Translator from Fullprof to Mantid for initial fitting param starting value

[Anders Markvardsen]

An algorithm which converts initial fitting parameters

InputFile Compulsory

OutputFile Compulsory

Append true/false default to false

We can only translate gsas values for the fitting functions which we have currently defined in Mantid

​http://www.ill.eu/sites/fullprof/

[Karl Palmen]

Add non-functioning ConvertFullprofToXml algorithm re #7617

I've left some code in it from LoadFullprofResolution, which could be useful. If I end up using a lot of the code without much modification, then it should go in a class for use by both algorithms.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: f25c76724517463fdc36d142961c794b93b68427

[Karl Palmen]

Change error message re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: c09e85f28381f01a9e976bde88d8e615a468668c

[Karl Palmen]

Correct file properties re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 168bbbacb618937f143be99287d5b3319f97e5a0

[Karl Palmen]

Enable LoadFullprofResolution to read a file without a CWL re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 03bdf2abd3da76842e5f1956fb9e79b2d64c6e86

[Karl Palmen]

Rename to end in XML instead of Xml re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 043f6cbbd68bf62ec0ff725f9ee9dd3742c45b8b

[Karl Palmen]

Correct reference to include file re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: cc6a2ca2e3ca1ddb5468f779b06c21f61b78a998

[Karl Palmen]

Use LoadFullprofResolution as child algorithm re #7617

Code to read the table and put it into the output parameter file is still to be written.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: c60425d3eeaa481df4775607a286739d9b43543c

[Karl Palmen]

Create parameter file stub re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: bc2441c0e67cb6d44256e90be4bc2046882fbd2a

[Karl Palmen]

Use current time as date re #7617

Also remove optional attribute of instrument (hard to determine).

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 8819f68a4aae2752284bd4afd07ce569e79ab559

[Karl Palmen]

Add empty banks to parameter file re #7617

Also tidied up the child algorithm code with help of Martyn

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: c02bd67c8fe5a59b2cc1a6fd0efe50e871f175ba

[Karl Palmen]

Make LoadFullprofResolution ignore END of bank line re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 4045674c51baea6e3751da08dd8a2df66c24c6a6

[Karl Palmen]

Extend LoadFullprofResolutionTest.h re #7617

Test extended to test the names of parameters I'll use later on.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 6847cd0268da173b8a704d5332c793e80258192d

[Karl Palmen]

Improve XML and other changes re #7617

Use component-link format for banks and whole instrument Tidy up includes Prepare for use of table workspace columns.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 1c17fa2a68a7c6e6390b1350e5b8417c718fbd42

[Karl Palmen]

Begin work on translation of parameters re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: b96fed5aba1d2edefbb21ce8d6a7ee249c5e88f3

[Russell Taylor]

Compiler warning alert! ​https://builds.sns.gov/job/ornl_clean_rhel6_develop/2278/warnings16Result/source.13574/#149

[Karl Palmen]

Preparation for getting parameter values re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 5e9d17067fee54c1a27e31462bb004632c214d76

[Karl Palmen]

Correct bank numbers when not in numerical sequence re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 99a5bb2f815db45908d35ca1aa9ab337a6ec954b

[Karl Palmen]

Complete the whole instrument parameters re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 59806989dace08adf111178decb08039ec2fcbb8

[Karl Palmen]

Correct use of std::to_string re #7617

and some other string usage improvements

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: af76a9ac412f80b30ddb2bc918f588b554c634be

[Karl Palmen]

Remove accidental use of ConvertFullprofToXML:: in .h file re #7617

Windows but not Unix allows this.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 4480a0982135e699a530e1bba205a73347daf6ec

[Karl Palmen]

Complete the translation re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 24fadac4440a617bc2f0d494a9d02a62d9ca3d05

[Karl Palmen]

Created skeleton unit test re #7617

It now verifies that the algorithm initializes and executes without error and produces an output file in accordance with its outputFile property.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 83e0b741196fd6752141b3f3d39874bb90b46e72

[Karl Palmen]

Unit test checks that Output file can be parsed as XML file re #7617

Also some unnecessary includes were removed from the ConvertFullprofToXML.cpp.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 7704157246cddef19ae62cb111e2fed34f9e133b

[Karl Palmen]

Add check for child nodes re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: b311cb249cde035b97e684580bc1c2620105360f

[Karl Palmen]

Make a start in testing the contents of the output file re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: f3e6452e43d9c029566c59d9332f21e51e0f57bd

[Russell Taylor]

There's another GCC compiler warning from this: ​https://builds.sns.gov/job/ornl_clean_rhel6_develop/2300/warnings16Result/?

[Karl Palmen]

Test parameters of whole instrument re #7617

The double valued 'eq' still needs testing.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: afdb3832ca14c7e5bd7c5468c6bb44af45bf8da3

[Karl Palmen]

Test all except 'eq' attribute re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: dfcfbc1f9cfc33ad71e174c4cef1b1b574c15a49

[Karl Palmen]

Begin creating function to test eq value re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: c2d59071ed32a1c469c7ec1330037d02435184fe

[Karl Palmen]

Test 'eq' value of parameters re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 4f421d9a07e3d934390ad8348a48a23cdc1d960e

[Karl Palmen]

Tidy up code improve comments re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 80dc1c51efc5e039d346d857004199f211798698

[Karl Palmen]

Rename 'Bank...' to 'bank...' as for GEM instrument re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 41d64e2f5d89fea67e9dd6b246a340283348894a

[Karl Palmen]

Set instrument to GEM re #7617

This is because fitting requires the instrument name to be specified in the parameter file as well as the IDF file. LoadFullprofResolution does not take the instrument name.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: c93b90a49fc7c155e835e22667ce6a990b456344

[Karl Palmen]

Put change to "GEM" into unit test re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: ccae6fe00d99821fe52194f2ccf1ae537f0ce53a

[Karl Palmen]

Add instrument property and test it re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: f050bcd760933d61b4298d0a376130b7cfe74fbc

[Karl Palmen]

Fullprof file for suggested test

[Karl Palmen]

A simple GEM file for testing

[Karl Palmen]

To test download the fullprof file attached.

Run the ConvertFullprofToXML on this file with instrument='GEM', check that it produces a well formed XML file.

Load a GEM file such as the one attached. Load it again into a second workspace. Run Loadparameter file on one of these two workspaces using the parameter file created by the run of ConvertFullprofToXML.

For each workspace plot the same spectrum. Then for each graph press the fit button on the toolbar clock on the graph to select a peak, choose IkedaCarapenterPV as the peak type then click on the top of the peak selected. Then some red markings should appear around the peak.

Look at the values of the parameters of the function in the Fit Function window. Check that they are different for the two workspaces and that for the workspace that had the parameters loaded the values for Alpha0, Alpha1, Beta0 and Kappa are the same as in the fullprof file allowing for floating point rounding errors.

Also check that the unit test is adequate and so is the wiki.

[Karl Palmen]

Also the tester can check that the parameter file generated corresponds to the fullprof file as described in http://www.mantidproject.org/CreateIkedaCarpenterParameters .

[Karl Palmen]

The append property is covered by ticket #8071. Do not test for this property.

[Gesner Passos]

I failed to see the fitting parameters showing the values inside the fullprof file. We will investigate the reason. In the mean time, we discussed some improvements to the code.

[Karl Palmen]

Make changes recommended by Gesner re #7617

Corrected comments, use ManditoryValidator and use AutoPtr.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: f21c0173a0995d3e105408a6bc55a376f061ceaf

[Karl Palmen]

Reduce arguments and improve efficiency re #7617

as suggested by Gesner Passos

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: fc0ea5aaaa0ef422c260d5abafcd353f4ec403d1

[Gesner Passos]

It turned out that it was my fault that I could not test and I got the result described in comment:43. I tried to get the result described here using the GEM58654. But, I tried in one invalid spectrum. Today, I tried on valid spectrum, and I got the expected result.

So, everything is working fine up to the commit on comment:36.

[Karl Palmen]

Unit test has been crashing since I made the changes recommended by Gesner.

[Karl Palmen]

Use AutoPtr in unit test re #7617

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 52c5aa66219726c2c066495f57dc15d12d730aab

[Karl Palmen]

Fix unit test to cope with validator on instrument name re #7617

Also use AutoPtr in unit test where appropriate.

Signed-off-by: Karl Palmen <karl.palmen@…>

Changeset: 04ac658801996da0a7c5d07c59000abbdd62a9de

[Wenduo Zhou]

Very nice work. We should make it work for other profiles.

[Wenduo Zhou]

Merge remote-tracking branch 'origin/feature/7617_fullprof_to_xml'

Full changeset: ​31a5ed2e56937e602e171c2ae4bd32d697bc794e

[Stuart Campbell]

This ticket has been transferred to github issue ​8462