Implement Connected Component Analysis in Mantid

[anonymous]

Connected component analysis: This is an exploratory method for peak finding and integration. Theoretically both can be achieved in the same set of steps very rapidly. Arbitrary shaped peaks, in both detector space, and in reciprocal space can be identified.

Initial implementation will use MDHistoWorkspaces, but the intention is to open this up to Workspace2Ds later.

[Nick Draper]

Please put the proposed Algorithm name in the title

[Owen Arnold]

Just attached the results of some preliminary work in python to establish how we can determine nearest touching neighbours in an n-dimensional fashion. This was a useful exercise prior to coding in c++.

[Owen Arnold]

refs #9155. 1D and 2D neighbour cases verified.

Extensive tests for these. Refactoring still neeeded.

Changeset: 7305ba6a6512f77848e4a5100d654a7c13fbdd55

[Owen Arnold]

refs #9155. Extend test cases to 3D.

Still need to refactor the working code for this.

Changeset: 8a1fb0f9b83d49c4fcb77f8542dfdae29de63dce

[Owen Arnold]

refs #9155. Refactor current working.

Avoid all vector resizing possible. Pre-cache as much as possible.

Changeset: 8da661ae9976b0b25b6c5dfda0bc1420f13017cb

[Owen Arnold]

Ticket references above should be against 9115 not 9155

[Owen Arnold]

refs #9115. Implement ConnectedComponentsLabelling with 1d tests.

Implement simple testing for connected component labelling.

Changeset: 7228a39fa6430e7b3545e4c1837d30f52520d179

[Owen Arnold]

refs #9115. Extensive testing to check that MD clustering is working.

Changeset: 411b8edde83b0726a76df8562fce962bda0312cf

[Owen Arnold]

refs #9115. Performance tests added.

As of yet, I have paid no attention at all to performance. This will be the subject of future work, but I want to make sure that any performance improvements are actually incremental improvements, and not unmeasured hand-waving type changes. Hence this performance test.

Changeset: cc0453469aa519b4137dbc93b7c69932dad2d92f

[Owen Arnold]

refs #9115. Rename class and associated files.

Changeset: 7e08cf1c1d8d36fc38b33a7b24ee88cbc47f365e

[Owen Arnold]

refs #9115. Warns and errors fixed. Perf tests.

I also added some peformance tests directly over the implementation of findNeighbourIndexes. I noticed that one of the performance tests around masking in the iterators was taking far too long, of the orer of 10s of seconds. So I refactored that peformance test to make the test itself do less work.

Changeset: ef4c1e36dc228b6827f3ad87853890169806fc2f

[Owen Arnold]

For future improvements. Benchmarks on my win64 debug build are:

• 1.7 seconds for findNearestNeighbours of IMDHistoWorkspaceTestPerformance
• 1.86 seconds for ConnectedComponentLabelingTestPeformance

[Owen Arnold]

refs #9115. Fix issue around auto usage.

Changeset: 1232ae9bf71f6d153004ef5080421052330ddf6d

[Owen Arnold]

refs #9115. Fix GCC 4.4 errors.

Changeset: 3b71da06c295286c4ff4e28c9cc9c9f8e2f35ca4

[Owen Arnold]

refs #9115. Fix pointless check warning.

Changeset: fb93911acbe004f1c50586e14c0ecf8a6e705522

[Owen Arnold]

refs #9115. Fix boost list_of usage.

Changeset: 79145a4c1585acedeb2607f84764e89f8d2fe3e7

[Owen Arnold]

refs #9115. Add missing tests.

Changeset: 763729618204d6d1581783ebf89c32746938eeed

[Owen Arnold]

refs #9115. Fix type warnings.

Changeset: 78fae90e875a10073f716546216da1363e7e3a1d

[Owen Arnold]

Tester: The major ouput of this work is Code/Mantid/Framework/Crystal/test/ConnectedComponentLabelingTest.h which should be used to demonstrate that the functionality is working correctly. The code has not yet been wired-up into algorithm form. That will be the subject of a future ticket to prevent the tickets from getting too big. Please review the changes by eye and check that the relevant jenkins jobs are passing correctly.

[Owen Arnold]

refs #9115. Fix more type conversion warnings.

Changeset: 16046401f7c9a64c5629642079c610019d07aa4a

[Martyn Gigg]

The code looks good and a nice use of strategies for the background determination.

All tests are passing.

[Martyn Gigg]

Merge remote-tracking branch 'origin/feature/9115_connected_components'

Full changeset: ​2611b7dc48eb65904bc36eb4248131fe6723391f

[Stuart Campbell]

This ticket has been transferred to github issue ​9958