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Numpy 2.0 and Scipy 1.16 updates #1

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10 changes: 5 additions & 5 deletions PulseShape/PulseShape.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import numpy as np
from scipy.interpolate import interp1d, pchip_interpolate
from scipy.integrate import cumtrapz
from scipy.integrate import cumulative_trapezoid
from .modulations import AmplitudeModulations, FrequencyModulations
from .utils import sop, pulse_propagation, transmitter

Expand Down Expand Up @@ -205,12 +205,12 @@ def bw_comp(self):
if self.fm_func.__name__ == 'uniformq' or self.shape == 'sech/tanh':
profile *= A0

int = cumtrapz(profile ** -2, nu0, initial=0)
int = cumulative_trapezoid(profile ** -2, nu0, initial=0)
tf = self.time[-1] * int / int[-1]
nu_adapted = pchip_interpolate(tf, nu0, self.time)

self.frequency_modulation = nu_adapted
self.phase = 2 * np.pi * cumtrapz(self.frequency_modulation, self.time, initial=0)
self.phase = 2 * np.pi * cumulative_trapezoid(self.frequency_modulation, self.time, initial=0)
self.phase += np.abs(np.min(self.phase))

if self.fm_func.__name__ == 'uniformq' or self.shape == 'sech/tanh':
Expand All @@ -223,7 +223,7 @@ def _compute_flip_amp(self):
"""Compute flip angle if not supplied by user"""

if self.fm_func.__name__ == 'none':
self.amp = self.flip / (2 * np.pi * np.trapz(self.amplitude_modulation, self.time))
self.amp = self.flip / (2 * np.pi * np.trapezoid(self.amplitude_modulation, self.time))
else:
if self.Qcrit is None:
with np.errstate(divide='ignore'):
Expand Down Expand Up @@ -282,7 +282,7 @@ def estimate_timestep(self):
# perform FFT and calculate bandwidth
A0fft = np.abs(np.fft.fftshift(np.fft.fft(tpulse.amplitude_modulation, zf)))
f = np.fft.fftshift(np.fft.fftfreq(zf, dt))
intg = cumtrapz(A0fft, initial=0)
intg = cumulative_trapezoid(A0fft, initial=0)
idx = np.argmin(np.abs(intg - 0.5 * np.max(intg)))
indbw = np.squeeze(np.argwhere(A0fft[idx:] > 0.1 * max(A0fft)))
AM_BW = 2 * (f[idx + indbw[-1] + 1] - f[idx])
Expand Down
6 changes: 3 additions & 3 deletions PulseShape/modulations.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from functools import wraps
import numpy as np
from scipy.integrate import cumtrapz
from scipy.integrate import cumulative_trapezoid

AmplitudeModulations = {}
FrequencyModulations = {}
Expand Down Expand Up @@ -387,8 +387,8 @@ def uniformq(Pulse):
------
None"""

freq = cumtrapz(Pulse.amplitude_modulation**2, Pulse.ti, initial=0) / np.trapz(Pulse.amplitude_modulation**2, Pulse.ti, )
freq = cumulative_trapezoid(Pulse.amplitude_modulation**2, Pulse.ti, initial=0) / np.trapezoid(Pulse.amplitude_modulation**2, Pulse.ti, )
freq = (Pulse.freq[1] - Pulse.freq[0]) * (freq - 1/2)
phase = 2 * np.pi * cumtrapz(freq, Pulse.ti, initial=0)
phase = 2 * np.pi * cumulative_trapezoid(freq, Pulse.ti, initial=0)
phase += np.abs(min(phase))
return freq, phase
4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@

setup(
name='PulseShape',
version='0.1.4',
version='0.1.5',
packages=['PulseShape'],
python_requires='>=3.6',
install_requires=['numpy>=1.19', 'scipy>=1.5', 'matplotlib>=3.0'],
install_requires=['numpy>=2.0', 'scipy>=1.6', 'matplotlib>=3.0'],
url='https://gitlab.com/mtessmer/PulseShape',
project_urls = {'Source': 'https://gitlab.com/mtessmer/PulseShape'},
license='GNU GPLv3',
Expand Down