def isregistered(function):
status, msg = True, ""
try:
FunctionFactory.createFunction(function)
except RuntimeError as exc:
status, msg = False, 'Could not create {} function: {}'.format(function, str(exc))
return status, msg
def initByName(self, name, *args, **kwargs):
"""
intialise composite function of named type.
E.g. "ProductFunction"
This function would be protected in c++
and should not be called directly except
by :meth:`__init__` functions of this class
and subclasses.
:param name: name of class calling this.
:param args: names of functions in composite function
:param kwargs: any parameters or attributes that must be passed to the
composite function itself.
"""
if len(args) == 1 and not isinstance(args[0], FunctionWrapper):
# We have a composite function to wrap
self.fun = args[0]
else:
self.fun = FunctionFactory.createCompositeFunction(name)
# Add the functions, checking for Composite & Product functions
for a in args:
if not isinstance(a, int):
if isinstance(a, CompositeFunctionWrapper):
if self.pureAddition:
self.pureAddition = a.pureAddition
if self.pureMultiplication:
self.pureMultiplication = a.pureMultiplication
functionToAdd = FunctionFactory.createInitialized(a.fun.__str__())
self.fun.add(functionToAdd)
self.init_paramgeters_and_attributes(**kwargs)
def test_members_can_be_added(self):
func = CompositeFunction()
f1 = FunctionFactory.createInitialized('name=FlatBackground,A0=1')
f2 = FunctionFactory.createInitialized('name=FlatBackground,A0=2')
f3 = FunctionFactory.createInitialized('name=FlatBackground,A0=3')
func.add(f1)
func.add(f2)
func.add(f3)
self.assertEqual(len(func), 3)
self.assertEqual(str(func[0]), 'name=FlatBackground,A0=1')
self.assertEqual(str(func[1]), 'name=FlatBackground,A0=2')
self.assertEqual(str(func[2]), 'name=FlatBackground,A0=3')
def is_registered(function_name):
"""
Check whether the function with the specified name has been registered.
:param function_name: The name of the function to check for registration.
:return: A tuple of the status (True if function is registered,
false otherwise) and the error message (empty if the
function is registered).
"""
try:
FunctionFactory.createFunction(function_name)
except RuntimeError as exc:
return False, 'Could not create {} function: {}'.format(function_name,
str(exc))
return True, ""
def skip(self):
"""
Override and return a string depending on whether the directive
should be skipped. If empty then the directive should be processed
otherwise the string should contain the error message
The default is to skip (and warn) if the algorithm is not known.
Returns:
str: Return error mesage string if the directive should be skipped
"""
from mantid.api import AlgorithmFactory, FunctionFactory
name, version = self.algorithm_name(), self.algorithm_version()
msg = ""
if version is None: # it is a fit function
if name in FunctionFactory.getFunctionNames():
return ""
else:
msg = "No fit function '%s', skipping directive" % name
else:
if AlgorithmFactory.exists(name, version):
return ""
else:
msg = "No algorithm '%s' version '%d', skipping directive" % (name, version)
# warn the user
if len(msg) > 0:
env = self.state.document.settings.env
env.app.verbose(msg)
return msg
def test_parameters_can_be_get_and_set(self):
func = FunctionFactory.createInitialized('name=FlatBackground,A0=1;name=FlatBackground,A0=2')
self.assertEqual(func.getParameterValue('f0.A0'), 1.0)
self.assertEqual(func.getParameterValue('f1.A0'), 2.0)
func.setParameter('f0.A0', 10.0)
self.assertEqual(func.getParameterValue('f0.A0'), 10.0)
func.setParameter('f1.A0', 20.0)
self.assertEqual(func.getParameterValue('f1.A0'), 20.0)
def test_nested_functions(self):
s = 'name=FlatBackground,A0=1;(name=FlatBackground,A0=2;name=FlatBackground,A0=3)'
func = FunctionFactory.createInitialized(s)
self.assertEqual(len(func), 2)
self.assertFalse(isinstance(func[0], CompositeFunction))
self.assertTrue(isinstance(func[1], CompositeFunction))
self.assertEqual(len(func[1]), 2)
self.assertEqual(func.getParameterValue('f0.A0'), 1.0)
self.assertEqual(func.getParameterValue('f1.f0.A0'), 2.0)
self.assertEqual(func.getParameterValue('f1.f1.A0'), 3.0)
self.assertEqual(func.nParams(), 3)
def create_mantid_ifunction(self, function_name):
"""
Create and initiializes a Mantid IFunction.
Args:
function_name (str): The name of the function to use.
Returns:
ifunction: An instance of a Mantid IFunction
"""
from mantid.api import FunctionFactory
return FunctionFactory.createFunction(function_name)
def test_function_existing_function_can_be_unsubscribed(self):
FunctionFactory.subscribe(TestFunctionCorrectForm)
nfuncs_before = len(FunctionFactory.getFunctionNames())
FunctionFactory.unsubscribe("TestFunctionCorrectForm")
available_functions = FunctionFactory.getFunctionNames()
self.assertEquals(nfuncs_before - 1, len(available_functions))
self.assertTrue("TestFunctionCorrectForm" not in available_functions)
def test_function_subscription(self):
nfuncs_orig = len(FunctionFactory.getFunctionNames())
FunctionFactory.subscribe(TestFunction)
new_funcs = FunctionFactory.getFunctionNames()
self.assertEquals(nfuncs_orig+1, len(new_funcs))
self.assertTrue("TestFunction" in new_funcs)
FunctionFactory.unsubscribe("TestFunction")
new_funcs = FunctionFactory.getFunctionNames()
self.assertEquals(nfuncs_orig, len(new_funcs))
self.assertTrue("TestFunction" not in new_funcs)
def __init__(self, name, **kwargs):
"""
Called when creating an instance
:param name: name of fitting function to create or
an Ifunction object to wrap.
:param kwargs: standard argument for initializing fit
function
"""
if not isinstance(name, str):
self.fun = name
else:
self.fun = FunctionFactory.createFunction(name)
self.init_paramgeters_and_attributes(**kwargs)
# Active fitting parameters
self.declareParameter("Tau", 1.0, 'Residence time')
self.declareParameter("L", 0.2, 'Jump length')
def function1D(self, xvals):
tau = self.getParameterValue("Tau")
l = self.getParameterValue("L")
l = l**2 / 2
xvals = np.array(xvals)
hwhm = (1.0 - np.exp( -l * xvals * xvals )) / tau
return hwhm
def functionDeriv1D(self, xvals, jacobian):
tau = self.getParameterValue("Tau")
l = self.getParameterValue("L")
l = l**2 / 2
i = 0
for x in xvals:
ex = math.exp(-l*x*x)
h = (1.0-ex)/tau
jacobian.set(i,0,-h/tau)
jacobian.set(i,1,x*x*ex/tau)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(HallRoss)
def init(self):
# Active fitting parameters
self.declareParameter("Tau", 1.0, 'Residence time')
self.declareParameter("L", 1.5, 'Jump length')
def function1D(self, xvals):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
length = length**2
xvals = np.array(xvals)
hwhm = xvals * xvals * length / (tau * (1 + xvals * xvals * length))
return hwhm
def functionDeriv1D(self, xvals, jacobian):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
length = length**2
i = 0
for x in xvals:
h = x*x*length/(tau*(1+x*x*length))
jacobian.set(i,0,-h/tau)
jacobian.set(i,1,h*(1.0-h*tau)/length)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(TeixeiraWater)
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=invalid-name, anomalous-backslash-in-string, attribute-defined-outside-init
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
class PCRmagnetfnorm(IFunction1D):
def category(self):
return "Muon\\MuonSpecific"
def init(self):
self.declareParameter("A0", 0.2, 'Amplitude')
self.declareParameter("SigmaOverW", 0.1, 'Normalised relaxation rate')
self.declareParameter("H0", 3.0, 'Local magnetic field')
self.declareParameter("Toff", 0.1, 'Time offset')
def function1D(self, x):
A0 = self.getParameterValue("A0")
sigma = self.getParameterValue("SigmaOverW")
H0 = self.getParameterValue("H0")
Toff = self.getParameterValue("Toff")
gmu = 2 * np.pi * 0.01355342
w = H0 * gmu
x = x - Toff
return A0 * (1./3 + 2./3 * np.exp(- (sigma * w * x) ** 2 / 2) * np.cos(w * x))
FunctionFactory.subscribe(PCRmagnetfnorm)
# pylint: disable=invalid-name, anomalous-backslash-in-string, attribute-defined-outside-init
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
class RFresonance(IFunction1D):
def category(self):
return "Muon\\MuonSpecific"
def init(self):
self.declareParameter("A0", 0.2)
self.declareParameter("Boffset", 10, 'Relaxation rate (G)')
self.declareParameter("B1", 10, 'Fluctuation (G)')
self.declareParameter("B1GauWidth", 0.2, 'Width of resonance (MHz)')
def function1D(self, x):
A0 = self.getParameterValue("A0")
Bcentre = self.getParameterValue("Boffset")
B = self.getParameterValue("B1")
width = self.getParameterValue("B1GauWidth")
gmu = 0.0135538817 * 2 * np.pi
Beff = np.sqrt(Bcentre**2 + B**2)
RelAmp = (B / Beff)**2
return A0 * (
1 +
(np.cos(Beff * gmu * x) * np.exp(-(width * x)**2) - 1) * RelAmp)
FunctionFactory.subscribe(RFresonance)
def category(self):
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("Height", 1.0, 'Height')
self.declareParameter("MSD", 0.05, 'Mean square displacement')
def function1D(self, xvals):
height = self.getParameterValue("Height")
msd = self.getParameterValue("MSD")
xvals = np.array(xvals)
intensity = height * np.exp(-msd * xvals**2)
return intensity
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
msd = self.getParameterValue("MSD")
for i, x in enumerate(xvals):
e = math.exp(-msd * x**2)
jacobian.set(i, 0, e)
jacobian.set(i, 1, -(x**2) * e * height)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(MsdGauss)
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=invalid-name, anomalous-backslash-in-string, attribute-defined-outside-init
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
class StretchedKT(IFunction1D):
def category(self):
return "Muon\\MuonGeneric"
def init(self):
self.declareParameter("A0", 1)
self.declareParameter("Beta", 1)
self.declareParameter("Sigma", 0.1)
def function1D(self, x):
A0 = self.getParameterValue("A0")
beta = self.getParameterValue("Beta")
Sigma = self.getParameterValue("Sigma")
product = Sigma * x
A = (2./3.) * (1 - product ** beta)
B = np.exp(- product ** beta / beta)
return A0*(1./3. + A * B)
FunctionFactory.subscribe(StretchedKT)
----------
xvals : sequence of floats
The domain where to evaluate the function
jacobian: 2D array
partial derivative of the function with respect to the fitting
parameters evaluated at the domain.
Returns
-------
numpy.ndarray
Function values
"""
radius = self.getParameterValue('R')
length = self.getParameterValue('L')
x = np.asarray(xvals) # Q values
z = length * np.outer(x, self.cos_theta)
# EISF along cylinder Z-axis
a = np.square(np.where(z < 1e-9, 1 - z * z / 6, np.sin(z) / z))
z = radius * np.outer(x, self.sin_theta)
# EISF on cylinder cross-section (diffusion on a disc)
b = np.square(
np.where(z < 1e-6, 1 - z * z / 10,
3 * (np.sin(z) - z * np.cos(z)) / (z * z * z)))
# integrate in theta
eisf = self.d_theta * np.sum(self.sin_theta * a * b, axis=1)
return self.getParameterValue('A') * eisf
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(EISFDiffCylinder)
along with this program. If not, see <http://www.gnu.org/licenses/>.
File change history is stored at: <https://github.com/mantidproject/mantid>
Code Documentation is available at: <http://doxygen.mantidproject.org>
'''
from __future__ import (absolute_import, division, print_function)
from mantid.api import IFunction1D, FunctionFactory
class FickDiffusion(IFunction1D):
def category(self):
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("D", 1.0, 'Diffusion constant')
def function1D(self, xvals):
return self.getParameterValue("D")*xvals*xvals
def functionDeriv1D(self, xvals, jacobian):
i = 0
for x in xvals:
jacobian.set(i,0,2.0*x)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(FickDiffusion)
Evaluate the model
@param xvals: numpy array of q-values
"""
# parameters
scale = self.getParameterValue('Scale')
bgd = self.getParameterValue('Background')
output = np.zeros(len(xvals), dtype=float)
for i in range(len(xvals)):
output[i] = scale * self._guinier_porod_core(xvals[i]) + bgd
return output
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
for x in xvals:
jacobian.set(i, 0, self._guinier_porod_core(x))
jacobian.set(i, 1, self._first_derivative_dim(x))
jacobian.set(i, 2, self._first_derivative_rg(x))
jacobian.set(i, 3, self._first_derivative_m(x))
jacobian.set(i, 4, 1.0)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(GuinierPorod)
# pylint: disable=no-init,invalid-name
'''
@author Spencer Howells, ISIS
@date December 05, 2013
'''
from __future__ import (absolute_import, division, print_function)
from mantid.api import IFunction1D, FunctionFactory
class FickDiffusion(IFunction1D):
def category(self):
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("D", 1.0, 'Diffusion constant')
def function1D(self, xvals):
return self.getParameterValue("D") * xvals * xvals
def functionDeriv1D(self, xvals, jacobian):
i = 0
for x in xvals:
jacobian.set(i, 0, 2.0 * x)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(FickDiffusion)
def setUp(self):
context = setup_context()
self.model = BasicFittingModel(context, context.fitting_context)
self.dataset_names = ["EMU20884; Group; fwd; Asymmetry", "EMU20884; Group; top; Asymmetry"]
self.fit_function = FunctionFactory.createFunction("FlatBackground")
self.single_fit_functions = [self.fit_function.clone(), self.fit_function.clone()]
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=invalid-name, anomalous-backslash-in-string, attribute-defined-outside-init
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
from scipy import special as sp
class Bessel(IFunction1D):
def category(self):
return "Muon"
def init(self):
self.declareParameter("A0", 1, 'Amplitude')
self.declareParameter("Phi", 0.1, 'Phase(rad)')
self.declareParameter("Nu", 0.1, 'Frequency(MHz)')
def function1D(self, x):
A0 = self.getParameterValue("A0")
Phi = self.getParameterValue("Phi")
Nu = self.getParameterValue("Nu")
return A0 * sp.j0(2 * np.pi * Nu * x + Phi)
FunctionFactory.subscribe(Bessel)
self.declareParameter("FreqD", 0.2,
'Anisotropic hyperfine coupling constant (MHz)')
self.declareParameter("FCut", 1.0, 'Frequency cut (MHz)')
self.declareParameter("Phi", 0.0, 'Phase')
self.addConstraints("FreqA > 0")
self.addConstraints("FreqD > 0")
self.addConstraints("FCut > 0")
def function1D(self, x):
A0 = self.getParameterValue("A0")
FreqA = self.getParameterValue("FreqA")
FreqD = self.getParameterValue("FreqD")
Fcut = self.getParameterValue("FCut")
Phi = self.getParameterValue("Phi")
W1 = 2 * np.pi * (FreqA - FreqD)
W2 = 2 * np.pi * (FreqA + FreqD / 2)
W3 = 3 * np.pi * FreqD
if Fcut > 0:
A1 = 1 / (1 + (W1 / (2 * np.pi * Fcut))**2)
A2 = 2 / (1 + (W2 / (2 * np.pi * Fcut))**2)
A3 = 2 / (1 + (W3 / (2 * np.pi * Fcut))**2)
else:
A1 = 1
A2 = 2
A3 = 2
return A0 * (A1 * np.cos(W1 * x + Phi) + A2 * np.cos(W2 * x + Phi) +
A3 * np.cos(W3 * x + Phi)) / 6
FunctionFactory.subscribe(ZFMuonium)
Nmax = 16000 # increase short-times resolution, increase the resolution of the structure factor tail
while ( emax / de ) < Nmax:
emax = 2 * emax
N = int( emax / de )
dt = ( float(N) / ( 2 * N + 1 ) ) * (self._h / emax) # extent to negative times and t==0
sampled_times = dt * np.arange(-N, N+1) # len( sampled_times ) < 64000
exponent = -(np.abs(sampled_times)/p['tau'])**p['beta']
freqs = de * np.arange(-N, N+1)
fourier = p['height']*np.abs( scipy.fftpack.fft( np.exp(exponent) ).real )
fourier = np.concatenate( (fourier[N+1:],fourier[0:N+1]) )
interpolator = scipy.interpolate.interp1d(freqs, fourier)
fourier = interpolator(xvals)
return fourier
def functionDeriv1D(self, xvals, jacobian):
'''Numerical derivative'''
p = self.validateParams()
f0 = self.function1D(xvals)
dp = {}
for (key,val) in p.items(): dp[key] = 0.1 * val #modify by ten percent
for name in self._parmset:
pp = copy.copy(p)
pp[name] += dp[name]
df = (self.function1D(xvals, **pp) - f0) / dp[name]
ip = self._parm2index[name]
for ix in range(len(xvals)):
jacobian.set(ix, ip, df[ix])
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(StretchedExpFT)
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source,
# Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=invalid-name, anomalous-backslash-in-string, attribute-defined-outside-init
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
class CombGaussLorentzKT(IFunction1D):
def category(self):
return "Muon\\MuonGeneric"
def init(self):
self.declareParameter("A0", 0.5, 'Amplitude')
self.declareParameter("Lambda", 0.1, 'Exponential decay rate')
self.declareParameter("Sigma", 0.2, 'KuboToyabe decay rate')
def function1D(self, x):
A0 = self.getParameterValue("A0")
Lambda = self.getParameterValue("Lambda")
Sigma = self.getParameterValue("Sigma")
return A0 * ((1. / 3.) + (2. / 3.) * (1. -
(Sigma * x)**2 - Lambda * x) *
np.exp(-0.5 * (Sigma * x)**2 - Lambda * x))
FunctionFactory.subscribe(CombGaussLorentzKT)
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("Tau", 1.0, 'Residence time')
self.declareParameter("L", 0.2, 'Jump length')
def function1D(self, xvals):
tau = self.getParameterValue("Tau")
l = self.getParameterValue("L")
xvals = np.array(xvals)
hwhm = (1.0 - np.exp( -l * xvals * xvals )) / tau
return hwhm
def functionDeriv1D(self, xvals, jacobian):
tau = self.getParameterValue("Tau")
l = self.getParameterValue("L")
i = 0
for x in xvals:
ex = math.exp(-l*x*x)
h = (1.0-ex)/tau
jacobian.set(i,0,-h/tau);
jacobian.set(i,1,x*x*ex/tau);
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(SingwiSjolander)
#Get the trial values
f_trial = self.function1D(xvals)
#Now return to the orignial
for i in range(self.numParams()):
self.setParameter(i, c[i])
return f_trial
# Construction the Jacobian (df) for the function
def functionDeriv1D(self, xvals, jacobian, eps=1.e-3):
f_int = self.function1D(xvals)
#Fetch parameters into array c
c = np.zeros(self.numParams())
for i in range(self.numParams()):
c[i] = self.getParamValue(i)
nc = np.prod(np.shape(c))
for k in range(nc):
dc = np.zeros(nc)
if k == 1 or k == 2:
epsUse = 1.e-3
else:
epsUse = eps
dc[k] = max(epsUse, epsUse * c[k])
f_new = self.function1DDiffParams(xvals, c + dc)
for i, dF in enumerate(f_new - f_int):
jacobian.set(i, k, dF / dc[k])
FunctionFactory.subscribe(BivariateGaussian)
def fwhm(self):
"""
Return what should be considered the 'fwhm' of this function.
"""
return 2.0*math.sqrt(2.0*math.log(2.0))*self.getParameterValue("Sigma")
def setCentre(self, new_centre):
"""
Called by an external entity, probably a GUI, in response to a mouse click
that gives a guess at the centre.
"""
self.setParameter("PeakCentre",new_centre)
def setHeight(self, new_height):
"""
Called by an external entity, probably a GUI, in response to a user guessing
the height.
"""
self.setParameter("Height", new_height)
def setFwhm(self, new_fwhm):
"""
Called by an external entity, probably a GUI, in response to a user guessing
the height.
"""
sigma = new_fwhm/(2.0*math.sqrt(2.0*math.log(2.0)))
self.setParameter("Sigma",sigma)
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(ExamplePeakFunction)
class StandardSC(IFunction1D):
def category(self):
return "Muon\\MuonGeneric"
def init(self):
self.declareParameter(
"A0", 0.16, 'Amplitude of interal field oscillation')
self.declareParameter("Sigma", 0.2, 'Gaussian decay rate')
self.declareParameter("FieldSC", 300.0, 'Internal Field (G)')
self.declareParameter("FieldBG", 300.0, 'External Field (G)')
self.declareParameter("Phi", 0.0, 'Phase')
self.declareParameter(
"Abg", 0.1, 'Amplitude of external field oscillation')
def function1D(self, x):
A0 = self.getParameterValue("A0")
sigma = self.getParameterValue("Sigma")
FieldSC = self.getParameterValue("FieldSC")
FieldBG = self.getParameterValue("FieldBG")
phi = self.getParameterValue("Phi")
Abg = self.getParameterValue("Abg")
omegaSC = FieldSC * 0.1355 * 2 * np.pi
omegaBG = FieldBG * 0.1355 * 2 * np.pi
return A0 * np.exp(- 0.5 * sigma * sigma * x * x) * np.cos(omegaSC * x + phi) + Abg * np.cos(omegaBG * x + phi)
FunctionFactory.subscribe(StandardSC)
F(E) is normalized:
\int_{-infty}^{infty} dE F(E) = 1
"""
parms, de, energies, fourier = function1Dcommon(
self, xvals, **optparms)
if parms is None:
return fourier #return zeros if parameters not valid
transform = parms['Height'] * np.interp(xvals - parms['Centre'],
energies, fourier)
return transform
@surrogate
def fillJacobian(self, xvals, jacobian, partials):
"""Fill the jacobian object with the dictionary of partial derivatives
:param xvals: domain where the derivatives are to be calculated
:param jacobian: jacobian object
:param partials: dictionary with partial derivates with respect to the
fitting parameters
"""
pass
@surrogate
def functionDeriv1D(self, xvals, jacobian):
"""Numerical derivative except for Height parameter"""
# partial derivatives with respect to the fitting parameters
pass
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(StretchedExpFT)
def setUp(self):
self.dataset_names = ["Name1", "Name2"]
self.current_dataset_index = 0
self.start_x = 0.0
self.end_x = 15.0
self.fit_status = "success"
self.chi_squared = 1.5
self.function_name = "FlatBackground"
self.minimizer = "Levenberg-Marquardt"
self.evaluation_type = "eval type"
self.fit_to_raw = True
self.plot_guess = True
self.simultaneous_fitting_mode = True
self.simultaneous_fit_by = "Group/Pair"
self.simultaneous_fit_by_specifier = "fwd"
self.global_parameters = ["A0"]
self.fit_function = FunctionFactory.createFunction("FlatBackground")
self.single_fit_functions = [
self.fit_function.clone(),
self.fit_function.clone()
]
self._setup_mock_view()
self._setup_mock_model()
self._setup_presenter()
self.mock_view_minimizer.assert_called_once_with()
self.mock_view_evaluation_type.assert_called_once_with()
self.mock_view_fit_to_raw.assert_called_once_with()
self.mock_view_simultaneous_fit_by.assert_called_once_with()
self.mock_view_simultaneous_fit_by_specifier.assert_called_once_with()
self.mock_view_global_parameters.assert_called_once_with()
self.mock_model_minimizer.assert_called_once_with(self.minimizer)
self.mock_model_evaluation_type.assert_called_once_with(
self.evaluation_type)
self.mock_model_fit_to_raw.assert_called_once_with(self.fit_to_raw)
self.mock_model_simultaneous_fit_by.assert_called_once_with(
self.simultaneous_fit_by)
self.mock_model_simultaneous_fit_by_specifier.assert_called_once_with(
self.simultaneous_fit_by_specifier)
self.mock_model_global_parameters.assert_called_once_with(
self.global_parameters)
self.assertEqual(
self.view.set_slot_for_fit_generator_clicked.call_count, 1)
self.assertEqual(self.view.set_slot_for_fit_button_clicked.call_count,
1)
self.assertEqual(self.view.set_slot_for_undo_fit_clicked.call_count, 1)
self.assertEqual(self.view.set_slot_for_plot_guess_changed.call_count,
1)
self.assertEqual(self.view.set_slot_for_fit_name_changed.call_count, 1)
self.assertEqual(
self.view.set_slot_for_function_structure_changed.call_count, 1)
self.assertEqual(
self.view.set_slot_for_function_parameter_changed.call_count, 1)
self.assertEqual(self.view.set_slot_for_start_x_updated.call_count, 1)
self.assertEqual(self.view.set_slot_for_end_x_updated.call_count, 1)
self.assertEqual(self.view.set_slot_for_minimizer_changed.call_count,
1)
self.assertEqual(
self.view.set_slot_for_evaluation_type_changed.call_count, 1)
self.assertEqual(self.view.set_slot_for_use_raw_changed.call_count, 1)
self.assertEqual(self.view.set_slot_for_dataset_changed.call_count, 1)
self.assertEqual(
self.view.set_slot_for_fitting_mode_changed.call_count, 1)
self.assertEqual(
self.view.set_slot_for_simultaneous_fit_by_changed.call_count, 1)
self.assertEqual(
self.view.set_slot_for_simultaneous_fit_by_specifier_changed.
call_count, 1)
def category(self):
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("Height", 1.0, 'Height')
self.declareParameter("Msd", 0.05, 'Mean square displacement')
def function1D(self, xvals):
height = self.getParameterValue("Height")
msd = self.getParameterValue("Msd")
xvals = np.array(xvals)
intensity = height * np.exp((-msd * xvals**2) / 6)
return intensity
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
msd = self.getParameterValue("Msd")
for i, x in enumerate(xvals):
e = math.exp((-msd * x**2) / 6)
jacobian.set(i, 0, e)
jacobian.set(i, 1, -((x**2) / 6) * e * height)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(MsdGauss)
def test_instance_can_be_created_from_factory(self):
FunctionFactory.subscribe(Times2)
func_name = Times2.__name__
func = FunctionFactory.createFunction(func_name)
self.assertTrue(isinstance(func, IFunction1D))
FunctionFactory.unsubscribe(func_name)
def test_get_Gaussian(self):
name = "Gaussian"
func = FunctionFactory.createFunction(name)
self.assertTrue(func.name() == name)
self.assertTrue(len(func.__repr__()) > len(name))
self.assertTrue("Peak" in func.categories())
def test_category_with_no_override_returns_default_category(self):
FunctionFactory.subscribe(NoCatgeoryFunction)
func = FunctionFactory.createFunction("NoCatgeoryFunction")
self.assertEquals("General", func.category())
FunctionFactory.unsubscribe("NoCatgeoryFunction")
import numpy as np
from scipy.special import kn
from mantid.api import IFunction1D, FunctionFactory
import numpy as np
class BesselFunction(IFunction1D):
def category(self):
return "SESANS"
def init(self):
self.declareParameter("length_scale", 0.2)
self.declareParameter("Const", 1)
def function1D(self, x):
c = self.getParameterValue("length_scale")
C = self.getParameterValue("Const")
kappa = c*x**2
return C*kappa*kn(1, kappa)
FunctionFactory.subscribe(BesselFunction)
def test_category_override_returns_overridden_result(self):
FunctionFactory.subscribe(Times2)
func = FunctionFactory.createFunction("Times2")
self.assertEquals("SimpleFunction", func.category())
FunctionFactory.unsubscribe("Times2")
"""
def category(self):
return "SANS"
def init(self):
# Active fitting parameters
self.declareParameter("Scale", 1.0, 'Scale')
self.declareParameter("Background", 0.0, 'Background')
def function1D(self, xvals):
"""
Evaluate the model
@param xvals: numpy array of q-values
"""
return self.getParameterValue("Scale") * np.power(xvals, -4) + self.getParameterValue('Background')
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
for x in xvals:
jacobian.set(i,0, math.pow(x, -4))
jacobian.set(i,1, 1.0)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(Porod)
def init(self):
self.declareParameter("A0", 0.2, 'Asymmetry')
self.declareParameter(
"Width", 0.1,
'Half-width half maximum of the local field Lorentzian Distribution'
)
self.declareParameter("Nu", 1, 'Rate of Markovian modulation')
self.declareParameter("Q", 0.1, 'Order Parameter')
self.addConstraints("Nu > 0")
self.addConstraints("0 < Q < 1")
def function1D(self, x):
A0 = self.getParameterValue("A0")
a = self.getParameterValue("Width")
nu = self.getParameterValue("Nu")
q = self.getParameterValue("Q")
x = x[1:np.size(x)]
term1 = 4 * (a**2) * (1 - q) * x / nu
term2 = q * (a**2) * (x**2)
term13 = np.exp(-np.sqrt(term1))
term23 = (
1 -
(term2 / np.sqrt(term1 + term2))) * np.exp(-np.sqrt(term1 + term2))
SpinGlass = A0 * ((1. / 3.) * term13 + (2. / 3.) * term23)
SpinGlass = np.insert(SpinGlass, 0, A0)
return SpinGlass
FunctionFactory.subscribe(SpinGlass)
"""
Evaluate the model
@param xvals: numpy array of q-values
"""
# parameters
scale = self.getParameterValue('Scale')
bgd = self.getParameterValue('Background')
output = np.zeros(len(xvals), dtype=float)
for i in range(len(xvals)):
output[i] = scale * self._guinier_porod_core(xvals[i]) + bgd
return output
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
for x in xvals:
jacobian.set(i,0, self._guinier_porod_core(x))
jacobian.set(i,1, self._first_derivative_dim(x))
jacobian.set(i,2, self._first_derivative_rg(x))
jacobian.set(i,3, self._first_derivative_m(x))
jacobian.set(i,4, 1.0)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(GuinierPorod)
def category(self):
return "QuasiElastic"
def init(self):
# Active fitting parameters
self.declareParameter("Tau", 1.0, 'Residence time')
self.declareParameter("L", 1.5, 'Jump length')
def function1D(self, xvals):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
xvals = np.array(xvals)
hwhm = (1.0 - np.sin(xvals * length) / (xvals * length)) / tau
return hwhm
def functionDeriv1D(self, xvals, jacobian):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
i = 0
for x in xvals:
s = math.sin(x*length)/(x*length)
h = (1.0-s)/tau
jacobian.set(i,0,-h/tau);
jacobian.set(i,1,(math.cos(x*length)-s)/(length*tau));
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(ChudleyElliot)
Parameters
----------
xvals : sequence of floats
The domain where to evaluate the function
jacobian: 2D array
partial derivative of the function with respect to the fitting
parameters evaluated at the domain.
Returns
-------
numpy.ndarray
Function values
"""
radius = self.getParameterValue('R')
length = self.getParameterValue('L')
x = np.asarray(xvals) # Q values
z = length * np.outer(x, self.cos_theta)
# EISF along cylinder Z-axis
a = np.square(np.where(z < 1e-9, 1 - z * z / 6, np.sin(z) / z))
z = radius * np.outer(x, self.sin_theta)
# EISF on cylinder cross-section (diffusion on a disc)
b = np.square(np.where(z < 1e-6, 1 - z * z / 10,
3 * (np.sin(z) - z * np.cos(z)) / (z * z * z)))
# integrate in theta
eisf = self.d_theta * np.sum(self.sin_theta * a * b, axis=1)
return self.getParameterValue('A') * eisf
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(EISFDiffCylinder)
import numpy as np
class HighTFMuonium(IFunction1D):
def category(self):
return "Muon\\MuonSpecific"
def init(self):
self.declareParameter("A0", 0.1)
self.declareParameter("Field", 100, "Magnetic field (G)")
self.declareParameter("Freq", 0.2,
'Isotropic hyperfine coupling constant (MHz)')
self.declareParameter("Phi", 0.0, 'Phi (rad)')
def function1D(self, x):
A0 = self.getParameterValue("A0")
Field = self.getParameterValue("Field")
Freq = self.getParameterValue("Freq")
Phi = self.getParameterValue("Phi")
gmu = 0.01355342
ge = 2.8024
OmegaMinus = (ge - gmu) * Field * np.pi
Omega = 2 * np.pi * \
(np.sqrt(Freq ** 2 + ((ge + gmu) * Field) ** 2) / 2 - Freq / 2)
Omega2 = Omega - OmegaMinus
Omega1 = Omega2 + Freq * 2 * np.pi
return A0 * 0.5 * (np.cos(Omega1 * x + Phi) + np.cos(Omega2 * x + Phi))
FunctionFactory.subscribe(HighTFMuonium)
def init(self):
# Active fitting parameters
self.declareParameter("Scale", 1.0, 'Scale')
self.declareParameter("Length", 50.0, 'Length')
self.declareParameter("Background", 0.0, 'Background')
def function1D(self, xvals):
"""
Evaluate the model
@param xvals: numpy array of q-values
"""
return self.getParameterValue("Scale") / (1.0 + np.power(xvals*self.getParameterValue('Length'), 2)) + self.getParameterValue('Background')
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
for x in xvals:
jacobian.set(i,0, 1.0 / (1.0 + np.power(x*self.getParameterValue('Length'), 2)))
denom = math.pow(1.0 + math.pow(x*self.getParameterValue('Length'), 2), -2)
jacobian.set(i,1, -2.0 * self.getParameterValue("Scale") * x * x * self.getParameterValue('Length') * denom)
jacobian.set(i,2, 1.0)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(Lorentz)
See ExamplePeakFunction for more on attributes
"""
# Active fitting parameters
self.declareParameter("A0")
self.declareParameter("A1")
def function1D(self, xvals):
"""
Computes the function on the set of values given and returns
the answer as a numpy array of floats
"""
return self.getParameterValue("A0") + self.getParameterValue("A1")*xvals
def functionDeriv1D(self, xvals, jacobian):
"""
Computes the partial derivatives of the function on the set of values given
and the sets these values in the given jacobian. The Jacobian is essentially
a matrix where jacobian.set(iy,ip,value) takes 3 parameters:
iy = The index of the data value whose partial derivative this corresponds to
ip = The index of the parameter value whose partial derivative this corresponds to
value = The value of the derivative
"""
i = 0
for x in xvals:
jacobian.set(i,0,1);
jacobian.set(i,1,x);
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(Example1DFunction)
-------
numpy.ndarray
Function values
"""
zs = self.getParameterValue('R') * np.asarray(xvals)
return self.getParameterValue('A') * np.square(3 * self.vecbessel(zs))
def functionDeriv1D(self, xvals, jacobian):
r"""Calculate the partial derivatives
Parameters
----------
xvals : sequence of floats
The domain where to evaluate the function
jacobian: 2D array
partial derivatives of the function with respect to the fitting
parameters, evaluated at the domain.
"""
amplitude = self.getParameterValue('A')
radius = self.getParameterValue('R')
i = 0
for x in xvals:
z = radius * x
j = j1(z)/z
jacobian.set(i, 0, np.square(3 * j))
jacobian.set(i,1, amplitude * 2 * 9 * j * (j1d(z) - j) / radius)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(EISFDiffSphere)
def test_instance_can_be_created_from_factory(self):
func = FunctionFactory.createInitialized(
'name=FlatBackground;name=FlatBackground')
self.assertTrue(isinstance(func, CompositeFunction))
self.assertEqual(len(func), 2)
self.assertEqual(func.nParams(), 2)
dsf = Dsf()
dsf.SetIntensities( mtd[ self._InputWorkspaces[idsf] ].dataY(self._WorkspaceIndex) )
dsf.errors = None # do not incorporate error data
if self._LoadErrors:
dsf.SetErrors(mtd[ self._InputWorkspaces[idsf] ].dataE(self._WorkspaceIndex))
dsf.SetFvalue( self._ParameterValues[idsf] )
dsfgroup.InsertDsf(dsf)
# Create the interpolator
from dsfinterp.channelgroup import ChannelGroup
self._channelgroup = ChannelGroup()
self._channelgroup.InitFromDsfGroup(dsfgroup)
if self._LocalRegression:
self._channelgroup.InitializeInterpolator(running_regr_type=self._RegressionType, windowlength=self._RegressionWindow)
else:
self._channelgroup.InitializeInterpolator(windowlength=0)
# channel group has been initialized, so evaluate the interpolator
dsf = self._channelgroup(p['TargetParameter'])
# Linear interpolation between the energies of the channels and the xvalues we require
# NOTE: interpolator evaluates to zero for any of the xvals outside of the domain defined by self._xvalues
intensities_interpolator = scipy.interpolate.interp1d(self._xvalues, p['Intensity']*dsf.intensities, kind='linear')
return intensities_interpolator(xvals) # can we pass by reference?
# Required to have Mantid recognize the new function
#pylint: disable=unused-import
try:
import dsfinterp
FunctionFactory.subscribe(DSFinterp1DFit)
except ImportError:
logger.debug('Failed to subscribe fit function DSFinterp1DFit. '+\
'Python package dsfinterp may be missing (https://pypi.python.org/pypi/dsfinterp)')
xvals = np.array(xvals)
i1 = 1.0 + (msd * xvals**2 / (6.0 * beta))
i2 = np.power(i1, beta)
intensity = height / i2
return intensity
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
msd = self.getParameterValue("Msd")
beta = self.getParameterValue("Beta")
for i, x in enumerate(xvals):
x_sq = x**2
q = msd * x_sq
q6 = q / 6
a1 = 1.0 + q6 / beta
a = 1.0 / math.pow(a1, beta)
b1 = q6 * x / beta + 1
b = -(x_sq / 6) * math.pow(b1, (-beta - 1))
cqx = q6 + beta
c1 = math.pow((cqx / beta), -beta)
c2 = q6 - cqx * math.log(cqx / beta)
c = c1 * c2 / cqx
jacobian.set(i, 0, a)
jacobian.set(i, 1, b * height)
jacobian.set(i, 2, c * height)
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(MsdPeters)
Return what should be considered the 'fwhm' of this function.
"""
return 2.0 * math.sqrt(
2.0 * math.log(2.0)) * self.getParameterValue("Sigma")
def setCentre(self, new_centre):
"""
Called by an external entity, probably a GUI, in response to a mouse click
that gives a guess at the centre.
"""
self.setParameter("PeakCentre", new_centre)
def setHeight(self, new_height):
"""
Called by an external entity, probably a GUI, in response to a user guessing
the height.
"""
self.setParameter("Height", new_height)
def setFwhm(self, new_fwhm):
"""
Called by an external entity, probably a GUI, in response to a user guessing
the height.
"""
sigma = new_fwhm / (2.0 * math.sqrt(2.0 * math.log(2.0)))
self.setParameter("Sigma", sigma)
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(ExamplePeakFunction)
# Active fitting parameters
self.declareParameter("Tau", 1.0, 'Residence time')
self.declareParameter("L", 1.5, 'Jump length')
def function1D(self, xvals):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
length = length**2
xvals = np.array(xvals)
hwhm = xvals * xvals * length / (tau * (1 + xvals * xvals * length))
return hwhm
def functionDeriv1D(self, xvals, jacobian):
tau = self.getParameterValue("Tau")
length = self.getParameterValue("L")
length = length**2
i = 0
for x in xvals:
h = x * x * length / (tau * (1 + x * x * length))
jacobian.set(i, 0, -h / tau)
jacobian.set(i, 1,
h * (1.0 - h * tau) / length)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(TeixeiraWater)
c = np.zeros(self.numParams())
for i in range(self.numParams()):
c[i] = self.getParamValue(i)
self.setParameter(i, trialc[i])
# Get the trial values
f_trial = self.function1D(xvals)
# Now return to the orignial
for i in range(self.numParams()):
self.setParameter(i, c[i])
return f_trial
# Construction the Jacobian (df) for the function
def functionDeriv1D(self, xvals, jacobian, eps=1.e-3):
f_int = self.function1D(xvals)
#Fetch parameters into array c
c = np.zeros(self.numParams())
for i in range(self.numParams()):
c[i] = self.getParamValue(i)
nc = np.prod(np.shape(c))
for k in range(nc):
dc = np.zeros(nc)
dc[k] = max(eps,eps*c[k])
f_new = self.function1DDiffParams(xvals,c+dc)
for i,dF in enumerate(f_new-f_int):
jacobian.set(i,k,dF/dc[k])
FunctionFactory.subscribe(IkedaCarpenterConvoluted)
def function1D(self, xvals):
"""
Evaluate the model
@param xvals: numpy array of q-values
"""
return self.getParameterValue("Scale") / (1.0 + np.power(xvals*self.getParameterValue('Length'), 2)) +\
self.getParameterValue('Background')
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
for x in xvals:
jacobian.set(
i, 0, 1.0 /
(1.0 + np.power(x * self.getParameterValue('Length'), 2)))
denom = math.pow(
1.0 + math.pow(x * self.getParameterValue('Length'), 2), -2)
jacobian.set(
i, 1, -2.0 * self.getParameterValue("Scale") * x * x *
self.getParameterValue('Length') * denom)
jacobian.set(i, 2, 1.0)
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(Lorentz)
def category(self):
return "SANS"
def init(self):
# Active fitting parameters
self.declareParameter("Scale", 1.0, 'Scale')
self.declareParameter("Rg", 60.0, 'Radius of gyration')
def function1D(self, xvals):
"""
Evaluate the model
@param xvals: numpy array of q-values
"""
return self.getParameterValue("Scale") * np.exp(-(self.getParameterValue('Rg')*xvals)**2/3.0 )
def functionDeriv1D(self, xvals, jacobian):
"""
Evaluate the first derivatives
@param xvals: numpy array of q-values
@param jacobian: Jacobian object
"""
i = 0
rg = self.getParameterValue('Rg')
for x in xvals:
jacobian.set(i,0, math.exp(-(rg*x)**2/3.0 ) )
jacobian.set(i,1, -self.getParameterValue("Scale") * math.exp(-(rg*x)**2/3.0 )*2.0/3.0*rg*x*x );
i += 1
# Required to have Mantid recognise the new function
FunctionFactory.subscribe(Guinier)
from matplotlib.lines import Line2D
from mantid.plots import MantidAxes
from mantid.simpleapi import CreateSampleWorkspace
from mantidqt.widgets.fitpropertybrowser import FitPropertyBrowser
from mantidqt.widgets.fitpropertybrowser.fitpropertybrowserplotinteraction import FitPropertyBrowserPlotInteraction
from mantid.api import AnalysisDataService, FunctionFactory, WorkspaceFactory
import matplotlib
matplotlib.use('AGG') # noqa
X_COLUMN_LABEL = 'x_column'
Y_COLUMN_LABEL = 'y_column'
FULL_FUNCTION = FunctionFactory.createInitialized("name=FlatBackground,A0=1;name=LinearBackground,A0=1,"
"A1=2;name=GausOsc,A=0.2,Sigma=0.2,Frequency=0.1,Phi=0")
FUNCTION_1 = FunctionFactory.createInitialized("name=FlatBackground,A0=1")
FUNCTION_2 = FunctionFactory.createInitialized("name=LinearBackground,A0=1,A1=2")
FUNCTION_3 = FunctionFactory.createInitialized("name=GausOsc,A=0.2,Sigma=0.2,Frequency=0.1,Phi=0")
class FitPropertyBrowserPlotInteractionTest(unittest.TestCase):
def setup_mock_fit_browser(self, workspace_creator, workspace_name, function, function_prefix):
workspace_creator(workspace_name)
self.fit_browser.workspaceName = Mock(return_value=workspace_name)
self.fit_browser.currentHandler.return_value = self.create_mock_handler(function, function_prefix)
def create_table_workspace(self, table_name):
table = WorkspaceFactory.createTable()
table.addColumn('double', X_COLUMN_LABEL, 1)
