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Bug fixes in make_extended_trapezoid and add_gradients #167

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merged 6 commits into from
Feb 7, 2024
Merged

Bug fixes in make_extended_trapezoid and add_gradients #167

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7201025
Added missing `area` calculation to `make_extended_trapezoid`
FrankZijlstra Feb 5, 2024
20358a5
Fixed bug in `add_gradients`
FrankZijlstra Feb 5, 2024
a22879a
Fixed incorrect `shape_dur` in `make_extended_trapezoid` when a delay…
FrankZijlstra Feb 5, 2024
a3cdf82
Fixed a bug in `event_lib` which could give KeyError's when duplicate…
FrankZijlstra Feb 6, 2024
6a5109d
Revert cleanup in `add_gradients` because it broke other code...
FrankZijlstra Feb 7, 2024
a9d1e03
Fixed `Opts` to work properly with negative `gamma` (e.g. for Oxygen-17)
FrankZijlstra Feb 7, 2024
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4 changes: 2 additions & 2 deletions pypulseq/add_gradients.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ def add_gradients(
else:
times.extend(g.delay + g.tt)

times = np.sort(np.unique(times))
times = np.unique(times)
dt = times[1:] - times[:-1]
ieps = np.flatnonzero(dt < eps)
if np.any(ieps):
Expand Down Expand Up @@ -140,7 +140,7 @@ def add_gradients(
if abs(waveform[0]) > eps and tt[0] > eps:
tt[0] += eps

amplitudes += np.interp(xp=tt, fp=waveform, x=times)
amplitudes += np.interp(xp=tt, fp=waveform, x=times, left=0, right=0)

grad = make_extended_trapezoid(
channel=channel, amplitudes=amplitudes, times=times, system=system
Expand Down
7 changes: 6 additions & 1 deletion pypulseq/event_lib.py
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Expand Up @@ -219,7 +219,12 @@ def update(
data_type : str, default=str()
"""
if key_id in self.data:
del self.keymap[self.data[key_id]]
# TODO: When reading a sequence file we can end up with duplicate
# events due to rounding to 6 digits. update() calls to both
# duplicates would give a key error here on the second
# duplicate. Ideally no duplicates should exist though...
if self.data[key_id] in self.keymap:
del self.keymap[self.data[key_id]]

self.insert(key_id, new_data, data_type)

Expand Down
5 changes: 2 additions & 3 deletions pypulseq/make_extended_trapezoid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,9 +136,8 @@ def make_extended_trapezoid(
round(times[0] / system.grad_raster_time) * system.grad_raster_time
)
grad.tt = times - grad.delay
grad.shape_dur = (
round(times[-1] / system.grad_raster_time) * system.grad_raster_time
)
grad.shape_dur = grad.tt[-1]
grad.area = 0.5 * ((grad.tt[1:] - grad.tt[:-1]) * (grad.waveform[1:] + grad.waveform[:-1])).sum()

grad.first = amplitudes[0]
grad.last = amplitudes[-1]
Expand Down
4 changes: 2 additions & 2 deletions pypulseq/opts.py
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Expand Up @@ -82,14 +82,14 @@ def __init__(

if max_grad != None:
max_grad = convert(
from_value=max_grad, from_unit=grad_unit, to_unit="Hz/m", gamma=gamma
from_value=max_grad, from_unit=grad_unit, to_unit="Hz/m", gamma=abs(gamma)
)
else:
max_grad = Opts.default.max_grad

if max_slew != None:
max_slew = convert(
from_value=max_slew, from_unit=slew_unit, to_unit="Hz/m", gamma=gamma
from_value=max_slew, from_unit=slew_unit, to_unit="Hz/m", gamma=abs(gamma)
)
else:
max_slew = Opts.default.max_slew
Expand Down
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