Homec4science
Diffusion pypulseq (feature-spiral) Browse

pypulseq/sigpy2pulseq.py
1fa25251e5cdfeature-spiral

Last Change
Raw File

sigpy2pulseq.py
View Options

import math
from types import SimpleNamespace
from typing import Tuple, Union
import numpy as np
import pypulseq as pp
import sigpy.mri.rf as rf_ext
import sigpy.plot as pl
from matplotlib import pyplot as plt
from pypulseq.make_trap_pulse import make_trapezoid
from pypulseq.opts import Opts
from scipy import integrate
def sig_2_seq(pulse: float, flip_angle: float, delay: float = 0, duration: float = 0,
freq_offset: float = 0, center_pos: float = 0.5, max_grad: float = 0, max_slew: float = 0,
phase_offset: float = 0, return_gz: bool = True, slice_thickness: float = 0, system: Opts = Opts(),
time_bw_product: float = 4, rf_freq: float = 0,
use: str = str()) -> Union[SimpleNamespace,
Tuple[SimpleNamespace, SimpleNamespace,
SimpleNamespace]]:
"""
Creates a radio-frequency sinc pulse event using the sigpy rf pulse library and optionally accompanying slice select, slice select rephasing
trapezoidal gradient events.
Parameters
----------
pulse : float
Sigpy designed RF pulse
flip_angle : float
Flip angle in radians.
apodization : float, optional, default=0
Apodization.
center_pos : float, optional, default=0.5
Position of peak.5 (midway).
delay : float, optional, default=0
Delay in milliseconds (ms).
duration : float, optional, default=0
Duration in milliseconds (ms).
freq_offset : float, optional, default=0
Frequency offset in Hertz (Hz).
max_grad : float, optional, default=0
Maximum gradient strength of accompanying slice select trapezoidal event.
max_slew : float, optional, default=0
Maximum slew rate of accompanying slice select trapezoidal event.
phase_offset : float, optional, default=0
Phase offset in Hertz (Hz).
return_gz:bool, default=False
Boolean flag to indicate if slice-selective gradient has to be returned.
slice_thickness : float, optional, default=0
Slice thickness of accompanying slice select trapezoidal event. The slice thickness determines the area of the
slice select event.
system : Opts, optional
System limits. Default is a system limits object initialised to default values.
time_bw_product : float, optional, default=4
Time-bandwidth product.
rf_freq : float, optional, default = 0
frequency offset
use : str, optional, default=str()
Use of radio-frequency sinc pulse. Must be one of 'excitation', 'refocusing' or 'inversion'.
Returns
-------
rf : SimpleNamespace
Radio-frequency sinc pulse event.
gz : SimpleNamespace, optional
Accompanying slice select trapezoidal gradient event. Returned only if `slice_thickness` is provided.
gzr : SimpleNamespace, optional
Accompanying slice select rephasing trapezoidal gradient event. Returned only if `slice_thickness` is provided.
Raises
------
ValueError
If invalid `use` parameter was passed. Must be one of 'excitation', 'refocusing' or 'inversion'.
If `return_gz=True` and `slice_thickness` was not provided.
"""
valid_use_pulses = ['excitation', 'refocusing', 'inversion']
if use != '' and use not in valid_use_pulses:
raise ValueError(
f"Invalid use parameter. Must be one of 'excitation', 'refocusing' or 'inversion'. Passed: {use}")
if np.sum(rf_freq) == 0:
# Step 1: Get signal, t
[signal, t] = get_signal(pulse=pulse, duration=duration, flip_angle=flip_angle, system=system)
rfp = SimpleNamespace()
rfp.type = 'rf'
rfp.signal = signal
rfp.t = t
rfp.freq_offset = rf_freq
rfp.phase_offset = phase_offset
rfp.dead_time = system.rf_dead_time
rfp.ringdown_time = system.rf_ringdown_time
rfp.delay = delay
if use != '':
rfp.use = use
if rfp.dead_time > rfp.delay:
rfp.delay = rfp.dead_time
if return_gz:
if slice_thickness == 0:
raise ValueError('Slice thickness must be provided')
if max_grad > 0:
system.max_grad = max_grad
if max_slew > 0:
system.max_slew = max_slew
BW = time_bw_product / duration
amplitude = BW / slice_thickness
area = amplitude * duration
gz = make_trapezoid(channel='z', system=system, flat_time=duration, flat_area=area)
gzr = make_trapezoid(channel='z', system=system, area=-area * (1 - center_pos) - 0.5 * (gz.area - area))
if rfp.delay > gz.rise_time:
gz.delay = math.ceil((rfp.delay - gz.rise_time) / system.grad_raster_time) * system.grad_raster_time
if rfp.delay < (gz.rise_time + gz.delay):
rfp.delay = gz.rise_time + gz.delay
if rfp.ringdown_time > 0:
t_fill = np.arange(1, round(rfp.ringdown_time / 1e-6) + 1) * 1e-6
rfp.t = np.concatenate((rfp.t, rfp.t[-1] + t_fill))
rfp.signal = np.concatenate((rfp.signal, np.zeros(len(t_fill))))
# Following 2 lines of code are workarounds for numpy returning 3.14... for np.angle(-0.00...)
negative_zero_indices = np.where(rfp.signal == -0.0)
rfp.signal[negative_zero_indices] = 0
if return_gz:
return rfp, gz, gzr, pulse
else:
return rfp
else:
print('Working on a FM pulse')
rf_train = get_RF_train(am_pulse=pulse, fm_pulse=rf_freq, duration=duration, system=system,
flip_angle=flip_angle)
return rf_train
def get_signal(pulse: float, duration: float, flip_angle: float, system: Opts = Opts()):
# N = int(round(duration / 1e-6))
N = int(round(duration / system.rf_raster_time))
t = np.arange(1, N + 1) * system.rf_raster_time
flip = np.sum(pulse) * system.rf_raster_time * 2 * np.pi
signal = pulse * flip_angle / flip
return signal, t
def disp_pulse(am_pulse: float, fm_pulse: float = 0, tb=4, duration=3e-3, system: Opts = Opts()):
if np.sum(fm_pulse) == 0:
pl.LinePlot(am_pulse)
# Simulate it
# x =np.arange(-20 * tb, 20 * tb, 40 * tb / 2000)
a = 20
x = np.arange(-a * tb, a * tb, 40 * tb / 2000)
[a, b] = rf_ext.sim.abrm(am_pulse,
x,
True)
Mxy = 2 * np.multiply(np.conj(a), b)
pl.LinePlot(Mxy)
else:
T = duration
Ns = am_pulse.shape[0]
t = np.linspace(-T / 2, T / 2, Ns, endpoint=True) * 1000
plt.figure()
plt.plot(t, np.abs(am_pulse))
plt.xlabel('ms')
plt.ylabel('a.u.')
plt.title('|AM|')
plt.figure()
plt.plot(t, fm_pulse / 1000)
plt.xlabel('ms')
plt.ylabel('kHz')
plt.title('FM')
# Simulate it
b1 = np.arange(0, 1, 0.01) # b1 grid we simulate the pulse over, Gauss
b1 = np.reshape(b1, (np.size(b1), 1))
a = np.zeros(np.shape(b1), dtype='complex')
b = np.zeros(np.shape(b1), dtype='complex')
for ii in range(0, np.size(b1)):
[a[ii], b[ii]] = rf_ext.sim.abrm_nd(2 * np.pi * (T / t.shape[0]) * 4258 * b1[ii] * am_pulse, np.ones(1),
T / t.shape[0] * np.reshape(fm_pulse, (np.size(fm_pulse), 1)))
Mz = 1 - 2 * np.abs(b) ** 2
plt.figure()
plt.plot(b1, Mz)
plt.xlabel('Gauss')
plt.ylabel('Mz')
def get_RF_train(am_pulse, fm_pulse, duration, system, flip_angle):
#scale the amplitude according to pulseq requirements
RF_train = []
Ns = am_pulse.shape[0]
Tseg = np.round(duration / Ns, 6)
t_rf_raster = system.rf_raster_time
system.rf_raster_time = Tseg
[signal, _] = get_signal(pulse=am_pulse, duration=duration, flip_angle=flip_angle, system=system)
t_block = np.round(0.5 * Tseg, 6) # Fixed at 50% duty cycle
system.rf_raster_time = t_rf_raster
system.rf_ringdown_time = np.round(0.5 * Tseg, 6) # To ensure 50% duty cycle
ph = 0
alpha = 0
for n in range(1, Ns):
flip_angle_block = 2 * math.pi * signal[n - 1] * t_block
pulse = pp.make_block_pulse(flip_angle=flip_angle_block, duration=t_block,
phase_offset=ph, system=system)
rfp = SimpleNamespace()
rfp.type = 'rf'
rfp.signal = pulse.signal
rfp.t = pulse.t
rfp.freq_offset = pulse.freq_offset
rfp.phase_offset = pulse.phase_offset
rfp.dead_time = 0
rfp.ringdown_time = system.rf_ringdown_time
rfp.delay = 0
RF_train.append(rfp)
alpha = alpha + 2 * math.pi * signal[n] * (Tseg)
del_ph = integrate.trapz([fm_pulse[n], fm_pulse[n - 1]], x=None, dx=t_block)
ph = ph + del_ph * 2 * math.pi
print(flip_angle)
print(alpha)
return RF_train
c4science · Help