Skip to content

np.trapz is deprecated. Updating to np.trapezoid #45

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bd-j merged 2 commits into from
May 29, 2025
Merged

np.trapz is deprecated. Updating to np.trapezoid #45

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
168f4f8
np.trapz is deprecated. Updating to np.trapezoid
sbruto May 21, 2025
bd683ff
try import of trapezoid, fall back to importing trapz
sbruto May 29, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 16 additions & 11 deletions sedpy/observate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,11 @@
"""

import numpy as np
try:
from numpy import trapezoid
except(ImportError):
from numpy import trapz as trapezoid

import os
try:
from pkg_resources import resource_filename, resource_listdir
Expand Down Expand Up @@ -238,13 +243,13 @@ def get_properties(self):
of many of these quantities.
"""
# Calculate some useful integrals
i0 = np.trapz(self.transmission * np.log(self.wavelength),
i0 = trapezoid(self.transmission * np.log(self.wavelength),
np.log(self.wavelength))
i1 = np.trapz(self.transmission,
i1 = trapezoid(self.transmission,
np.log(self.wavelength))
i2 = np.trapz(self.transmission * self.wavelength,
i2 = trapezoid(self.transmission * self.wavelength,
self.wavelength)
i3 = np.trapz(self.transmission,
i3 = trapezoid(self.transmission,
self.wavelength)

tmax = self.transmission.max()
Expand All @@ -262,14 +267,14 @@ def get_properties(self):
rind = np.argmin(self.wavelength[sel])
self.red_edge = self.wavelength[sel][rind]

i4 = np.trapz(self.transmission *
i4 = trapezoid(self.transmission *
(np.log(self.wavelength / self.wave_effective))**2.0,
np.log(self.wavelength))
self.gauss_width = (i4 / i1)**(0.5)
self.effective_width = (2.0 * np.sqrt(2. * np.log(2.)) *
self.gauss_width *
self.wave_effective)
# self.norm = np.trapz(transmission,wavelength)
# self.norm = trapezoid(transmission,wavelength)

# Get zero points and AB to Vega conversion
self.ab_zero_counts = self.obj_counts(self.wavelength,
Expand Down Expand Up @@ -340,7 +345,7 @@ def obj_counts_hires(self, sourcewave, sourceflux, sourceflux_unc=0):
# assert ~edge, "Source spectrum does not span filter."
ind = slice(max(positive.min() - 1, 0),
min(positive.max() + 2, len(sourcewave)))
counts = np.trapz(sourcewave[ind] * newtrans[ind] *
counts = trapezoid(sourcewave[ind] * newtrans[ind] *
sourceflux[..., ind],
sourcewave[ind], axis=-1)
return np.squeeze(counts)
Expand Down Expand Up @@ -376,7 +381,7 @@ def obj_counts_lores(self, sourcewave, sourceflux, sourceflux_unc=0):

# Integrate lambda*f_lambda*R
if True in (newflux > 0.):
counts = np.trapz(self.wavelength * self.transmission * newflux,
counts = trapezoid(self.wavelength * self.transmission * newflux,
self.wavelength)
return np.squeeze(counts)
else:
Expand Down Expand Up @@ -564,7 +569,7 @@ def _build_super_trans(self):
"""
# TODO: investigate using arrays that cover different wavelength
# intervals (but same number of elements) for each filter. Then when
# integrating (with dot or vectorized trapz) the source spectrum must be
# integrating (with dot or vectorized trapezoid) the source spectrum must be
# offset for each filter. This would remove the vast majority of zeros

ab_counts = np.array([f.ab_zero_counts for f in self.filters])
Expand Down Expand Up @@ -664,7 +669,7 @@ def get_sed_maggies_trapz(self, sourceflux, sourcewave=None):
flux = sourceflux
y = self.trans_dw * flux[self.finds]
x = self.lam[self.finds]
maggies = np.trapz(y, x, axis=-1)
maggies = trapezoid(y, x, axis=-1)
return maggies

def get_sed_maggies_numba(self, sourceflux, sourcewave=None):
Expand Down Expand Up @@ -854,7 +859,7 @@ def Lbol(wave, spec, wave_min=90, wave_max=1e6):
of length (...nsource)
"""
inds = np.where(np.logical_and(wave < wave_max, wave >= wave_min))
return np.trapz(spec[..., inds[0]], wave[inds])
return trapezoid(spec[..., inds[0]], wave[inds])


def air2vac(air):
Expand Down
13 changes: 9 additions & 4 deletions sedpy/smoothing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,11 @@
# * more testing of the smooth_lsf* methods.

import numpy as np
try:
from numpy import trapezoid
except(ImportError):
from numpy import trapz as trapezoid

from numpy.fft import fft, ifft, fftfreq, rfftfreq

__all__ = ["smoothspec", "smooth_wave", "smooth_vel", "smooth_lsf",
Expand Down Expand Up @@ -229,7 +234,7 @@ def smooth_vel(wave, spec, outwave, sigma, nsigma=10, inres=0, **extras):
else:
_spec = spec
f = np.exp(-0.5 * x**2)
flux[i] = np.trapz(f * _spec, x) / np.trapz(f, x)
flux[i] = trapezoid(f * _spec, x) / trapezoid(f, x)
return flux


Expand Down Expand Up @@ -352,7 +357,7 @@ def smooth_wave(wave, spec, outwave, sigma, nsigma=10, inres=0, in_vel=False,
else:
_spec = spec
f = np.exp(-0.5 * x**2)
flux[i] = np.trapz(f * _spec, x) / np.trapz(f, x)
flux[i] = trapezoid(f * _spec, x) / trapezoid(f, x)
return flux


Expand Down Expand Up @@ -463,8 +468,8 @@ def smooth_lsf(wave, spec, outwave, sigma=None, lsf=None, return_kernel=False,
# should this be axis=0 or axis=1?
kernel = kernel / kernel.sum(axis=1)[:, None]
newspec = np.dot(kernel, spec)
# kernel /= np.trapz(kernel, wave, axis=1)[:, None]
# newspec = np.trapz(kernel * spec[None, :], wave, axis=1)
# kernel /= trapezoid(kernel, wave, axis=1)[:, None]
# newspec = trapezoid(kernel * spec[None, :], wave, axis=1)
if return_kernel:
return newspec, kernel
return newspec
Expand Down