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Allow even number of ToF bins #1334

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Allow even number of ToF bins #1334

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5bedd93
changing timing index
Oct 3, 2023
5b9d603
furter adaptation to timing_pos_num from 0 to num_tof_bin -1, more s…
Oct 10, 2023
da07d94
furter adaptation to timing_pos_num from 0 to num_tof_bin -1, fixed g…
Oct 17, 2023
e9ffdd4
more tof swaps and fixes for even tof bins
Jan 15, 2024
c807500
merging master and fixing conflicts
Jan 15, 2024
605f950
fixing symmetry test issues
Jan 22, 2024
fcfb1ca
fixing asserts and tests
Jan 26, 2024
3afc3fa
Merge remote-tracking branch 'origin/master' into changetofidx
KrisThielemans Jan 27, 2024
5cf36d9
Merge remote-tracking branch 'origin/master' into changetofidx
KrisThielemans Jan 29, 2024
ab7c5df
fixing symmetry indeces
Mar 11, 2024
8246115
fixing conflincts and merge origin/master
danieldeidda Mar 11, 2024
ab23474
fix Datasymmetry timeshift;
danieldeidda Mar 25, 2024
ab7265d
Update src/IO/stir_ecat_common.cxx
danieldeidda Mar 26, 2024
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13 changes: 5 additions & 8 deletions src/buildblock/ProjDataInfo.cxx
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Expand Up @@ -68,10 +68,7 @@ START_NAMESPACE_STIR
float
ProjDataInfo::get_k(const Bin& bin) const
{
if (!(num_tof_bins%2))
return bin.timing_pos_num() * tof_increament_in_mm + tof_increament_in_mm / 2.f;
else
return (bin.timing_pos_num() * tof_increament_in_mm);
return (bin.timing_pos_num() - (num_tof_bins-1)/2.f)* tof_increament_in_mm ;
}

double
Expand Down Expand Up @@ -223,14 +220,14 @@ ProjDataInfo::set_tof_mash_factor(const int new_num)
tof_increament_in_mm = tof_delta_time_to_mm(tof_mash_factor * scanner_ptr->get_size_of_timing_pos());

// TODO cope with even numbers!
min_tof_pos_num = - (scanner_ptr->get_max_num_timing_poss() / tof_mash_factor)/2;
max_tof_pos_num = min_tof_pos_num + (scanner_ptr->get_max_num_timing_poss() / tof_mash_factor) -1;
min_tof_pos_num = 0;//- (scanner_ptr->get_max_num_timing_poss() / tof_mash_factor)/2;
max_tof_pos_num = (scanner_ptr->get_max_num_timing_poss() / tof_mash_factor)-1 ;//min_tof_pos_num + (scanner_ptr->get_max_num_timing_poss() / tof_mash_factor) -1;

num_tof_bins = max_tof_pos_num - min_tof_pos_num +1 ;

// Ensure that we have a central tof bin.
if (num_tof_bins%2 == 0)
error("ProjDataInfo: Number of TOF bins should be an odd number. Abort.");
// if (num_tof_bins%2 == 0)
// error("ProjDataInfo: Number of TOF bins should be an odd number. Abort.");

// Upper and lower boundaries of the timing poss;
tof_bin_boundaries_mm.grow(min_tof_pos_num, max_tof_pos_num);
Expand Down
4 changes: 2 additions & 2 deletions src/buildblock/ProjDataInfoCylindrical.cxx
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Expand Up @@ -582,13 +582,13 @@ get_LOR(LORInAxialAndNoArcCorrSinogramCoordinates<float>& lor,
const float z1 = (m_in_mm - max_a*tantheta);
const float z2 = (m_in_mm - min_a*tantheta);

const bool swap = false;//get_tof_delta_time(bin)<0;
lor =
LORInAxialAndNoArcCorrSinogramCoordinates<float>(z1, z2,
phi,
asin(s_in_mm/get_ring_radius()),
get_ring_radius(),
false);// needs to set "swapped" to false given above code
swap);// needs to set "swapped" to false given above code
}

#if 0
Expand Down
23 changes: 15 additions & 8 deletions src/buildblock/ProjDataInfoCylindricalNoArcCorr.cxx
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Expand Up @@ -334,7 +334,7 @@ get_num_det_pos_pairs_for_bin(const Bin& bin, bool ignore_non_spatial_dimensions
{
return
get_num_ring_pairs_for_segment_axial_pos_num(bin.segment_num(),
bin.axial_pos_num())*
bin.axial_pos_num())*
get_view_mashing_factor()*
(ignore_non_spatial_dimensions ? 1 : std::max(1,get_tof_mash_factor()));
}
Expand Down Expand Up @@ -362,8 +362,12 @@ get_all_det_pos_pairs_for_bin(vector<DetectionPositionPair<> >& dps,
// not sure how to handle even tof mashing
assert(!is_tof_data() || (get_tof_mash_factor() % 2 == 1)); // TODOTOF
// we will need to add all (unmashed) timing_pos for the current bin
min_timing_pos_num = bin.timing_pos_num()*get_tof_mash_factor() - (get_tof_mash_factor() / 2);
max_timing_pos_num = bin.timing_pos_num()*get_tof_mash_factor() + (get_tof_mash_factor() / 2);
min_timing_pos_num = bin.timing_pos_num()*get_tof_mash_factor();//bin.timing_pos_num()*get_tof_mash_factor() - (get_tof_mash_factor() / 2);
if (get_tof_mash_factor()==0)
max_timing_pos_num = bin.timing_pos_num();//bin.timing_pos_num()*get_tof_mash_factor() + (get_tof_mash_factor() / 2);
else
max_timing_pos_num = bin.timing_pos_num()*get_tof_mash_factor() + (get_tof_mash_factor())-1;

}

unsigned int current_dp_num=0;
Expand All @@ -387,6 +391,7 @@ get_all_det_pos_pairs_for_bin(vector<DetectionPositionPair<> >& dps,
dps[current_dp_num].pos2().tangential_coord() = det2_num;
dps[current_dp_num].pos2().axial_coord() = rings_iter->second;
dps[current_dp_num].timing_pos() = uncompressed_timing_pos_num;

++current_dp_num;
}
}
Expand Down Expand Up @@ -494,8 +499,8 @@ find_cartesian_coordinates_given_scanner_coordinates (CartesianCoordinate3D<floa
const int num_detectors_per_ring =
get_scanner_ptr()->get_num_detectors_per_ring();

int d1, d2, r1, r2;
int tpos = timing_pos_num;

int d1, d2, r1, r2, tpos;

this->initialise_det1det2_to_uncompressed_view_tangpos_if_not_done_yet();

Expand All @@ -505,14 +510,15 @@ find_cartesian_coordinates_given_scanner_coordinates (CartesianCoordinate3D<floa
d2 = det1;
r1 = Ring_B;
r2 = Ring_A;
tpos *= -1;
tpos=get_max_tof_pos_num()-timing_pos_num;
}
else
{
d1 = det1;
d2 = det2;
r1 = Ring_A;
r2 = Ring_B;
tpos=timing_pos_num;
}

#if 0
Expand Down Expand Up @@ -543,8 +549,9 @@ find_cartesian_coordinates_given_scanner_coordinates (CartesianCoordinate3D<floa
coord_2 = lor.p2();

#endif
if (tpos < 0)
std::swap(coord_1, coord_2);

if (tpos -get_max_tof_pos_num()/2.F < 0)
std::swap(coord_1, coord_2);
}

void
Expand Down
6 changes: 3 additions & 3 deletions src/include/stir/ProjDataInfoCylindricalNoArcCorr.inl
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Expand Up @@ -138,7 +138,7 @@ get_bin_for_det_pair(Bin& bin,
}
else
{
bin.timing_pos_num() = -timing_pos_num;
bin.timing_pos_num() = get_max_tof_pos_num()-timing_pos_num;
return get_segment_axial_pos_num_for_ring_pair(bin.segment_num(), bin.axial_pos_num(), ring_num2, ring_num1);
}
}
Expand All @@ -156,7 +156,7 @@ get_bin_for_det_pos_pair(Bin& bin,
dp.pos2().axial_coord(),
this->get_tof_mash_factor()==0
? 0 // use timing_pos==0 in the nonTOF case
: stir::round((float)dp.timing_pos()/this->get_tof_mash_factor()));
: (int)(dp.timing_pos()/this->get_tof_mash_factor()));
}
void
ProjDataInfoCylindricalNoArcCorr::
Expand Down Expand Up @@ -189,7 +189,7 @@ get_det_pos_pair_for_bin(
//lousy work around because types don't match (short/int). TODO remove!
int t1, a1, t2, a2;
get_det_pair_for_bin(t1, a1, t2, a2, bin);
if (bin.timing_pos_num()>=0)
if (bin.timing_pos_num()-get_max_tof_pos_num()/2.F>=0)
{
dp.pos1().tangential_coord()=t1;
dp.pos1().axial_coord()=a1;
Expand Down
8 changes: 4 additions & 4 deletions src/include/stir/recon_buildblock/DataSymmetriesForBins_PET_CartesianGrid.inl
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Expand Up @@ -353,7 +353,7 @@ find_sym_op_general_bin(
if ( !do_symmetry_swap_segment || segment_num > 0)
{
if ( do_symmetry_swap_s && s < 0)
return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq(view180, axial_pos_shift, z_shift, transform_z);
return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq(view180, axial_pos_shift, z_shift, transform_z, proj_data_info_ptr->get_scanner_ptr()->get_max_num_timing_poss()-1);
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else
{
if (z_shift==0)
Expand All @@ -369,13 +369,13 @@ find_sym_op_general_bin(
return new SymmetryOperation_PET_CartesianGrid_swap_zq(view180, axial_pos_shift, z_shift, transform_z);
else*/
if ( do_symmetry_swap_s && s < 0)
return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(view180, axial_pos_shift, z_shift);
return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(view180, axial_pos_shift, z_shift, proj_data_info_ptr->get_scanner_ptr()->get_max_num_timing_poss()-1);
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else
return new SymmetryOperation_PET_CartesianGrid_swap_zq(view180, axial_pos_shift, z_shift, transform_z); // s > 0
}
else // segment_num = 0
{
if ( do_symmetry_swap_s && s < 0) return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(view180, axial_pos_shift, z_shift);
if ( do_symmetry_swap_s && s < 0) return new SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(view180, axial_pos_shift, z_shift, proj_data_info_ptr->get_scanner_ptr()->get_max_num_timing_poss()-1);
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else
{
if (z_shift==0)
Expand Down Expand Up @@ -484,7 +484,7 @@ find_basic_bin(int &segment_num, int &view_num, int &axial_pos_num, int &tangent
{
//when swap_s, must invert timing pos for lor probs. Symmetry operation should correct bin
tangential_pos_num *= -1;
timing_pos_num *= -1;
timing_pos_num = proj_data_info_ptr->get_max_tof_pos_num() - timing_pos_num;
change=true;
}
if ( do_symmetry_shift_z && axial_pos_num != 0 ) { axial_pos_num = 0; change = true; }
Expand Down
7 changes: 4 additions & 3 deletions src/include/stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.h
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Expand Up @@ -179,7 +179,7 @@ public RegisteredParsingObject<PoissonLogLikelihoodWithLinearModelForMeanAndPro
const ProjData& get_proj_data() const;
const shared_ptr<ProjData>& get_proj_data_sptr() const;
const int get_max_segment_num_to_process() const;
const int get_max_timing_pos_num_to_process() const;
const int get_max_num_central_timing_poss_to_process() const;
const bool get_zero_seg0_end_planes() const;
const ProjData& get_additive_proj_data() const;
const shared_ptr<ProjData>& get_additive_proj_data_sptr() const;
Expand All @@ -201,7 +201,7 @@ public RegisteredParsingObject<PoissonLogLikelihoodWithLinearModelForMeanAndPro
int set_num_subsets(const int num_subsets);
void set_proj_data_sptr(const shared_ptr<ProjData>&);
void set_max_segment_num_to_process(const int);
void set_max_timing_pos_num_to_process(const int);
void set_max_num_central_timing_poss_to_process(const int);
void set_zero_seg0_end_planes(const bool);
//N.E. Changed to ExamData
virtual void set_additive_proj_data_sptr(const shared_ptr<ExamData>&);
Expand Down Expand Up @@ -311,7 +311,8 @@ public RegisteredParsingObject<PoissonLogLikelihoodWithLinearModelForMeanAndPro

//! the maximum absolute time-of-flight bin number to use in the reconstruction
/*! convention: if -1, use get_max_tof_pos_num()*/
int max_timing_pos_num_to_process;
int max_num_central_timing_poss_to_process;
int tof_bin_shift;

/**********************/
ParseAndCreateFrom<TargetT, ProjData> target_parameter_parser;
Expand Down
10 changes: 6 additions & 4 deletions src/include/stir/recon_buildblock/SymmetryOperations_PET_CartesianGrid.h
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Expand Up @@ -339,8 +339,8 @@ class SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq : public SymmetryOpera
private:
typedef SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq self;
public:
SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq(const int num_views, const int axial_pos_shift, const int z_shift, const int q)
: view180(num_views), axial_pos_shift(axial_pos_shift), z_shift(z_shift), q(q)
SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq(const int num_views, const int axial_pos_shift, const int z_shift, const int q, const int max_tof_pos_num)
: view180(num_views), axial_pos_shift(axial_pos_shift), z_shift(z_shift), q(q), timing_shift(max_tof_pos_num)
{}

inline void
Expand All @@ -364,6 +364,7 @@ class SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq : public SymmetryOpera
int axial_pos_shift;
int z_shift;
int q;
int timing_shift;
};

class SymmetryOperation_PET_CartesianGrid_swap_xy_ymx_zq : public SymmetryOperation
Expand Down Expand Up @@ -497,8 +498,8 @@ class SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy : public SymmetryOperatio
private:
typedef SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy self;
public:
SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(const int num_views, const int axial_pos_shift, const int z_shift)
: view180(num_views), axial_pos_shift(axial_pos_shift), z_shift(z_shift)
SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy(const int num_views, const int axial_pos_shift, const int z_shift, const int max_tof_pos_num)
: view180(num_views), axial_pos_shift(axial_pos_shift), z_shift(z_shift), timing_shift(max_tof_pos_num)
{}

inline void
Expand All @@ -521,6 +522,7 @@ class SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy : public SymmetryOperatio
int view180;
int axial_pos_shift;
int z_shift;
int timing_shift;
};

class SymmetryOperation_PET_CartesianGrid_swap_xmy_ymx_zq : public SymmetryOperation
Expand Down
4 changes: 2 additions & 2 deletions src/include/stir/recon_buildblock/SymmetryOperations_PET_CartesianGrid.inl
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Expand Up @@ -351,7 +351,7 @@ SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy_zq::
{
b.axial_pos_num() += axial_pos_shift;
b.tangential_pos_num() *= -1;
b.timing_pos_num() *= -1;
b.timing_pos_num() = timing_shift - b.timing_pos_num();
}

void
Expand Down Expand Up @@ -553,7 +553,7 @@ SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy::
b.axial_pos_num() += axial_pos_shift;
b.segment_num() *= -1;
b.tangential_pos_num() *= -1;
b.timing_pos_num() *= -1;
b.timing_pos_num() = timing_shift - b.timing_pos_num();
}
void
SymmetryOperation_PET_CartesianGrid_swap_xmx_ymy::
Expand Down
36 changes: 20 additions & 16 deletions src/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx
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Expand Up @@ -95,7 +95,7 @@ set_defaults()

this->input_filename="";
this->max_segment_num_to_process=-1;
this->max_timing_pos_num_to_process=0;
this->max_num_central_timing_poss_to_process=-1;
// KT 20/06/2001 disabled
//num_views_to_add=1;
this->proj_data_sptr.reset(); //MJ added
Expand Down Expand Up @@ -322,8 +322,8 @@ get_max_segment_num_to_process() const
template <typename TargetT>
const int
PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT>::
get_max_timing_pos_num_to_process() const
{ return this->max_timing_pos_num_to_process; }
get_max_num_central_timing_poss_to_process() const
{ return this->max_num_central_timing_poss_to_process; }

template <typename TargetT>
const bool
Expand Down Expand Up @@ -416,10 +416,10 @@ set_max_segment_num_to_process(const int arg)
template<typename TargetT>
void
PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT>::
set_max_timing_pos_num_to_process(const int arg)
set_max_num_central_timing_poss_to_process(const int arg)
{
this->already_set_up = this->already_set_up && (this->max_timing_pos_num_to_process == arg);
this->max_timing_pos_num_to_process = arg;
this->already_set_up = this->already_set_up && (this->max_num_central_timing_poss_to_process == arg);
this->max_num_central_timing_poss_to_process = arg;
}

template<typename TargetT>
Expand Down Expand Up @@ -614,8 +614,11 @@ set_up_before_sensitivity(shared_ptr<const TargetT > const& target_sptr)
return Succeeded::no;
}

this->max_timing_pos_num_to_process =
this->proj_data_sptr->get_max_tof_pos_num();
this->max_num_central_timing_poss_to_process =
this->proj_data_sptr->get_max_tof_pos_num();
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I think is wrong, it probably needs a divide by 2 or so

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mh not sure than the shift is different then zero if we want to use them all

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in fact, we don't support this yet, but having wrong code is a bad idea. Add a comment and throw an error if the argument isn't what we expect?

However, it seems hard to know what the argument should be. For 2 TOF bins, the max number of central should be 1. For 3 TOF bins, it should also be 1.5... (1 could work, but how would one say then we only want to do the central one). Looks like the name is still wrong.

Or remove...

// The following "shift"is used to estimate the maximum and minimum tof position number to process
// i.e. min_pos= num_tof_bins+shift and max_pos= num_tof_bins-shift if we use all than shift =0
this->tof_bin_shift = (proj_data_sptr->get_num_tof_poss()-this->max_num_central_timing_poss_to_process)/2;

shared_ptr<ProjDataInfo> proj_data_info_sptr(this->proj_data_sptr->get_proj_data_info_sptr()->clone());

Expand Down Expand Up @@ -745,8 +748,8 @@ actual_compute_subset_gradient_without_penalty(TargetT& gradient,
this->additive_proj_data_sptr,
this->normalisation_sptr,
caching_info_ptr,
-this->max_timing_pos_num_to_process,
this->max_timing_pos_num_to_process,
proj_data_sptr->get_min_tof_pos_num() + tof_bin_shift,
proj_data_sptr->get_max_tof_pos_num() - tof_bin_shift,
add_sensitivity);
}

Expand Down Expand Up @@ -789,8 +792,8 @@ actual_compute_objective_function_without_penalty(const TargetT& current_estimat
this->get_time_frame_definitions().get_start_time(this->get_time_frame_num()),
this->get_time_frame_definitions().get_end_time(this->get_time_frame_num()),
this->caching_info_ptr,
-this->max_timing_pos_num_to_process,
this->max_timing_pos_num_to_process
proj_data_sptr->get_min_tof_pos_num() + tof_bin_shift,
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proj_data_sptr->get_max_tof_pos_num() - tof_bin_shift
);


Expand All @@ -805,10 +808,11 @@ sum_projection_data() const
{

float counts=0.0F;

int min_timing_poss_to_process = proj_data_sptr->get_min_tof_pos_num() + tof_bin_shift;
int max_timing_poss_to_process = proj_data_sptr->get_max_tof_pos_num() - tof_bin_shift;
for (int segment_num = -max_segment_num_to_process; segment_num <= max_segment_num_to_process; ++segment_num)
{
for (int timing_pos_num = -max_timing_pos_num_to_process; timing_pos_num <= max_timing_pos_num_to_process; ++timing_pos_num)
for (int timing_pos_num = min_timing_poss_to_process; timing_pos_num <= max_timing_poss_to_process; ++timing_pos_num)
{
for (int view_num = proj_data_sptr->get_min_view_num();
view_num <= proj_data_sptr->get_max_view_num();
Expand Down Expand Up @@ -901,8 +905,8 @@ add_subset_sensitivity(TargetT& sensitivity, const int subset_num) const
this->get_time_frame_definitions().get_start_time(this->get_time_frame_num()),
this->get_time_frame_definitions().get_end_time(this->get_time_frame_num()),
this->caching_info_ptr,
use_tofsens ? -this->max_timing_pos_num_to_process : 0,
use_tofsens ? this->max_timing_pos_num_to_process : 0);
use_tofsens ? proj_data_sptr->get_min_tof_pos_num() + tof_bin_shift : 0,
use_tofsens ? proj_data_sptr->get_max_tof_pos_num() - tof_bin_shift : 0);

std::transform(sensitivity.begin_all(), sensitivity.end_all(),
sensitivity_this_subset_sptr->begin_all(), sensitivity.begin_all(),
Expand Down
12 changes: 2 additions & 10 deletions src/recon_test/test_DataSymmetriesForBins_PET_CartesianGrid.cxx
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Expand Up @@ -128,16 +128,8 @@ run_tests_2_proj_matrices_1_bin(const ProjMatrixByBin& proj_matrix_no_symm,
{
// SYM const Bin bin=*bin_iter;

cerr << "\nCurrent bin: \tsegment = " << bin.segment_num()
<< ", \taxial pos " << bin.axial_pos_num()
<< ", \tview = " << bin.view_num()
<< ", \ttangential_pos_num = " << bin.tangential_pos_num()
<< ", timing position index = " << bin.timing_pos_num()
<< "\nSymm bin: \t\tsegment = " << elems_with_sym.get_bin().segment_num()
<< ", \taxial pos " << elems_with_sym.get_bin().axial_pos_num()
<< ", \tview = " << elems_with_sym.get_bin().view_num()
<< ", \ttangential_pos_num = " << elems_with_sym.get_bin().tangential_pos_num()
<< ", timing position index = " << bin.timing_pos_num() << "\n";
cerr << "\nCurrent bin: " << elems_no_sym.get_bin()
<< "\nSymm bin: " << elems_with_sym.get_bin()<< "\n";

if (elems_no_sym != elems_with_sym)
{
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