Investigate & fix differences between vesuvio reduction in Mantid & Matlab

[Martyn Gigg]

The VESUVIO group have found some differences in the results of the fitting in Mantid vs MATLAB. Investigate & fix them.

[Martyn Gigg]

Fix value of angular width parameter on VESUVIO. Refs #7199

Changeset: 9e5a6a9c37b7360f67ad8b4161eb19c78dadd2ad

[Martyn Gigg]

Add logging to ComptonProfile. Refs #7199

Changeset: 01b3c217d7e107f989dbaf243e32c82d07ccf636

[Martyn Gigg]

Allow the absolute error to be specified in SimplexMinimizer.

Refs #7199

Changeset: 180bfba419563ef8b26f6882ca3ec2f41a2938b9

[Martyn Gigg]

Add a specialized CostFunction to minimize a set of linear eqns ...

that includes equality & inequality constraints. The simplex minizer eventually gets to a good answer after restarting with updated values a few times. Refs #7199

Changeset: e5c50acf28b0d73ac6ce90e65566b9924d34eff4

[Martyn Gigg]

Refactor ComptonProfile to calculate resolution & Y-space once.

Refs #7199

Changeset: beb7b89f971038b2d74836f2bbb13ada60a0fab8

[Martyn Gigg]

ComptonProfile functions can now populate a constraint matrix

This can be used by a composite of the functions to compute the mass profile for various parameters. Refs #7199

Changeset: db7b5cf902eaefd3fa9c92a621691312962a4e51

[Martyn Gigg]

Significant caching in GramCharlierComptonProfile.

Leads to a roughly 400% speed increase (of the system test) as it currently is. The Voigt function was expensive to compute and identical with each function iteration. It is now cached when the workspace is set. Refs #7199

Changeset: f73586cb963b70e3fe9602f8ba2bdca191c166d6

[Martyn Gigg]

Refactor GramCharlierComptonProfile to allow calculation of

each contribution separately. Refs #7199

Changeset: 6822152f6f1c386505f90416fcd9476884b64e22

[Martyn Gigg]

Pass errors through to fill constraint matrix in ComptonProfile.

Refs #7199

Changeset: 2bb501a450e2122bad7fc943318b82769bfa47d3

[Martyn Gigg]

Fix value of angular width parameter on VESUVIO. Refs #7199

Changeset: 9e5a6a9c37b7360f67ad8b4161eb19c78dadd2ad

[Martyn Gigg]

Add logging to ComptonProfile. Refs #7199

Changeset: 01b3c217d7e107f989dbaf243e32c82d07ccf636

[Martyn Gigg]

Allow the absolute error to be specified in SimplexMinimizer.

Refs #7199

Changeset: 180bfba419563ef8b26f6882ca3ec2f41a2938b9

[Martyn Gigg]

Refactor ComptonProfile to calculate resolution & Y-space once.

Refs #7199

Changeset: c29f961da252b25009ef748c9c9799072c7b29a8

[Martyn Gigg]

ComptonProfile functions can now populate a constraint matrix

This can be used by a composite of the functions to compute the mass profile for various parameters. Refs #7199

Changeset: 6baa8fc2416c58a766b8c28e35baf7b82462fa7f

[Martyn Gigg]

Significant caching in GramCharlierComptonProfile.

Leads to a roughly 400% speed increase (of the system test) as it currently is. The Voigt function was expensive to compute and identical with each function iteration. It is now cached when the workspace is set. Refs #7199

Changeset: 9b24229966e3831156b26261ec7d1075958f09af

[Martyn Gigg]

Refactor GramCharlierComptonProfile to allow calculation of

each contribution separately. Refs #7199

Changeset: b2af3c162e7fb3e06b0d2ab092dc72689d896d89

[Martyn Gigg]

Pass errors through to fill constraint matrix in ComptonProfile.

Refs #7199

Changeset: 12cb61c574c053e2651d363552af115b4ebaf171

[Martyn Gigg]

Added class to perform least-square minimzation on eqn set.

It uses the same implementation that scipy uses for slsqp. Refs #7199

Changeset: 2fb44fd46c4ba89ac91c5b4cd14eaea2c0769778

[Martyn Gigg]

Fix doxygen comment. Refs #7199

Changeset: ac60c5692781ae4c4b4e3800c7455725ac99b702

[Martyn Gigg]

Remove dead-time correction from Vesuvio loader

Refs #7199

Changeset: a26728a3b487f7ebe90830dfa5f67952b43450b3

[Martyn Gigg]

Output a non-histogram workspace from LoadVesuvio in difference mode

Refs #7199

Changeset: 64d9d30a5a3d12f6156cba9d84c06cc715a3a263

[Martyn Gigg]

Fix error calculation in LoadVesuvio. Refs #7199

The errors should have be computed from the data itself and not the errors computed by LoadRaw. There was also a bug with how the tof values were calculated.

Changeset: 7f5f010011088d38dc122c342037f480fa72f6ee

[Martyn Gigg]

Fix intensity parameters in ComptonScatteringCountRate

This allows them to be computed based on the current profile values and taken out of the main fit. Refs #7199

Changeset: 77f7c05392001459c0d0653d8c69f6f66cfc3f38

[Martyn Gigg]

Fix value of angular width parameter on VESUVIO. Refs #7199

Changeset: 98ee33590eeef355f5b79bb56a17692de93f5756

[Martyn Gigg]

Add logging to ComptonProfile. Refs #7199

Changeset: 099377a338bd48371a6918984dfb865e608620e5

[Martyn Gigg]

Allow the absolute error to be specified in SimplexMinimizer.

Refs #7199

Changeset: cbf364377c98c50f6be9d905dfae267fd3c640c4

[Martyn Gigg]

Refactor ComptonProfile to calculate resolution & Y-space once.

Refs #7199

Changeset: 11bca6c63ceab2d0f2246028dcbf9f2797fd7aee

[Martyn Gigg]

ComptonProfile functions can now populate a constraint matrix

This can be used by a composite of the functions to compute the mass profile for various parameters. Refs #7199

Changeset: fc37cefc25d95e5d84fde9d0545e197d6b1aa170

[Martyn Gigg]

Significant caching in GramCharlierComptonProfile.

Leads to a roughly 400% speed increase (of the system test) as it currently is. The Voigt function was expensive to compute and identical with each function iteration. It is now cached when the workspace is set. Refs #7199

Changeset: c2f18fb8c3ad1b360b63eb17e38ebc586a7e778f

[Martyn Gigg]

Refactor GramCharlierComptonProfile to allow calculation of

each contribution separately. Refs #7199

Changeset: 54c7b39bb76560f5eb912b37414a04a0a7bc886d

[Martyn Gigg]

Pass errors through to fill constraint matrix in ComptonProfile.

Refs #7199

Changeset: 4117bcabdf02f94701be8b5bd9749edc0b01822c

[Martyn Gigg]

Added class to perform least-square minimzation on eqn set.

It uses the same implementation that scipy uses for slsqp. Refs #7199

Changeset: cf07d4b4e4e5c3633d65830f2c3201f06f587391

[Martyn Gigg]

Fix doxygen comment. Refs #7199

Changeset: 050bc09459a7812069180e876e01d9683bed0118

[Martyn Gigg]

Remove dead-time correction from Vesuvio loader

Refs #7199

Changeset: f98bf8cd79a2a35d9888ae3fbde1c9bcf6af0d06

[Martyn Gigg]

Output a non-histogram workspace from LoadVesuvio in difference mode

Refs #7199

Changeset: eb5b5bf22a67569c7aa81a8e7174864bb7630cf2

[Martyn Gigg]

Fix error calculation in LoadVesuvio. Refs #7199

The errors should have be computed from the data itself and not the errors computed by LoadRaw. There was also a bug with how the tof values were calculated.

Changeset: d1a10d7f7a4ac26a75a8562b5af38dedd57443bd

[Martyn Gigg]

Fix intensity parameters in ComptonScatteringCountRate

This allows them to be computed based on the current profile values and taken out of the main fit. Refs #7199

Changeset: 0b784475466ab50719d98b486911dd97ecfec965

[Martyn Gigg]

Allow custom delimiter when reading/writing matrices from streams.

The stream operators still use commas as before but the free functions now allows users to specify the delimiter. Refs #7199

Changeset: 158712d262d3668655a8c845ad7f804f9c613298

[Martyn Gigg]

Add intensity constraint matrix as attr on ComptonScatteringCountRate

Refs #7199

Changeset: a18f90074795abfde5235b8816310b7ad95e7312

[Martyn Gigg]

Include FSE parameter in intensity coeffs when free. Refs #7199

Changeset: 630d2d6ebb283ac84a73a2392d854024a3d1a445

[Martyn Gigg]

Check fixing of FSE coefficient in the correct place. Refs #7199

Changeset: 17f399aa59b9c4765059b181a33f35ed3f567d22

[Martyn Gigg]

Add tests for concrete ComptonProfile result values. Refs #7199

Also includes a separate test helper method to create a similar workspace for the tests to use as they share a large amount of setup

Changeset: 974f0df8dac945c5d56921b69022a26bbb8016f5

[Martyn Gigg]

Add test for ComptonScatteringCountRate values. Refs #7199

Changeset: 2edc35454672500f7e3adc1fe6b1cc781ebd6a57

[Martyn Gigg]

Fix bug with empty equality constraints. Refs #7199

They are now allowed by just not setting the attribute value.

Changeset: 52a5dcb78318c58cee79c26afb992a1019a3c28c

[Martyn Gigg]

Fix memory error bug in filling equality matrix

It was writing to memory that it shouldn't have been. Refs #7199

Changeset: 2e53e0a302c2734863514a3be5181de1cf45735a

[Martyn Gigg]

Allow absolute & relative errors to be specifed in LM minimizer

Gives more flexibility rather than being stuck with the hard-coded 1e-4. The default is set to replicate the old behaviour. Refs #7199

Changeset: 6e75e81e417db026f509a8f6c2a32b448736ccab

[Martyn Gigg]

Added more detail to Fit at information log level. Refs #7199

• The value of the cost function is printed after each iteration
• The Covariance & Hessian matrix are output at the end of the fit

Changeset: 87521c32079a1221088ab6c3db8239eafd56c221

[Martyn Gigg]

Update VesuvioFittingTest

Now uses ComptonScatteringCountRate instead of basic CompositeFunction to give a better overall fit. Refs #7199

Changeset: 59774490bea0bfedc33f8388604086f8592d3682

[Martyn Gigg]

Update values for LoadVesuvio test.

The output is now a point data set in the difference case and the errors were being calculated incorrectly before. Refs #7199

Changeset: 46f936ecafd7b033a017e0a2be3d7acc4bc53caa

[Martyn Gigg]

Remove local extern qualifiers in SLSQPMinimzer Refs #7199

Changeset: 95424ae831e7d75b2ed94e17b48212bd67f8165e

[Martyn Gigg]

Branch: bugfix/7199_vesuvio_fitting_diffs

Repositories: Main code & System test

Tester: This is difficult to test as it is work that must ultimately be verified by the users.

The fit to some Vesuvio data can be run with the following scripts. Make sure the system test data directory is in your data search path. The output from Fit, which can be plotted by plotting the data vs calculated, should give a reasonable match to the data.

LoadVesuvio(Filename='14188-14190',OutputWorkspace='raw_ws',SpectrumList='135',Mode='SingleDifference',
                    InstrumentParFile=r'IP0005.dat')
        CropWorkspace(InputWorkspace='raw_ws',OutputWorkspace='raw_ws',XMin=50,XMax=562)

        function_str = \
            "composite=ComptonScatteringCountRate,NumDeriv=1,IntensityConstraints=\"Matrix(1|3)0|-1|3\";"\
            "name=GramCharlierComptonProfile,WorkspaceIndex=0,Mass=1.007940,HermiteCoeffs=1 0 1;"\
            "name=GaussianComptonProfile,WorkspaceIndex=0,Mass=27.000000;"\
            "name=GaussianComptonProfile,WorkspaceIndex=0,Mass=91.000000"

        ties_str = "f1.Width=10.000000,f2.Width=25.000000,f0.FSECoeff=f0.Width*sqrt(2)/12"
        constraints_str = "2.000000 < f0.Width < 7.000000"

        ws_prefix = "fit"
        Fit(InputWorkspace='raw_ws',Function=function_str,Ties=ties_str,Constraints=constraints_str,
            Output=ws_prefix, CreateOutput=True,OutputCompositeMembers=True,MaxIterations=5000,
            Minimizer="Levenberg-Marquardt,AbsError=1e-08,RelError=1e-08")

[Martyn Gigg]

Move local struct to namespace level. Refs #7199

Some older compilers can't deal with a function call where the template type is only defined locally within the function.

Changeset: 2feb5151d660b52297577e957b60c33d76b93dbf

[Martyn Gigg]

Fix std::pow call for unsigned types on OS X. Refs #7199

Changeset: b3fcc3412ea5db92180c1b46069862f4266eb3e6

[Martyn Gigg]

Relax tolerance for test slightly for intel compiler on OS X.

Refs #7199

Changeset: af3a7489b1d9780ad41616121893905811d4bf11

[Martyn Gigg]

Relax tolerance for GaussianComptonProfileTest for Intel on OSX 10.8

Refs #7199

Changeset: baf2fb1d77eba944a29100f881de10c5bc83de12

[Martyn Gigg]

Relax tolerancance for GaussianComptonProfileTest for Intel on OSX

even more...Refs #7199

Changeset: 5099daab4aafdef32a03f334154db0a89a71ac5e

[Martyn Gigg]

Relax VesuvioFittingTest tolerance (slightly) to account for OS X

Refs #7199

Changeset: 2cebf40e98f36d6068a43d27d7712bd9f6f5ba0f

[Alex Buts]

It works and it indeed up to the users to check if it work correctly

[Alex Buts]

refs #7199 Merge branch 'master' into

bugfix/7189_ConvertToMD_V2_inSysTests Conflicts:

SystemTests/AnalysisTests/MDWorkspaceTests.py

Changeset: d64e7162ffc3fe7e9c77c5f3f377554e0d924232

[Stuart Campbell]

This ticket has been transferred to github issue ​8045