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Example 1 with Resequencer

use of uk.ac.sussex.gdsc.core.match.Resequencer in project GDSC-SMLM by aherbert.

the class ClassificationMatchCalculator method runCompareClassifications.

private void runCompareClassifications(MemoryPeakResults results1, MemoryPeakResults results2) {
    final List<PointPair> allMatches = new LinkedList<>();
    // Optionally exclude results which do not have an id and/or category
    Predicate<PeakResult> test = settings.useId == ClassAnalysis.IGNORE_ZERO ? r -> r.getId() != 0 : null;
    if (settings.useCategory == ClassAnalysis.IGNORE_ZERO) {
        final Predicate<PeakResult> test2 = r -> r.getCategory() != 0;
        test = test == null ? test2 : test.and(test2);
    } else if (test == null) {
        test = r -> true;
    }
    // Divide the results into time points
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates1 = getCoordinates(results1, test);
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates2 = getCoordinates(results2, test);
    // Process each time point
    int n1 = 0;
    int n2 = 0;
    for (final int t : getTimepoints(coordinates1, coordinates2)) {
        final Coordinate[] c1 = getCoordinates(coordinates1, t);
        final Coordinate[] c2 = getCoordinates(coordinates2, t);
        n1 += c1.length;
        n2 += c2.length;
        final List<PointPair> matches = new LinkedList<>();
        MatchCalculator.analyseResults3D(c1, c2, settings.matchDistance, null, null, null, matches);
        allMatches.addAll(matches);
    }
    if (allMatches.isEmpty()) {
        IJ.error(TITLE, "No localisation matches between the two results sets");
        return;
    }
    // Get the unique Ids and Categories in the matches.
    final Mapper ids = getMapper(allMatches, PeakResult::getId, settings.useId);
    final Mapper cats = getMapper(allMatches, PeakResult::getCategory, settings.useCategory);
    // Map id/category to an index = stride * cat + id
    final int stride = ids.size();
    // Any integer is allowed as an index
    if ((long) stride * cats.size() > 1L << 32) {
        IJ.error(TITLE, "Too many combinations of id and category to assigne unique labels");
        return;
    }
    // Extract indices
    final int[] set1 = new int[allMatches.size()];
    final int[] set2 = new int[allMatches.size()];
    int i = 0;
    for (final PointPair r : allMatches) {
        set1[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint1()).getPeakResult());
        set2[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint2()).getPeakResult());
        i++;
    }
    final Resequencer re = new Resequencer();
    re.setCacheMap(true);
    re.renumber(set1);
    re.renumber(set2);
    // Compare
    final RandIndex r = new RandIndex().compute(set1, set2);
    final TextWindow resultsWindow = ImageJUtils.refresh(resultsWindowRef, () -> new TextWindow(TITLE + " Results", "Results1\tResults2\tID\tCategory\tn1\tc1\tn2\tc2\tMatched\tRand Index\tAdjusted RI", "", 900, 300));
    try (BufferedTextWindow bw = new BufferedTextWindow(resultsWindow)) {
        final StringBuilder sb = new StringBuilder(2048);
        sb.append(results1.getName()).append('\t');
        sb.append(results2.getName()).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useId.ordinal()]).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useCategory.ordinal()]).append('\t');
        sb.append(n1).append('\t');
        sb.append(MathUtils.max(set1) + 1).append('\t');
        sb.append(n2).append('\t');
        sb.append(MathUtils.max(set2) + 1).append('\t');
        sb.append(set1.length).append('\t');
        sb.append(MathUtils.rounded(r.getRandIndex())).append('\t');
        sb.append(MathUtils.rounded(r.getAdjustedRandIndex())).append('\t');
        bw.append(sb.toString());
    }
}
Also used : PeakResultPoint(uk.ac.sussex.gdsc.smlm.results.PeakResultPoint) TIntObjectHashMap(gnu.trove.map.hash.TIntObjectHashMap) Arrays(java.util.Arrays) ConfigurationException(uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException) Prefs(ij.Prefs) TextWindow(ij.text.TextWindow) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) AtomicReference(java.util.concurrent.atomic.AtomicReference) ConversionException(com.thoughtworks.xstream.converters.ConversionException) TIntProcedure(gnu.trove.procedure.TIntProcedure) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) LinkedList(java.util.LinkedList) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) RandIndex(uk.ac.sussex.gdsc.core.match.RandIndex) Predicate(java.util.function.Predicate) BufferedTextWindow(uk.ac.sussex.gdsc.core.ij.BufferedTextWindow) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) InputSource(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager.InputSource) ToIntFunction(java.util.function.ToIntFunction) TIntIntHashMap(gnu.trove.map.hash.TIntIntHashMap) NamedObject(uk.ac.sussex.gdsc.smlm.data.NamedObject) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) Coordinate(uk.ac.sussex.gdsc.core.match.Coordinate) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) TIntHashSet(gnu.trove.set.hash.TIntHashSet) XyzrResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.XyzrResultProcedure) List(java.util.List) PointPair(uk.ac.sussex.gdsc.core.match.PointPair) Resequencer(uk.ac.sussex.gdsc.core.match.Resequencer) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) IJ(ij.IJ) MatchCalculator(uk.ac.sussex.gdsc.core.match.MatchCalculator) PlugIn(ij.plugin.PlugIn) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) BufferedTextWindow(uk.ac.sussex.gdsc.core.ij.BufferedTextWindow) Resequencer(uk.ac.sussex.gdsc.core.match.Resequencer) RandIndex(uk.ac.sussex.gdsc.core.match.RandIndex) LinkedList(java.util.LinkedList) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) PeakResultPoint(uk.ac.sussex.gdsc.smlm.results.PeakResultPoint) TextWindow(ij.text.TextWindow) BufferedTextWindow(uk.ac.sussex.gdsc.core.ij.BufferedTextWindow) Coordinate(uk.ac.sussex.gdsc.core.match.Coordinate) LinkedList(java.util.LinkedList) List(java.util.List) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) PointPair(uk.ac.sussex.gdsc.core.match.PointPair) PeakResultPoint(uk.ac.sussex.gdsc.smlm.results.PeakResultPoint)

Aggregations

ConversionException (com.thoughtworks.xstream.converters.ConversionException)1 TIntIntHashMap (gnu.trove.map.hash.TIntIntHashMap)1 TIntObjectHashMap (gnu.trove.map.hash.TIntObjectHashMap)1 TIntProcedure (gnu.trove.procedure.TIntProcedure)1 TIntHashSet (gnu.trove.set.hash.TIntHashSet)1 IJ (ij.IJ)1 Prefs (ij.Prefs)1 PlugIn (ij.plugin.PlugIn)1 TextWindow (ij.text.TextWindow)1 Arrays (java.util.Arrays)1 LinkedList (java.util.LinkedList)1 List (java.util.List)1 AtomicReference (java.util.concurrent.atomic.AtomicReference)1 Predicate (java.util.function.Predicate)1 ToIntFunction (java.util.function.ToIntFunction)1 BufferedTextWindow (uk.ac.sussex.gdsc.core.ij.BufferedTextWindow)1 ImageJUtils (uk.ac.sussex.gdsc.core.ij.ImageJUtils)1 ExtendedGenericDialog (uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog)1 Coordinate (uk.ac.sussex.gdsc.core.match.Coordinate)1 MatchCalculator (uk.ac.sussex.gdsc.core.match.MatchCalculator)1