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make_arbitrary_rf.py
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Thu, Jun 6, 10:34

make_arbitrary_rf.py
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import math
from types import SimpleNamespace
from typing import Tuple, Union
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, bandwidth: float = 0, delay: float = 0,
freq_offset: float = 0, max_grad: float = 0, max_slew: float = 0, phase_offset: float = 0,
return_gz: bool = False, slice_thickness: float = 0, system: Opts = Opts(),
time_bw_product: float = 0,
use: str = str()) -> Union[SimpleNamespace, Tuple[SimpleNamespace, SimpleNamespace]]:
"""
Creates a radio-frequency pulse event with arbitrary pulse shape and optionally an accompanying slice select
trapezoidal gradient event.
Parameters
----------
signal : numpy.ndarray
Arbitrary waveform.
flip_angle : float
Flip angle in radians.
bandwidth : float, default=0
Bandwidth in Hertz (Hz).
delay : float, default=0
Delay in milliseconds (ms) of accompanying slice select trapezoidal event.
freq_offset : float, default=0
Frequency offset in Hertz (Hz).
max_grad : float, default=system.max_grad
Maximum gradient strength of accompanying slice select trapezoidal event.
max_slew : float, default=system.max_slew
Maximum slew rate of accompanying slice select trapezoidal event.
phase_offset : float, default=0
Phase offset in Hertz (Hz).a
return_gz : bool, default=False
Boolean flag to indicate if slice-selective gradient has to be returned.
slice_thickness : float, default=0
Slice thickness of accompanying slice select trapezoidal event. The slice thickness determines the area of the
slice select event.
system : Opts, default=Opts()
System limits.
time_bw_product : float, default=4
Time-bandwidth product.
use : str, default=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, if return_gz=True
Slice select trapezoidal gradient event accompanying the arbitrary radio-frequency pulse event.
Raises
------
ValueError
If invalid `use` parameter is passed. Must be one of 'excitation', 'refocusing' or 'inversion'.
If `signal` with ndim > 1 is passed.
If `return_gz=True`, and `slice_thickness` and `bandwith` are not passed.
"""
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}")
signal = np.squeeze(signal)
if signal.ndim > 1:
raise ValueError(f'signal should have ndim=1. Passed ndim={signal.ndim}')
signal = signal / bp.abs(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 != '':
rf.use = use
if rf.dead_time > rf.delay:
rf.delay = rf.dead_time
if return_gz:
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
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 if return_gz else rf

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