_type& wmh); // read collimator parameters from a file
 
 // void which_hole();
 
-void fill_pcf(wmh_mph_type& wmh, pcf_type& pcf); // fill precalculated functions
-
-// void free_pcf ();                                      // fill precalculated functions
+void fill_pcf(const wmh_mph_type& wmh, pcf_type& pcf); // fill precalculated functions
 
 void calc_cumsum(discrf2d_type* f);
 
-void generate_msk_mph(bool* msk_3d, float* att, wmh_mph_type& wmh); // create a boolean mask for wm (no weights outside the msk)
-
-// void read_msk_file_mph ( bool * msk );                 // read mask from a file
-
-std::string wm_SPECT_read_value_1d(std::ifstream* stream1, char DELIMITER);
-
-void wm_SPECT_read_hvalues_mph(std::ifstream* stream1, char DELIMITER, int* nh, bool do_cyl, wmh_mph_type& wmh);
-
-// void read_att_map_mph ( float *attmap );               // read attenuation map from a file
-
-// char *itoa ( int n, char *s);                      // to convert integer to ascii
+void generate_msk_mph(bool* msk_3d,
+                      const float* att,
+                      const wmh_mph_type& wmh); // create a boolean mask for wm (no weights outside the msk)
 
 void error_wmtools_SPECT_mph(int nerr, int ip, std::string txt); // error messages in wm_SPECT
 

src/include/stir/recon_buildblock/PinholeSPECTUB_Weight3d.h

@@ -4,8 +4,7 @@
     Copyright (C) 2014, 2021, University College London
     This file is part of STIR.
 
-    This software is distributed WITHOUT ANY WARRANTY;
-    without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+    SPDX-License-Identifier: Apache-2.0
 
     See STIR/LICENSE.txt for details
 
@@ -24,49 +23,15 @@ void wm_calculation_mph(bool do_estim,
                         psf2d_type* psf2d_bin,
                         psf2d_type* psf_subs,
                         psf2d_type* psf2d_aux,
-                        psf2d_type* kern,
-                        float* attmap,
-                        bool* msk_3d,
+                        const psf2d_type* kern,
+                        const float* attmap,
+                        const bool* msk_3d,
                         int* Nitems,
-                        wmh_mph_type& wmh,
+                        const wmh_mph_type& wmh,
                         wm_da_type& wm,
-                        pcf_type& pcf);
+                        const pcf_type& pcf);
 
-//... geometric component ............................................
-
-bool check_xang_par(voxel_type* vox, hole_type* h);
-
-bool check_zang_par(voxel_type* vox, hole_type* h);
-
-// bool check_xang_obl( lor_type * l, voxel_type * vox, hole_type * h);
-
-// bool check_zang_obl( lor_type * l, voxel_type * vox, hole_type * h);
-
-void voxel_projection_mph(lor_type* l, voxel_type* v, hole_type* h, wmh_mph_type& wmh);
-
-void fill_psfi(psf2d_type* kern, wmh_mph_type& wmh);
-
-void downsample_psf(psf2d_type* psf_in, psf2d_type* psf_out, int factor, bool do_calc);
-
-void psf_convol(psf2d_type* psf1, psf2d_type* psf_aux, psf2d_type* psf2, bool do_calc);
-
-float bresenh_f(int i1, int j1, int i2, int j2, float** f, int imax, int jmax, float dcr, wmh_mph_type& wmh, pcf_type& pcf);
-
-void fill_psf_geo(psf2d_type* psf2d, lor_type* l, discrf2d_type* f, int factor, bool do_calc, wmh_mph_type& wmh);
-
-void fill_psf_depth(psf2d_type* psf2d, lor_type* l, discrf2d_type* f, int factor, bool do_calc, wmh_mph_type& wmh, pcf_type& pcf);
-
-void psf_convol(psf2d_type* psf2d, psf2d_type* psf_aux, psf2d_type* kern);
-
-void downsample_psf(psf2d_type* psf_subs, psf2d_type* psf_bin);
-
-//... attenuation...................................................
-
-float calc_att_mph(bin_type bin, voxel_type vox, float* attmap, wmh_mph_type& wmh);
-
-int comp_dist(float dx, float dy, float dz, float dlast);
-
-void error_weight3d(int nerr, std::string txt); // error messages in weight3d_SPECT
+void fill_psfi(psf2d_type* kern, const wmh_mph_type& wmh);
 
 } // namespace SPECTUB_mph
 

src/include/stir/recon_buildblock/SPECTUB_Tools.h

@@ -13,9 +13,6 @@
 #ifndef _WM_SPECTUB_H
 #define _WM_SPECTUB_H
 
-#include <iostream>
-#include <vector>
-
 #include <string>
 
 namespace SPECTUB
@@ -317,75 +314,29 @@ typedef struct
 
 //... functions from wmtools_SPECT.cpp .........................................
 
-void write_wm_FC(wm_da_type& wm); // to write double array weight matrix
-
-void write_wm_hdr(wm_da_type& wm, wmh_type& wmh); // to write header of a matrix
-
-void write_wm_STIR(SPECTUB::wm_da_type& wm); // to write matrix in STIR format
-
-void index_calc(int* indexs, wmh_type& wmh); // to calculate projection index order in subsets
-
-void read_Rrad(float* Rrad, wmh_type& wmh); // to read variable rotation radius from a text file (1 radius per line)
+void index_calc(int* indexs, const wmh_type& wmh); // to calculate projection index order in subsets
 
 //
 // 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, wmh_type& wmh, const float* Rrad); // to fill angle structure
+void fill_ang(angle_type* ang, const wmh_type& wmh, const float* Rrad); // to fill angle structure
 
 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, wmh_type& wmh); // to read mask from a file
-
-void read_att_map(float* attmap, wmh_type& wmh); // to read attenuation map from a file
+                  const float* att,
+                  const volume_type* vol,
+                  const wmh_type& wmh); // to create a boolean mask for wm (no weights outside the msk)
 
-int max_psf_szb(angle_type* ang, wmh_type& wmh);
+int max_psf_szb(const angle_type* ang, const wmh_type& wmh);
 
 float calc_sigma_h(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
+float calc_sigma_v(voxel_type vox, collim_type COL);
 
 void free_wm(wm_type* f); // to free weight_mat
 
 void free_wm_da(wm_da_type* f); // to free weight_mat_da
 
-void error_wmtools_SPECT(int nerr, std::string txt); // error messages in wm_SPECT
-
-//... functions from wm_SPECT.2.0............................
-
-// int wm_SPECT( std::string inputFile);
-
-// void error_wm_SPECT( int nerr, std::string txt);      //list of error messages
-
-////void wm_inputs( std::string fileName, proj_type * prj, volume_type *vol, voxel_type *vox, bin_type *bin );
-// void wm_inputs(char **argv,
-//			   int argc,
-//			   proj_type *prj,
-//			   volume_type *vol,
-//			   voxel_type *vox,
-//	       bin_type *bin);
-//
-//
-////void read_inputs( std::string param, proj_type * prj, volume_type *vol, voxel_type *vox, bin_type *bin );
-// void read_inputs(vector<std::string> param,
-//				 proj_type *prj,
-//				 volume_type *vol,
-//				 voxel_type *vox,
-////		 bin_type *bin);
-//
-// extern wmh_type wmh;           // weight matrix header. Global variable
-//
-// extern wm_da_type wm;          // double array weight matrix structure. Global variable
-//
-// extern float * Rrad;           // variable projection radius (in acquisition order)
-
 } // namespace SPECTUB
 
 #endif //_WM_SPECT_H

src/include/stir/recon_buildblock/SPECTUB_Weight3d.h

@@ -41,7 +41,7 @@ void wm_calculation(const int kOS,
                     const SPECTUB::discrf_type* const gaussdens,
                     const int* const NITEMS,
                     SPECTUB::wm_da_type& wm,
-                    SPECTUB::wmh_type& wmh,
+                    const SPECTUB::wmh_type& wmh,
                     const float* Rrad);
 
 void wm_size_estimation(int kOS,
@@ -55,7 +55,7 @@ void wm_size_estimation(int kOS,
                         const int maxszb,
                         const SPECTUB::discrf_type* const gaussdens,
                         int* NITEMS,
-                        SPECTUB::wmh_type& wmh,
+                        const SPECTUB::wmh_type& wmh,
                         const float* Rrad);
 
 //... geometric component ............................................
@@ -64,21 +64,21 @@ void calc_gauss(SPECTUB::discrf_type* gaussdens);
 
 void calc_vxprj(SPECTUB::angle_type* ang);
 
-void voxel_projection(SPECTUB::voxel_type* vox, float* eff, float lngcmd2, SPECTUB::wmh_type& wmh);
+void voxel_projection(SPECTUB::voxel_type* vox, float* eff, float lngcmd2, const SPECTUB::wmh_type& wmh);
 
 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);
+                 const SPECTUB::wmh_type& wmh);
 
 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);
+                 const SPECTUB::wmh_type& wmh);
 
 void fill_psf_3d(SPECTUB::psf2da_type* psf,
                  SPECTUB::psf1d_type* psf1d_h,
@@ -88,10 +88,13 @@ void fill_psf_3d(SPECTUB::psf2da_type* psf,
                  float szdx,
                  float thdx,
                  float thcmd2,
-                 wmh_type& wmh);
+                 const wmh_type& wmh);
 
-void calc_psf_bin(
-    float center_psf, float binszcm, SPECTUB::discrf_type const* const vxprj, SPECTUB::psf1d_type* psf, SPECTUB::wmh_type& wmh);
+void calc_psf_bin(float center_psf,
+                  float binszcm,
+                  SPECTUB::discrf_type const* const vxprj,
+                  SPECTUB::psf1d_type* psf,
+                  const SPECTUB::wmh_type& wmh);
 
 //... attenuation...................................................
 
@@ -103,7 +106,7 @@ void calc_psf_bin(
 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 SPECTUB::attpth_type* const attpth, const float* const attmap, int islc, SPECTUB::wmh_type& wmh);
+float calc_att(const SPECTUB::attpth_type* const attpth, const float* const attmap, int islc, const SPECTUB::wmh_type& wmh);
 
 int comp_dist(float dx, float dy, float dz, float dlast);