Examples with ResultsImageSettings uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageSettings used on opensource projects

Example 1 with ResultsImageSettings

use of uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageSettings in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method showPulseAnalysisDialog.

private boolean showPulseAnalysisDialog() {
    final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(title);
    gd.addMessage("Plot molecules activated after a pulse");
    String[] correctionNames = null;
    String[] assignmentNames = null;
    if (settings.channels > 1) {
        if (settings.channels == 2) {
            gd.addNumericField("Crosstalk_21", settings.ct[Settings.C21], 3);
            gd.addNumericField("Crosstalk_12", settings.ct[Settings.C12], 3);
        } else {
            for (int i = 0; i < Settings.ctNames.length; i++) {
                gd.addNumericField("Crosstalk_" + Settings.ctNames[i], settings.ct[i], 3);
            }
        }
        gd.addNumericField("Local_density_radius", settings.densityRadius, 0, 6, "nm");
        gd.addSlider("Min_neighbours", 0, 15, settings.minNeighbours);
        correctionNames = SettingsManager.getNames((Object[]) Settings.specificCorrection);
        gd.addChoice("Crosstalk_correction", correctionNames, correctionNames[settings.specificCorrectionIndex]);
        for (int c = 1; c <= settings.channels; c++) {
            gd.addSlider("Crosstalk_correction_cutoff_C" + c + " (%)", 0, 100, settings.specificCorrectionCutoff[c - 1]);
        }
        assignmentNames = SettingsManager.getNames((Object[]) Settings.nonSpecificCorrection);
        gd.addChoice("Nonspecific_assigment", assignmentNames, assignmentNames[settings.nonSpecificCorrectionIndex]);
        gd.addSlider("Nonspecific_assignment_cutoff (%)", 0, 100, settings.nonSpecificCorrectionCutoff);
    }
    resultsSettingsBuilder = SettingsManager.readResultsSettings(0).toBuilder();
    ResultsManager.addImageResultsOptions(gd, resultsSettingsBuilder, ResultsManager.FLAG_IMAGE_NO_LUT);
    final Checkbox previewCheckBox = gd.addAndGetCheckbox("Preview", false);
    final String buttonLabel = "Draw loop";
    gd.addMessage("Click '" + buttonLabel + "' to draw the current ROIs in a loop view");
    gd.addAndGetButton(buttonLabel, this::actionPerformed);
    magnificationChoice = gd.addAndGetChoice("Magnification", Settings.magnifications, settings.magnification);
    gd.addDialogListener(this::dialogItemChanged);
    gd.addOptionCollectedListener(event -> addWork(previewCheckBox.getState()));
    gd.addHelp(HelpUrls.getUrl(helpKey));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    // The dialog was OK'd so run if work was staged in the workflow.
    if (workflow.isStaged()) {
        workflow.runStaged();
    }
    // Record options for a macro since the NonBlockingDialog does not
    if (Recorder.record) {
        if (settings.channels > 1) {
            // Suppress null warnings
            if (correctionNames == null || assignmentNames == null) {
                throw new IllegalStateException();
            }
            if (settings.channels == 2) {
                Recorder.recordOption("Crosstalk_21", Double.toString(settings.ct[Settings.C21]));
                Recorder.recordOption("Crosstalk_12", Double.toString(settings.ct[Settings.C12]));
            } else {
                for (int i = 0; i < Settings.ctNames.length; i++) {
                    Recorder.recordOption("Crosstalk_" + Settings.ctNames[i], Double.toString(settings.ct[i]));
                }
            }
            Recorder.recordOption("Local_density_radius", Double.toString(settings.densityRadius));
            Recorder.recordOption("Min_neighbours", Integer.toString(settings.minNeighbours));
            Recorder.recordOption("Crosstalk_correction", correctionNames[settings.specificCorrectionIndex]);
            for (int c = 1; c <= settings.channels; c++) {
                Recorder.recordOption("Crosstalk_correction_cutoff_C" + c, Double.toString(settings.specificCorrectionCutoff[c - 1]));
            }
            Recorder.recordOption("Nonspecific_assigment", assignmentNames[settings.nonSpecificCorrectionIndex]);
            Recorder.recordOption("Nonspecific_assignment_cutoff (%)", Double.toString(settings.nonSpecificCorrectionCutoff));
        }
        final ResultsImageSettings s = resultsSettingsBuilder.getResultsImageSettings();
        Recorder.recordOption("Image", SettingsManager.getResultsImageTypeNames()[s.getImageTypeValue()]);
        if (s.getWeighted()) {
            Recorder.recordOption("Weighted");
        }
        if (s.getEqualised()) {
            Recorder.recordOption("Equalised");
        }
        Recorder.recordOption("Image_Precision", Double.toString(s.getAveragePrecision()));
        Recorder.recordOption("Image_Size_mode", SettingsManager.getResultsImageSizeModeNames()[s.getImageSizeModeValue()]);
        Recorder.recordOption("Image_Scale", Double.toString(s.getScale()));
        Recorder.recordOption("Image_Size", Integer.toString(s.getImageSize()));
        Recorder.recordOption("Image_Pixel_size", Double.toString(s.getPixelSize()));
    }
    SettingsManager.writeSettings(resultsSettingsBuilder);
    return true;
}

Example 2 with ResultsImageSettings

use of uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageSettings in project GDSC-SMLM by aherbert.

the class ResultsManager method addImageResults.

/**
 * Adds the image results.
 *
 * <p>Note: This always uses {@link ResultsImageMode#IMAGE_ADD}.
 *
 * @param resultsList the results list
 * @param resultsSettings the results settings
 * @param bounds the bounds
 * @param flags the flags
 */
public static void addImageResults(PeakResultsList resultsList, ResultsImageSettings resultsSettings, Rectangle bounds, int flags) {
    if (resultsSettings.getImageTypeValue() > 0) {
        final ResultsImageSettings.Builder builder = resultsSettings.toBuilder();
        builder.setImageMode(ResultsImageMode.IMAGE_ADD);
        final ImageJImagePeakResults image = ImagePeakResultsFactory.createPeakResultsImage(builder, resultsList.getName(), bounds, resultsList.getNmPerPixel());
        // Rolling window size is set by the factory method. Unset it if not using extra options.
        if (!BitFlagUtils.anySet(flags, FLAG_EXTRA_OPTIONS)) {
            image.setRollingWindowSize(0);
        }
        image.setRepaintDelay(2000);
        resultsList.addOutput(image);
    }
}

Example 3 with ResultsImageSettings

use of uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageSettings in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method addImageResults.

private void addImageResults(PeakResultsList resultsList, String title, Rectangle bounds, double nmPerPixel, ResultsImageSettings imageSettings) {
    if (imageSettings.getImageTypeValue() > 0) {
        final ResultsImageSettings.Builder builder = imageSettings.toBuilder();
        builder.setImageMode(ResultsImageMode.IMAGE_ADD);
        final ImageJImagePeakResults image = ImagePeakResultsFactory.createPeakResultsImage(builder, title, bounds, nmPerPixel);
        image.setLiveImage(false);
        image.setDisplayImage(settings.channels == 1);
        resultsList.addOutput(image);
    }
}