From d4c02aa092116b6402fb378f3cbcb294bb0e283d Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Thu, 11 Jul 2024 15:49:00 +0000
Subject: [PATCH] CI fixes
---
bilby/core/sampler/dynesty.py | 6 +-
bilby/core/utils/calculus.py | 89 ++++++----------------
bilby/gw/likelihood/base.py | 8 +-
bilby/gw/likelihood/roq.py | 6 +-
examples/core_examples/logo/sample_logo.py | 2 +-
requirements.txt | 5 +-
test/core/sampler/dynesty_test.py | 2 +-
test/core/utils_test.py | 2 +-
8 files changed, 38 insertions(+), 82 deletions(-)
diff --git a/bilby/core/sampler/dynesty.py b/bilby/core/sampler/dynesty.py
index 70480c6b8..f1617f1ef 100644
--- a/bilby/core/sampler/dynesty.py
+++ b/bilby/core/sampler/dynesty.py
@@ -691,6 +691,8 @@ class Dynesty(NestedSampler):
)
while True:
self.finalize_sampler_kwargs(sampler_kwargs)
+ if getattr(self.sampler, "added_live", False):
+ self.sampler._remove_live_points()
self.sampler.run_nested(**sampler_kwargs)
if self.sampler.ncall == old_ncall:
break
@@ -705,8 +707,8 @@ class Dynesty(NestedSampler):
if last_checkpoint_s > self.check_point_delta_t:
self.write_current_state()
self.plot_current_state()
- if getattr(self.sampler, "added_live", False):
- self.sampler._remove_live_points()
+ if getattr(self.sampler, "added_live", False):
+ self.sampler._remove_live_points()
self.sampler.run_nested(**sampler_kwargs)
self.write_current_state()
diff --git a/bilby/core/utils/calculus.py b/bilby/core/utils/calculus.py
index 618061f48..ac6fcefcd 100644
--- a/bilby/core/utils/calculus.py
+++ b/bilby/core/utils/calculus.py
@@ -1,7 +1,7 @@
import math
-from numbers import Number
+
import numpy as np
-from scipy.interpolate import interp2d
+from scipy.interpolate import RectBivariateSpline
from scipy.special import logsumexp
from .log import logger
@@ -189,79 +189,34 @@ def logtrapzexp(lnf, dx):
return C + logsumexp([logsumexp(lnfdx1), logsumexp(lnfdx2)])
-class UnsortedInterp2d(interp2d):
- def __call__(self, x, y, dx=0, dy=0, assume_sorted=False):
- """Modified version of the interp2d call method.
-
- This avoids the outer product that is done when two numpy
- arrays are passed.
-
- Parameters
- ==========
- x: See superclass
- y: See superclass
- dx: See superclass
- dy: See superclass
- assume_sorted: bool, optional
- This is just a place holder to prevent a warning.
- Overwriting this will not do anything
+class BoundedRectBivariateSpline(RectBivariateSpline):
- Returns
- =======
- array_like: See superclass
+ def __init__(self, x, y, z, bbox=[None] * 4, kx=3, ky=3, s=0, fill_value=None):
+ self.x_min, self.x_max, self.y_min, self.y_max = bbox
+ if self.x_min is None:
+ self.x_min = min(x)
+ if self.x_max is None:
+ self.x_max = max(x)
+ if self.y_min is None:
+ self.y_min = min(y)
+ if self.y_max is None:
+ self.y_max = max(y)
+ self.fill_value = fill_value
+ super().__init__(x=x, y=y, z=z, bbox=bbox, kx=kx, ky=ky, s=s)
- """
- from scipy.interpolate.dfitpack import bispeu
-
- x, y = self._sanitize_inputs(x, y)
+ def __call__(self, x, y, dx=0, dy=0, grid=False):
+ result = super().__call__(x=x, y=y, dx=dx, dy=dy, grid=grid)
out_of_bounds_x = (x < self.x_min) | (x > self.x_max)
out_of_bounds_y = (y < self.y_min) | (y > self.y_max)
bad = out_of_bounds_x | out_of_bounds_y
- if isinstance(x, Number) and isinstance(y, Number):
+ result[bad] = self.fill_value
+ if result.size == 1:
if bad:
- output = self.fill_value
- ier = 0
+ return self.fill_value
else:
- output, ier = bispeu(*self.tck, x, y)
- output = float(output)
+ return result.item()
else:
- output = np.empty_like(x)
- output[bad] = self.fill_value
- if np.any(~bad):
- output[~bad], ier = bispeu(*self.tck, x[~bad], y[~bad])
- else:
- ier = 0
- if ier == 10:
- raise ValueError("Invalid input data")
- elif ier:
- raise TypeError("An error occurred")
- return output
-
- @staticmethod
- def _sanitize_inputs(x, y):
- if isinstance(x, np.ndarray) and x.size == 1:
- x = float(x)
- if isinstance(y, np.ndarray) and y.size == 1:
- y = float(y)
- if isinstance(x, np.ndarray) and isinstance(y, np.ndarray):
- original_shapes = (x.shape, y.shape)
- if x.shape != y.shape:
- while x.ndim > y.ndim:
- y = np.expand_dims(y, -1)
- while y.ndim > x.ndim:
- x = np.expand_dims(x, -1)
- try:
- x = x * np.ones(y.shape)
- y = y * np.ones(x.shape)
- except ValueError:
- raise ValueError(
- f"UnsortedInterp2d received incompatibly shaped arrays: {original_shapes}"
- )
- elif isinstance(x, np.ndarray) and not isinstance(y, np.ndarray):
- y = y * np.ones_like(x)
- elif not isinstance(x, np.ndarray) and isinstance(y, np.ndarray):
- x = x * np.ones_like(y)
- return x, y
+ return result
def round_up_to_power_of_two(x):
diff --git a/bilby/gw/likelihood/base.py b/bilby/gw/likelihood/base.py
index e0a09c1e9..d04b28d82 100644
--- a/bilby/gw/likelihood/base.py
+++ b/bilby/gw/likelihood/base.py
@@ -7,7 +7,7 @@ import numpy as np
from scipy.special import logsumexp
from ...core.likelihood import Likelihood
-from ...core.utils import logger, UnsortedInterp2d, create_time_series
+from ...core.utils import logger, BoundedRectBivariateSpline, create_time_series
from ...core.prior import Interped, Prior, Uniform, DeltaFunction
from ..detector import InterferometerList, get_empty_interferometer, calibration
from ..prior import BBHPriorDict, Cosmological
@@ -752,7 +752,7 @@ class GravitationalWaveTransient(Likelihood):
d_inner_h_ref = np.real(d_inner_h_ref)
return self._interp_dist_margd_loglikelihood(
- d_inner_h_ref, h_inner_h_ref)
+ d_inner_h_ref, h_inner_h_ref, grid=False)
def phase_marginalized_likelihood(self, d_inner_h, h_inner_h):
d_inner_h = ln_i0(abs(d_inner_h))
@@ -891,9 +891,9 @@ class GravitationalWaveTransient(Likelihood):
self._create_lookup_table()
else:
self._create_lookup_table()
- self._interp_dist_margd_loglikelihood = UnsortedInterp2d(
+ self._interp_dist_margd_loglikelihood = BoundedRectBivariateSpline(
self._d_inner_h_ref_array, self._optimal_snr_squared_ref_array,
- self._dist_margd_loglikelihood_array, kind='cubic', fill_value=-np.inf)
+ self._dist_margd_loglikelihood_array.T, fill_value=-np.inf)
@property
def cached_lookup_table_filename(self):
diff --git a/bilby/gw/likelihood/roq.py b/bilby/gw/likelihood/roq.py
index 12d5212f2..b0bac463d 100644
--- a/bilby/gw/likelihood/roq.py
+++ b/bilby/gw/likelihood/roq.py
@@ -1110,11 +1110,11 @@ class ROQGravitationalWaveTransient(GravitationalWaveTransient):
f_high: float
The maximum frequency which must be considered
"""
- from scipy.integrate import simps
+ from scipy.integrate import simpson
integrand1 = np.power(freq, -7. / 3) / psd
- integral1 = simps(integrand1, freq)
+ integral1 = simpson(y=integrand1, x=freq)
integrand3 = np.power(freq, 2. / 3.) / (psd * integral1)
- f_3_bar = simps(integrand3, freq)
+ f_3_bar = simpson(y=integrand3, x=freq)
f_high = scaling * f_3_bar**(1 / 3)
diff --git a/examples/core_examples/logo/sample_logo.py b/examples/core_examples/logo/sample_logo.py
index 6b5b7225a..a9993d8ec 100644
--- a/examples/core_examples/logo/sample_logo.py
+++ b/examples/core_examples/logo/sample_logo.py
@@ -18,7 +18,7 @@ for letter in ["B", "I", "L", "Y"]:
img = 1 - io.imread("{}.png".format(letter), as_gray=True)[::-1, :]
x = np.arange(img.shape[0])
y = np.arange(img.shape[1])
- interp = si.interpolate.interp2d(x, y, img.T)
+ interp = si.RectBivariateSpline(x, y, img, kx=1, ky=1)
likelihood = Likelihood(interp)
diff --git a/requirements.txt b/requirements.txt
index 05c8c4fad..37bdb21f5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,11 +1,10 @@
bilby.cython>=0.3.0
-# remove pin after https://git.ligo.org/lscsoft/bilby/-/merge_requests/1368
-dynesty>=2.0.1,<2.1.4
+dynesty>=2.0.1
emcee
corner
numpy
matplotlib
-# remove pin after https://git.ligo.org/lscsoft/bilby/-/merge_requests/1368
+# see https://github.com/healpy/healpy/pull/953
scipy>=1.5,<1.14
pandas
dill
diff --git a/test/core/sampler/dynesty_test.py b/test/core/sampler/dynesty_test.py
index d33cc2e23..5d1c534a0 100644
--- a/test/core/sampler/dynesty_test.py
+++ b/test/core/sampler/dynesty_test.py
@@ -216,7 +216,7 @@ class TestCustomSampler(unittest.TestCase):
self.sampler = cls(
loglikelihood=lambda x: 1,
prior_transform=lambda x: x,
- npdim=4,
+ ndim=4,
live_points=(np.zeros((1000, 4)), np.zeros((1000, 4)), np.zeros(1000)),
update_interval=None,
first_update=dict(),
diff --git a/test/core/utils_test.py b/test/core/utils_test.py
index d6b3e8902..ed63916a3 100644
--- a/test/core/utils_test.py
+++ b/test/core/utils_test.py
@@ -320,7 +320,7 @@ class TestUnsortedInterp2d(unittest.TestCase):
self.xx = np.linspace(0, 1, 10)
self.yy = np.linspace(0, 1, 10)
self.zz = np.random.random((10, 10))
- self.interpolant = bilby.core.utils.UnsortedInterp2d(self.xx, self.yy, self.zz)
+ self.interpolant = bilby.core.utils.BoundedRectBivariateSpline(self.xx, self.yy, self.zz)
def tearDown(self):
pass
--
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