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Commit c96cd97a authored by Matthew David Pitkin's avatar Matthew David Pitkin
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Run black to fix formatting issues that break the pipeline

parent c52d5226
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1 merge request!983Allow logtrapzexp to work on a non-uniform grid
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bilby/core/utils/calculus.py
+ 29
− 19
View file @ c96cd97a
......@@ -6,8 +6,16 @@ from scipy.special import logsumexp
from .logger import logger
def derivatives(vals, func, releps=1e-3, abseps=None, mineps=1e-9, reltol=1e-3,
epsscale=0.5, nonfixedidx=None):
def derivatives(
vals,
func,
releps=1e-3,
abseps=None,
mineps=1e-9,
reltol=1e-3,
epsscale=0.5,
nonfixedidx=None,
):
"""
Calculate the partial derivatives of a function at a set of values. The
derivatives are calculated using the central difference, using an iterative
......@@ -54,19 +62,19 @@ def derivatives(vals, func, releps=1e-3, abseps=None, mineps=1e-9, reltol=1e-3,
grads = np.zeros(len(nonfixedidx))
# maximum number of times the gradient can change sign
flipflopmax = 10.
flipflopmax = 10.0
# set steps
if abseps is None:
if isinstance(releps, float):
eps = np.abs(vals) * releps
eps[eps == 0.] = releps # if any values are zero set eps to releps
eps[eps == 0.0] = releps # if any values are zero set eps to releps
teps = releps * np.ones(len(vals))
elif isinstance(releps, (list, np.ndarray)):
if len(releps) != len(vals):
raise ValueError("Problem with input relative step sizes")
eps = np.multiply(np.abs(vals), releps)
eps[eps == 0.] = np.array(releps)[eps == 0.]
eps[eps == 0.0] = np.array(releps)[eps == 0.0]
teps = releps
else:
raise RuntimeError("Relative step sizes are not a recognised type!")
......@@ -107,8 +115,10 @@ def derivatives(vals, func, releps=1e-3, abseps=None, mineps=1e-9, reltol=1e-3,
cureps *= epsscale
if cureps < mineps or flipflop > flipflopmax:
# if no convergence set flat derivative (TODO: check if there is a better thing to do instead)
logger.warning("Derivative calculation did not converge: setting flat derivative.")
grads[count] = 0.
logger.warning(
"Derivative calculation did not converge: setting flat derivative."
)
grads[count] = 0.0
break
leps *= epsscale
......@@ -122,10 +132,10 @@ def derivatives(vals, func, releps=1e-3, abseps=None, mineps=1e-9, reltol=1e-3,
break
# check whether previous diff and current diff are the same within reltol
rat = (cdiff / cdiffnew)
if np.isfinite(rat) and rat > 0.:
rat = cdiff / cdiffnew
if np.isfinite(rat) and rat > 0.0:
# gradient has not changed sign
if np.abs(1. - rat) < reltol:
if np.abs(1.0 - rat) < reltol:
grads[count] = cdiffnew
break
else:
......@@ -157,18 +167,20 @@ def logtrapzexp(lnf, dx):
=======
The natural logarithm of the area under the function.
"""
lnfdx1 = lnf[:-1]
lnfdx2 = lnf[1:]
if isinstance(dx, (int, float)):
C = np.log(dx / 2.)
C = np.log(dx / 2.0)
elif isinstance(dx, (list, np.ndarray)):
if len(dx) != len(lnf) - 1:
raise ValueError("Step size array must have length one less than the function length")
raise ValueError(
"Step size array must have length one less than the function length"
)
lndx = np.log(dx)
lnfdx1 = lnfdx1.copy() + lndx
lnfdx2 = lnfdx2.copy() + lndx
lnfdx2 = lnfdx2.copy() + lndx
C = -np.log(2.0)
else:
raise TypeError("Step size must be a single value or array-like")
......@@ -177,9 +189,8 @@ def logtrapzexp(lnf, dx):
class UnsortedInterp2d(interp2d):
def __call__(self, x, y, dx=0, dy=0, assume_sorted=False):
""" Modified version of the interp2d call method.
"""Modified version of the interp2d call method.
This avoids the outer product that is done when two numpy
arrays are passed.
......@@ -200,6 +211,7 @@ class UnsortedInterp2d(interp2d):
"""
from scipy.interpolate.dfitpack import bispeu
x, y = self._sanitize_inputs(x, y)
out_of_bounds_x = (x < self.x_min) | (x > self.x_max)
out_of_bounds_y = (y < self.y_min) | (y > self.y_max)
......@@ -232,9 +244,7 @@ class UnsortedInterp2d(interp2d):
y = float(y)
if isinstance(x, np.ndarray) and isinstance(y, np.ndarray):
if x.shape != y.shape:
raise ValueError(
"UnsortedInterp2d received unequally shaped arrays"
)
raise ValueError("UnsortedInterp2d received unequally shaped arrays")
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):
......
test/core/utils_test.py
+ 12
− 19
View file @ c96cd97a
......@@ -270,6 +270,7 @@ class TestLatexPlotFormat(unittest.TestCase):
fig, ax = plt.subplots()
ax.plot(self.x, self.y)
fig.savefig(self.filename)
plot()
self.assertTrue(os.path.isfile(self.filename))
......@@ -279,6 +280,7 @@ class TestLatexPlotFormat(unittest.TestCase):
fig, ax = plt.subplots()
ax.plot(self.x, self.y)
fig.savefig(self.filename)
plot(BILBY_MATHDEFAULT=1)
self.assertTrue(os.path.isfile(self.filename))
......@@ -288,6 +290,7 @@ class TestLatexPlotFormat(unittest.TestCase):
fig, ax = plt.subplots()
ax.plot(self.x, self.y)
fig.savefig(self.filename)
plot(BILBY_MATHDEFAULT=0)
self.assertTrue(os.path.isfile(self.filename))
......@@ -313,14 +316,11 @@ class TestLatexPlotFormat(unittest.TestCase):
class TestUnsortedInterp2d(unittest.TestCase):
def setUp(self):
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.UnsortedInterp2d(self.xx, self.yy, self.zz)
def tearDown(self):
pass
......@@ -333,22 +333,15 @@ class TestUnsortedInterp2d(unittest.TestCase):
self.assertIsNone(self.interpolant(-0.5, 0.5))
def test_returns_float_for_float_and_array(self):
self.assertIsInstance(self.interpolant(0.5, np.random.random(10)), np.ndarray)
self.assertIsInstance(self.interpolant(np.random.random(10), 0.5), np.ndarray)
self.assertIsInstance(
self.interpolant(0.5, np.random.random(10)), np.ndarray
)
self.assertIsInstance(
self.interpolant(np.random.random(10), 0.5), np.ndarray
)
self.assertIsInstance(
self.interpolant(np.random.random(10), np.random.random(10)),
np.ndarray
self.interpolant(np.random.random(10), np.random.random(10)), np.ndarray
)
def test_raises_for_mismatched_arrays(self):
with self.assertRaises(ValueError):
self.interpolant(
np.random.random(10), np.random.random(20)
)
self.interpolant(np.random.random(10), np.random.random(20))
def test_returns_fill_in_correct_place(self):
x_data = np.random.random(10)
......@@ -364,11 +357,11 @@ class TestTrapeziumRuleIntegration(unittest.TestCase):
self.dx = self.dxs[0]
with np.errstate(divide="ignore"):
self.lnfunc1 = np.log(self.x)
self.func1int = (self.x[-1] ** 2 - self.x[0] ** 2) / 2
self.func1int = (self.x[-1] ** 2 - self.x[0] ** 2) / 2
with np.errstate(divide="ignore"):
self.lnfunc2 = np.log(self.x ** 2)
self.func2int = (self.x[-1] ** 3 - self.x[0] ** 3) / 3
self.irregularx = np.array(
[
self.x[0],
......@@ -397,7 +390,7 @@ class TestTrapeziumRuleIntegration(unittest.TestCase):
def test_inconsistent_step_length(self):
with self.assertRaises(ValueError):
utils.logtrapzexp(self.lnfunc1, self.x[0:len(self.x) // 2])
utils.logtrapzexp(self.lnfunc1, self.x[0 : len(self.x) // 2])
def test_integral_func1(self):
res1 = utils.logtrapzexp(self.lnfunc1, self.dx)
......@@ -405,7 +398,7 @@ class TestTrapeziumRuleIntegration(unittest.TestCase):
self.assertTrue(np.abs(res1 - res2) < 1e-12)
self.assertTrue(np.abs((np.exp(res1) - self.func1int) / self.func1int) < 1e-12)
def test_integral_func2(self):
res = utils.logtrapzexp(self.lnfunc2, self.dxs)
self.assertTrue(np.abs((np.exp(res) - self.func2int) / self.func2int) < 1e-4)
......
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