Examples with ExtendedGenericDialog ij.gui.ExtendedGenericDialog used on opensource projects

Example 41 with ExtendedGenericDialog

use of ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method refreshSettings.

private void refreshSettings(String newFilename) {
    if (newFilename != null && new File(newFilename).exists()) {
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Reload settings from file");
        gd.showDialog();
        if (gd.wasOKed()) {
            // Reload the settings and update the GUI
            GlobalSettings settings = SettingsManager.unsafeLoadSettings(newFilename, false);
            if (settings == null)
                return;
            Calibration calibration = settings.getCalibration();
            refreshSettings(calibration);
            FitEngineConfiguration config = settings.getFitEngineConfiguration();
            refreshSettings(config, true);
            ResultsSettings resultsSettings = settings.getResultsSettings();
            refreshSettings(resultsSettings);
        }
    }
}

Example 42 with ExtendedGenericDialog

use of ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class PeakFit method configureFitSolver.

/**
	 * Show a dialog to configure the fit solver. The updated settings are saved to the settings file. An error
	 * message is shown if the dialog is cancelled or the configuration is invalid.
	 * 
	 * @param settings
	 * @param filename
	 * @param extraOptions
	 *            True if extra configuration options should be allowed
	 * @param ignoreCalibration
	 *            True if the calibration should not be configured
	 * @return True if the configuration succeeded
	 */
public static boolean configureFitSolver(GlobalSettings settings, String filename, boolean extraOptions, boolean ignoreCalibration) {
    FitEngineConfiguration config = settings.getFitEngineConfiguration();
    FitConfiguration fitConfig = config.getFitConfiguration();
    Calibration calibration = settings.getCalibration();
    boolean isBoundedLVM = fitConfig.getFitSolver() == FitSolver.LVM_MLE || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM_WEIGHTED;
    if (fitConfig.getFitSolver() == FitSolver.MLE) {
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Maximum Likelihood Estimation requires additional parameters");
        if (!ignoreCalibration) {
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
            gd.addCheckbox("Model_camera_noise", fitConfig.isModelCamera());
            gd.addNumericField("Read_noise (ADUs)", calibration.getReadNoise(), 2);
            gd.addNumericField("Amplification (ADU/electron)", calibration.getAmplification(), 2);
            gd.addCheckbox("EM-CCD", calibration.isEmCCD());
        }
        String[] searchNames = SettingsManager.getNames((Object[]) MaximumLikelihoodFitter.SearchMethod.values());
        gd.addChoice("Search_method", searchNames, searchNames[fitConfig.getSearchMethod().ordinal()]);
        gd.addStringField("Relative_threshold", "" + fitConfig.getRelativeThreshold());
        gd.addStringField("Absolute_threshold", "" + fitConfig.getAbsoluteThreshold());
        gd.addNumericField("Max_iterations", fitConfig.getMaxIterations(), 0);
        gd.addNumericField("Max_function_evaluations", fitConfig.getMaxFunctionEvaluations(), 0);
        if (extraOptions)
            gd.addCheckbox("Gradient_line_minimisation", fitConfig.isGradientLineMinimisation());
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        if (!ignoreCalibration) {
            calibration.setBias(Math.abs(gd.getNextNumber()));
            fitConfig.setModelCamera(gd.getNextBoolean());
            calibration.setReadNoise(Math.abs(gd.getNextNumber()));
            calibration.setAmplification(Math.abs(gd.getNextNumber()));
            calibration.setEmCCD(gd.getNextBoolean());
            fitConfig.setBias(calibration.getBias());
            fitConfig.setReadNoise(calibration.getReadNoise());
            fitConfig.setAmplification(calibration.getAmplification());
            fitConfig.setEmCCD(calibration.isEmCCD());
        }
        fitConfig.setSearchMethod(gd.getNextChoiceIndex());
        try {
            fitConfig.setRelativeThreshold(Math.abs(Double.parseDouble(gd.getNextString())));
            fitConfig.setAbsoluteThreshold(Math.abs(Double.parseDouble(gd.getNextString())));
        } catch (NumberFormatException e) {
            fitConfig.setRelativeThreshold(0);
            fitConfig.setAbsoluteThreshold(0);
        }
        fitConfig.setMaxIterations((int) gd.getNextNumber());
        fitConfig.setMaxFunctionEvaluations((int) gd.getNextNumber());
        if (extraOptions)
            fitConfig.setGradientLineMinimisation(gd.getNextBoolean());
        else
            // This option is for the Conjugate Gradient optimiser and makes it less stable
            fitConfig.setGradientLineMinimisation(false);
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
        try {
            Parameters.isAboveZero("Relative threshold", fitConfig.getRelativeThreshold());
            Parameters.isAboveZero("Absolute threshold", fitConfig.getAbsoluteThreshold());
            Parameters.isAboveZero("Max iterations", fitConfig.getMaxIterations());
            Parameters.isAboveZero("Max function evaluations", fitConfig.getMaxFunctionEvaluations());
            fitConfig.getFunctionSolver();
        } catch (IllegalArgumentException e) {
            IJ.error(TITLE, e.getMessage());
            return false;
        }
    } else if (isBoundedLVM || fitConfig.getFitSolver() == FitSolver.LVM || fitConfig.getFitSolver() == FitSolver.LVM_WEIGHTED) {
        boolean isWeightedLVM = fitConfig.getFitSolver() == FitSolver.LVM_WEIGHTED || fitConfig.getFitSolver() == FitSolver.BOUNDED_LVM_WEIGHTED;
        boolean requireGain = fitConfig.getFitSolver() == FitSolver.LVM_MLE;
        boolean requireBias = isWeightedLVM || requireGain;
        // Collect options for LVM fitting
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage(fitConfig.getFitSolver().getShortName() + " requires additional parameters");
        String[] criteriaNames = SettingsManager.getNames((Object[]) FitCriteria.values());
        gd.addChoice("Fit_criteria", criteriaNames, criteriaNames[fitConfig.getFitCriteria().ordinal()]);
        gd.addNumericField("Significant_digits", fitConfig.getSignificantDigits(), 0);
        gd.addNumericField("Coord_delta", fitConfig.getDelta(), 4);
        gd.addNumericField("Lambda", fitConfig.getLambda(), 4);
        if (extraOptions)
            gd.addNumericField("Min_iterations", fitConfig.getMinIterations(), 0);
        gd.addNumericField("Max_iterations", fitConfig.getMaxIterations(), 0);
        // Extra parameters are needed for the weighted LVM
        if (isWeightedLVM && !ignoreCalibration) {
            gd.addMessage("Weighted LVM fitting requires a CCD camera noise model");
            gd.addNumericField("Read_noise (ADUs)", calibration.getReadNoise(), 2);
        }
        if (requireBias)
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
        if (requireGain)
            gd.addNumericField("Gain (ADU/photon)", calibration.getGain(), 2);
        if (isBoundedLVM) {
            gd.addCheckbox("Use_clamping", fitConfig.isUseClamping());
            gd.addCheckbox("Dynamic_clamping", fitConfig.isUseDynamicClamping());
            if (extraOptions) {
                gd.addNumericField("Clamp_background", fitConfig.getClampBackground(), 2);
                gd.addNumericField("Clamp_signal", fitConfig.getClampSignal(), 2);
                gd.addNumericField("Clamp_angle", fitConfig.getClampAngle(), 2);
                gd.addNumericField("Clamp_x", fitConfig.getClampX(), 2);
                gd.addNumericField("Clamp_y", fitConfig.getClampY(), 2);
                gd.addNumericField("Clamp_sd0", fitConfig.getClampXSD(), 2);
                gd.addNumericField("Clamp_sd1", fitConfig.getClampYSD(), 2);
            }
        }
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        fitConfig.setFitCriteria(gd.getNextChoiceIndex());
        fitConfig.setSignificantDigits((int) gd.getNextNumber());
        fitConfig.setDelta(gd.getNextNumber());
        fitConfig.setLambda(gd.getNextNumber());
        if (extraOptions)
            fitConfig.setMinIterations((int) gd.getNextNumber());
        fitConfig.setMaxIterations((int) gd.getNextNumber());
        if (isWeightedLVM && !ignoreCalibration) {
            calibration.setReadNoise(Math.abs(gd.getNextNumber()));
        }
        if (requireBias) {
            calibration.setBias(Math.abs(gd.getNextNumber()));
            fitConfig.setBias(calibration.getBias());
        }
        if (requireGain) {
            calibration.setGain(Math.abs(gd.getNextNumber()));
            fitConfig.setGain(calibration.getGain());
        }
        if (isBoundedLVM) {
            fitConfig.setUseClamping(gd.getNextBoolean());
            fitConfig.setUseDynamicClamping(gd.getNextBoolean());
            if (extraOptions) {
                fitConfig.setClampBackground(Math.abs(gd.getNextNumber()));
                fitConfig.setClampSignal(Math.abs(gd.getNextNumber()));
                fitConfig.setClampAngle(Math.abs(gd.getNextNumber()));
                fitConfig.setClampX(Math.abs(gd.getNextNumber()));
                fitConfig.setClampY(Math.abs(gd.getNextNumber()));
                fitConfig.setClampXSD(Math.abs(gd.getNextNumber()));
                fitConfig.setClampYSD(Math.abs(gd.getNextNumber()));
            }
        }
        if (isWeightedLVM && !ignoreCalibration) {
            fitConfig.setNoiseModel(CameraNoiseModel.createNoiseModel(calibration.getReadNoise(), calibration.getBias(), calibration.isEmCCD()));
        }
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
        try {
            Parameters.isAboveZero("Significant digits", fitConfig.getSignificantDigits());
            Parameters.isAboveZero("Delta", fitConfig.getDelta());
            Parameters.isAboveZero("Lambda", fitConfig.getLambda());
            Parameters.isAboveZero("Max iterations", fitConfig.getMaxIterations());
            fitConfig.getFunctionSolver();
        } catch (IllegalArgumentException e) {
            IJ.error(TITLE, e.getMessage());
            return false;
        }
    } else if (fitConfig.getFitSolver() == FitSolver.LVM_QUASI_NEWTON) {
        // No options yet for Apache LVM fitting. Save options for consistency
        if (filename != null)
            SettingsManager.saveSettings(settings, filename);
    }
    if (config.isIncludeNeighbours()) {
        if (!fitConfig.getFunctionSolver().isBounded()) {
            IJ.error(TITLE, "Including neighbours requires a bounded fit solver");
            return false;
        }
    }
    return true;
}

Example 43 with ExtendedGenericDialog

use of ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class TraceDiffusion method checkCalibration.

/**
	 * Check the results have a calibrated exposure time and pixel pitch. If not then show a dialog to collect the
	 * calibration.
	 * 
	 * @param results
	 * @return True if calibrated
	 */
private boolean checkCalibration(MemoryPeakResults results) {
    if (results.getCalibration() == null || results.getCalibration().getExposureTime() <= 0 || results.getCalibration().getNmPerPixel() <= 0) {
        Calibration cal = results.getCalibration();
        if (cal == null)
            cal = new Calibration();
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Uncalibrated results! Please enter the calibration:");
        gd.addNumericField("Exposure_time (ms)", cal.getExposureTime(), 2);
        gd.addNumericField("Pixel_pitch (nm)", cal.getNmPerPixel(), 2);
        gd.showDialog();
        if (gd.wasCanceled() || gd.invalidNumber())
            return false;
        cal.setExposureTime(gd.getNextNumber());
        cal.setNmPerPixel(gd.getNextNumber());
        if (cal.getExposureTime() <= 0 || cal.getNmPerPixel() <= 0)
            return false;
    }
    return true;
}

Example 44 with ExtendedGenericDialog

use of ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class TraceMatchCalculator method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Compare the points in two results sets\nand compute the match statistics");
    ResultsManager.addInput(gd, "Results1", inputOption1, InputSource.MEMORY_MULTI_FRAME);
    ResultsManager.addInput(gd, "Results2", inputOption2, InputSource.MEMORY_MULTI_FRAME);
    ResultsManager.addInput(gd, "Results3", inputOption3, InputSource.NONE, InputSource.MEMORY_MULTI_FRAME);
    gd.addNumericField("Distance", dThreshold, 2);
    gd.addNumericField("Beta", beta, 2);
    gd.addCheckbox("Show_pairs", showPairs);
    gd.addChoice("Sort_pairs", SORT_OPTIONS, SORT_OPTIONS[sortIndex]);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption1 = gd.getNextChoice();
    inputOption2 = gd.getNextChoice();
    inputOption3 = gd.getNextChoice();
    dThreshold = gd.getNextNumber();
    beta = gd.getNextNumber();
    showPairs = gd.getNextBoolean();
    sortIndex = gd.getNextChoiceIndex();
    // Check arguments
    try {
        Parameters.isAboveZero("Distance threshold", dThreshold);
        Parameters.isPositive("Beta", beta);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}

Example 45 with ExtendedGenericDialog

use of ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class TraceDiffusion method readDialog.

private boolean readDialog(ExtendedGenericDialog gd) {
    settings.truncate = gd.getNextBoolean();
    settings.internalDistances = gd.getNextBoolean();
    //settings.subSampledDistances = gd.getNextBoolean();
    settings.fitLength = (int) Math.abs(gd.getNextNumber());
    settings.msdCorrection = gd.getNextBoolean();
    settings.precisionCorrection = gd.getNextBoolean();
    settings.mle = gd.getNextBoolean();
    settings.fitRestarts = (int) Math.abs(gd.getNextNumber());
    settings.jumpDistance = (int) Math.abs(gd.getNextNumber());
    minDifference = Math.abs(gd.getNextNumber());
    minFraction = Math.abs(gd.getNextNumber());
    if (extraOptions)
        myMinN = minN = (int) Math.abs(gd.getNextNumber());
    maxN = (int) Math.abs(gd.getNextNumber());
    debugFitting = gd.getNextBoolean();
    saveTraceDistances = gd.getNextBoolean();
    saveRawData = gd.getNextBoolean();
    settings.showHistograms = gd.getNextBoolean();
    title = gd.getNextString();
    if (gd.invalidNumber())
        return false;
    if (settings.showHistograms) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Select the histograms to display");
        gd.addCheckbox("Remove_outliers", settings.removeOutliers);
        gd.addNumericField("Histogram_bins", settings.histogramBins, 0);
        for (int i = 0; i < displayHistograms.length; i++) gd.addCheckbox(NAMES[i].replace(' ', '_'), displayHistograms[i]);
        gd.addCheckbox("MSD/Molecule", displayMSDHistogram);
        gd.addCheckbox("D/Molecule", displayDHistogram);
        gd.addCheckbox("Trace_length", displayTraceLength);
        gd.addCheckbox("Trace_size", displayTraceSize);
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        settings.removeOutliers = gd.getNextBoolean();
        settings.histogramBins = (int) Math.abs(gd.getNextNumber());
        for (int i = 0; i < displayHistograms.length; i++) displayHistograms[i] = gd.getNextBoolean();
        displayMSDHistogram = gd.getNextBoolean();
        displayDHistogram = gd.getNextBoolean();
        displayTraceLength = gd.getNextBoolean();
        displayTraceSize = gd.getNextBoolean();
    }
    // Check arguments
    try {
        Parameters.isAboveZero("Histogram bins", settings.histogramBins);
        Parameters.isAbove("Fit length", settings.fitLength, 1);
        Parameters.isAboveZero("Jump distance", settings.jumpDistance);
        Parameters.isEqualOrAbove("Maximum N", maxN, myMinN);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}