Refactor PoldiSpectrumDomainFunction to use arbitrary profile functions

[Michael Wedel]

In its current form with all the parameter transformations it will be very hard (or impossible) to replace the profile function that is used in PoldiSpectrumDomainFunction. After some experiments I came to the conclusion that there's an equivalent way of calculation the function that does not require any parameter transformation. This means that PoldiSpectrumDomainFunction can be seen as a wrapper for an IPeakFunction, which makes it possible to finally use other profile functions and easily add others (which are then general and not limited to POLDI).

In the scope of this ticket I would like to implement those changes.

[Michael Wedel]

Refs #10996. Alternative approach for calculation of POLDI 2D-spectrum

Changeset: 06a6c1b655727389fd3d7e01b4a409966fc5f2d5

[Michael Wedel]

Refs #10996. Removing comments, debug output, adjusting unit test.

Changeset: 0b60fd5b9f73903c94d458c52cf133752b4bf635

[Michael Wedel]

Refs #10996. Checkpointing work.

Changeset: b08cc36603edf966c75ad25d87e0496eb57e5295

[Michael Wedel]

Refs #10996. Added test function (area based gaussian)

Changeset: b64ae3331156ad29d6011a1a651abb22b010f5fc

[Michael Wedel]

Refs #10996. Adding local jacobian to handle derivatives.

Changeset: 4e10784fcfe66a6d9e42a1503d105fc568e43224

[Michael Wedel]

Refs #10996. Format correction

Changeset: 0d6e5dd35ddd7c687a9c5cda3faa2d626106adb6

[Michael Wedel]

Refs #10996. factoring out profile function

Changeset: 0fdf943206d55b0752647b3765347542a59b290d

[Michael Wedel]

Refs #10996. Removing AreaGaussian

This is no longer required and is removed.

Changeset: 6b88ed7fdc0a2310fe60bde3b58ff21d36c7f993

[Michael Wedel]

Refs #10996. Removing debugging statements

Changeset: 2c91349ad7de58a6667d49fcfc116c5fd75bf96f

[Michael Wedel]

Refs #10996. Fixing PoldiFitPeaks2DTest

Changeset: c75cfb170d01bc20bb665eda68c89a97f13fc490

[Michael Wedel]

Refs #10996. Remove actualFunction from PoldiSpectrumDomainFunction

Changeset: d0268f96eef1422abf57e38899945eff318aeefd

[Michael Wedel]

Refs #10996. Fix PoldiSpectrumDomainFunctionTest

Changeset: bd126a3c35f29b5f71910c931f548856249d1a14

[Michael Wedel]

Replacing peak integration with new intensity methods of IPeakFunction

Refs #10996.

Changeset: b17e83d92780c9834f6048cd15d0f86b40177465

[Michael Wedel]

Refs #10996. Cleaning up PoldiSpectrumDomainFunction

Changeset: 2a63581662114f61d0cf7aed39e30d4e1cdeb6e7

[Michael Wedel]

Refs #10996. Adding unit tests for LocalJacobian

Changeset: 5a1ac75297384f497cc2c29841e19b4299e23758

[Michael Wedel]

Refs #10996. Providing fallback peak profile

When PoldiPeakCollection has no profile function set, the one provided to PoldiFitPeaks2D should be used.

Changeset: c44d496b258d714301e97b4379888e2ff3786720

[Michael Wedel]

Refs #10996. Adjusting system test for POLDIFitPeaks2D

Since intensity calculation changed slightly, it's not so useful to compare those. Instead a fit is performed and it's checked whether the fitted parameters are within acceptable ranges.

Changeset: a3e51c4ffabb983ffa418aa9dab791112acb8e8e

[Michael Wedel]

Refs #10996. Actually using fallback profile

Changeset: 14eaf02a3098262fff5c0431b654bee1de489657

[Michael Wedel]

Refs #10996. Removing unused code from PoldiTimeTransformer

Changeset: 1177aef436748274e707bc7e0c97fb1b19dae322

[Michael Wedel]

This is being verified as ​pull request #270.

[Michael Wedel]

Jenkins retest this please

[Michael Wedel]

Jenkins retest this please

[Michael Wedel]

Testing information Make sure the modified system test for PoldiFitPeaks2D passes. For manual testing you can try the usage examples of PoldiFitPeaks2D to see if they give reasonable results. To test the new feature, you could add the PeakProfilFunction-parameter to the algorithm call, for example with Lorentzian (assuming you already executed the usage example):

` PoldiFitPeaks2D(InputWorkspace=truncated_6904,

PoldiPeakWorkspace="peaks_refined_6904", PeakProfileFunction="Lorentzian", OutputWorkspace="simulated_6904", RefinedPoldiPeakWorkspace="peaks_fit_2d_6904", Calculated1DSpectrum="simulated_1d_6904", LinearBackgroundParameter=0.01)

`

In this case the spectrum has much higher values and in the 1D spectrum the Lorentzian peaks are nicely visible.

[Michael Wedel]

This is being verified as ​pull request #16.

[Michael Wedel]

Refs #10996. Correcting unit test

The unit test for the derivative was disabled, re-enabled it.

Changeset: dede5b36681e67aa1f6257919bf62b4c574c80ac

[Federico M Pouzols]

All looks perfect to me and the examples seem to work well. But I found an issue in one POLDI system test. POLDIFitPeaks2DTest fails with this error:

`

File "<string>", line 1, in <module> File "/home/fedemp/mantid-repos/systemtests/StressTestFramework/stresstesting.py", line 194, in execute

self.runTest()

File "/home/fedemp/mantid-repos/systemtests/SystemTests/AnalysisTests/POLDIFitPeaks2DTest.py", line 15, in runTest

self.analyseResults(dataFiles)

File "/home/fedemp/mantid-repos/systemtests/SystemTests/AnalysisTests/POLDIFitPeaks2DTest.py", line 56, in analyseResults

self.assertTrue(np.all(absDiff < 7e-4))

File "/usr/lib/python2.7/unittest/case.py", line 422, in assertTrue

raise self.failureException(msg)

AssertionError: False is not true `

Can you check if you also get this issue. It looks like a small numerical difference could have broken the test, but it could be something local here. For me, there are values in absDiff that are definitely bigger than the 7e-4, and one of them is as big as 0.42630710526.

Otherwise I think this is ready to be merged.

[Michael Wedel]

This is still the old system test. I modified it, because the intensity calculation is a bit different now and it simply does not give the same intensities anymore. For the new system test there is also a pull request, it's this one: ​https://github.com/mantidproject/systemtests/pull/16. Sorry for not making it more prominent in the testing comment.

[Federico M Pouzols]

Ops, sorry I had missed this parallel branch. When I use this modified test with PR #270(​https://github.com/mantidproject/mantid/pull/270) I get what appears to be an approximation issue:

`

File "<string>", line 1, in <module> File "/home/fedemp/mantid-repos/systemtests/StressTestFramework/stresstesting.py", line 194, in execute

self.runTest()

File "/home/fedemp/mantid-repos/systemtests/SystemTests/AnalysisTests/POLDIFitPeaks2DTest.py", line 15, in runTest

self.analyseResults(dataFiles)

File "/home/fedemp/mantid-repos/systemtests/SystemTests/AnalysisTests/POLDIFitPeaks2DTest.py", line 67, in analyseResults

self.assertLessThan(np.fabs(value - reference), error)

File "/home/fedemp/mantid-repos/systemtests/StressTestFramework/stresstesting.py", line 402, in assertLessThan

raise Exception(msg)

Exception: Expected 7.1583e-05 < 6.9e-05 `

When I enable the debug print I see this: ` 0 d 0.153846153851 1.108644 0 FWHM (rel.) 0.256706666667 0.002475747 0 Intensity 0.42762694823 3286.152 1 d 0.333333333331 1.637539 1 FWHM (rel.) 1.03743478261 0.002516417 `

It looks perfectly acceptable to me to have an approximation error in the 6th digit when using single precision. I'm not sure what Python (in different versions) may be doing here, especially when it casts the values as strings to floats. It these number above look good to you maybe the solution could be to increase a bit the error threshold and/or use double precision.

[Michael Wedel]

Refs #10996. Removing FWHM from test until #10515 is solved.

Changeset: 4ed667abbc93314d0b87737c49e22e3673e7c388

[Michael Wedel]

Jenkins retest this please

[Michael Wedel]

Jenkins retest this please

[Michael Wedel]

Refs #10996. Updating PoldiAnalyseResiduals doctest

Because of different intensity calculation, the residuals are of course also slightly different, I forgot about that before.

Changeset: e079688d63d2b47ce0fa5527c9c70f86976fde5a

[Michael Wedel]

Refs #10996. Small fix to FunctionParameterDecorator

Forwarding of active parameters was not implemented.

Changeset: c46c8a63fc16d15ca9b95a36d85b218c8d8a2ccd

[Michael Wedel]

Re #10996. PoldiSpectrumDomainFunction uses FunctionParameterDecorator

Changeset: 714929fbd84a9cfddf4ba4a31af74d9d9caf0370

[Michael Wedel]

Refs #10996. Adjusting unit test.

Changeset: 9c5e78c120fc7e3bc8c2e0fceacd8c360bbadc7e

[Michael Wedel]

Refs #10996. Adjusting unit test for PeakParameterFunction

Changeset: 5152fbccf20353beaf343d6a49c539b469a80a90

[Michael Wedel]

Refs #10996. Fixing system test for PoldiFitPeaks2D

Changeset: 5924fced90f869d942bdce23585a7efe777121e3

[Michael Wedel]

PoldiSpectrumDomainFunction has been updated to use changes from ticket #11102(​http://trac.mantidproject.org/mantid/ticket/11102), so that wrapping of the peak function is simpler. This is just an implementation detail, it does not change the testing information.

Additionally, the system test has been updated, so the systemtests pull request is obsolete.

[Michael Wedel]

Jenkins retest this please

[Federico Montesino Pouzols]

All is good after the system tests transition to the main repo.

[Federico Montesino Pouzols]

Merge pull request #270 from mantidproject/feature/10996_refactor_poldi_spectrum_domain_function

Refactor PoldiSpectrumDomainFunction to use arbitrary peak profile functions

Full changeset: ​a70d395ad6a79d86a02b25a4f385a14efbc3ab7f

[Michael Wedel]

System test is in main repo now, so I'm closing this pull request.

[Stuart Campbell]

This ticket has been transferred to github issue ​11835