Examples with Label java.awt.Label used on opensource projects

Example 51 with Label

use of java.awt.Label in project GDSC-SMLM by aherbert.

the class ResultsManager method showDialog.

private boolean showDialog() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("results-manager"));
    settings = Settings.load();
    resultsSettings = SettingsManager.readResultsSettings(0).toBuilder();
    gd.addMessage("Read the Peak Results and output to a new format");
    gd.addMessage("Select the Peak Results");
    addInput(gd, INPUT_NAME, settings.inputOption, new FilenameLoadOption[] { new FilenameLoadOption(settings.inputFilename) }, InputSource.MEMORY, InputSource.FILE);
    final Choice inputChoice = gd.getLastChoice();
    addTableResultsOptions(gd, resultsSettings, FLAG_TABLE_FORMAT);
    addImageResultsOptions(gd, resultsSettings);
    addFileResultsOptions(gd, resultsSettings, 0);
    addInMemoryResultsOptions(gd, resultsSettings);
    final Label messageLabel = (Label) gd.getMessage();
    final Checkbox saveCheckbox = gd.getLastCheckbox();
    // Hide the in-memory settings if the input is not a file
    if (ImageJUtils.isShowGenericDialog()) {
        final Label saveLabel = gd.getLastLabel();
        final ItemListener listener = event -> {
            final boolean enable = INPUT_FILE.equals(inputChoice.getSelectedItem());
            if (enable != messageLabel.isVisible()) {
                messageLabel.setVisible(enable);
                saveCheckbox.setVisible(enable);
                saveLabel.setVisible(enable);
                gd.pack();
            }
        };
        // Run once to set up
        listener.itemStateChanged(null);
        inputChoice.addItemListener(listener);
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.inputOption = ResultsManager.getInputSource(gd);
    settings.inputFilename = gd.getNextString();
    resultsSettings.getResultsTableSettingsBuilder().setResultsTableFormatValue(gd.getNextChoiceIndex());
    resultsSettings.getResultsImageSettingsBuilder().setImageTypeValue(gd.getNextChoiceIndex());
    resultsSettings.getResultsFileSettingsBuilder().setFileFormatValue(gd.getNextChoiceIndex());
    resultsSettings.getResultsFileSettingsBuilder().setResultsFilename(gd.getNextString());
    resultsSettings.getResultsInMemorySettingsBuilder().setInMemory(gd.getNextBoolean());
    gd.collectOptions();
    // Check arguments
    try {
        final ResultsImageSettings.Builder imageSettings = resultsSettings.getResultsImageSettingsBuilder();
        if (imageSettings.getImageType() == ResultsImageType.DRAW_INTENSITY_AVERAGE_PRECISION || imageSettings.getImageType() == ResultsImageType.DRAW_LOCALISATIONS_AVERAGE_PRECISION) {
            ParameterUtils.isAboveZero("Image precision", imageSettings.getAveragePrecision());
        }
        ParameterUtils.isAboveZero("Image scale", imageSettings.getScale());
        if (extraOptions) {
            ParameterUtils.isPositive("Image rolling window", imageSettings.getRollingWindowSize());
        }
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    settings.save();
    SettingsManager.writeSettings(resultsSettings.build());
    return true;
}

Example 52 with Label

use of java.awt.Label in project GDSC-SMLM by aherbert.

the class PsfDrift method showHwhm.

private void showHwhm() {
    // Build a list of suitable images
    final List<String> titles = createImageList(false);
    if (titles.isEmpty()) {
        IJ.error(TITLE, "No suitable PSF images");
        return;
    }
    final GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Approximate the volume of the PSF as a Gaussian and\n" + "compute the equivalent Gaussian width.");
    settings = Settings.load();
    gd.addChoice("PSF", titles.toArray(new String[0]), settings.title);
    gd.addCheckbox("Use_offset", settings.useOffset);
    gd.addSlider("Smoothing", 0, 0.5, settings.smoothing);
    gd.addHelp(HelpUrls.getUrl("psf-hwhm"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.title = gd.getNextChoice();
    settings.useOffset = gd.getNextBoolean();
    settings.smoothing = gd.getNextNumber();
    settings.save();
    imp = WindowManager.getImage(settings.title);
    if (imp == null) {
        IJ.error(TITLE, "No PSF image for image: " + settings.title);
        return;
    }
    psfSettings = getPsfSettings(imp);
    if (psfSettings == null) {
        IJ.error(TITLE, "No PSF settings for image: " + settings.title);
        return;
    }
    final int size = imp.getStackSize();
    final ImagePsfModel psf = createImagePsf(1, size, 1);
    final double[] w0 = psf.getAllHwhm0();
    final double[] w1 = psf.getAllHwhm1();
    // Get current centre
    final int centre = psfSettings.getCentreImage();
    // Extract valid values (some can be NaN)
    double[] sw0 = new double[w0.length];
    double[] sw1 = new double[w1.length];
    final TDoubleArrayList s0 = new TDoubleArrayList(w0.length);
    final TDoubleArrayList s1 = new TDoubleArrayList(w0.length);
    int c0 = 0;
    int c1 = 0;
    for (int i = 0; i < w0.length; i++) {
        if (Double.isFinite(w0[i])) {
            s0.add(i + 1);
            sw0[c0++] = w0[i];
        }
        if (Double.isFinite(w1[i])) {
            s1.add(i + 1);
            sw1[c1++] = w1[i];
        }
    }
    if (c0 == 0 && c1 == 0) {
        IJ.error(TITLE, "No computed HWHM for image: " + settings.title);
        return;
    }
    double[] slice0 = s0.toArray();
    sw0 = Arrays.copyOf(sw0, c0);
    double[] slice1 = s1.toArray();
    sw1 = Arrays.copyOf(sw1, c1);
    // Smooth
    if (settings.smoothing > 0) {
        final LoessInterpolator loess = new LoessInterpolator(settings.smoothing, 1);
        sw0 = loess.smooth(slice0, sw0);
        sw1 = loess.smooth(slice1, sw1);
    }
    final TDoubleArrayList minWx = new TDoubleArrayList();
    final TDoubleArrayList minWy = new TDoubleArrayList();
    for (int i = 0; i < w0.length; i++) {
        double weight = 0;
        if (Double.isFinite(w0[i])) {
            if (Double.isFinite(w1[i])) {
                weight = w0[i] * w1[i];
            } else {
                weight = w0[i] * w0[i];
            }
        } else if (Double.isFinite(w1[i])) {
            weight = w1[i] * w1[i];
        }
        if (weight != 0) {
            minWx.add(i + 1);
            minWy.add(Math.sqrt(weight));
        }
    }
    // Smooth the combined line
    final double[] cx = minWx.toArray();
    double[] cy = minWy.toArray();
    if (settings.smoothing > 0) {
        final LoessInterpolator loess = new LoessInterpolator(settings.smoothing, 1);
        cy = loess.smooth(cx, cy);
    }
    final int newCentre = SimpleArrayUtils.findMinIndex(cy);
    // Convert to FWHM
    final double fwhm = psfSettings.getFwhm();
    // Widths are in pixels
    final String title = TITLE + " HWHM";
    final Plot plot = new Plot(title, "Slice", "HWHM (px)");
    double[] limits = MathUtils.limits(sw0);
    limits = MathUtils.limits(limits, sw1);
    final double maxY = limits[1] * 1.05;
    plot.setLimits(1, size, 0, maxY);
    plot.setColor(Color.red);
    plot.addPoints(slice0, sw0, Plot.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(slice1, sw1, Plot.LINE);
    plot.setColor(Color.magenta);
    plot.addPoints(cx, cy, Plot.LINE);
    plot.setColor(Color.black);
    plot.addLabel(0, 0, "X=red; Y=blue, Combined=Magenta");
    final PlotWindow pw = ImageJUtils.display(title, plot);
    // Show a non-blocking dialog to allow the centre to be updated ...
    // Add a label and dynamically update when the centre is moved.
    final NonBlockingExtendedGenericDialog gd2 = new NonBlockingExtendedGenericDialog(TITLE);
    final double scale = psfSettings.getPixelSize();
    // @formatter:off
    ImageJUtils.addMessage(gd2, "Update the PSF information?\n \n" + "Current z-centre = %d, FHWM = %s px (%s nm)\n", centre, MathUtils.rounded(fwhm), MathUtils.rounded(fwhm * scale));
    // @formatter:on
    gd2.addSlider("z-centre", cx[0], cx[cx.length - 1], newCentre);
    final TextField tf = gd2.getLastTextField();
    gd2.addMessage("");
    gd2.addAndGetButton("Reset", event -> tf.setText(Integer.toString(newCentre)));
    final Label label = gd2.getLastLabel();
    gd2.addCheckbox("Update_centre", settings.updateCentre);
    gd2.addCheckbox("Update_HWHM", settings.updateHwhm);
    gd2.enableYesNoCancel();
    gd2.hideCancelButton();
    final UpdateDialogListener dl = new UpdateDialogListener(cx, cy, maxY, newCentre, scale, pw, label);
    gd2.addDialogListener(dl);
    gd.addHelp(HelpUrls.getUrl("psf-hwhm"));
    gd2.showDialog();
    if (gd2.wasOKed() && (settings.updateCentre || settings.updateHwhm)) {
        final ImagePSF.Builder b = psfSettings.toBuilder();
        if (settings.updateCentre) {
            b.setCentreImage(dl.centre);
        }
        if (settings.updateHwhm) {
            b.setFwhm(dl.getFwhm());
        }
        imp.setProperty("Info", ImagePsfHelper.toString(b));
    }
}

Example 53 with Label

use of java.awt.Label in project GDSC-SMLM by aherbert.

the class PeakFit method addRelativeParameterOptions.

/**
 * Adds the relative parameter options.
 *
 * @param gd the dialog
 * @param rp the relative parameter
 */
static void addRelativeParameterOptions(final ExtendedGenericDialog gd, final RelativeParameterProvider rp) {
    final String label = rp.getDialogName();
    gd.addSlider(label, rp.getMin(), rp.getMax(), rp.getValue(), new OptionListener<Double>() {

        @Override
        public boolean collectOptions(Double value) {
            // Nothing depends on the input double value so just collect the options
            return collectOptions(false);
        }

        @Override
        public boolean collectOptions() {
            return collectOptions(true);
        }

        private boolean collectOptions(boolean silent) {
            final ExtendedGenericDialog egd = new ExtendedGenericDialog(rp.name + " Options", null);
            final boolean oldValue = rp.isAbsolute();
            egd.addCheckbox(rp.getDialogName() + "_absolute", oldValue);
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            final boolean newValue = egd.getNextBoolean();
            rp.setAbsolute(newValue);
            return oldValue != newValue;
        }
    });
    // Add a label after the button.
    // The button is added in a panel with a GridBagLayout.
    final Panel p = gd.getLastPanel();
    final GridBagConstraints pc = new GridBagConstraints();
    pc.gridy = 0;
    pc.gridx = 3;
    pc.insets = new Insets(5, 5, 0, 0);
    pc.anchor = GridBagConstraints.EAST;
    final Label flagLabel = new Label();
    updateFlag(flagLabel, rp.isAbsolute());
    p.add(flagLabel, pc);
    gd.addOptionCollectedListener(event -> {
        if (label.equals(event.getLabel())) {
            updateFlag(flagLabel, rp.isAbsolute());
        }
    });
}

Example 54 with Label

use of java.awt.Label in project mzmine2 by mzmine.

the class FeatureOverviewWindow method addFeatureDataSummary.

private JPanel addFeatureDataSummary(PeakListRow row) {
    JPanel featureDataSummary = new JPanel(new GridLayout(0, 1));
    featureDataSummary.setBackground(Color.WHITE);
    featureDataSummary.add(new Label("Feature: " + row.getID()));
    if (row.getPreferredPeakIdentity() != null)
        featureDataSummary.add(new Label("Identity: " + row.getPreferredPeakIdentity().getName()));
    if (row.getComment() != null)
        featureDataSummary.add(new Label("Comment: " + row.getComment()));
    featureDataSummary.add(new Label("Raw File: " + rawFiles[0].getName()));
    featureDataSummary.add(new Label("Intensity: " + MZmineCore.getConfiguration().getIntensityFormat().format(feature.getHeight())));
    featureDataSummary.add(new Label("Area: " + MZmineCore.getConfiguration().getIntensityFormat().format(feature.getArea())));
    featureDataSummary.add(new Label("Charge: " + feature.getCharge()));
    featureDataSummary.add(new Label("m/z: " + MZmineCore.getConfiguration().getMZFormat().format(feature.getMZ())));
    featureDataSummary.add(new Label("Retention time: " + MZmineCore.getConfiguration().getRTFormat().format(feature.getRT())));
    featureDataSummary.add(new Label("Asymmetry factor " + MZmineCore.getConfiguration().getRTFormat().format(feature.getAsymmetryFactor())));
    featureDataSummary.add(new Label("Tailing Factor factor " + MZmineCore.getConfiguration().getRTFormat().format(feature.getTailingFactor())));
    featureDataSummary.add(new Label("Status: " + feature.getFeatureStatus()));
    return featureDataSummary;
}