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make_sinc.py
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Fri, Sep 27, 13:10

make_sinc.py
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import numpy as np
from pulseq.core.holder import Holder
from pulseq.core.make_trap import make_trapezoid
from pulseq.core.opts import Opts
def make_sinc_pulse(kwargs, nargout=1):
"""
Makes a Holder object for an RF pulse Event.
Parameters
----------
kwargs : dict
Key value mappings of RF Event parameters_params and values.
nargout: int
Number of output arguments to be returned. Default is 1, only RF Event is returned. Passing any number greater
than 1 will return the Gz Event along with the RF Event.
Returns
-------
rf : Holder
RF Event configured based on supplied kwargs.
gz : Holder
Slice select trapezoidal gradient Event.
"""
flip_angle = kwargs.get("flip_angle")
system = kwargs.get("system", Opts())
duration = kwargs.get("duration", 0)
freq_offset = kwargs.get("freq_offset", 0)
phase_offset = kwargs.get("phase_offset", 0)
time_bw_product = kwargs.get("time_bw_product", 4)
apodization = kwargs.get("apodization", 0)
max_grad = kwargs.get("max_grad", 0)
max_slew = kwargs.get("max_slew", 0)
slice_thickness = kwargs.get("slice_thickness", 0)
BW = time_bw_product / duration
alpha = apodization
N = int(round(duration / 1e-6))
t = np.zeros((1, N))
for x in range(1, N + 1):
t[0][x - 1] = x * system.rf_raster_time
tt = t - (duration / 2)
window = np.zeros((1, tt.shape[1]))
for x in range(0, tt.shape[1]):
window[0][x] = 1.0 - alpha + alpha * np.cos(2 * np.pi * tt[0][x] / duration)
signal = np.multiply(window, np.sinc(BW * tt))
flip = np.sum(signal) * system.rf_raster_time * 2 * np.pi
signal = signal * flip_angle / flip
rf = Holder()
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.ring_down_time = system.rf_ring_down_time
fill_time = 0
if nargout > 1:
if slice_thickness == 0:
raise ValueError('Slice thickness must be provided')
system.max_grad = max_grad if max_grad > 0 else system.max_grad
system.max_slew = max_slew if max_slew > 0 else system.max_slew
amplitude = BW / slice_thickness
area = amplitude * duration
kwargs_for_trap = {"channel": 'z', "system": system, "flat_time": duration, "flat_area": area}
gz = make_trapezoid(kwargs_for_trap)
fill_time = gz.rise_time
nfill_time = int(round(fill_time / 1e-6))
t_fill = np.zeros((1, nfill_time))
for x in range(1, nfill_time + 1):
t_fill[0][x - 1] = x * 1e-6
temp = np.concatenate((t_fill[0], rf.t[0] + t_fill[0][-1]))
temp = temp.reshape((1, len(temp)))
rf.t = np.resize(rf.t, temp.shape)
rf.t[0] = temp
z = np.zeros((1, t_fill.shape[1]))
temp2 = np.concatenate((z[0], rf.signal[0]))
temp2 = temp2.reshape((1, len(temp2)))
rf.signal = np.resize(rf.signal, temp2.shape)
rf.signal[0] = temp2
# Add dead time to start of pulse, if required
if fill_time < rf.dead_time:
fill_time = rf.dead_time - fill_time
t_fill = (np.arange(int(round(fill_time / 1e-6))) * 1e-6)[np.newaxis, :]
rf.t = np.concatenate((t_fill, (rf.t + t_fill[0, -1])), axis=1)
rf.signal = np.concatenate((np.zeros(t_fill.shape), rf.signal), axis=1)
if rf.ring_down_time > 0:
t_fill = (np.arange(1, round(rf.ring_down_time / 1e-6) + 1) * 1e-6)[np.newaxis, :]
rf.t = np.concatenate((rf.t, rf.t[0, -1] + t_fill), axis=1)
rf.signal = np.concatenate((rf.signal, np.zeros(t_fill.shape)), axis=1)
# Following 2 lines of code are workarounds for numpy returning 3.14... for np.angle(-0.00...)
negative_zero_indices = np.where(rf.signal == -0.0)
rf.signal[negative_zero_indices] = 0
if nargout > 1:
return rf, gz
else:
return rf

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