def my_func():
grid_radius = 1
fig_params = 'T1-100ms_T2-10ms_TE-4ms_TR-100ms_x-0.0_y-minus-0.5'
see_sequence = False
run_sim = True
plot_sim_results = True
reconstruction_name = 'reconstruction_'+fig_params+'.pdf'
# Place ems
r0 = np.array([[0.0,-0.5,0.0]])*1e-2
em_positions = np.tile(r0,(8000,1))
num_ems = em_positions.shape[0]
em_gyromagnetic_ratio = 2.675e8
main_field = 3.0
em_equilibrium_magnetization = 1.0
em_magnetizations = np.zeros([num_ems,3])
em_magnetizations[:,1] = 1.0
em_shielding_constants = np.zeros(num_ems)
em_velocities = np.zeros([num_ems,3],dtype=float)
# Compute the pulse sequence
Gz_amplitude = 10.0e-3
slice_width = 5e-2
delta_t = 1e-6
xlim = 1e-2
ylim = xlim
fe_sample_radius = grid_radius
pe_sample_radius = grid_radius
kx_max = grid_radius/(2*xlim)
ky_max = grid_radius/(2*ylim)
kmove_time = 1e-3
kread_time = 8e-3
read_all = False
T1_max = 100e-3
T2_max = 10e-3
repetition_time = 100e-3
gyromagnetic_ratio = em_gyromagnetic_ratio
# Create pulse sequence
## pulse_length = int(4e6)
## Gx = np.zeros(pulse_length)
## Gy = np.zeros(pulse_length)
## Gz = np.zeros(pulse_length)
## readout = np.zeros(pulse_length,dtype=bool)
## delta_t = 1e-6
## pulse_sequence = [Pulse(mode='free',Gx=Gx,Gy=Gy,Gz=Gz,readout=readout,delta_t=delta_t)]
pulse_sequence = generate_2DFT_sequence(main_field,Gz_amplitude,slice_width,gyromagnetic_ratio,fe_sample_radius,pe_sample_radius,kx_max,ky_max,kmove_time,kread_time,repetition_time,delta_t,read_all)
# Initialize simulation
def T1_map(position): return T1_max
def T2_map(position): return T2_max
print('beginning sim with ' + str(num_ems) + ' ems')
sim = Sim(em_magnetizations,em_positions,em_velocities,em_gyromagnetic_ratio,em_shielding_constants,em_equilibrium_magnetization,T1_map,T2_map,main_field,pulse_sequence)
em_shielding_constants = np.zeros(num_ems)
em_velocities = np.zeros([num_ems, 3], dtype=float)
# Compute the pulse sequence
Gz_amplitude = 10.0e-3
slice_width = 5e-2
delta_t = 1e-6
fe_sample_radius = grid_radius
pe_sample_radius = grid_radius
kx_max = grid_radius / (2 * xlim)
ky_max = grid_radius / (2 * ylim)
kmove_time = 1e-3
adc_rate = 5e3
pulse_sequence = generate_2DFT_sequence(main_field, Gz_amplitude, slice_width,
em_gyromagnetic_ratio,
fe_sample_radius, pe_sample_radius,
kx_max, ky_max, kmove_time, adc_rate,
delta_t)
if see_sequence:
see_2DFT_sequence(pulse_sequence)
# Run simulation
if run_sim:
def T1_map(position):
return 1e6
def T2_map(position):
return 1e6
print('beginning sim with ' + str(num_ems) + ' ems')
ylim = xlim
fe_sample_radius = grid_radius
pe_sample_radius = grid_radius
kx_max = grid_radius / (2 * xlim)
ky_max = grid_radius / (2 * ylim)
kmove_time = 1e-3
kread_time = 8e-3
read_all = False
T1_max = 100e-3
T2_max = 10e-3
repetition_time = 100e-3
gyromagnetic_ratio = em_gyromagnetic_ratio
# Create pulse sequence
pulse_sequence = generate_2DFT_sequence(main_field, Gz_amplitude, slice_width,
gyromagnetic_ratio, fe_sample_radius,
pe_sample_radius, kx_max, ky_max,
kmove_time, kread_time,
repetition_time, pulse_delta_t,
read_all)
if see_sequence: see_readout_pulses(pulse_sequence)
##tip_angle = np.pi/2.0
##gyromagnetic_ratio = em_gyromagnetic_ratio
##pulse_tip = generate_tipping_pulse(gyromagnetic_ratio,main_field,Gz_amplitude,slice_width,tip_angle,delta_t)
##pulse_sequence = generate_kspace_pulses(pulse_tip,fe_sample_radius,pe_sample_radius,kx_max,ky_max,kmove_time,adc_rate,gyromagnetic_ratio,delta_t,read_all)
if run_sim:
# Run simulation
def T1_map(position):
return T1_max
def T2_map(position):
return T2_max