diff --git a/Framework/PythonInterface/mantid/fitfunctions.py b/Framework/PythonInterface/mantid/fitfunctions.py
index ee7dace2df3d09f2b705492176285343b479da54..55b3c78a001a3d3569b5c3d4ce737f16ffc2321b 100644
--- a/Framework/PythonInterface/mantid/fitfunctions.py
+++ b/Framework/PythonInterface/mantid/fitfunctions.py
@@ -23,7 +23,7 @@ class FunctionWrapper(object):
return wrapper(fun, *args, **kwargs)
return FunctionWrapper(fun, **kwargs)
- def __init__ (self, name, **kwargs):
+ def __init__(self, name, **kwargs):
"""
Called when creating an instance
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSDFit.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSDFit.py
index c2070b3f8379190e2cb2c970ece8d363ecdf41a2..3824447f5e1400ee7fb57850e62c91f2029e3023 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSDFit.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/MSDFit.py
@@ -31,7 +31,8 @@ class MSDFit(DataProcessorAlgorithm):
self.declareProperty(MatrixWorkspaceProperty('InputWorkspace', '', direction=Direction.Input),
doc='Sample input workspace')
self.declareProperty(name='Model', defaultValue='Gauss',
- validator=StringListValidator(['Gauss', 'Peters', 'Yi']),
+ validator=StringListValidator(
+ ['Gauss', 'Peters', 'Yi']),
doc='Model options : Gauss, Peters, Yi')
self.declareProperty(name='XStart', defaultValue=0.0,
@@ -100,9 +101,12 @@ class MSDFit(DataProcessorAlgorithm):
progress = Progress(self, 0.0, 0.05, 3)
self._original_ws = self._input_ws
- rename_alg = self.createChildAlgorithm("RenameWorkspace", enableLogging=False)
+ rename_alg = self.createChildAlgorithm(
+ "RenameWorkspace", enableLogging=False)
rename_alg.setProperty("InputWorkspace", self._input_ws)
- rename_alg.setProperty("OutputWorkspace", self._input_ws + "_" + self._model)
+ rename_alg.setProperty(
+ "OutputWorkspace",
+ self._input_ws + "_" + self._model)
rename_alg.execute()
self._input_ws = self._input_ws + "_" + self._model
input_params = [self._input_ws + ',i%d' % i for i in range(self._spec_range[0],
@@ -111,19 +115,19 @@ class MSDFit(DataProcessorAlgorithm):
# Fit line to each of the spectra
if self._model == 'Gauss':
logger.information('Model : Gaussian approximation')
- function = 'name=MsdGauss, Height=1.0, MSD=0.1'
- function += ',constraint=(Height>0.0, MSD>0.0)'
- params_list = ['Height', 'MSD']
+ function = 'name=MsdGauss, Height=1.0, Msd=0.1'
+ function += ',constraint=(Height>0.0, Msd>0.0)'
+ params_list = ['Height', 'Msd']
elif self._model == 'Peters':
logger.information('Model : Peters & Kneller')
- function = 'name=MsdPeters, Height=1.0, MSD=1.0, Beta=1.0'
- function += ',constraint=(Height>0.0, MSD>0.0, 100.0>Beta>0.3)'
- params_list = ['Height', 'MSD', 'Beta']
+ function = 'name=MsdPeters, Height=1.0, Msd=1.0, Beta=1.0'
+ function += ',constraint=(Height>0.0, Msd>0.0, 100.0>Beta>0.3)'
+ params_list = ['Height', 'Msd', 'Beta']
elif self._model == 'Yi':
logger.information('Model : Yi et al')
- function = 'name=MsdYi, Height=1.0, MSD=1.0, Sigma=0.1'
- function += ',constraint=(Height>0.0, MSD>0.0, Sigma>0.0)'
- params_list = ['Height', 'MSD', 'Sigma']
+ function = 'name=MsdYi, Height=1.0, Msd=1.0, Sigma=0.1'
+ function += ',constraint=(Height>0.0, Msd>0.0, Sigma>0.0)'
+ params_list = ['Height', 'Msd', 'Sigma']
else:
raise ValueError('No Model defined')
@@ -137,12 +141,20 @@ class MSDFit(DataProcessorAlgorithm):
FitType='Sequential',
CreateOutput=True)
- delete_alg = self.createChildAlgorithm("DeleteWorkspace", enableLogging=False)
- delete_alg.setProperty("Workspace", self._output_msd_ws + '_NormalisedCovarianceMatrices')
+ delete_alg = self.createChildAlgorithm(
+ "DeleteWorkspace", enableLogging=False)
+ delete_alg.setProperty(
+ "Workspace",
+ self._output_msd_ws +
+ '_NormalisedCovarianceMatrices')
delete_alg.execute()
- delete_alg.setProperty("Workspace", self._output_msd_ws + '_Parameters')
+ delete_alg.setProperty(
+ "Workspace",
+ self._output_msd_ws +
+ '_Parameters')
delete_alg.execute()
- rename_alg = self.createChildAlgorithm("RenameWorkspace", enableLogging=False)
+ rename_alg = self.createChildAlgorithm(
+ "RenameWorkspace", enableLogging=False)
rename_alg.setProperty("InputWorkspace", self._output_msd_ws)
rename_alg.setProperty("OutputWorkspace", self._output_param_ws)
rename_alg.execute()
@@ -154,31 +166,50 @@ class MSDFit(DataProcessorAlgorithm):
for par in params_list:
ws_name = self._output_msd_ws + '_' + par
parameter_ws_group.append(ws_name)
- convert_alg = self.createChildAlgorithm("ConvertTableToMatrixWorkspace", enableLogging=False)
+ convert_alg = self.createChildAlgorithm(
+ "ConvertTableToMatrixWorkspace", enableLogging=False)
convert_alg.setProperty("InputWorkspace", self._output_param_ws)
convert_alg.setProperty("OutputWorkspace", ws_name)
convert_alg.setProperty("ColumnX", 'axis-1')
convert_alg.setProperty("ColumnY", par)
convert_alg.setProperty("ColumnE", par + '_Err')
convert_alg.execute()
- mtd.addOrReplace(ws_name, convert_alg.getProperty("OutputWorkspace").value)
-
- append_alg = self.createChildAlgorithm("AppendSpectra", enableLogging=False)
- append_alg.setProperty("InputWorkspace1", self._output_msd_ws + '_' + params_list[0])
- append_alg.setProperty("InputWorkspace2", self._output_msd_ws + '_' + params_list[1])
+ mtd.addOrReplace(
+ ws_name, convert_alg.getProperty("OutputWorkspace").value)
+
+ append_alg = self.createChildAlgorithm(
+ "AppendSpectra", enableLogging=False)
+ append_alg.setProperty(
+ "InputWorkspace1",
+ self._output_msd_ws +
+ '_' +
+ params_list[0])
+ append_alg.setProperty(
+ "InputWorkspace2",
+ self._output_msd_ws +
+ '_' +
+ params_list[1])
append_alg.setProperty("ValidateInputs", False)
append_alg.setProperty("OutputWorkspace", self._output_msd_ws)
append_alg.execute()
- mtd.addOrReplace(self._output_msd_ws, append_alg.getProperty("OutputWorkspace").value)
+ mtd.addOrReplace(
+ self._output_msd_ws,
+ append_alg.getProperty("OutputWorkspace").value)
if len(params_list) > 2:
append_alg.setProperty("InputWorkspace1", self._output_msd_ws)
- append_alg.setProperty("InputWorkspace2", self._output_msd_ws + '_' + params_list[2])
+ append_alg.setProperty(
+ "InputWorkspace2",
+ self._output_msd_ws +
+ '_' +
+ params_list[2])
append_alg.setProperty("ValidateInputs", False)
append_alg.setProperty("OutputWorkspace", self._output_msd_ws)
append_alg.execute()
- mtd.addOrReplace(self._output_msd_ws, append_alg.getProperty("OutputWorkspace").value)
+ mtd.addOrReplace(self._output_msd_ws,
+ append_alg.getProperty("OutputWorkspace").value)
for par in params_list:
- delete_alg.setProperty("Workspace", self._output_msd_ws + '_' + par)
+ delete_alg.setProperty(
+ "Workspace", self._output_msd_ws + '_' + par)
delete_alg.execute()
progress.report('Change axes')
@@ -187,7 +218,9 @@ class MSDFit(DataProcessorAlgorithm):
sort_alg.setProperty("InputWorkspace", self._output_msd_ws)
sort_alg.setProperty("OutputWorkspace", self._output_msd_ws)
sort_alg.execute()
- mtd.addOrReplace(self._output_msd_ws, sort_alg.getProperty("OutputWorkspace").value)
+ mtd.addOrReplace(
+ self._output_msd_ws,
+ sort_alg.getProperty("OutputWorkspace").value)
# Create a new x axis for the Q and Q**2 workspaces
xunit = mtd[self._output_msd_ws].getAxis(0).setUnit('Label')
xunit.setLabel('Temperature', 'K')
@@ -200,7 +233,10 @@ class MSDFit(DataProcessorAlgorithm):
# Rename fit workspace group
original_fit_ws_name = self._output_msd_ws + '_Workspaces'
if original_fit_ws_name != self._output_fit_ws:
- rename_alg.setProperty("InputWorkspace", self._output_msd_ws + '_Workspaces')
+ rename_alg.setProperty(
+ "InputWorkspace",
+ self._output_msd_ws +
+ '_Workspaces')
rename_alg.setProperty("OutputWorkspace", self._output_fit_ws)
rename_alg.execute()
@@ -213,7 +249,8 @@ class MSDFit(DataProcessorAlgorithm):
copy_alg.setProperty("OutputWorkspace", self._output_fit_ws)
copy_alg.execute()
- rename_alg = self.createChildAlgorithm("RenameWorkspace", enableLogging=False)
+ rename_alg = self.createChildAlgorithm(
+ "RenameWorkspace", enableLogging=False)
rename_alg.setProperty("InputWorkspace", self._input_ws)
rename_alg.setProperty("OutputWorkspace", self._original_ws)
rename_alg.execute()
diff --git a/Framework/PythonInterface/plugins/functions/MsdGauss.py b/Framework/PythonInterface/plugins/functions/MsdGauss.py
index 0f7f8e9d0ed1cdcdf829e1ded284740b3f61db9a..1f796e1367d63d2ffeb8958a373ed7ee264b97e7 100644
--- a/Framework/PythonInterface/plugins/functions/MsdGauss.py
+++ b/Framework/PythonInterface/plugins/functions/MsdGauss.py
@@ -27,11 +27,11 @@ class MsdGauss(IFunction1D):
def init(self):
# Active fitting parameters
self.declareParameter("Height", 1.0, 'Height')
- self.declareParameter("MSD", 0.05, 'Mean square displacement')
+ self.declareParameter("Msd", 0.05, 'Mean square displacement')
def function1D(self, xvals):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
xvals = np.array(xvals)
intensity = height * np.exp(-msd * xvals**2)
@@ -40,7 +40,7 @@ class MsdGauss(IFunction1D):
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
for i, x in enumerate(xvals):
e = math.exp(-msd * x**2)
diff --git a/Framework/PythonInterface/plugins/functions/MsdPeters.py b/Framework/PythonInterface/plugins/functions/MsdPeters.py
index b3278bc1eaf8dff62ed1e409c7eda2c0751201f3..9974d21ec72df219503536a556219a5e35656c07 100644
--- a/Framework/PythonInterface/plugins/functions/MsdPeters.py
+++ b/Framework/PythonInterface/plugins/functions/MsdPeters.py
@@ -28,12 +28,12 @@ class MsdPeters(IFunction1D):
def init(self):
# Active fitting parameters
self.declareParameter("Height", 1.0, 'Height')
- self.declareParameter("MSD", 0.05, 'Mean square displacement')
+ self.declareParameter("Msd", 0.05, 'Mean square displacement')
self.declareParameter("Beta", 1.0, 'beta')
def function1D(self, xvals):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
beta = self.getParameterValue("Beta")
xvals = np.array(xvals)
@@ -44,7 +44,7 @@ class MsdPeters(IFunction1D):
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
beta = self.getParameterValue("Beta")
for i, x in enumerate(xvals):
diff --git a/Framework/PythonInterface/plugins/functions/MsdYi.py b/Framework/PythonInterface/plugins/functions/MsdYi.py
index 50c25f4fd24c6e63a488317727d3f2d15eef8813..3e92154c30074bd59135b1da19897c175ad7f517 100644
--- a/Framework/PythonInterface/plugins/functions/MsdYi.py
+++ b/Framework/PythonInterface/plugins/functions/MsdYi.py
@@ -1,43 +1,46 @@
-# Mantid Repository : https://github.com/mantidproject/mantid
-#
-# Copyright © 2007 ISIS Rutherford Appleton Laboratory UKRI,
-# NScD Oak Ridge National Laboratory, European Spallation Source
-# & Institut Laue - Langevin
-# SPDX - License - Identifier: GPL - 3.0 +
-# pylint: disable=no-init,invalid-name
'''
@author Spencer Howells, ISIS
@date December 05, 2013
+
+Copyright © 2007-8 ISIS Rutherford Appleton Laboratory,
+NScD Oak Ridge National Laboratory & European Spallation Source
+
+pylint: disable=no-init,invalid-name
+
+This file is part of Mantid.
+Mantid Repository : https://github.com/mantidproject/mantid
+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)
-
import math
import numpy as np
-
from mantid.api import IFunction1D, FunctionFactory
-
# The model of Yi et al(J Phys Chem B 1316 5029 2012) takes into account motional heterogeneity.
-# The elastic intensity is propotional to exp(-1/6*Q^2*msd)*(1+Q^4*sigma/72)
+# The elastic intensity is proportional to exp(-(1/6)*Q^2*msd)*(1+Q^4*sigma/72)
# where the mean square displacement msd = <r^2> and sigma^2 is the variance of the msd.
+# In the limit sigma = 0 the model becomes Gaussian.
+
class MsdYi(IFunction1D):
+
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')
+ self.declareParameter("Msd", 0.05, 'Mean square displacement')
self.declareParameter("Sigma", 1.0, 'Sigma')
def function1D(self, xvals):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
sigma = self.getParameterValue("Sigma")
xvals = np.array(xvals)
- i1 = np.exp(-1.0 / (6.0 * xvals**2 * msd))
+ i1 = np.exp((-1.0 / 6.0) * xvals * xvals * msd)
i2 = 1.0 + (np.power(xvals, 4) * sigma / 72.0)
intensity = height * i1 * i2
@@ -45,13 +48,12 @@ class MsdYi(IFunction1D):
def functionDeriv1D(self, xvals, jacobian):
height = self.getParameterValue("Height")
- msd = self.getParameterValue("MSD")
+ msd = self.getParameterValue("Msd")
sigma = self.getParameterValue("Sigma")
for i, x in enumerate(xvals):
- q = msd * x**2
- f1 = math.exp(-1.0 / (6.0 * q))
- df1 = f1 / (6.0 * x * q)
+ f1 = math.exp((-1.0 / 6.0) * x * x * msd)
+ df1 = -f1 * ((2.0 / 6.0) * x * msd)
x4 = math.pow(x, 4)
f2 = 1.0 + (x4 * sigma / 72.0)
df2 = x4 / 72.0
diff --git a/Framework/PythonInterface/test/python/plugins/functions/MsdGaussTest.py b/Framework/PythonInterface/test/python/plugins/functions/MsdGaussTest.py
index 60f0cba3d67a5d7c06789a26dc548e2eff9047b5..2126d5f4edc9f23ae6b2f98bf2dceced5a42265a 100644
--- a/Framework/PythonInterface/test/python/plugins/functions/MsdGaussTest.py
+++ b/Framework/PythonInterface/test/python/plugins/functions/MsdGaussTest.py
@@ -23,15 +23,15 @@ class MsdGaussTest(unittest.TestCase):
input = np.array([[0, 1], [2, 3]])
expected = np.array([[1., 0.95122942], [0.81873075, 0.63762815]])
tolerance = 0.000001
- status, output = check_output("MsdGauss", input, expected, tolerance, Height=1.0, MSD=0.05)
+ status, output = check_output("MsdGauss", input, expected, tolerance, Height=1.0, Msd=0.05)
if not status:
self.fail("Computed output " + str(output) + " from input " + str(input) +
" is not equal to the expected output: " + str(expected))
def test_use_in_fit(self):
- workspace = create_test_workspace(create_model("MsdGauss", Height=1.0, MSD=0.05), 1000)
- function_string = create_function_string("MsdGauss", Height=1.0, MSD=0.05)
+ workspace = create_test_workspace(create_model("MsdGauss", Height=1.0, Msd=0.05), 1000)
+ function_string = create_function_string("MsdGauss", Height=1.0, Msd=0.05)
Fit(Function=function_string, InputWorkspace=workspace, StartX=1.2, EndX=1200)
diff --git a/Framework/PythonInterface/test/python/plugins/functions/MsdPetersTest.py b/Framework/PythonInterface/test/python/plugins/functions/MsdPetersTest.py
index 62797361d291a8747625b2e835738f7f18b532bc..86ff0730ccdaf2d7c59367c7aa96855ba4c57474 100644
--- a/Framework/PythonInterface/test/python/plugins/functions/MsdPetersTest.py
+++ b/Framework/PythonInterface/test/python/plugins/functions/MsdPetersTest.py
@@ -23,15 +23,15 @@ class MsdPetersTest(unittest.TestCase):
input = np.array([[0, 1], [2, 3]])
expected = np.array([[1., 0.99173554], [0.96774194, 0.93023256]])
tolerance = 0.000001
- status, output = check_output("MsdPeters", input, expected, tolerance, Height=1.0, MSD=0.05, Beta=1.0)
+ status, output = check_output("MsdPeters", input, expected, tolerance, Height=1.0, Msd=0.05, Beta=1.0)
if not status:
self.fail("Computed output " + str(output) + " from input " + str(input) +
" is not equal to the expected output: " + str(expected))
def test_use_in_fit(self):
- workspace = create_test_workspace(create_model("MsdPeters", Height=1.0, MSD=0.05, Beta=1.0), 1000)
- function_string = create_function_string("MsdPeters", Height=1.0, MSD=0.05, Beta=1.0)
+ workspace = create_test_workspace(create_model("MsdPeters", Height=1.0, Msd=0.05, Beta=1.0), 1000)
+ function_string = create_function_string("MsdPeters", Height=1.0, Msd=0.05, Beta=1.0)
Fit(Function=function_string, InputWorkspace=workspace, StartX=1.2, EndX=1200)
diff --git a/Framework/PythonInterface/test/python/plugins/functions/MsdYiTest.py b/Framework/PythonInterface/test/python/plugins/functions/MsdYiTest.py
index 2558863e09090090db257620551250cf09e50232..4a1e5431d573283d2c73a486801b50ac2adc5d42 100644
--- a/Framework/PythonInterface/test/python/plugins/functions/MsdYiTest.py
+++ b/Framework/PythonInterface/test/python/plugins/functions/MsdYiTest.py
@@ -21,18 +21,30 @@ class MsdYiTest(unittest.TestCase):
def test_function_output(self):
input = np.array([[1, 2], [3, 4]])
- expected = np.array([[0.03616947, 0.53117559], [1.46726692, 3.69882113]])
+ expected = np.array(
+ [[1.00547492, 1.18215301], [1.97145491, 3.98690068]])
tolerance = 0.000001
- status, output = check_output("MsdYi", input, expected, tolerance, Height=1.0, MSD=0.05, Sigma=1.0)
+ status, output = check_output(
+ "MsdYi", input, expected, tolerance, Height=1.0, Msd=0.05, Sigma=1.0)
if not status:
self.fail("Computed output " + str(output) + " from input " + str(input) +
" is not equal to the expected output: " + str(expected))
def test_use_in_fit(self):
- workspace = create_test_workspace(create_model("MsdYi", Height=1.0, MSD=0.05, Sigma=1.0), 1000)
- function_string = create_function_string("MsdYi", Height=1.0, MSD=0.05, Sigma=1.0)
- Fit(Function=function_string, InputWorkspace=workspace, StartX=1.2, EndX=1200)
+ workspace = create_test_workspace(
+ create_model(
+ "MsdYi",
+ Height=1.0,
+ Msd=0.05,
+ Sigma=1.0),
+ 1000)
+ function_string = create_function_string(
+ "MsdYi", Height=1.0, Msd=0.05, Sigma=1.0)
+ Fit(Function=function_string,
+ InputWorkspace=workspace,
+ StartX=1.2,
+ EndX=1200)
if __name__ == '__main__':
diff --git a/docs/source/algorithms/MSDFit-v1.rst b/docs/source/algorithms/MSDFit-v1.rst
index f7b51e2cda468e30da3ebfe74171c9a69af73817..4e01c6d43b5b051247d008e7ace9b83591a1d160 100644
--- a/docs/source/algorithms/MSDFit-v1.rst
+++ b/docs/source/algorithms/MSDFit-v1.rst
@@ -61,8 +61,8 @@ Output:
A0: [ 0.87079958]
A1: [ 0.03278263]
Using Yi Model
- A0: [ 0.75677983]
- A1: [ 1.76943372]
+ A0: [ 0.95770532]
+ A1: [ 0.58819225]
.. categories::
diff --git a/docs/source/release/v3.14.0/indirect_inelastic.rst b/docs/source/release/v3.14.0/indirect_inelastic.rst
index 44567e5958ffcdf0a4f416bdb9c632d8ca1a88d8..c9fd7a9a92b6c0e5eeb7ef7ee757a27b39b64fbb 100644
--- a/docs/source/release/v3.14.0/indirect_inelastic.rst
+++ b/docs/source/release/v3.14.0/indirect_inelastic.rst
@@ -49,6 +49,7 @@ Bugfixes
message is now displayed.
- The Probability Density Functions (PDF) workspaces for the FABADA minimiser in ConvFit no longer overwrite each other.
Various other improvements in the display of the FABADA PDF's have also been finished.
+- The expression for the Fit type Yi in MSDFit was incorrect and has now been corrected.
Data Corrections Interface