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Changes radius in Invariant Guinier extrapolation to radius squared #3841

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Changes radius in Invariant Guinier extrapolation to radius squared #3841

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31 changes: 11 additions & 20 deletions src/sas/sascalc/invariant/invariant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,14 +113,14 @@ class of type Transform that performs operations related to guinier
function
"""

def __init__(self, scale=1, radius=60):
def __init__(self, scale=1, Rg_squared=3600):
Transform.__init__(self)
self.scale = scale
self.radius = radius
self.Rg_squared = Rg_squared
## Uncertainty of scale parameter
self.dscale = 0
## Unvertainty of radius parameter
self.dradius = 0
## Uncertainty of Rg squared parameter
self.dRg_squared = 0

def linearize_q_value(self, value):
"""
Expand All @@ -137,18 +137,12 @@ def extract_model_parameters(self, constant, slope, dconstant=0, dslope=0):
assign new value to the scale and the radius
"""
self.scale = math.exp(constant)
if slope > 0:
slope = 0.0
self.radius = math.sqrt(-3 * slope)
self.Rg_squared = -3.0 * slope
# Errors
self.dscale = math.exp(constant) * dconstant
if slope == 0.0:
n_zero = -1.0e-24
self.dradius = -3.0 / 2.0 / math.sqrt(-3 * n_zero) * dslope
else:
self.dradius = -3.0 / 2.0 / math.sqrt(-3 * slope) * dslope
self.dRg_squared = 3.0 * dslope

return [self.radius, self.scale], [self.dradius, self.dscale]
return [self.Rg_squared, self.scale], [self.dRg_squared, self.dscale]

def evaluate_model(self, x):
r"""
Expand All @@ -165,10 +159,10 @@ def evaluate_model_errors(self, x):

:param x: array of q-values
"""
p1 = np.array([self.dscale * math.exp(-((self.radius * q) ** 2 / 3)) for q in x])
p1 = np.array([self.dscale * math.exp(-(self.Rg_squared * q**2 / 3.0)) for q in x])
p2 = np.array(
[
self.scale * math.exp(-((self.radius * q) ** 2 / 3)) * (-(q**2 / 3)) * 2 * self.radius * self.dradius
self.scale * math.exp(-(self.Rg_squared * q**2 / 3.0)) * (-(q**2 / 3.0)) * self.dRg_squared
for q in x
]
)
Expand All @@ -185,16 +179,13 @@ def _guinier(self, x):

Also uses:
- self.scale: $s$, the scale value
- self.radius: $r$, the guinier radius value
- self.Rg_squared: $r$, the guinier radius value squared

:return: F(x)
"""
# transform the radius of coming from the inverse guinier function to a
# a radius of a guinier function
if self.radius <= 0:
msg = "Rg expected positive value, but got %s" % self.radius
raise ValueError(msg)
value = np.array([math.exp(-((self.radius * i) ** 2 / 3)) for i in x])
value = np.array([math.exp(-(self.Rg_squared * i**2 / 3.0)) for i in x])
return self.scale * value


Expand Down
8 changes: 4 additions & 4 deletions test/sasinvariant/utest_data_handling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -430,8 +430,8 @@ def test_low_q(self):
power=inv._low_extrapolation_power)
self.assertAlmostEqual(self.scale,
inv._low_extrapolation_function.scale, 6)
self.assertAlmostEqual(self.rg,
inv._low_extrapolation_function.radius, 6)
self.assertAlmostEqual(self.rg**2,
inv._low_extrapolation_function.Rg_squared, 6)


class TestPowerLawExtrapolation(unittest.TestCase):
Expand Down Expand Up @@ -573,8 +573,8 @@ def test_low_q(self):
power=inv._low_extrapolation_power)
self.assertAlmostEqual(self.scale,
inv._low_extrapolation_function.scale, 6)
self.assertAlmostEqual(self.rg,
inv._low_extrapolation_function.radius, 6)
self.assertAlmostEqual(self.rg**2,
inv._low_extrapolation_function.Rg_squared, 6)

qstar = inv.get_qstar(extrapolation='low')
test_y = inv._low_extrapolation_function.evaluate_model(x=self.data.x)
Expand Down