import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from pyreconstruct import reconstruct_from_2DFT,adjust_phase
# Opts
np.set_printoptions(precision=3)
# Import S
S_real = pd.read_csv('S_real.csv',sep=',',header=None).values
S_imag = pd.read_csv('S_imag.csv',sep=',',header=None).values
S = S_real+1j*S_imag
img = reconstruct_from_2DFT(S)
plt.figure()
plt.imshow(img)
plt.colorbar(label='intensity')
plt.xlabel('X position (a.u.)')
plt.ylabel('Y position (a.u.)')
plt.show()
'lac_2_pyr_rate': 0.0,
'pyr_sigma': 0.0,
'lac_sigma': 10e-6
}
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, em_delta_t, conversion_dict,
T1_map, T2_map, main_field, pulse_sequence)
ems, mrs = sim.run_sim()
num_pe_samples = int(2 * pe_sample_radius + 1)
num_fe_samples = int(2 * fe_sample_radius + 1)
S = np.empty([num_pe_samples, num_fe_samples], dtype=complex)
for line_no in range(num_pe_samples):
S[line_no, :] = mrs[line_no]
img, x, y = reconstruct_from_2DFT(S, kx_max, ky_max)
np.savetxt('em-positions_' + fig_params + '.csv',
em_positions,
delimiter=',')
np.savetxt('img_' + fig_params + '.csv', img, delimiter=',')
np.savetxt('x_' + fig_params + '.csv', x, delimiter=',')
np.savetxt('y_' + fig_params + '.csv', y, delimiter=',')
if plot_sim_results:
em_positions = np.loadtxt('em-positions_' + fig_params + '.csv',
delimiter=',')
if em_positions.ndim == 1: em_positions = np.array([em_positions])
img = np.loadtxt('img_' + fig_params + '.csv', delimiter=',')
x = np.loadtxt('x_' + fig_params + '.csv', delimiter=',')
y = np.loadtxt('y_' + fig_params + '.csv', delimiter=',')
x = x * 1e2
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from pyreconstruct import reconstruct_from_2DFT
S_real = pd.read_csv('S_real.csv', sep=',', header=None).values
S_imag = pd.read_csv('S_imag.csv', sep=',', header=None).values
S = S_real + 1j * S_imag
img = np.abs(reconstruct_from_2DFT(S))
plt.figure()
plt.imshow(img)
plt.colorbar()
plt.savefig('reconstruction.pdf')