import math
from copy import copy
from types import SimpleNamespace
from typing import Tuple, Union
from warnings import warn
import numpy as np
from pypulseq.calc_rf_center import calc_rf_center
from pypulseq.make_trapezoid import make_trapezoid
from pypulseq.opts import Opts
from pypulseq.supported_labels_rf_use import get_supported_rf_uses
from pypulseq.utils.tracing import trace, trace_enabled
[docs]
def make_arbitrary_rf(
signal: np.ndarray,
flip_angle: float,
bandwidth: float = 0.0,
delay: float = 0.0,
dwell: float = 0.0,
freq_offset: float = 0.0,
no_signal_scaling: bool = False,
max_grad: float = 0.0,
max_slew: float = 0.0,
phase_offset: float = 0.0,
return_gz: bool = False,
slice_thickness: float = 0.0,
system: Union[Opts, None] = None,
time_bw_product: float = 0.0,
use: str = 'undefined',
freq_ppm: float = 0.0,
phase_ppm: float = 0.0,
center: Union[float, None] = None,
) -> Union[SimpleNamespace, Tuple[SimpleNamespace, SimpleNamespace]]:
"""
Create an RF pulse with the given pulse shape.
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 seconds (s) of accompanying slice select trapezoidal event.
dwell : float, default=0
Temporal sampling step of waveform. If set to 0, will use `system.rf_raster_time`.
freq_offset : float, default=0
Frequency offset in Hertz (Hz).
no_signal_scaling : bool, default=False
If set to True no rescaling of the RF amplitude will happen. E.g. for adiabatic pulses.
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 (m) 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=0
Time-bandwidth product.
use : str, default='undefined'
Use of arbitrary radio-frequency pulse event.
Must be one of 'excitation', 'refocusing', 'inversion',
'saturation', 'preparation', 'other', 'undefined'.
freq_ppm : float, default=0
PPM frequency offset.
phase_ppm : float, default=0
PPM phase offset.
center : float, default=None
RF center (s).
Returns
-------
rf : SimpleNamespace
Radio-frequency pulse event with arbitrary pulse shape.
gz : SimpleNamespace, optional
Slice select trapezoidal gradient event accompanying the arbitrary radio-frequency pulse event.
Raises
------
ValueError
If invalid `use` parameter is passed.
If `signal` with ndim > 1 is passed.
If `return_gz=True`, and `slice_thickness` and `bandwidth` are not passed.
"""
if system is None:
system = Opts.default
valid_pulse_uses = get_supported_rf_uses()
if use != '' and use not in valid_pulse_uses:
raise ValueError(f'Invalid use parameter. Must be one of {valid_pulse_uses}. Passed: {use}')
if dwell == 0:
dwell = system.rf_raster_time
signal = np.squeeze(signal)
if signal.ndim > 1:
raise ValueError(f'signal should have ndim=1. Passed ndim={signal.ndim}')
if not no_signal_scaling:
signal = signal / np.abs(np.sum(signal * dwell)) * flip_angle / (2 * np.pi)
n_samples = len(signal)
duration = n_samples * dwell
t = (np.arange(1, n_samples + 1) - 0.5) * dwell
rf = SimpleNamespace()
rf.type = 'rf'
rf.signal = signal
rf.t = t
rf.shape_dur = duration
rf.freq_offset = freq_offset
rf.phase_offset = phase_offset
rf.freq_ppm = freq_ppm
rf.phase_ppm = phase_ppm
rf.dead_time = system.rf_dead_time
rf.ringdown_time = system.rf_ringdown_time
rf.delay = delay
rf.use = use
if rf.dead_time > rf.delay:
warn(
f'Specified RF delay {rf.delay * 1e6:.2f} us is less than the dead time {rf.dead_time * 1e6:.0f} us. Delay was increased to the dead time.',
stacklevel=2,
)
rf.delay = rf.dead_time
if center is not None:
rf.center = center
if rf.center < 0:
rf.center = 0
if rf.center > rf.shape_dur:
rf.center = rf.shape_dur
else:
rf.center, _ = calc_rf_center(rf)
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 = copy(system)
system.max_grad = max_grad
if max_slew > 0:
system = copy(system)
system.max_slew = max_slew
if time_bw_product > 0:
bandwidth = time_bw_product / duration
amplitude = bandwidth / slice_thickness
area = amplitude * duration
gz = make_trapezoid(channel='z', system=system, flat_time=duration, flat_area=area)
if rf.delay > gz.rise_time:
# Round-up to gradient raster
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 trace_enabled():
rf.trace = trace()
if return_gz:
return rf, gz
else:
return rf
