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

Example 41 with GenericDialog

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

the class ConfigurationTemplate method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if ("images".equals(arg)) {
        showTemplateImages();
        return;
    }
    TITLE = "Template Configuration";
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addCheckbox("Select_standard_templates", selectStandardTemplates);
    gd.addCheckbox("Select_custom_directory", selectCustomDirectory);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    selectStandardTemplates = gd.getNextBoolean();
    selectCustomDirectory = gd.getNextBoolean();
    if (selectStandardTemplates)
        loadSelectedStandardTemplates();
    if (selectCustomDirectory)
        loadTemplatesFromDirectory();
}

Example 42 with GenericDialog

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

the class ResultsManager method addTableResults.

private void addTableResults(MemoryPeakResults results, PeakResultsList resultsList, boolean showDeviations, boolean showEndFrame) {
    if (resultsSettings.getResultsTable() != ResultsTable.NONE) {
        IJTablePeakResults r = new IJTablePeakResults(showDeviations);
        r.setPeakIdColumnName("Frame");
        r.setShowCalibratedValues(resultsSettings.getResultsTable() == ResultsTable.CALIBRATED);
        // Get a bias if required
        Calibration calibration = results.getCalibration();
        if (r.isShowCalibratedValues() && calibration.getBias() == 0) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.addMessage("Calibrated results requires a camera bias");
            gd.addNumericField("Camera_bias (ADUs)", calibration.getBias(), 2);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                calibration.setBias(Math.abs(gd.getNextNumber()));
            }
        }
        r.setShowEndFrame(showEndFrame);
        resultsList.addOutput(r);
    }
}

Example 43 with GenericDialog

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

the class ResultsManager method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (arg != null && arg.startsWith("clear")) {
        Collection<MemoryPeakResults> allResults;
        boolean removeAll = false;
        if (arg.contains("multi")) {
            MultiDialog md = new MultiDialog(TITLE, new MultiDialog.MemoryResultsItems());
            md.addSelected(selected);
            md.showDialog();
            if (md.wasCanceled())
                return;
            selected = md.getSelectedResults();
            if (selected.isEmpty())
                return;
            allResults = new ArrayList<MemoryPeakResults>(selected.size());
            for (String name : selected) {
                MemoryPeakResults r = MemoryPeakResults.getResults(name);
                if (r != null)
                    allResults.add(r);
            }
        } else {
            removeAll = true;
            allResults = MemoryPeakResults.getAllResults();
        }
        if (allResults.isEmpty())
            return;
        long memorySize = 0;
        int size = 0;
        for (MemoryPeakResults results : allResults) {
            memorySize += MemoryPeakResults.estimateMemorySize(results.getResults());
            size += results.size();
        }
        String memory = MemoryPeakResults.memorySizeString(memorySize);
        String count = Utils.pleural(size, "result");
        String sets = Utils.pleural(allResults.size(), "set");
        GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage(String.format("Do you want to remove %s from memory (%s, %s)?", count, sets, memory));
        gd.enableYesNoCancel();
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        if (removeAll)
            MemoryPeakResults.clearMemory();
        else {
            for (MemoryPeakResults results : allResults) MemoryPeakResults.removeResults(results.getName());
        }
        SummariseResults.clearSummaryTable();
        IJ.log(String.format("Cleared %s (%s, %s)", count, sets, memory));
        return;
    }
    if (!showDialog())
        return;
    MemoryPeakResults results = loadResults(inputOption);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    results = cropToRoi(results);
    if (results.size() == 0) {
        IJ.error(TITLE, "No results within the crop region");
        return;
    }
    if (resultsSettings.resultsInMemory && fileInput)
        MemoryPeakResults.addResults(results);
    IJ.showStatus("Processing outputs ...");
    Rectangle bounds = results.getBounds(true);
    boolean showDeviations = resultsSettings.showDeviations && canShowDeviations(results);
    boolean showEndFrame = canShowEndFrame(results);
    boolean showId = canShowId(results);
    // Display the configured output
    PeakResultsList outputList = new PeakResultsList();
    outputList.copySettings(results);
    //String title = results.getSource();
    //if (title == null || title.length() == 0)
    //	output.setSource(TITLE);
    addTableResults(results, outputList, showDeviations, showEndFrame);
    addImageResults(outputList, results.getName(), bounds, results.getNmPerPixel(), results.getGain());
    addFileResults(outputList, showDeviations, showEndFrame, showId);
    // Reduce to single object for speed
    PeakResults output = (outputList.numberOfOutputs() == 1) ? outputList.toArray()[0] : outputList;
    output.begin();
    // Process in batches to provide progress
    List<PeakResult> list = results.getResults();
    int progress = 0;
    int totalProgress = list.size();
    int stepProgress = Utils.getProgressInterval(totalProgress);
    TurboList<PeakResult> batch = new TurboList<PeakResult>(stepProgress);
    for (PeakResult result : list) {
        if (progress % stepProgress == 0) {
            IJ.showProgress(progress, totalProgress);
        }
        progress++;
        batch.addf(result);
        if (batch.size() == stepProgress) {
            output.addAll(batch);
            batch.clearf();
            if (isInterrupted())
                break;
        }
    }
    IJ.showProgress(1);
    output.end();
    IJ.showStatus(String.format("Processed %d result%s", results.size(), (results.size() > 1) ? "s" : ""));
}

Example 44 with GenericDialog

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

the class PSFEstimator method showDialog.

/**
	 * @param imp
	 * @return
	 */
private int showDialog(ImagePlus imp) {
    // Keep class variables for the parameters we are fitting 
    FitConfiguration fitConfig = config.getFitConfiguration();
    initialPeakStdDev0 = fitConfig.getInitialPeakStdDev0();
    initialPeakStdDev1 = fitConfig.getInitialPeakStdDev1();
    initialPeakAngle = fitConfig.getInitialAngle();
    if (!extraOptions) {
        interlacedData = false;
        integrateFrames = 1;
    }
    this.imp = imp;
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Estimate 2D Gaussian to fit maxima");
    gd.addNumericField("Initial_StdDev0", initialPeakStdDev0, 3);
    gd.addNumericField("Initial_StdDev1", initialPeakStdDev1, 3);
    gd.addNumericField("Initial_Angle", initialPeakAngle, 3);
    gd.addNumericField("Number_of_peaks", settings.numberOfPeaks, 0);
    // pValue sets the smallest significance level probability level at which they are said to be different.
    // i.e. p <= pValue they are different
    // lower pValue means harder to be found different.
    // lower pValue means easier to be found the same.
    gd.addNumericField("p-Value", settings.pValue, 4);
    gd.addCheckbox("Update_preferences", settings.updatePreferences);
    gd.addCheckbox("Log_progress", settings.debugPSFEstimator);
    gd.addCheckbox("Iterate", settings.iterate);
    gd.addCheckbox("Show_histograms", settings.showHistograms);
    gd.addNumericField("Histogram_bins", settings.histogramBins, 0);
    String[] filterTypes = SettingsManager.getNames((Object[]) DataFilterType.values());
    gd.addChoice("Spot_filter_type", filterTypes, filterTypes[config.getDataFilterType().ordinal()]);
    String[] filterNames = SettingsManager.getNames((Object[]) DataFilter.values());
    gd.addChoice("Spot_filter", filterNames, filterNames[config.getDataFilter(0).ordinal()]);
    gd.addSlider("Smoothing", 0, 2.5, config.getSmooth(0));
    gd.addSlider("Search_width", 0.5, 2.5, config.getSearch());
    gd.addSlider("Border", 0.5, 2.5, config.getBorder());
    gd.addSlider("Fitting_width", 2, 4.5, config.getFitting());
    if (extraOptions) {
        gd.addCheckbox("Interlaced_data", optionInterlacedData);
        gd.addSlider("Integrate_frames", 1, 5, optionIntegrateFrames);
    }
    gd.addMessage("--- Gaussian fitting ---");
    Component splitLabel = gd.getMessage();
    String[] solverNames = SettingsManager.getNames((Object[]) FitSolver.values());
    gd.addChoice("Fit_solver", solverNames, solverNames[fitConfig.getFitSolver().ordinal()]);
    String[] functionNames = SettingsManager.getNames((Object[]) FitFunction.values());
    gd.addChoice("Fit_function", functionNames, functionNames[fitConfig.getFitFunction().ordinal()]);
    // Parameters specific to each Fit solver are collected in a second dialog 
    gd.addNumericField("Fail_limit", config.getFailuresLimit(), 0);
    gd.addCheckbox("Include_neighbours", config.isIncludeNeighbours());
    gd.addSlider("Neighbour_height", 0.01, 1, config.getNeighbourHeightThreshold());
    gd.addSlider("Residuals_threshold", 0.01, 1, config.getResidualsThreshold());
    gd.addMessage("--- Peak filtering ---\nDiscard fits that shift; are too low; or expand/contract");
    gd.addCheckbox("Smart_filter", fitConfig.isSmartFilter());
    gd.addCheckbox("Disable_simple_filter", fitConfig.isDisableSimpleFilter());
    gd.addSlider("Shift_factor", 0.01, 2, fitConfig.getCoordinateShiftFactor());
    gd.addNumericField("Signal_strength", fitConfig.getSignalStrength(), 2);
    gd.addNumericField("Min_photons", fitConfig.getMinPhotons(), 0);
    gd.addSlider("Min_width_factor", 0, 0.99, fitConfig.getMinWidthFactor());
    gd.addSlider("Width_factor", 1.01, 5, fitConfig.getWidthFactor());
    gd.addNumericField("Precision", fitConfig.getPrecisionThreshold(), 2);
    if (gd.getLayout() != null) {
        GridBagLayout grid = (GridBagLayout) gd.getLayout();
        int xOffset = 0, yOffset = 0;
        int lastY = -1, rowCount = 0;
        for (Component comp : gd.getComponents()) {
            // Check if this should be the second major column
            if (comp == splitLabel) {
                xOffset += 2;
                yOffset -= rowCount;
            }
            // Reposition the field
            GridBagConstraints c = grid.getConstraints(comp);
            if (lastY != c.gridy)
                rowCount++;
            lastY = c.gridy;
            c.gridx = c.gridx + xOffset;
            c.gridy = c.gridy + yOffset;
            c.insets.left = c.insets.left + 10 * xOffset;
            c.insets.top = 0;
            c.insets.bottom = 0;
            grid.setConstraints(comp, c);
        }
        if (IJ.isLinux())
            gd.setBackground(new Color(238, 238, 238));
    }
    gd.showDialog();
    if (gd.wasCanceled() || !readDialog(gd))
        return DONE;
    return flags;
}

Example 45 with GenericDialog

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

the class PSFEstimator method readDialog.

private boolean readDialog(GenericDialog gd) {
    initialPeakStdDev0 = gd.getNextNumber();
    initialPeakStdDev1 = gd.getNextNumber();
    initialPeakAngle = gd.getNextNumber();
    settings.numberOfPeaks = (int) gd.getNextNumber();
    settings.pValue = gd.getNextNumber();
    settings.updatePreferences = gd.getNextBoolean();
    settings.debugPSFEstimator = gd.getNextBoolean();
    settings.iterate = gd.getNextBoolean();
    settings.showHistograms = gd.getNextBoolean();
    settings.histogramBins = (int) gd.getNextNumber();
    config.setDataFilterType(gd.getNextChoiceIndex());
    config.setDataFilter(gd.getNextChoiceIndex(), Math.abs(gd.getNextNumber()), 0);
    config.setSearch(gd.getNextNumber());
    config.setBorder(gd.getNextNumber());
    config.setFitting(gd.getNextNumber());
    if (extraOptions) {
        interlacedData = optionInterlacedData = gd.getNextBoolean();
        integrateFrames = optionIntegrateFrames = (int) gd.getNextNumber();
    }
    FitConfiguration fitConfig = config.getFitConfiguration();
    fitConfig.setFitSolver(gd.getNextChoiceIndex());
    fitConfig.setFitFunction(gd.getNextChoiceIndex());
    config.setFailuresLimit((int) gd.getNextNumber());
    config.setIncludeNeighbours(gd.getNextBoolean());
    config.setNeighbourHeightThreshold(gd.getNextNumber());
    config.setResidualsThreshold(gd.getNextNumber());
    fitConfig.setSmartFilter(gd.getNextBoolean());
    fitConfig.setDisableSimpleFilter(gd.getNextBoolean());
    fitConfig.setCoordinateShiftFactor(gd.getNextNumber());
    fitConfig.setSignalStrength(gd.getNextNumber());
    fitConfig.setMinPhotons(gd.getNextNumber());
    fitConfig.setMinWidthFactor(gd.getNextNumber());
    fitConfig.setWidthFactor(gd.getNextNumber());
    fitConfig.setPrecisionThreshold(gd.getNextNumber());
    if (gd.invalidNumber())
        return false;
    // Check arguments
    try {
        Parameters.isAboveZero("Initial SD0", initialPeakStdDev0);
        Parameters.isAboveZero("Initial SD1", initialPeakStdDev1);
        Parameters.isPositive("Initial angle", initialPeakAngle);
        Parameters.isPositive("Number of peaks", settings.numberOfPeaks);
        Parameters.isAboveZero("P-value", settings.pValue);
        Parameters.isEqualOrBelow("P-value", settings.pValue, 0.5);
        if (settings.showHistograms)
            Parameters.isAboveZero("Histogram bins", settings.histogramBins);
        Parameters.isAboveZero("Search width", config.getSearch());
        Parameters.isAboveZero("Fitting width", config.getFitting());
        Parameters.isPositive("Failures limit", config.getFailuresLimit());
        Parameters.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
        Parameters.isPositive("Residuals threshold", config.getResidualsThreshold());
        Parameters.isPositive("Coordinate Shift factor", fitConfig.getCoordinateShiftFactor());
        Parameters.isPositive("Signal strength", fitConfig.getSignalStrength());
        Parameters.isPositive("Min photons", fitConfig.getMinPhotons());
        Parameters.isPositive("Min width factor", fitConfig.getMinWidthFactor());
        Parameters.isPositive("Width factor", fitConfig.getWidthFactor());
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    if (fitConfig.getFitFunction() != FitFunction.FREE && fitConfig.getFitFunction() != FitFunction.FREE_CIRCULAR && fitConfig.getFitFunction() != FitFunction.CIRCULAR) {
        String msg = "ERROR: A width-fitting function must be selected (i.e. not fixed-width fitting)";
        IJ.error(TITLE, msg);
        log(msg);
        return false;
    }
    final String filename = SettingsManager.getSettingsFilename();
    SettingsManager.saveSettings(globalSettings, filename);
    if (!PeakFit.configureSmartFilter(globalSettings, filename))
        return false;
    if (!PeakFit.configureDataFilter(globalSettings, filename, false))
        return false;
    if (!PeakFit.configureFitSolver(globalSettings, filename, false))
        return false;
    // Extra parameters are needed for interlaced data
    if (interlacedData) {
        gd = new GenericDialog(TITLE);
        gd.addMessage("Interlaced data requires a repeating pattern of frames to process.\n" + "Describe the regular repeat of the data:\n \n" + "Start = The first frame that contains data\n" + "Block = The number of continuous frames containing data\n" + "Skip = The number of continuous frames to ignore before the next data\n \n" + "E.G. 2:9:1 = Data was imaged from frame 2 for 9 frames, 1 frame to ignore, then repeat.");
        gd.addNumericField("Start", optionDataStart, 0);
        gd.addNumericField("Block", optionDataBlock, 0);
        gd.addNumericField("Skip", optionDataSkip, 0);
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        if (!gd.wasCanceled()) {
            dataStart = (int) gd.getNextNumber();
            dataBlock = (int) gd.getNextNumber();
            dataSkip = (int) gd.getNextNumber();
            if (dataStart > 0 && dataBlock > 0 && dataSkip > 0) {
                // Store options for next time
                optionInterlacedData = true;
                optionDataStart = dataStart;
                optionDataBlock = dataBlock;
                optionDataSkip = dataSkip;
            }
        } else {
            interlacedData = false;
        }
    }
    return true;
}