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Fix sigpy tests #227

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merged 3 commits into from
Feb 13, 2025
Merged

Fix sigpy tests #227

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4ba19f7
Fix sigpy tests
btasdelen Dec 30, 2024
2f07fd9
Correct sigpy_pulse doc.
btasdelen Dec 30, 2024
5da0bf3
Merge branch 'master' into fix_sigpy_pulse
schuenke Feb 13, 2025
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26 changes: 22 additions & 4 deletions src/pypulseq/make_sigpy_pulse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,16 +45,14 @@ def sigpy_n_seq(
----------
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 seconds (s).
duration : float, optional, default=4e-3
Duration in seconds (s).
freq_offset : float, optional, default=0
Frequency offset in Hertz (Hz).
center_pos : float, optional, default=0.5
Position of peak.5 (midway).
max_grad : float, optional, default=0
Maximum gradient strength of accompanying slice select trapezoidal event.
max_slew : float, optional, default=0
Expand All @@ -70,6 +68,26 @@ def sigpy_n_seq(
System limits. Default is a system limits object initialized to default values.
time_bw_product : float, optional, default=4
Time-bandwidth product.
pulse_cfg: SigpyPulseOpts, optional, default=None
Pulse configuration options. Possible keys are:
- pulse_type: str, optional, default='slr'
Pulse type. Must be one of 'slr' or 'sms'.
- ptype: str, optional, default='st'
Pulse design method. Must be one of 'st', 'ex', 'inv', 'sat', 'se', 'fi', 'fs', 'se'.
- ftype: str, optional, default='ls'
Filter type. Must be one of 'ls', 'pm', 'min', 'max', 'ap'.
- d1: float, optional, default=0.01
Passband ripple.
- d2: float, optional, default=0.01
Stopband ripple.
- cancel_alpha_phs: bool, optional, default=False
Cancel alpha phase.
- n_bands: int, optional, default=3
Number of bands. SMS only.
- band_sep: float, optional, default=20
Band separation. SMS only.
- phs_0_pt: str, optional, default='None'
Phase 0 point. SMS only.
use : str, optional, default=str()
Use of radio-frequency sinc pulse. Must be one of 'excitation', 'refocusing' or 'inversion'.
plot: bool, optional, default=True
Expand Down
89 changes: 48 additions & 41 deletions tests/test_sigpy.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
# sms - check MB
# slr - check slice profile
"""Tests for SigPy pulse generation."""

import importlib.util

Expand All @@ -21,11 +20,13 @@ def test_sigpy_import():

@pytest.mark.sigpy
def test_slr():
import sigpy.mri.rf as sigpy_rf
from pypulseq.make_sigpy_pulse import sigpy_n_seq

slice_thickness = 3e-3
flip_angle = np.pi / 2
duration = 3e-3
time_bw_product = 4

system = Opts(
max_grad=32,
Expand All @@ -35,6 +36,7 @@ def test_slr():
rf_ringdown_time=30e-6,
rf_dead_time=100e-6,
)

pulse_cfg = SigpyPulseOpts(
pulse_type='slr',
ptype='st',
Expand All @@ -46,47 +48,49 @@ def test_slr():
band_sep=20,
phs_0_pt='None',
)

rfp, _, _ = sigpy_n_seq( # type: ignore
flip_angle=flip_angle,
system=system,
delay=100e-6,
duration=duration,
slice_thickness=slice_thickness,
time_bw_product=4,
return_gz=True,
slice_thickness=slice_thickness,
system=system,
time_bw_product=time_bw_product,
pulse_cfg=pulse_cfg,
plot=False,
delay=system.rf_dead_time,
)

# Check that the number of samples in the pulse is correct
assert rfp.signal.shape[0] == pytest.approx((duration + system.rf_ringdown_time) / system.rf_raster_time)

# Check that the pulse can be added to a PyPulseq Sequence
seq = pp.Sequence(system=system)
seq.add_block(rfp)

assert rfp.signal.shape[0] == pytest.approx((duration + system.rf_ringdown_time) / system.rf_raster_time)

# [a, b] = rf.sim.abrm(
# rfp.signal,
# np.arange(-20 * time_bw_product, 20 * time_bw_product, 40 * time_bw_product / 2000),
# True,
# )
# mag_xy = 2 * np.multiply(np.conj(a), b)
# # pl.LinePlot(Mxy)
# # print(np.sum(np.abs(Mxy)))
# # peaks, dict = sis.find_peaks(np.abs(Mxy),threshold=0.5, plateau_size=40)
# plateau_widths = np.sum(np.abs(mag_xy) > 0.8)
# assert plateau_widths == 29
# Check that the pulse shape is correct
pulse = (rfp.signal * system.rf_raster_time * 2 * np.pi) / flip_angle
[a, b] = sigpy_rf.sim.abrm(
pulse,
np.arange(-20 * time_bw_product, 20 * time_bw_product, 40 * time_bw_product / 2000),
True,
)
mag_xy = 2 * np.multiply(np.conj(a), b)
plateau_widths = np.sum(np.abs(mag_xy) > 0.8)
assert plateau_widths == 29


@pytest.mark.sigpy
def test_sms():
import sigpy.mri.rf as sigpy_rf
from pypulseq.make_sigpy_pulse import sigpy_n_seq

print('Testing SMS design')

slice_thickness = 3e-3 # Slice thickness
slice_thickness = 3e-3
flip_angle = np.pi / 2
duration = 3e-3
n_bands = 3
# Set system limits
time_bw_product = 4

system = Opts(
max_grad=32,
grad_unit='mT/m',
Expand All @@ -95,6 +99,7 @@ def test_sms():
rf_ringdown_time=30e-6,
rf_dead_time=100e-6,
)

pulse_cfg = SigpyPulseOpts(
pulse_type='sms',
ptype='st',
Expand All @@ -106,32 +111,34 @@ def test_sms():
band_sep=20,
phs_0_pt='None',
)

rfp, _, _ = sigpy_n_seq( # type: ignore
flip_angle=flip_angle,
system=system,
delay=100e-6,
duration=duration,
slice_thickness=slice_thickness,
time_bw_product=4,
return_gz=True,
slice_thickness=slice_thickness,
system=system,
time_bw_product=time_bw_product,
pulse_cfg=pulse_cfg,
plot=False,
delay=system.rf_dead_time,
)

# Check that the number of samples in the pulse is correct
assert rfp.signal.shape[0] == pytest.approx((duration + system.rf_ringdown_time) / system.rf_raster_time)

# Check that the pulse can be added to a PyPulseq Sequence
seq = pp.Sequence(system=system)
seq.add_block(rfp)

assert rfp.signal.shape[0] == pytest.approx((duration + system.rf_ringdown_time) / system.rf_raster_time)

# [a, b] = rf.sim.abrm(
# rfp.signal,
# np.arange(-20 * time_bw_product, 20 * time_bw_product, 40 * time_bw_product / 2000),
# True,
# )
# mag_xy = 2 * np.multiply(np.conj(a), b)
# # pl.LinePlot(Mxy)
# # print(np.sum(np.abs(Mxy)))
# # peaks, dict = sis.find_peaks(np.abs(Mxy),threshold=0.5, plateau_size=40)
# plateau_widths = np.sum(np.abs(mag_xy) > 0.8)
# # if slr has 29 > 0.8, then sms with MB = n_bands
# assert (29 * n_bands) == plateau_widths
# Check that the pulse shape is correct
pulse = (rfp.signal * system.rf_raster_time * 2 * np.pi) / flip_angle
[a, b] = sigpy_rf.sim.abrm(
pulse,
np.arange(-20 * time_bw_product, 20 * time_bw_product, 40 * time_bw_product / 2000),
True,
)
mag_xy = 2 * np.multiply(np.conj(a), b)
plateau_widths = np.sum(np.abs(mag_xy) > 0.8)
# if slr has 29 > 0.8, then sms with MB = n_bands
assert (29 * n_bands) == plateau_widths
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