Create Workflow-algorithm for POLDI

[Michael Wedel]

Now that more or less all algorithms necessary for POLDI are in place, I would like to create one or more Workflow-algorithms using these.

The first step is to check back with the beamline scientists which workflows are most important and most used and then implement them.

[Michael Wedel]

Refs #10702. Small fix to PoldiMerge

Changeset: 603a8a6b18402625d7ce1c6e7daa2db459fc0e2c

[Michael Wedel]

Refs #10702. Adding 2014f parameters for POLDI

Changeset: eec5a10a51a9a23a9ffcf63a0fb97b2a97f171da

[Michael Wedel]

Refs #10702. Change naming of indexed peak workspaces.

Changeset: 382508a5488102a80d2fd0bc012d6dcaa2595986

[Michael Wedel]

Refs #10702. First draft of workflow algorithm

Changeset: ef36cfee5f24f0986b466fca892dc1ea45356f57

[Michael Wedel]

Refs #10702. Clang-formatting PoldiIndexKnownCompounds.cpp

Changeset: 6b116adddda5949352748741458c9d87838fa16f

[Michael Wedel]

Refs #10702. Fixing small problem in PoldiFitPeaks1Dv2

Changeset: 0c334e1e0c9f229af147b22ddf626d41c9dbf0e6

[Michael Wedel]

Refs #10702. Adjusting unit test of PoldiIndexKnownCompounds

Changeset: 06088106b72fb4c7e707c2b4239d2df8dc630396

[Michael Wedel]

Refs #10702. Small changes to algorithm and formatting

Changeset: e4db272418d181bb3ac5ac479ff2ebb6ef886137

[Michael Wedel]

Refs #10702. Addressing some pylint issues

Changeset: 1e0832490a22b4f963776535a5c8d1633ad9dbfd

[Michael Wedel]

Refs #10702. Fixing typo.

Changeset: c025c411233c174ecf8634902c5e6ea5dc099b31

[Michael Wedel]

Refs #10702. Checkpointing work.

Changeset: 24435d5a1d24e7a806b06a6f71b14960b757f8fd

[Michael Wedel]

Refs #10702. Starting algorithm from scratch

The first approach to writing a workflow algorithm was too focused on one (complex) use case, which made it way to difficult to use the algorithm for more common cases. After further discussion with the scientists, the scope of the algorithm is better defined.

Changeset: de84c52e844a9624c85d13fa8ac637ed4f209d61

[Michael Wedel]

Refs #10702. Using PointGroupFactory in PoldiPeakCollection

Changeset: 0521e7cf949bfc4d534b19eff3cbec026cdfa40d

[Michael Wedel]

Refs #10702. Adding unit cell to PoldiPeakCollection

This will make InitialCell and CrystalSystem of PoldiFitPeaks2D obsolete, as PoldiIndexKnownCompounds now stores the cell and point group.

Changeset: 6c8f8616831b47fd8be413ed4a0e1d36a8038753

[Michael Wedel]

Refs #10702. Change naming scheme of PoldiIndexKnownCompounds output

Previous naming scheme would overwrite indexed workspaces when using a compound multiple times.

Changeset: 48cced7483a815106c0ac23256eca258be637f61

[Michael Wedel]

Refs #10702. Extracting crystal system names into PointGroup.h

This way it's easier to convert between strings/enum in different places.

Changeset: 9b35cf5ed55a19f4aa90b7392d2b5472a0cd646f

[Michael Wedel]

Refs #10702. PoldiPeakCollection clone also unit cell and point group

Point group also has a default now, which is better than having a null pointer around.

Changeset: b1931e8043a0c72556f041c21028d57e85e5fc9a

[Michael Wedel]

Refs #10702. Remove InitialCell and CrystalSystem from PoldiFitPeaks2D

These need to be present in the logs of the peak tables now, which they are when PoldiIndexKnownCompounds has been used to generate them. The docs contain a hint what to do when a custom indexing method has been used.

Changeset: 2447b05389f6f3941d498b242a8a36a4f6a7f819

[Michael Wedel]

Refs #10702. Fixing typo in algorithm property doc

Changeset: 59341ab7fc6f3d36c1b3af0a5120f87f93c1c020

[Michael Wedel]

Refs #10702. PoldiFitPeaks2D now accepts WorkspaceGroup for peaks

In this first step, workspace groups are accepted, but only the first one is used. Everything still works as expected.

Changeset: 351424c52ef8bcb5d3c6a43efd54fe683a088c5a

[Michael Wedel]

Refs #10702. PoldiFitPeaks2D handles multiple phases

Changeset: 1f6f4e9317982dc5d76f932b0b898961b74af76e

[Michael Wedel]

Refs #10702. Cleaning up order and comments in PoldiFitPeaks2D

Changeset: fe210d87c36de84b65f01a6886870b8e8045d2f4

[Michael Wedel]

Refs #10702. Small fix to default point group in PoldiPeakCollection

Changeset: 104539529dcb5fb2b0d436b35d9875e5aff37386

[Michael Wedel]

Refs #10702. Fixing system test for PoldiFitPeaks2D

Changeset: 88b6869654551e2f106f43aa3bd6fecb6d9fbae6

[Michael Wedel]

Refs #10702. Declaring properties.

Changeset: c098bfaa347062c1dba9477f5e231a6a9e2df51a

[Michael Wedel]

Refs #10702. Assign indices for all phases

Changeset: 90347b1b0c98d4767d55d3dea92292c865fd21d5

[Michael Wedel]

Refs #10702. Small fix in PoldiFitPeaks1D

Returning the right workspace which has gone through multiple refinements, making peak criteria more strict.

Changeset: 17d859d7c0adfd80a03fae991d1753cd3a91caaa

[Michael Wedel]

Refs #10702. Working algorithm.

Changeset: 813123322589e34097b7398caf1bd46d7887403a

[Michael Wedel]

Refs #10702. Changing import of plotting

Changeset: 3fdad0a9c7b28e25df43bc5e2bc8ee2bdb510ed5

[Michael Wedel]

Refs #10702. Added systemtest

Changeset: 6567f435f8e008bc385d2837ceb8390015637b0c

[Michael Wedel]

Refs #10702. Added documentation for PoldiDataAnalysis.

Updated algorithm category as well.

Changeset: 62e965a5e9c9083d17be6bf63be5a44781e87d9c

[Michael Wedel]

Refs #10702. Small fixes to doctests

As a result of the bug fixed in PoldiFitPeaks1D, one unindexed peak that is not actually a peak is excluded, so the numbers need to be adjusted by one.

Changeset: fc62c657a2752393e3c0ce0f071c3956ecf0d9f5

[Michael Wedel]

Refs #10702. Correcting doc-test of PoldiDataAnalysis

Changeset: e55f4ce3b0ad38511bf9ff5b02cc73497ca46eb6

[Michael Wedel]

Refs #10702. Small fix to PoldiCreatePeaksFromFile

Fixing space group symbol parsing (did not allow /) and allow rational numbers.

Changeset: 0d672978f2fe0db2311157ad9e6ddf2e058864b1

[Michael Wedel]

Refs #10702. Added small output comment

Changeset: c9b1524e97ae88c4aaa2d7694a1e5be3246d6f88

[Michael Wedel]

This is being verified as ​pull request #649.

[Michael Wedel]

Refs #10702. Fixing system test after automatic masking

Changeset: c200ca182f9cf28a440bc11d9f7c1e24141c9e93

[Michael Wedel]

Refs #10702. Fixing PawleyFit doctest

Changeset: 2db786db4991ac74db6d03778902cb6d05590ca3

[Andrei Savici]

You should fix your pylint warnings:

• for unused variables (say a=Load(filename), then unused a) just use dummy_variable_name instead
• add newlines at the end of the files
• add a statement to ignore variables defined outside init. Most python algorithms have this

[Michael Wedel]

Refs #10702. Fixing pyling warnings

Changeset: c2ff80386f13a6e0c332052bf3bbb47dc15e6f6d

[Michael Wedel]

Thanks Andrei, I missed the pylint warnings. But why was the indicator green?

[Andrei Savici]

For now the threshold is set to 4000 warnings. We need to fix a few more, to slowly get it down

[Federico Montesino Pouzols]

All looks good, and extensively documented and tested. I run the system and unit tests locally just in case, without surprises.

Maybe one small thing that could be added to the tests later on is some test cases with wrong properties (users mistype or forget a required property, etc.). And I am not sure if it is possible to have wrong combinations of properties (and/or property values), that could also be added in the unit tests.

I also have a general comment about unit tests, actually forwarding a comment from Owen some days ago on one of my PRs. The idea is to prefer the TSM_... versions of the CxxTest asserts rather than the TS_... adding informative messages wherever it makes sense, so that we can quickly get an idea of what's the issue when a unit test fails. Hum, but I see now that TSM is already used in many places already in these tests ;)

[Federico Montesino Pouzols]

Merge pull request #649 from mantidproject/10702_poldi_workflow_algorithm

Add workflow algorithm for POLDI analysis

Full changeset: ​435d4dab38a9a325ca472a1265f8953cd72ac362

[Michael Wedel]

Thanks for testing thoroughly! You're right, I do not use TSM_ too often, I will pay more attention to this in the future. So far I tried to use them in "bulk" tests where the same check is run for similar data in the same test. Another thing I'm trying to work on is to make smaller, more specific test-cases, which makes it also easier to spot where an error originated, just from the name of the test-case.

[Stuart Campbell]

This ticket has been transferred to github issue ​11544