CCL clustering defect

[Owen Arnold]

Some issues have been fixed with the connected component analysis, and some others have been discovered as part of #9509. Generally the CCL works well, and only a very small number of pixels are misplaced.

The issues seem to stem from resolving a unified label id across neighbouring pixels (this is not a multi-threaded issue). This is probably due to the fact that the neighbours are being stored as independent copies, so updates to one parent DisjointElement, don't affect other connected elements (when they should). I therefore suggest that the solution to this is to:

a) Prove my theory above. A few unit tests in CCL should do this

b) If (a) is proved. Fix it by storing smart_pointers in the neighbours array.

This is a (rather large) unit test, which I used as part of CCL to quickly reproduce the issue. I'm also attaching a script, which produces cluster outputs, which demonstrate the issue via IntegratePeaksUsingClusters

void xtest_on_real_md_peak()
  {
    auto createAlg = Mantid::API::AlgorithmManager::Instance().createUnmanaged("CreateMDHistoWorkspace");
    createAlg->setChild(true);
    createAlg->initialize();
    createAlg->setPropertyValue("SignalInput",
        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    createAlg->setProperty("Dimensionality", 3);
    createAlg->setPropertyValue("Extents", "4.9,5.3,0.87,1.27,3.78,4.18");
    createAlg->setPropertyValue("NumberOfBins", "20,20,20");
    createAlg->setPropertyValue("Names", "Q_lab_x,Q_lab_y,Q_lab_z");
    createAlg->setPropertyValue("Units", "Q,Q,Q");
    createAlg->setPropertyValue("OutputWorkspace", "out_ws");
    createAlg->execute();
    IMDHistoWorkspace_sptr inWS = createAlg->getProperty("OutputWorkspace");

    size_t labelingId = 1;
    int nThreads = 1;

    HardThresholdBackground backgroundStrategy(0.7, NoNormalization);

    Progress prog;
    ConnectedComponentLabeling ccl(labelingId, nThreads);
    auto outWS = ccl.execute(inWS, &backgroundStrategy, prog);

    std::set<size_t> uniqueEntries = connection_workspace_to_set_of_labels(outWS.get());
    //TSM_ASSERT_EQUALS("1 object covering entire space", 2, uniqueEntries.size());
    //TS_ASSERT(does_set_contain(uniqueEntries, labelingId));

    auto saveAlg = AlgorithmManager::Instance().createUnmanaged("SaveMD");
    saveAlg->setChild(true);
    saveAlg->initialize();
    saveAlg->setProperty("InputWorkspace", outWS);
    saveAlg->setProperty("Filename", "/Users/spu92482/Desktop/CCL.nxs");
    saveAlg->execute();
  }

[Owen Arnold]

refs #9539. Fix bridge link unit tests.

The issue here is that new DisjointElements are being placed on the stack as temporaries at the time that m_parent is set. When they go out of scope the same address can be used in the next round of the loop, therefore all m_parents get set to the same value.

Changeset: ac7fa8c6a6567cda1947328094aa2541a730aa06

[Owen Arnold]

refs #9539. Add another test

Changeset: c4627343d6c69904e774a26703b1fbcbaf909dcc

[Owen Arnold]

Tester: Ignore the attached script and the original guess about what was happening here.

The issue came about because the DisjointElement tree was not being constructed properly. Our CCL implementation is a two step process. 1) Generate the tree. 2) Find the root of each tree and use that to label the respective element in the resulting image. Step 1 was not being performed properly. More specifically parent elements of each node were not being updated in the right way.

• Check the code changes
• Verify that the new unit tests work.
• If you want to, copy, as a temporary change, the dummy unit test above in the description and use it to create CCL.nxs. When opening CCL.nxs in the SliceViewer, you should find that any elements next to each other (8 connectivity) have the same colour.

[Martyn Gigg]

There is an MSBuild compiler warning that would be good to catch here:

​http://builds.mantidproject.org/view/Develop%20Builds/job/develop_clean_win7_debug/44/warnings33Result/

[Owen Arnold]

refs #9539. Fix type conversion issue.

Changeset: 6f568b0d0b649733004114f3fd22e12859f6e14f

[Martyn Gigg]

Merge remote-tracking branch 'origin/feature/9539_bridge_link_issue'

Full changeset: ​1604ccaee22135726c174e80a42fa17d20c94856

[Owen Arnold]

Cherry-pick fixes from feature/9539_bridge_link_issue into next

Changes:

refs #9539. Fix bridge link unit tests.

The issue here is that new DisjointElements are being placed on the stack as temporaries at the time that m_parent is set. When they go out of scope the same address can be used in the next round of the loop, therefore all m_parents get set to the same value. (cherry picked from commit ac7fa8c6a6567cda1947328094aa2541a730aa06)

refs #9539. Add another test (cherry picked from commit c4627343d6c69904e774a26703b1fbcbaf909dcc)

refs #9539. Fix type conversion issue. (cherry picked from commit 6f568b0d0b649733004114f3fd22e12859f6e14f)

Changeset: 832545342a68ca695a8cd79e90f41d457fe183f9

[Stuart Campbell]

This ticket has been transferred to github issue ​10382