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make_arbitrary_rf.py
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Mon, Jun 10, 13:14

make_arbitrary_rf.py
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import math
from types import SimpleNamespace
import numpy as np
from pypulseq.make_trap_pulse import make_trapezoid
from pypulseq.opts import Opts
def make_arbitrary_rf(signal: np.ndarray, flip_angle: float, system: Opts = Opts(), freq_offset: float = 0,
phase_offset: float = 0, time_bw_product: float = 0, bandwidth: float = 0, max_grad: float = 0,
max_slew: float = 0, slice_thickness: float = 0, delay: float = 0,
use: str = None) -> SimpleNamespace:
"""
Creates a radio-frequency pulse event with arbitrary pulse shape and optionally an accompanying slice select
trapezoidal gradient event.
Parameters
----------
signal : np.ndarray
Arbitrary waveform.
flip_angle : float
Flip angle in radians.
system : Opts
System limits. Default is a system limits object initialised to default values.
freq_offset : float
Frequency offset in Hertz (Hz). Default is 0.
phase_offset : float
Phase offset in Hertz (Hz). Default is 0.
time_bw_product : float
Time-bandwidth product. Default is 4.
bandwidth : float
Bandwidth in Hertz (Hz).
max_grad : float
Maximum gradient strength of accompanying slice select trapezoidal event. Default is `system`'s `max_grad`.
max_slew : float
Maximum slew rate of accompanying slice select trapezoidal event. Default is `system`'s `max_slew`.
slice_thickness : float
Slice thickness of accompanying slice select trapezoidal event. The slice thickness determines the area of the
slice select event.
delay : float
Delay in milliseconds (ms) of accompanying slice select trapezoidal event.
use : str
Use of arbitrary radio-frequency pulse event. Must be one of 'excitation', 'refocusing' or 'inversion'.
Returns
-------
rf : SimpleNamespace
Radio-frequency pulse event with arbitrary pulse shape.
gz : SimpleNamespace
Slice select trapezoidal gradient event accompanying the arbitrary radio-frequency pulse event.
"""
valid_use_pulses = ['excitation', 'refocusing', 'inversion']
if use is not None and use not in valid_use_pulses:
raise ValueError(
f'Invalid use parameter. Must be one of excitation, refocusing or inversion. You passed: {use}')
signal = np.squeeze(signal)
if signal.ndim > 1:
raise ValueError(f'signal should have ndim=1. You passed ndim={signal.ndim}')
signal = signal / np.sum(signal * system.rf_raster_time) * flip_angle / (2 * np.pi)
N = len(signal)
duration = N * system.rf_raster_time
t = np.arange(1, N + 1) * system.rf_raster_time
rf = SimpleNamespace()
rf.type = 'rf'
rf.signal = signal
rf.t = t
rf.freq_offset = freq_offset
rf.phase_offset = phase_offset
rf.dead_time = system.rf_dead_time
rf.ringdown_time = system.rf_ringdown_time
rf.delay = delay
if use is not None:
rf.use = use
if rf.dead_time > rf.delay:
rf.delay = rf.dead_time
try:
if slice_thickness <= 0:
raise ValueError('Slice thickness must be provided.')
if bandwidth <= 0:
raise ValueError('Bandwidth of pulse must be provided.')
if max_grad > 0:
system.max_grad = max_grad
if max_slew > 0:
system.max_slew = max_slew
BW = bandwidth
if time_bw_product > 0:
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)
if rf.delay > gz.rise_time:
gz.delay = math.ceil((rf.delay - gz.rise_time) / system.grad_raster_time) * system.grad_raster_time
if rf.delay < (gz.rise_time + gz.delay):
rf.delay = gz.rise_time + gz.delay
except:
gz = None
if rf.ringdown_time > 0:
t_fill = np.arange(1, round(rf.ringdown_time / 1e-6) + 1) * 1e-6
rf.t = np.concatenate((rf.t, rf.t[-1] + t_fill))
rf.signal = np.concatenate((rf.signal, np.zeros(len(t_fill))))
return rf, gz

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