Examples with FitEngineConfiguration uk.ac.sussex.gdsc.smlm.engine.FitEngineConfiguration used on opensource projects

Example 41 with FitEngineConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitEngineConfiguration in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method resetParametersFromFitting.

private void resetParametersFromFitting() {
    final FitEngineConfiguration config = BenchmarkSpotFit.getFitEngineConfiguration();
    settings.failCount = config.getFailuresLimit();
    settings.duplicateDistance = config.getDuplicateDistance();
    settings.duplicateDistanceAbsolute = config.getDuplicateDistanceAbsolute();
    residualsThreshold = settings.residualsThreshold = (BenchmarkSpotFit.getComputeDoublets()) ? BenchmarkSpotFit.getMultiFilter().residualsThreshold : 1;
}

Example 42 with FitEngineConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitEngineConfiguration in project GDSC-SMLM by aherbert.

the class ConfigurationTemplate method createInlineTemplates.

private static Map<String, Template> createInlineTemplates() {
    final Map<String, Template> inlineTemplates = new LinkedHashMap<>();
    // Add the default.
    // This will be a simple least squares estimator applicable to non-calibrated data.
    final FitEngineConfiguration config = FitEngineConfiguration.create();
    addInlineTemplate(inlineTemplates, "Default", config);
    return inlineTemplates;
}

Example 43 with FitEngineConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitEngineConfiguration in project GDSC-SMLM by aherbert.

the class PeakFit method configureDataFilter.

/**
 * Show a dialog to configure the data filter. The data filter type and the first data filter must
 * ALREADY be set in the configuration. The subsequent filters are then configured, e.g. for
 * difference and jury filters.
 *
 * <p>The updated settings are saved to the settings file. An error message is shown if the dialog
 * is cancelled or the configuration is invalid.
 *
 * <p>If the configuration is for a per-pixel camera type (e.g. sCMOS) then the camera model will
 * be loaded using the configured camera model name. This will be used to validate the filter to
 * check the filter supports the per-pixel camera type.
 *
 * @param config the config
 * @param flags the flags
 * @return True if the configuration succeeded
 */
public static boolean configureDataFilter(final FitEngineConfiguration config, int flags) {
    // Check we have at least the first filter.
    if (config.getDataFiltersCount() == 0) {
        throw new IllegalStateException("No primary filter is configured");
    }
    int filterCount;
    switch(config.getDataFilterType()) {
        case JURY:
            filterCount = Integer.MAX_VALUE;
            break;
        case DIFFERENCE:
            filterCount = 2;
            break;
        case SINGLE:
        default:
            filterCount = 1;
            break;
    }
    int numberOfFilters = 1;
    final String[] filterNames = SettingsManager.getDataFilterMethodNames();
    final DataFilterMethod[] filterValues = SettingsManager.getDataFilterMethodValues();
    final FitEngineConfigurationProvider fitEngineConfigurationProvider = () -> config;
    for (int i = 1; i < filterCount; i++) {
        final int filter = i + 1;
        final int ii = i;
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        if (filter == filterCount) {
            // This is maximum filter count so no continue option
            ImageJUtils.addMessage(gd, "Configure the %s filter.", FitProtosHelper.getName(config.getDataFilterType()));
        } else {
            gd.enableYesNoCancel("Add", "Continue");
            ImageJUtils.addMessage(gd, "Configure the %s filter.\nClick continue to proceed with the current set of %d.", FitProtosHelper.getName(config.getDataFilterType()), i);
        }
        final String fieldName = "Spot_filter" + filter;
        if (IJ.isMacro()) {
            // Use blank default value so bad macro parameters return nothing
            gd.addStringField(fieldName, "");
        } else {
            gd.addChoice(fieldName, filterNames, filterNames[config.getDataFilterMethod(ii, config.getDataFilterMethod(ii - 1)).ordinal()]);
        }
        addRelativeParameterOptions(gd, new RelativeParameterProvider(0, 4.5, "Smoothing" + filter, fitEngineConfigurationProvider, true) {

            @Override
            void setAbsolute(boolean absolute) {
                // Get the current settings
                final FitEngineConfiguration c = fitEngineConfigurationProvider.getFitEngineConfiguration();
                final DataFilterMethod m = c.getDataFilterMethod(ii);
                final double smooth = c.getDataFilterParameter(ii).getValue();
                // Reset with the new absolute value
                c.setDataFilter(m, smooth, absolute, ii);
            }

            @Override
            boolean isAbsolute() {
                final FitEngineConfiguration c = fitEngineConfigurationProvider.getFitEngineConfiguration();
                return c.getDataFilterParameterAbsolute(ii, c.getDataFilterParameterAbsolute(ii - 1));
            }

            @Override
            double getValue() {
                final FitEngineConfiguration c = fitEngineConfigurationProvider.getFitEngineConfiguration();
                return c.getDataFilterParameterValue(ii, c.getDataFilterParameterValue(ii - 1));
            }
        });
        gd.showDialog();
        if (gd.wasCanceled()) {
            return false;
        }
        if (gd.wasOKed()) {
            int filterIndex = -1;
            if (IJ.isMacro()) {
                final String filterName = gd.getNextString();
                for (int j = 0; j < filterNames.length; j++) {
                    if (filterNames[j].equals(filterName)) {
                        filterIndex = j;
                        break;
                    }
                }
                if (filterIndex < 0) {
                    break;
                }
            } else {
                filterIndex = gd.getNextChoiceIndex();
            }
            // Note: The absolute flag is set in extra options
            config.setDataFilter(filterValues[filterIndex], Math.abs(gd.getNextNumber()), i);
            gd.collectOptions();
            numberOfFilters++;
        } else {
            break;
        }
    }
    config.setNumberOfFilters(numberOfFilters);
    if (BitFlagUtils.anyNotSet(flags, FLAG_NO_SAVE)) {
        saveFitEngineSettings(config);
    }
    final FitConfiguration fitConfig = config.getFitConfiguration();
    final CalibrationReader calibration = fitConfig.getCalibrationReader();
    if (calibration.isScmos()) {
        fitConfig.setCameraModel(CameraModelManager.load(fitConfig.getCameraModelName()));
    }
    try {
        config.createSpotFilter();
    } catch (final IllegalStateException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    return true;
}