def test_calibration_fit_from_points(name, args):
"""Test Calibration.fit and from_points methods."""
# test fit()
cal1 = make_calibration(name, args)
cal1.add_points(points_x, points_y)
cal1.fit()
# alternate: call fit_points() instead of add_points() and fit()
cal1.fit_points(points_x, points_y)
# skip any instances that require a factory method
if len(args) != 2:
cal2 = None
else:
# test from_points()
cal2 = Calibration.from_points(args[0], points_x, points_y)
cal2 = Calibration.from_points(args[0], points_x, points_y, params0=args[1])
assert cal2 == cal1
# test fit() with weights
cal1 = make_calibration(name, args)
cal1.add_points(points_x, points_y, weights)
cal1.fit()
# alternate: call fit_points() with weights
cal1.fit_points(points_x, points_y, weights)
# skip any instances that require a factory method
if len(args) != 2:
cal2 = None
else:
# test from_points() with weights
cal2 = Calibration.from_points(args[0], points_x, points_y, weights)
cal2 = Calibration.from_points(
args[0], points_x, points_y, weights, params0=args[1]
)
assert cal2 == cal1
plt.figure()
plt.title(cal1.expression)
x_fine1 = np.linspace(0, 3000, num=500)
plt.plot(
x_fine1,
cal1(x_fine1),
"b-",
lw=2,
alpha=0.5,
label="fitted function",
)
plt.plot(points_x, points_y, "ro", label="calibration points")
plt.xlabel("x")
plt.xlabel("y")
plt.xlim(0)
plt.ylim(0)
plt.legend()
plt.savefig(os.path.join(TEST_OUTPUTS, f"calibration__fit__{name}.png"))
# Test statistics
assert len(cal1.fit_y) > 0
assert cal1.fit_R_squared > 0.8 # note: this is flexible
assert 0 <= cal1.fit_reduced_chi_squared <= 200 # note: this is flexible
cal1.plot()
def make_calibration(name, args):
"""Make an instance of the desired Calibration type."""
attrs = {"comment": "Test of Calibration class", "name": name}
if name.startswith("lin"):
cal = Calibration.from_linear(*args, **attrs, domain=domain)
elif name.startswith("poly"):
cal = Calibration.from_polynomial(*args, **attrs, domain=domain)
elif name.startswith("sqrt"):
cal = Calibration.from_sqrt_polynomial(*args, **attrs, domain=domain)
elif name.startswith("interp"):
cal = Calibration.from_interpolation(points_x, points_y, **attrs, domain=domain)
else:
cal = Calibration(*args, **attrs, domain=domain)
return cal
def test_calibration_read_failures():
"""Test miscellaneous HDF5 reading failures."""
fname = os.path.join(TEST_OUTPUTS, "calibration__read_failures.h5")
cal = Calibration.from_linear([2.0, 3.0])
cal.add_points([0, 1000, 2000], [0, 1000, 2000])
# remove datasets from the file and show that read raises an error
for dset_name in ["params", "expression", "domain", "range"]:
cal.write(fname)
with h5.open_h5(fname, "r+") as f:
del f[dset_name]
with pytest.raises(CalibrationError):
Calibration.read(fname)
# remove datasets from the file and show that read does *not* raise error
for dset_name in ["points_x", "points_y"]:
cal.write(fname)
with h5.open_h5(fname, "r+") as f:
del f[dset_name]
Calibration.read(fname)
# add unexpected dataset to the file and show that read raises an error
cal.write(fname)
with h5.open_h5(fname, "r+") as f:
f.create_dataset("unexpected", data=[0, 1, 2])
with pytest.raises(CalibrationError):
Calibration.read(fname)
def test_calibration_set_add_points(name, args):
"""Test Calibration.set_points and add_points methods."""
fname = os.path.join(TEST_OUTPUTS, f"calibration__add_points__{name}.h5")
cal = make_calibration(name, args)
# test set_points
cal.set_points()
cal.set_points(1000, 1000)
cal.set_points((0, 1000), (0, 1000))
cal.set_points([], [])
# test add_points
cal.add_points() # does nothing
for px, py in [[(), ()], [1000, 1000], [(0, 1000), (0, 1000)]]:
cal.add_points(px, py)
# test __str__() and __repr__()
str(cal)
repr(cal)
# test write()
cal.write(fname)
# test read()
cal2 = Calibration.read(fname)
# test __eq__()
assert cal2 == cal
# points_x is not 1D
with pytest.raises(CalibrationError):
points_1d = np.array([0, 1000, 2000])
points_2d = np.reshape(points_1d, (1, 3))
cal.add_points(points_2d, points_1d)
# points_y is not 1D
with pytest.raises(CalibrationError):
points_1d = np.array([0, 1000, 2000])
points_2d = np.reshape(points_1d, (1, 3))
cal.add_points(points_1d, points_2d)
# points have different lengths
with pytest.raises(CalibrationError):
points_1d = np.array([0, 1000, 2000])
points_2d = np.reshape(points_1d, (1, 3))
cal.add_points([0, 1000, 2000], [0, 2000])
# points_x contains negative values
with pytest.raises(CalibrationError):
cal.add_points([0, -2000], [0, 2000])
# points_y contains negative values
with pytest.raises(CalibrationError):
cal.add_points([0, 2000], [0, -2000])
def test_calibration(name, args):
"""Test the Calibration class."""
fname = os.path.join(TEST_OUTPUTS, f"calibration__init__{name}.h5")
# test __init__()
cal = make_calibration(name, args)
# test protections on setting parameters
with pytest.raises(CalibrationError):
cal.params = None
with pytest.raises(CalibrationError):
cal.params = np.ones((1, 2))
# test write()
cal.write(fname)
# test read()
cal2 = Calibration.read(fname)
# test __eq__()
assert cal2 == cal
# test copy()
cal3 = cal.copy()
assert cal3 == cal
# test __call__()
cal(100.0)
str(cal)
repr(cal)
def test_calibration_interpolation():
"""Test Calibration.from_interpolation."""
Calibration.from_interpolation(points_x[:2], points_y[:2])
with pytest.raises(CalibrationError):
Calibration.from_interpolation(points_x[:1], points_y[:1])
def test_calibration_misc():
"""Miscellaneous tests to increase test coverage."""
cal1 = Calibration.from_linear([2.0, 3.0])
cal2 = Calibration.from_polynomial([2.0, 3.0, 7.0])
with pytest.raises(CalibrationError):
cal1 != 0
assert cal1 != cal2
# bad number of arguments
with pytest.raises(CalibrationError):
Calibration.from_linear([2.0])
Calibration.from_linear([2.0, 3.0])
with pytest.raises(CalibrationError):
Calibration.from_linear([2.0, 3.0, 4.0])
# bad number of arguments
with pytest.raises(CalibrationError):
Calibration.from_polynomial([2.0])
Calibration.from_polynomial([2.0, 3.0])
Calibration.from_polynomial([2.0, 3.0, 4.0])
# bad number of arguments
with pytest.raises(CalibrationError):
Calibration.from_sqrt_polynomial([2.0])
Calibration.from_sqrt_polynomial([2.0, 3.0])
Calibration.from_sqrt_polynomial([2.0, 3.0, 4.0])
def test_calibration_inverse():
"""Test calibrations with and without inverse expression."""
fname = os.path.join(TEST_OUTPUTS, "calibration__inverse.h5")
# cal1 has an explicit inverse expression, cal2 does not
cal1 = Calibration("p[0] + p[1] * x", [5.0, 4.0],
inv_expression="(y - p[0]) / p[1]")
cal2 = Calibration(cal1.expression, [5.0, 4.0])
assert cal1 == cal2
# evaluate the inverse for a scalar
y = 100.0
x1 = cal1.inverse(y)
x2 = cal2.inverse(y)
assert np.isclose(x1, (y - 5.0) / 4.0)
assert np.isclose(x1, x2)
# evaluate the inverse for a scalar with initial guess
x1 = cal1.inverse(y, x0=25.0)
x2 = cal2.inverse(y, x0=25.0)
assert np.isclose(x1, (y - 5.0) / 4.0)
assert np.isclose(x1, x2)
# evaluate the inverse for an array
y = np.linspace(20.0, 500.0, num=100)
x1 = cal1.inverse(y)
x2 = cal2.inverse(y)
assert np.allclose(x1, (y - 5.0) / 4.0)
assert np.allclose(x1, x2)
# evaluate the inverse for an array with initial guesses
y = np.linspace(20.0, 500.0, num=100)
x0 = np.arange(len(y)) / 4.0
x1 = cal1.inverse(y, x0=x0)
x2 = cal2.inverse(y, x0=x0)
assert np.allclose(x1, (y - 5.0) / 4.0)
assert np.allclose(x1, x2)
# evaluate inverse for values inside the range with result inside domain
cal1.domain = [0, 1]
cal1.range = [-1e6, 1e6]
x0 = 0.5
y0 = cal1(x0)
cal1.range = [y0 - 1, y0 + 1]
cal1.inverse(y0)
# evaluate inverse for values inside the range with result outside domain
cal1.domain = [0, 2]
cal1.range = [-1e6, 1e6]
x0 = 2.0
y0 = cal1(x0)
cal1.domain = [0, 1]
cal1.range = [y0 - 1, y0 + 1]
with pytest.raises(CalibrationError):
cal1(x0)
with pytest.raises(CalibrationError):
cal1.inverse(y0)
# evaluate the inverse for a value outside the range and the domain
cal1.domain = [0, 2]
cal1.range = [-1e6, 1e6]
x0 = 2.0
y0 = cal1(x0)
cal1.domain = [x0 - 2, x0 - 1]
cal1.range = [y0 - 2, y0 - 1]
with pytest.raises(CalibrationError):
cal1(x0)
with pytest.raises(CalibrationError):
cal1.inverse(y0)
# test __str__() and __repr__()
str(cal1)
repr(cal1)
# test write() and read()
cal1.write(fname)
cal3 = Calibration.read(fname)
assert cal3.inv_expression is not None
assert cal3.inv_expression == cal1.inv_expression
def test_calibration_domain_range():
"""Test setting the domain and range of a calibration."""
cal = Calibration("p[0] + p[1] * x", [5.0, 4.0])
# set the domain and range to defaults
cal.domain = None
cal.range = None
# cannot set domain or range to infinite values
with pytest.raises(CalibrationError):
cal.domain = [-np.inf, np.inf]
with pytest.raises(CalibrationError):
cal.range = [-np.inf, np.inf]
# set the domain and range to specific values
x0 = 1
cal.domain = [x0 - 1, x0 + 1]
cal.range = [-1e6, 1e6]
# evaluate for x inside domain and result inside range
y0 = cal(x0)
# evaluate for x outside domain (fails)
x1 = cal.domain[1] + 3
with pytest.raises(CalibrationError):
cal(x1)
# expand domain and reevaluate
cal.domain = (cal.domain[0], x1 + 1)
cal(x1)
# evaluate for x inside domain and result outside range (warns)
cal.domain = [x0 - 1, x0 + 1]
cal.range = [y0 + 10, y0 + 20]
with pytest.warns(CalibrationWarning):
y2 = cal(x0)
# y value is not clipped to the range so should be the same as before
assert np.isclose(y0, y2)
# expand range and reevaluate
cal.range = [y0 - 1, y0 + 1]
cal(x0)