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reading gradient
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@aghaeifar
aghaeifar committed Feb 15, 2024
1 parent 8b58b52 commit bc5a0fa
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Showing 3 changed files with 82 additions and 34 deletions.
9 changes: 9 additions & 0 deletions config/config_default.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,15 @@ DEPHASING[2] =
DEPHASING_T[0] =
DEPHASING_T[1] =
DEPHASING_T[2] =
; Apply gradient in T/m for each axis. Gradients are active for one DWELL_TIME
GRADIENT_XYZ[0] = 0.0 0.0 0.0
GRADIENT_XYZ[1] = 0.0 0.0 0.0
GRADIENT_XYZ[2] = 0.0 0.0 0.0
; Time (sec) to apply gradient.
GRADIENT_T[0] = 0.0
GRADIENT_T[1] = 0.0
GRADIENT_T[2] = 0.0


DWELL_TIME = 50e-6

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81 changes: 50 additions & 31 deletions src/file_utils.h
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Original file line number Diff line number Diff line change
Expand Up @@ -162,16 +162,7 @@ bool read_config(std::string config_filename, simulation_parameters& param, std:
for(i=0; i<MAX_RF && ini.get("SCAN_PARAMETERS").has("RF_ST[" + std::to_string(i) + "]"); i++)
param.RF_ST[i] = std::stof(ini.get("SCAN_PARAMETERS").get("RF_ST[" + std::to_string(i) + "]")) / param.dt;

// check RF start time conditions
if (std::is_sorted(param.RF_ST, param.RF_ST + i) == false ||
std::adjacent_find(param.RF_ST, param.RF_ST + i) != param.RF_ST + i ||
param.RF_ST[0] != 0 ||
(param.n_RF = i) == 0)
{
std::copy(param.RF_ST, param.RF_ST + param.n_RF, std::ostream_iterator<int>(std::cout, " ")); std::cout << std::endl;
std::cout << ERR_MSG << "RF Times must be in ascending order, starts with 0 and must not have duplicates values" << std::endl;
return false;
}
param.n_RF = i;
// RF flip angles
for(i=0; i<param.n_RF && ini.get("SCAN_PARAMETERS").has("RF_FA[" + std::to_string(i) + "]"); i++)
param.RF_FA[i] = std::stof(ini.get("SCAN_PARAMETERS").get("RF_FA[" + std::to_string(i) + "]")) ;
Expand All @@ -191,39 +182,67 @@ bool read_config(std::string config_filename, simulation_parameters& param, std:
return false;
}

// ---------------- dephasing (start times, Flip angles ) ----------------
// Dephase start times
for(i=0; i<MAX_RF && ini.get("SCAN_PARAMETERS").has("DEPHASING_T[" + std::to_string(i) + "]"); i++)
{
try
{
param.dephasing_T[i] = std::stof(ini.get("SCAN_PARAMETERS").get("DEPHASING_T[" + std::to_string(i) + "]")) / param.dt;
}
catch(const std::exception& e)
{
break;
}
}

param.n_dephasing = i;

// check RF start time conditions
if (std::is_sorted(param.dephasing_T, param.dephasing_T + i) == false ||
std::adjacent_find(param.dephasing_T, param.dephasing_T + i) != param.dephasing_T + i )
if (std::is_sorted(param.RF_ST, param.RF_ST + i) == false ||
std::adjacent_find(param.RF_ST, param.RF_ST + i) != param.RF_ST + i ||
param.RF_ST[0] != 0 ||
param.n_RF == 0)
{
std::copy(param.RF_ST, param.RF_ST + param.n_RF, std::ostream_iterator<int>(std::cout, " ")); std::cout << std::endl;
std::cout << ERR_MSG << "RF Times must be in ascending order and must not have duplicates values" << std::endl;
std::cout << ERR_MSG << "RF Times must be in ascending order, starts with 0 and must not have duplicates values" << std::endl;
return false;
}
}

// ---------------- dephasing (start times, Flip angles ) ----------------
// Dephase start times
for(i=0; i<MAX_RF && ini.get("SCAN_PARAMETERS").has("DEPHASING_T[" + std::to_string(i) + "]"); i++)
param.dephasing_T[i] = std::stof(ini.get("SCAN_PARAMETERS").get("DEPHASING_T[" + std::to_string(i) + "]")) / param.dt;

param.n_dephasing = i;
// Dephase flip angles
for(i=0; i<param.n_dephasing && ini.get("SCAN_PARAMETERS").has("DEPHASING[" + std::to_string(i) + "]"); i++)
param.dephasing[i] = std::stof(ini.get("SCAN_PARAMETERS").get("DEPHASING[" + std::to_string(i) + "]")) ;

if(i != param.n_dephasing)
{
std::cout << ERR_MSG << "DEPHASING and DEPHASING_T must have the same number of elements" << std::endl;
return false;
}
}

// check Dephase start time conditions
if (std::is_sorted(param.dephasing_T, param.dephasing_T + i) == false ||
std::adjacent_find(param.dephasing_T, param.dephasing_T + i) != param.dephasing_T + i )
{
std::copy(param.dephasing_T, param.dephasing_T + param.n_dephasing, std::ostream_iterator<int>(std::cout, " ")); std::cout << std::endl;
std::cout << ERR_MSG << "dephasing Times must be in ascending order and must not have duplicates values" << std::endl;
return false;
}

// ---------------- Gradients (start times, strength (T/m) ) ----------------
// Gradient start times
for(i=0; i<MAX_GRADIENT && ini.get("SCAN_PARAMETERS").has("GRADIENT_T[" + std::to_string(i) + "]"); i++)
param.gradient_T[i] = std::stof(ini.get("SCAN_PARAMETERS").get("GRADIENT_T[" + std::to_string(i) + "]")) / param.dt;

param.n_gradient = i;
// Gradient strength
for(i=0; i<param.n_gradient && ini.get("SCAN_PARAMETERS").has("GRADIENT_XYZ[" + std::to_string(i) + "]"); i++)
param.gradient_xyz[i] = std::stof(ini.get("SCAN_PARAMETERS").get("GRADIENT_XYZ[" + std::to_string(i) + "]")) ;

if(i != param.n_gradient)
{
std::cout << ERR_MSG << "GRADIENT_XYZ and GRADIENT_T must have the same number of elements" << std::endl;
return false;
}

// check Dephase start time conditions
if (std::is_sorted(param.gradient_T, param.gradient_T + i) == false ||
std::adjacent_find(param.gradient_T, param.gradient_T + i) != param.gradient_T + i )
{
std::copy(param.gradient_T, param.gradient_T + param.n_gradient, std::ostream_iterator<int>(std::cout, " ")); std::cout << std::endl;
std::cout << ERR_MSG << "Gradient Times must be in ascending order and must not have duplicates values" << std::endl;
return false;
}

}

// ============== reading section SCAN_PARAMETERS ==============
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26 changes: 23 additions & 3 deletions src/miscellaneous.h
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Original file line number Diff line number Diff line change
Expand Up @@ -25,20 +25,36 @@
#define MAX_RF 128 // maximum number of RF
#define MAX_TE 256 // maximum number of echo times
#define MAX_DEPHASE 128 // maximum number of dephasing
#define MAX_GRADIENT 128 // maximum number of gradient

typedef struct simulation_parameters
{
float T1, T2, TR, dt, B0, e1, e12, e2, e22, c, s, c2, s2;
float RF_FA[MAX_RF], RF_PH[MAX_RF]; // refocusing FA
float dephasing[MAX_DEPHASE]; // dephasing in degree
int32_t RF_ST[MAX_RF], TE[MAX_TE], dephasing_T[MAX_DEPHASE]; // refocusing time in dt, echo times in dt, dephasing time in dt
float gradient_xyz[3*MAX_GRADIENT]; // gradient in T/m
int32_t RF_ST[MAX_RF], TE[MAX_TE], dephasing_T[MAX_DEPHASE], gradient_T[MAX_GRADIENT]; // refocusing time in dt, echo times in dt, dephasing time in dt
float sample_length[3], scale2grid[3], diffusion_const, phase_cycling;
int32_t n_timepoints, n_sample_length_scales, n_fieldmaps, n_TE, n_RF, n_dephasing;
int32_t n_timepoints, n_sample_length_scales, n_fieldmaps, n_TE, n_RF, n_dephasing, n_gradient;
int32_t n_dummy_scan;
uint32_t n_spins, fieldmap_size[3], seed;
uint64_t matrix_length;
bool enDebug, enApplyFA2, enCrossBoundry;
simulation_parameters():T1(2.2),T2(0.04),TR(0.04),dt(5e-5),B0(9.4),n_TE(0),n_RF(0),n_dummy_scan(0),phase_cycling(0.),enApplyFA2(false),enDebug(false),enCrossBoundry(true)
simulation_parameters():
T1(2.2),
T2(0.04),
TR(0.04),
dt(5e-5),
B0(9.4),
n_TE(0),
n_RF(0),
n_dephasing(0),
n_gradient(0),
n_dummy_scan(0),
phase_cycling(0.),
enApplyFA2(false),
enDebug(false),
enCrossBoundry(true)
{
memset(fieldmap_size, 0, 3*sizeof(fieldmap_size[0]));
memset(sample_length, 0, 3*sizeof(sample_length[0]));
Expand All @@ -48,6 +64,8 @@ typedef struct simulation_parameters
memset(RF_PH, 0, MAX_RF*sizeof(RF_PH[0]));
memset(dephasing, 0, MAX_DEPHASE*sizeof(dephasing[0]));
memset(dephasing_T, 0, MAX_DEPHASE*sizeof(dephasing_T[0]));
memset(gradient_xyz, 0, 3*MAX_GRADIENT*sizeof(gradient_xyz[0]));
memset(gradient_T, 0, MAX_GRADIENT*sizeof(gradient_T[0]));
}

void dump()
Expand All @@ -59,6 +77,8 @@ typedef struct simulation_parameters
std::cout<<"RF time = "; for(int i=0; i<n_RF; i++) std::cout<<RF_ST[i]*dt<<' '; std::cout<<'\n';
std::cout<<"dephasing degree = "; for(int i=0; i<n_dephasing; i++) std::cout<<dephasing[i]<<' '; std::cout<<'\n';
std::cout<<"dephasing time = "; for(int i=0; i<n_dephasing; i++) std::cout<<dephasing_T[i]*dt<<' '; std::cout<<'\n';
std::cout<<"gradient T/m = "; for(int i=0; i<3*n_gradient; i++) std::cout<<gradient_xyz[i]<<' '; std::cout<<'\n';
std::cout<<"gradient time = "; for(int i=0; i<n_gradient; i++) std::cout<<gradient_T[i]<<' '; std::cout<<'\n';
std::cout<<"sample length = "<< sample_length[0] << " x " << sample_length[1] << " x " << sample_length[2] << " m" << '\n';
std::cout<<"scale2grid = "<< scale2grid[0] << " x " << scale2grid[1] << " x " << scale2grid[2] << '\n';
std::cout<<"fieldmap size = "<< fieldmap_size[0] << " x " << fieldmap_size[1] << " x " << fieldmap_size[2] << '\n';
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