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SAFIR scanners updates #1563

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c2ee090
Initial commit:
Feb 10, 2025
30780c3
Adding two utilities for conversion and trimming of sinograms in gene…
Feb 10, 2025
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64 changes: 64 additions & 0 deletions src/buildblock/Scanner.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -1146,6 +1146,70 @@ Scanner::Scanner(Type scanner_type)
);
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"),
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2 changes: 2 additions & 0 deletions src/include/stir/Scanner.h
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Expand Up @@ -175,6 +175,8 @@ class Scanner
Allegro,
GeminiTF,
SAFIRDualRingPrototype,
SafirI,
SafirII,
UPENN_5rings,
UPENN_5rings_no_gaps,
UPENN_6rings,
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2 changes: 2 additions & 0 deletions src/utilities/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@ set(${dir_EXE_SOURCES}
find_sum_projection_of_viewgram_and_sinogram.cxx
separate_true_from_random_scatter_for_necr.cxx
stir_timings.cxx
convert_projdata_types.cxx
trim_projdata.cxx
)

if (HAVE_ITK)
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95 changes: 95 additions & 0 deletions src/utilities/convert_projdata_types.cxx
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Original file line number Diff line number Diff line change
@@ -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/DetectorCoordinateMap.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;
}
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