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

Example 6 with FilterSet

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

the class BenchmarkSpotFit method saveFilters.

private static boolean saveFilters(String filename, ArrayList<Filter> filters) {
    final ArrayList<FilterSet> filterList = new ArrayList<>(1);
    // Add Range keyword to identify as a range filter set
    filterList.add(new FilterSet("Range", filters));
    try (FileOutputStream fos = new FileOutputStream(filename)) {
        // Use the instance (not .toXML() method) to allow the exception to be caught
        FilterXStreamUtils.getXStreamInstance().toXML(filterList, fos);
        return true;
    } catch (final Exception ex) {
        IJ.log("Unable to save the filter set to file: " + ex.getMessage());
    }
    return false;
}

Example 7 with FilterSet

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

the class BenchmarkFilterAnalysis method runAnalysis.

private void runAnalysis(List<FilterSet> filterSets, ComplexFilterScore optimum, double rangeReduction) {
    filterAnalysisResult.plots.clear();
    filterAnalysisResult.bestFilter.clear();
    getCoordinateStore();
    filterAnalysisStopWatch = StopWatch.createStarted();
    IJ.showStatus("Analysing filters ...");
    int setNumber = 0;
    final DirectFilter currentOptimum = (optimum != null) ? optimum.result.filter : null;
    for (final FilterSet filterSet : filterSets) {
        setNumber++;
        if (filterAnalysis(filterSet, setNumber, currentOptimum, rangeReduction) < 0) {
            break;
        }
    }
    filterAnalysisStopWatch.stop();
    ImageJUtils.finished();
    final String timeString = filterAnalysisStopWatch.toString();
    IJ.log("Filter analysis time : " + timeString);
}

Example 8 with FilterSet

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

the class BenchmarkFilterAnalysis method iterate.

private void iterate() {
    // If this is run again immediately then provide options for reporting the results
    final Map<String, ComplexFilterScore> localIterBestFilter = iterBestFilter.get();
    // the result is from an iteration analysis.
    if (filterAnalysisResult.bestFilter.equals(localIterBestFilter)) {
        final GenericDialog gd = new GenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.addMessage("Iteration results are held in memory.\n \nReport these results?");
        gd.addHelp(HelpUrls.getUrl("iterate-filter-analysis"));
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
        if (gd.wasOKed()) {
            reportIterationResults();
            return;
        }
    }
    // Show this dialog first so we can run fully automated after interactive dialogs
    if (!showIterationDialog()) {
        return;
    }
    // Total the time from the interactive plugins
    long time = 0;
    // Run the benchmark fit once interactively, keep the instance
    final BenchmarkSpotFit fit = new BenchmarkSpotFit();
    // than has been optimised before)
    if (fit.resetMultiPathFilter() || invalidBenchmarkSpotFitResults(true)) {
        fit.run(null);
        if (!fit.isFinished()) {
            // The plugin did not complete
            return;
        }
        resetParametersFromFitting();
    }
    if (invalidBenchmarkSpotFitResults(false)) {
        return;
    }
    if (spotFitResults.stopWatch != null) {
        time += spotFitResults.stopWatch.getTime();
    }
    // Run filter analysis once interactively
    if (!loadFitResults()) {
        return;
    }
    // Collect parameters for optimising the parameters
    if (!showDialog(FLAG_OPTIMISE_FILTER | FLAG_OPTIMISE_PARAMS)) {
        return;
    }
    // Load filters from file
    final List<FilterSet> filterSets = readFilterSets();
    if (filterSets == null || filterSets.isEmpty()) {
        IJ.error(TITLE, "No filters specified");
        return;
    }
    ComplexFilterScore current = analyse(filterSets);
    if (current == null) {
        return;
    }
    time += filterAnalysisStopWatch.getTime();
    current = analyseParameters(current);
    if (current == null) {
        return;
    }
    time += parameterAnalysisStopWatch.getTime();
    // Time the non-interactive plugins as a continuous section
    iterationStopWatch = StopWatch.createStarted();
    // Remove the previous iteration results
    iterBestFilter.set(null);
    ImageJUtils.log(TITLE + " Iterating ...");
    final IterationConvergenceChecker checker = new IterationConvergenceChecker(current);
    // Iterate ...
    boolean outerConverged = false;
    int outerIteration = 1;
    double outerRangeReduction = 1;
    while (!outerConverged) {
        if (settings.iterationConvergeBeforeRefit) {
            // Optional inner loop so that the non-filter and filter parameters converge
            // before a refit
            boolean innerConverged = false;
            double innerRangeReduction = 1;
            // innerRangeReduction *= outerRangeReduction
            while (!innerConverged) {
                final ComplexFilterScore previous = current;
                // Re-use the filters as the user may be loading a custom set.
                current = analyse(filterSets, current, innerRangeReduction);
                if (current == null) {
                    return;
                }
                final double[] previousParameters = createParameters();
                current = analyseParameters(current, innerRangeReduction);
                if (current == null) {
                    return;
                }
                final double[] currentParameters = createParameters();
                innerConverged = checker.converged("Filter", previous, current, previousParameters, currentParameters);
            }
            // Check if we can continue (e.g. not max iterations or escape pressed)
            if (!checker.canContinue) {
                break;
            }
        }
        // Do the fit (using the current optimum filter)
        fit.run(current.result.filter, residualsThreshold, settings.failCount, settings.duplicateDistance, settings.duplicateDistanceAbsolute);
        if (invalidBenchmarkSpotFitResults(false)) {
            return;
        }
        if (!loadFitResults()) {
            return;
        }
        // is centred around the current optimum.
        if (settings.iterationMinRangeReduction < 1) {
            // Linear interpolate down to the min range reduction
            outerRangeReduction = MathUtils.max(settings.iterationMinRangeReduction, MathUtils.interpolateY(0, 1, settings.iterationMinRangeReductionIteration, settings.iterationMinRangeReduction, outerIteration++));
        }
        // Optimise the filter again.
        final ComplexFilterScore previous = current;
        // Re-use the filters as the user may be loading a custom set.
        current = analyse(filterSets, current, outerRangeReduction);
        if (current == null) {
            break;
        }
        final double[] previousParameters = createParameters();
        current = analyseParameters(current, outerRangeReduction);
        if (current == null) {
            return;
        }
        final double[] currentParameters = createParameters();
        outerConverged = checker.converged("Fit+Filter", previous, current, previousParameters, currentParameters);
    }
    if (current != null) {
        // Set-up the plugin so that it can be run again (in iterative mode)
        // and the results reported for the top filter.
        // If the user runs the non-iterative mode then the results will be lost.
        iterBestFilter.set(filterAnalysisResult.bestFilter);
    }
    time += iterationStopWatch.getTime();
    IJ.log("Iteration analysis time : " + TextUtils.millisToString(time));
    showFinished();
}

Example 9 with FilterSet

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

the class BenchmarkFilterAnalysis method initialise.

@Override
public void initialise(List<? extends Chromosome<FilterScore>> individuals) {
    gaIteration++;
    gaScoreIndex = 0;
    gaScoreResults = scoreFilters(setStrength(new FilterSet(populationToFilters(individuals))), false);
}

Example 10 with FilterSet

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

the class BenchmarkFilterAnalysis method expandFilters.

/**
 * If filters have been provided in FiltersSets of 3 then expand the filters into a set assuming
 * the three represent min:max:increment.
 *
 * @param filterSets the filter sets
 * @return the expanded filter sets
 */
private List<FilterSet> expandFilters(List<FilterSet> filterSets) {
    // Note:
    // Do not clear the search range map and step size map when reading a new set of filters.
    // The filters may be the same with slight modifications and so it is useful to keep the last
    // settings.
    final long[] expanded = new long[filterSets.size()];
    final String[] name = new String[expanded.length];
    int count = 0;
    boolean doIt = false;
    for (final FilterSet filterSet : filterSets) {
        if (filterSet.size() == 3 && filterSet.allSameType()) {
            name[count] = filterSet.getName();
            // Check we have min:max:increment by counting the combinations
            final Filter f1 = filterSet.getFilters().get(0);
            final Filter f2 = filterSet.getFilters().get(1);
            final Filter f3 = filterSet.getFilters().get(2);
            final int n = f1.getNumberOfParameters();
            final double[] parameters = new double[n];
            final double[] parameters2 = new double[n];
            final double[] increment = new double[n];
            for (int i = 0; i < n; i++) {
                parameters[i] = f1.getParameterValue(i);
                parameters2[i] = f2.getParameterValue(i);
                increment[i] = f3.getParameterValue(i);
            }
            final long combinations = countCombinations(parameters, parameters2, increment);
            if (combinations > 1) {
                expanded[count] = combinations;
                doIt = true;
            }
        }
        count++;
    }
    if (!doIt) {
        return filterSets;
    }
    final GenericDialog gd = new GenericDialog(TITLE);
    gd.hideCancelButton();
    final StringBuilder sb = new StringBuilder("The filter file contains potential triples of min:max:increment.\n \n");
    for (count = 0; count < expanded.length; count++) {
        if (expanded[count] > 0) {
            sb.append("Expand set [").append((count + 1)).append("]");
            if (!TextUtils.isNullOrEmpty(name[count])) {
                sb.append(" ").append(name[count]);
            }
            sb.append(" to ").append(expanded[count]).append(" filters\n");
        }
    }
    gd.addMessage(sb.toString());
    gd.addCheckbox("Expand_filters", settings.expandFilters);
    gd.showDialog();
    if (!gd.wasCanceled()) {
        settings.expandFilters = gd.getNextBoolean();
        if (!settings.expandFilters) {
            return filterSets;
        }
    }
    IJ.showStatus("Expanding filters ...");
    final List<FilterSet> filterList2 = new ArrayList<>(filterSets.size());
    for (final FilterSet filterSet : filterSets) {
        count = filterList2.size();
        if (expanded[count] == 0) {
            filterList2.add(filterSet);
            continue;
        }
        final Filter f1 = filterSet.getFilters().get(0);
        final Filter f2 = filterSet.getFilters().get(1);
        final Filter f3 = filterSet.getFilters().get(2);
        final int n = f1.getNumberOfParameters();
        final double[] parameters = new double[n];
        final double[] parameters2 = new double[n];
        final double[] increment = new double[n];
        for (int i = 0; i < n; i++) {
            parameters[i] = f1.getParameterValue(i);
            parameters2[i] = f2.getParameterValue(i);
            increment[i] = f3.getParameterValue(i);
        }
        final List<Filter> list = expandFilters(f1, parameters, parameters2, increment);
        filterList2.add(new FilterSet(filterSet.getName(), list));
    }
    IJ.showStatus("");
    ImageJUtils.log("Expanded input to %d filters in %s", countFilters(filterList2), TextUtils.pleural(filterList2.size(), "set"));
    return filterList2;
}