Examples with FilterSet uk.ac.sussex.gdsc.smlm.results.filter.FilterSet used on opensource projects

Example 11 with FilterSet

use of uk.ac.sussex.gdsc.smlm.results.filter.FilterSet in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method findOptimum.

@Nullable
@Override
public SearchResult<FilterScore> findOptimum(double[][] points) {
    gaIteration++;
    SimpleFilterScore max = filterScoreOptimum;
    final FilterScoreResult[] scoreResults = scoreFilters(setStrength(new FilterSet(searchSpaceToFilters(points))), false);
    if (scoreResults == null) {
        return null;
    }
    for (int index = 0; index < scoreResults.length; index++) {
        final FilterScoreResult scoreResult = scoreResults[index];
        final SimpleFilterScore result = new SimpleFilterScore(scoreResult, true, scoreResult.criteria >= minCriteria);
        if (result.compareTo(max) < 0) {
            max = result;
        }
    }
    filterScoreOptimum = max;
    // Add the best filter to the table
    // This filter may not have been part of the scored subset so use the entire results set for
    // reporting
    final DirectFilter filter = max.result.filter;
    final FractionClassificationResult r = scoreFilter(filter, defaultMinimalFilter, gaResultsList, coordinateStore);
    final StringBuilder text = createResult(filter, r);
    add(text, gaIteration);
    gaWindow.accept(text.toString());
    return new SearchResult<>(filter.getParameters(), max);
}

Example 12 with FilterSet

use of uk.ac.sussex.gdsc.smlm.results.filter.FilterSet in project GDSC-SMLM by aherbert.

the class FilterAnalysis method addPrecisionHysteresisFilters.

private void addPrecisionHysteresisFilters(List<FilterSet> filterSets) {
    if (!settings.hysteresisPrecisionFilter) {
        return;
    }
    for (int precisionGap = settings.minPrecisionGap; precisionGap <= settings.maxPrecisionGap; precisionGap += settings.incPrecisionGap) {
        final List<Filter> filters = new LinkedList<>();
        for (int precision = settings.minPrecision; precision <= settings.maxPrecision; precision++) {
            filters.add(new PrecisionHysteresisFilter(2, 0, 1, 0, precision, precisionGap));
        }
        filterSets.add(new FilterSet(filters));
    }
}

Example 13 with FilterSet

use of uk.ac.sussex.gdsc.smlm.results.filter.FilterSet in project GDSC-SMLM by aherbert.

the class FilterAnalysis method addSnrFilters.

private void addSnrFilters(List<FilterSet> filterSets) {
    if (!settings.snrFilter) {
        return;
    }
    for (double w = settings.minWidth; w <= settings.maxWidth; w += settings.incWidth) {
        final WidthFilter wf = new WidthFilter((float) w);
        final List<Filter> filters = new LinkedList<>();
        for (int snr = settings.minSnr; snr <= settings.maxSnr; snr++) {
            filters.add(new AndFilter(wf, new SnrFilter(snr)));
        }
        filterSets.add(new FilterSet(filters));
    }
}

Example 14 with FilterSet

use of uk.ac.sussex.gdsc.smlm.results.filter.FilterSet in project GDSC-SMLM by aherbert.

the class FilterAnalysis method analyse.

/**
 * Run different filtering methods on a set of labelled peak results outputting performance
 * statistics on the success of the filter to an ImageJ table.
 *
 * <p>If the peak result original value is set to 1 it is considered a true peak, 0 for a false
 * peak. Filtering is done using e.g. SNR threshold, Precision thresholds, etc. The statistics
 * reported are shown in a table, e.g. precision, Jaccard, F-score.
 *
 * <p>For each filter set a plot is shown of the Jaccard score verses the filter value, thus
 * filters should be provided in ascending numerical order otherwise they are sorted.
 *
 * @param resultsList the results list
 * @param filterSets the filter sets
 */
public void analyse(List<MemoryPeakResults> resultsList, List<FilterSet> filterSets) {
    final Consumer<String> output = createResultsWindow();
    plots = new ArrayList<>(settings.plotTopN);
    bestFilter = new HashMap<>();
    bestFilterOrder = new LinkedList<>();
    IJ.showStatus("Analysing filters ...");
    final int total = countFilters(filterSets);
    int count = 0;
    for (final FilterSet filterSet : filterSets) {
        IJ.showStatus("Analysing " + filterSet.getName() + " ...");
        count = runAnalysis(output, filterSet, resultsList, count, total);
    }
    ImageJUtils.finished();
    showPlots();
    calculateSensitivity(resultsList);
}

Example 15 with FilterSet

use of uk.ac.sussex.gdsc.smlm.results.filter.FilterSet in project GDSC-SMLM by aherbert.

the class FilterAnalysis method addSnrHysteresisFilters.

private void addSnrHysteresisFilters(List<FilterSet> filterSets) {
    if (!settings.hysteresisSnrFilter) {
        return;
    }
    for (double w = settings.minWidth; w <= settings.maxWidth; w += settings.incWidth) {
        final WidthFilter wf = new WidthFilter((float) w);
        for (int snrGap = settings.minSnrGap; snrGap <= settings.maxSnrGap; snrGap += settings.incSnrGap) {
            final List<Filter> filters = new LinkedList<>();
            for (int snr = settings.minSnr; snr <= settings.maxSnr; snr++) {
                filters.add(new AndFilter(wf, new SnrHysteresisFilter(2, 0, 1, 0, snr, snrGap)));
            }
            filterSets.add(new FilterSet(filters));
        }
    }
}