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

Example 1 with MultiPathFilter

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

the class BenchmarkSpotFit method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("fit-spot-data"));
    ImageJUtils.addMessage(gd, "Fit candidate spots in the benchmark image created by " + CreateData.TITLE + " plugin\nand identified by the " + BenchmarkSpotFilter.TITLE + " plugin.\nPSF width = %s nm (Square pixel adjustment = %s nm)\n \n" + "Configure the fitting:", MathUtils.rounded(simulationParameters.sd), MathUtils.rounded(getSa()));
    gd.addSlider("Fraction_positives", 50, 100, settings.fractionPositives);
    gd.addSlider("Fraction_negatives_after_positives", 0, 100, settings.fractionNegativesAfterAllPositives);
    gd.addSlider("Min_negatives_after_positives", 0, 30, settings.negativesAfterAllPositives);
    gd.addSlider("Match_distance", 0.5, 3.5, settings.distance);
    gd.addSlider("Lower_distance", 0, 3.5, settings.lowerDistance);
    gd.addSlider("Match_signal", 0, 3.5, settings.signalFactor);
    gd.addSlider("Lower_signal", 0, 3.5, settings.lowerSignalFactor);
    final FitEngineConfigurationProvider fitEngineConfigurationProvider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    // Collect options for fitting
    final double sa = getSa();
    final FitConfiguration fitConfig = config.getFitConfiguration();
    fitConfig.setInitialPeakStdDev(MathUtils.round(sa / simulationParameters.pixelPitch));
    PeakFit.addPsfOptions(gd, fitConfig);
    PeakFit.addFittingOptions(gd, fitEngineConfigurationProvider);
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), FitProtosHelper.getName(fitConfig.getFitSolver()));
    gd.addMessage("Multi-path filter (used to pick optimum results during fitting)");
    // Allow loading the best filter for these results
    final boolean benchmarkSettingsCheckbox = BenchmarkSpotFitResult.fitResultsId.get() == BenchmarkFilterAnalysis.getLastFittingId();
    Checkbox cbBenchmark = null;
    if (benchmarkSettingsCheckbox) {
        // This should always be an opt-in decision. Otherwise the user cannot use the previous
        // settings.
        cbBenchmark = gd.addAndGetCheckbox("Benchmark_settings", false);
    }
    gd.addTextAreas(XmlUtils.convertQuotes(multiFilter.toXml()), null, 6, 60);
    textFailLimit = gd.addAndGetNumericField("Fail_limit", config.getFailuresLimit(), 0);
    cbIncludeNeighbours = gd.addAndGetCheckbox("Include_neighbours", config.isIncludeNeighbours());
    gd.addAndGetSlider("Neighbour_height", 0.01, 1, config.getNeighbourHeightThreshold());
    textNeighbourHeight = gd.getLastTextField();
    cbComputeDoublets = gd.addAndGetCheckbox("Compute_doublets", settings.computeDoublets);
    PeakFit.addDuplicateDistanceOptions(gd, fitEngineConfigurationProvider);
    gd.addCheckbox("Show_score_histograms", settings.showFilterScoreHistograms);
    gd.addCheckbox("Show_correlation", settings.showCorrelation);
    gd.addCheckbox("Plot_rank_by_intensity", settings.rankByIntensity);
    gd.addCheckbox("Save_filter_range", settings.saveFilterRange);
    if (extraOptions) {
    // No extra options
    }
    // Add a mouse listener to the config file field
    if (cbBenchmark != null && ImageJUtils.isShowGenericDialog()) {
        taFilterXml = gd.getTextArea1();
        cbBenchmark.addItemListener(this);
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.fractionPositives = Math.abs(gd.getNextNumber());
    settings.fractionNegativesAfterAllPositives = Math.abs(gd.getNextNumber());
    settings.negativesAfterAllPositives = (int) Math.abs(gd.getNextNumber());
    settings.distance = Math.abs(gd.getNextNumber());
    settings.lowerDistance = Math.abs(gd.getNextNumber());
    settings.signalFactor = Math.abs(gd.getNextNumber());
    settings.lowerSignalFactor = Math.abs(gd.getNextNumber());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setFitting(gd.getNextNumber());
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    boolean myUseBenchmarkSettings = false;
    if (benchmarkSettingsCheckbox) {
        // useBenchmarkSettings =
        myUseBenchmarkSettings = gd.getNextBoolean();
    }
    // Read dialog settings
    final String xml = gd.getNextText();
    final int failLimit = (int) gd.getNextNumber();
    final boolean includeNeighbours = gd.getNextBoolean();
    final double neighbourHeightThreshold = gd.getNextNumber();
    final boolean myComputeDoublets = gd.getNextBoolean();
    final double myDuplicateDistance = gd.getNextNumber();
    gd.collectOptions();
    MultiPathFilter myMultiFilter = null;
    if (myUseBenchmarkSettings && !ImageJUtils.isShowGenericDialog()) {
        // Only copy the benchmark settings if not interactive
        final FitEngineConfiguration tmp = new FitEngineConfiguration();
        final FitConfiguration tmpFitConfig = tmp.getFitConfiguration();
        // Collect the residuals threshold
        tmpFitConfig.setComputeResiduals(true);
        if (BenchmarkFilterAnalysis.updateConfiguration(tmp, false)) {
            config.setFailuresLimit(tmp.getFailuresLimit());
            config.setIncludeNeighbours(tmp.isIncludeNeighbours());
            config.setNeighbourHeightThreshold(tmp.getNeighbourHeightThreshold());
            settings.computeDoublets = (tmp.getResidualsThreshold() < 1);
            config.setDuplicateDistance(tmp.getDuplicateDistance());
            config.setDuplicateDistanceAbsolute(tmp.getDuplicateDistanceAbsolute());
            final DirectFilter primaryFilter = tmpFitConfig.getSmartFilter();
            final double residualsThreshold = tmp.getResidualsThreshold();
            myMultiFilter = new MultiPathFilter(primaryFilter, FitWorker.createMinimalFilter(tmpFitConfig.getFilterPrecisionMethod()), residualsThreshold);
        }
    } else {
        myMultiFilter = MultiPathFilter.fromXml(xml);
        config.setFailuresLimit(failLimit);
        config.setIncludeNeighbours(includeNeighbours);
        config.setNeighbourHeightThreshold(neighbourHeightThreshold);
        settings.computeDoublets = myComputeDoublets;
        config.setDuplicateDistance(myDuplicateDistance);
    }
    if (myMultiFilter == null) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("The multi-path filter was invalid.\n \nContinue with a default filter?");
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.showDialog();
        if (!gd.wasOKed()) {
            return false;
        }
    } else {
        multiFilter = myMultiFilter;
    }
    if (settings.computeDoublets) {
        config.setResidualsThreshold(0);
        fitConfig.setComputeResiduals(true);
    } else {
        config.setResidualsThreshold(1);
        fitConfig.setComputeResiduals(false);
    }
    settings.showFilterScoreHistograms = gd.getNextBoolean();
    settings.showCorrelation = gd.getNextBoolean();
    settings.rankByIntensity = gd.getNextBoolean();
    settings.saveFilterRange = gd.getNextBoolean();
    // Avoid stupidness, i.e. things that move outside the fit window and are bad widths
    // TODO - Fix this for simple or smart filter...
    fitConfig.setDisableSimpleFilter(false);
    // Realistically we cannot fit lower than this
    fitConfig.setMinPhotons(15);
    // Disable shift as candidates may be re-mapped to alternative candidates so the initial
    // position is wrong.
    fitConfig.setCoordinateShiftFactor(0);
    fitConfig.setMinWidthFactor(1.0 / 5);
    fitConfig.setMaxWidthFactor(5);
    // Disable the direct filter
    fitConfig.setDirectFilter(null);
    if (extraOptions) {
    // No extra options
    }
    if (gd.invalidNumber()) {
        return false;
    }
    if (settings.lowerDistance > settings.distance) {
        settings.lowerDistance = settings.distance;
    }
    if (settings.lowerSignalFactor > settings.signalFactor) {
        settings.lowerSignalFactor = settings.signalFactor;
    }
    // Distances relative to sa (not s) as this is the same as the BenchmarkSpotFilter plugin
    distanceInPixels = settings.distance * sa / simulationParameters.pixelPitch;
    lowerDistanceInPixels = settings.lowerDistance * sa / simulationParameters.pixelPitch;
    // Copy simulation defaults if a new simulation.
    // if (lastSimulationId.get() != simulationParameters.id) {
    // This is needed to configure the fit solver.
    fitConfig.setNmPerPixel(simulationParameters.pixelPitch);
    fitConfig.setGain(simulationParameters.gain);
    fitConfig.setQuantumEfficiency(simulationParameters.qe);
    fitConfig.setReadNoise(simulationParameters.readNoise);
    fitConfig.setBias(simulationParameters.bias);
    fitConfig.setCameraType(simulationParameters.cameraType);
    fitConfig.setCameraModel(CreateData.getCameraModel(simulationParameters));
    // }
    if (!PeakFit.configurePsfModel(config)) {
        return false;
    }
    return PeakFit.configureFitSolver(config, IJImageSource.getBounds(imp), null, (extraOptions) ? PeakFit.FLAG_EXTRA_OPTIONS : 0);
}

Example 2 with MultiPathFilter

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

the class BenchmarkSpotFit method itemStateChanged.

@Override
public void itemStateChanged(ItemEvent event) {
    if (event.getSource() instanceof Checkbox) {
        final Checkbox checkbox = (Checkbox) event.getSource();
        int failLimit;
        boolean includeNeighbours;
        double neighbourHeightThrehsold;
        boolean computeDoublets;
        MultiPathFilter myMultiFilter;
        if (checkbox.getState()) {
            final FitEngineConfiguration tmp = new FitEngineConfiguration();
            final FitConfiguration tmpFitConfig = tmp.getFitConfiguration();
            // Collect residuals threshold
            tmpFitConfig.setComputeResiduals(true);
            if (BenchmarkFilterAnalysis.updateConfiguration(tmp, false)) {
                failLimit = tmp.getFailuresLimit();
                includeNeighbours = tmp.isIncludeNeighbours();
                neighbourHeightThrehsold = tmp.getNeighbourHeightThreshold();
                computeDoublets = tmp.getResidualsThreshold() < 1;
                final DirectFilter primaryFilter = tmpFitConfig.getSmartFilter();
                final double residualsThreshold = tmp.getResidualsThreshold();
                myMultiFilter = new MultiPathFilter(primaryFilter, FitWorker.createMinimalFilter(tmpFitConfig.getFilterPrecisionMethod()), residualsThreshold);
            } else {
                IJ.log("Failed to update settings using the filter analysis");
                checkbox.setState(false);
                return;
            }
        } else {
            failLimit = config.getFailuresLimit();
            includeNeighbours = config.isIncludeNeighbours();
            neighbourHeightThrehsold = config.getNeighbourHeightThreshold();
            computeDoublets = BenchmarkSpotFit.this.settings.computeDoublets;
            myMultiFilter = multiFilter;
        }
        // Update the dialog
        taFilterXml.setText(myMultiFilter.toXml());
        textFailLimit.setText("" + failLimit);
        cbIncludeNeighbours.setState(includeNeighbours);
        textNeighbourHeight.setText(MathUtils.rounded(neighbourHeightThrehsold));
        cbComputeDoublets.setState(computeDoublets);
    }
}

Example 3 with MultiPathFilter

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

the class BenchmarkSpotFit method run.

/**
 * Run the analysis non-interactively using the given filter settings.
 *
 * @param filter the filter
 * @param residualsThreshold the residuals threshold
 * @param failuresLimit the failures limit
 * @param duplicateDistance the duplicate distance
 * @param duplicateDistanceAbsolute the duplicate distance absolute
 */
void run(DirectFilter filter, double residualsThreshold, int failuresLimit, double duplicateDistance, boolean duplicateDistanceAbsolute) {
    clearFitResults();
    silent = true;
    finished = false;
    if (!initialise()) {
        return;
    }
    // Reset the filter
    multiFilter = new MultiPathFilter(filter, FitWorker.createMinimalFilter(getPrecisionMethod(filter)), residualsThreshold);
    // Update the appropriate fitting settings
    config.setFailuresLimit(failuresLimit);
    config.setDuplicateDistance(duplicateDistance);
    config.setDuplicateDistanceAbsolute(duplicateDistanceAbsolute);
    runFitting();
    finished = true;
}

Example 4 with MultiPathFilter

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

the class BenchmarkFilterAnalysis method readFilterSets.

@Nullable
@SuppressWarnings("unchecked")
private List<FilterSet> readFilterSets() {
    if (extraOptions) {
        final MultiPathFilter multiFilter = BenchmarkSpotFit.getMultiFilter();
        if (multiFilter != null) {
            final IDirectFilter f = multiFilter.getFilter();
            if (f instanceof DirectFilter) {
                final GenericDialog gd = new GenericDialog(TITLE);
                gd.addMessage("Use an identical filter to " + BenchmarkSpotFit.TITLE);
                gd.enableYesNoCancel();
                gd.hideCancelButton();
                gd.showDialog();
                if (gd.wasOKed()) {
                    final List<FilterSet> filterSets = new ArrayList<>(1);
                    final List<Filter> filters = new ArrayList<>(1);
                    filters.add((DirectFilter) f);
                    final FilterSet filterSet = new FilterSet(filters);
                    filterSets.add(filterSet);
                    resetParametersFromFitting();
                    createResultsPrefix2();
                    return filterSets;
                }
            }
        }
    }
    GUIFilterSettings filterSettings = SettingsManager.readGuiFilterSettings(0);
    final String filename = ImageJUtils.getFilename("Filter_File", filterSettings.getFilterSetFilename());
    if (filename != null) {
        IJ.showStatus("Reading filters ...");
        filterSettings = filterSettings.toBuilder().setFilterSetFilename(filename).build();
        // Allow the filters to be cached
        final Triple<String, Long, List<FilterSet>> filterCache = lastFilterList.get();
        if (isSameFile(filename, filterCache)) {
            final GenericDialog gd = new GenericDialog(TITLE);
            gd.hideCancelButton();
            gd.addMessage("The same filter file was selected.");
            gd.addCheckbox("Re-use_filters", settings.reUseFilters);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                settings.reUseFilters = gd.getNextBoolean();
                if (settings.reUseFilters) {
                    SettingsManager.writeSettings(filterSettings);
                    return filterCache.getRight();
                }
            }
        }
        final File file = new File(filename);
        try (BufferedReader input = new BufferedReader(new UnicodeReader(new FileInputStream(file), null))) {
            // Use the instance so we can catch the exception
            final Object o = FilterXStreamUtils.getXStreamInstance().fromXML(input);
            if (!(o instanceof List<?>)) {
                IJ.log("No filter sets defined in the specified file: " + filename);
                return null;
            }
            SettingsManager.writeSettings(filterSettings);
            List<FilterSet> filterSets = (List<FilterSet>) o;
            if (containsStandardFilters(filterSets)) {
                IJ.log("Filter sets must contain 'Direct' filters");
                return null;
            }
            // Check they are not empty lists
            final List<FilterSet> filterSets2 = new LinkedList<>();
            for (final FilterSet filterSet : filterSets) {
                if (filterSet.size() != 0) {
                    filterSets2.add(filterSet);
                } else {
                    IJ.log("Filter set empty: " + filterSet.getName());
                }
            }
            if (filterSets2.isEmpty()) {
                IJ.log("All Filter sets are empty");
                return null;
            }
            // Maintain the same list type
            filterSets.clear();
            filterSets.addAll(filterSets2);
            // Option to enumerate filters
            filterSets = expandFilters(filterSets);
            // Save for re-use
            lastFilterList.set(Triple.of(filename, getLastModified(file), filterSets));
            return filterSets;
        } catch (final Exception ex) {
            IJ.log("Unable to load the filter sets from file: " + ex.getMessage());
        } finally {
            IJ.showStatus("");
        }
    }
    return null;
}

Example 5 with MultiPathFilter

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

the class BenchmarkFilterAnalysis method scoreFilter.

private ParameterScoreResult scoreFilter(DirectFilter filter, DirectFilter minFilter, int failCount, double residualsThreshold, double duplicateDistance, CoordinateStore coordinateStore, boolean createTextResult) {
    final MultiPathFilter multiPathFilter = new MultiPathFilter(filter, minFilter, residualsThreshold);
    final FractionClassificationResult r = multiPathFilter.fractionScoreSubset(gaResultsListToScore, createFailCounter(failCount), fitResultData.countActual, null, null, coordinateStore);
    final double score = getScore(r);
    final double criteria = getCriteria(r);
    // Create the score output
    final String text = (createTextResult && criteria >= minCriteria) ? createResult(filter, r, buildResultsPrefix2(failCount, residualsThreshold, duplicateDistance)).toString() : null;
    final double[] parameters = new double[] { failCount, residualsThreshold, duplicateDistance };
    return new ParameterScoreResult(score, criteria, parameters, text);
}