SAFIR updates

src/buildblock/Scanner.cxx

@@ -1085,7 +1085,7 @@ Scanner::Scanner(Type scanner_type)
                  150,   // max_num_non_arccorrected_bins_v,
                  150,   // default_num_arccorrected_bins_v,
                  180,   // num_detectors_per_ring_v
-                 64.05, //  inner_ring_radius_v
+                 64.05, // inner_ring_radius_v
                  5,     // average_depth_of_interaction_v
                  2.2,   // ring_spacing_v
                  1.1,   // bin_size_v
@@ -1099,18 +1099,82 @@ Scanner::Scanner(Type scanner_type)
                  1,     // num_detector_layers_v
                  -1,    // energy_resolution_v
                  -1,    // reference_energy_v
-                 (short int)1,
-                 0.F,
-                 0.F,                   // non-TOF
-                 "BlocksOnCylindrical", // scanner_geometry_v
-                 2.2,                   // axial_crystal_spacing_v
-                 2.2,                   // transaxial_crystal_spacing_v
-                 18.1,                  // axial_block_spacing_v
-                 33.6,                  // transaxial_block_spacing_v
-                 ""                     // crystal_map_file_name_v
+                 (short int)1, // max_num_of_timing_poss_v,
+                 0.F,   // size_timing_pos_v,
+                 0.F,   // timing_resolution_v,
+                 "",    // scanner_geometry_v
+                 2.2,   // axial_crystal_spacing_v
+                 2.2,   // transaxial_crystal_spacing_v
+                 18.1,  // axial_block_spacing_v
+                 33.6,  // transaxial_block_spacing_v
+                 ""     // crystal_map_file_name_v
       );
       break;
 
+    case SafirI:
+      set_params(SafirI, string_list("SafirI"),
+               24,    // num_rings_v
+               150,   // max_num_non_arccorrected_bins_v,
+               150,   // default_num_arccorrected_bins_v,
+               180,   // num_detectors_per_ring_v
+               64.05, // inner_ring_radius_v
+               5,     // average_depth_of_interaction_v
+               2.2,   // ring_spacing_v
+               1.1,   // bin_size_v
+               0,     // intrinsic_tilt_v
+               3,     // num_axial_blocks_per_bucket_v
+               1,     // num_transaxial_blocks_per_bucket_v
+               8,     // num_axial_crystals_per_block_v
+               15,    // num_transaxial_crystals_per_block_v
+               1,     // num_axial_crystals_per_singles_unit_v
+               1,     // num_transaxial_crystals_per_singles_unit_v
+               1,     // num_detector_layers_v
+               0.12,  // energy_resolution_v
+               511,   // reference_energy_v
+               (short int)1, //max_num_of_timing_poss_v,
+               0.F,   // size_timing_pos_v,
+               0.F,   // timing_resolution_v,
+               "",    // scanner_geometry_v
+               2.2,   // axial_crystal_spacing_v
+               2.2,   // transaxial_crystal_spacing_v
+               18.1,  // axial_block_spacing_v
+               33.6,  // transaxial_block_spacing_v
+               ""     // crystal_map_file_name_v
+              );
+      break;
+
+    case SafirII:
+      set_params(SafirII, string_list("SafirII"),
+               64,    // num_rings_v
+               150,   // max_num_non_arccorrected_bins_v,
+               150,   // default_num_arccorrected_bins_v,
+               180,   // num_detectors_per_ring_v
+               64.05, // inner_ring_radius_v
+               5,     // average_depth_of_interaction_v
+               2.2,   // ring_spacing_v
+               1.1,   // bin_size_v
+               0,     // intrinsic_tilt_v
+               8,     // num_axial_blocks_per_bucket_v
+               1,     // num_transaxial_blocks_per_bucket_v
+               8,     // num_axial_crystals_per_block_v
+               15,    // num_transaxial_crystals_per_block_v
+               1,     // num_axial_crystals_per_singles_unit_v
+               1,     // num_transaxial_crystals_per_singles_unit_v
+               1,     // num_detector_layers_v
+               0.12,  // energy_resolution_v
+               511,   // reference_energy_v
+               (short int)1, // max_num_of_timing_poss_v,
+               0.F,   // size_timing_pos_v,
+               0.F,   // timing_resolution_v,
+               "",    // scanner_geometry_v
+               2.2,   // axial_crystal_spacing_v
+               2.2,   // transaxial_crystal_spacing_v
+               18.1,  // axial_block_spacing_v
+               33.6,  // transaxial_block_spacing_v
+               ""     // crystal_map_file_name_v
+              );
+      break;
+
     case UPENN_5rings:
       set_params(UPENN_5rings,
                  string_list("UPENN_5rings"),

src/include/stir/Scanner.h

@@ -174,6 +174,8 @@ class Scanner
     Allegro,
     GeminiTF,
     SAFIRDualRingPrototype,
+    SafirI,
+    SafirII,
     UPENN_5rings,
     UPENN_5rings_no_gaps,
     UPENN_6rings,

src/utilities/convert_projdata_types.cxx

@@ -0,0 +1,95 @@
+//
+//
+/*!
+  \file
+  \ingroup utilities
+
+  \brief This program takes a projection data from one type and converts it to another type.
+  \author Parisa Khateri
+
+*/
+/*
+*/
+#include "stir/ProjData.h"
+#include "stir/IO/interfile.h"
+#include "stir/utilities.h"
+#include "stir/Bin.h"
+
+#include <fstream>
+#include <iostream>
+#include "stir/ProjDataFromStream.h"
+#include "stir/Viewgram.h"
+#include "stir/IO/read_from_file.h"
+#include "stir/SegmentByView.h"
+#include "stir/ProjDataInterfile.h"
+#include "stir/ProjDataInfo.h"
+#include "stir/LORCoordinates.h"
+
+#include "stir/GeometryBlocksOnCylindrical.h"
+#include "stir/DetectionPosition.h"
+#include "stir/CartesianCoordinate3D.h"
+#include "stir/listmode/DetectorCoordinateMapFromFile.h"
+#include <boost/make_shared.hpp>
+#include "stir/CPUTimer.h"
+#include "stir/shared_ptr.h"
+
+
+#ifndef STIR_NO_NAMESPACES
+using std::cerr;
+#endif
+
+USING_NAMESPACE_STIR
+
+
+
+int main(int argc, char *argv[])
+{
+  CPUTimer timer0;
+
+  if(argc<4)
+  {
+    cerr<<"Usage: " << argv[0] << " output_filename input_filename template_blk_projdata\n";
+    exit(EXIT_FAILURE);
+  }
+  std::string output_filename=argv[1];
+  shared_ptr<ProjData> in_pd_ptr = ProjData::read_from_file(argv[2]);
+  shared_ptr<ProjData> template_pd_ptr = ProjData::read_from_file(argv[3]);
+
+  shared_ptr<ProjDataInfo> in_pdi_ptr(in_pd_ptr->get_proj_data_info_sptr()->clone());
+  shared_ptr<ProjDataInfo> out_pdi_ptr(template_pd_ptr->get_proj_data_info_sptr()->clone());
+  ProjDataInterfile out_proj_data(template_pd_ptr->get_exam_info_sptr(), out_pdi_ptr, output_filename+".hs");
+  write_basic_interfile_PDFS_header(output_filename+".hs", out_proj_data);
+
+  timer0.start();
+
+  assert(in_pdi_ptr->get_min_segment_num()==-1*in_pdi_ptr->get_max_segment_num());
+  for (int seg=in_pdi_ptr->get_min_segment_num(); seg<=in_pdi_ptr->get_max_segment_num();++seg)
+  {
+    std::cout<<"seg_num = "<<seg<<"\n";
+    // keep sinograms out of the loop to avoid reallocations
+    // initialise to something because there's no default constructor
+    Viewgram<float> viewgram_blk = out_proj_data.get_empty_viewgram(out_proj_data.get_min_view_num(),seg);
+    Viewgram<float> viewgram_cyl = in_pd_ptr->get_empty_viewgram(in_pd_ptr->get_min_view_num(),seg);
+
+    for(int view=in_pdi_ptr->get_min_view_num(); view<=in_pdi_ptr->get_max_view_num();++view)
+    {
+      viewgram_blk = out_proj_data.get_empty_viewgram(view,seg);
+      viewgram_cyl = in_pd_ptr->get_viewgram(view,seg);
+
+      for(int ax=in_pdi_ptr->get_min_axial_pos_num(seg); ax<=in_pdi_ptr->get_max_axial_pos_num(seg);++ax)
+      {
+        for(int tang=in_pdi_ptr->get_min_tangential_pos_num(); tang<=in_pdi_ptr->get_max_tangential_pos_num(); ++tang)
+        {
+          viewgram_blk[ax][tang] = viewgram_cyl[ax][tang];
+        }
+      }
+      if (!(out_proj_data.set_viewgram(viewgram_blk)== Succeeded::yes))
+        warning("Error set_segment for projdata_symm %d\n", seg);
+    }
+  }
+
+  timer0.stop();
+  std::cerr << "\nConverting from cylindrical projdata to block took " << timer0.value() << "s CPU time.\n\n";
+
+  return EXIT_SUCCESS;
+}