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

Example 1 with YesNoCancelDialog

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

the class PeakFit method setup.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
	 */
public int setup(String arg, ImagePlus imp) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    plugin_flags = FLAGS;
    extraOptions = Utils.isExtraOptions();
    maximaIdentification = (arg != null && arg.contains("spot"));
    fitMaxima = (arg != null && arg.contains("maxima"));
    simpleFit = (arg != null && arg.contains("simple"));
    boolean runSeries = (arg != null && arg.contains("series"));
    ImageSource imageSource = null;
    if (fitMaxima) {
        imp = null;
        // The image source will be found from the peak results.
        if (!showMaximaDialog())
            return DONE;
        MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
        if (results == null || results.size() == 0) {
            IJ.error(TITLE, "No results could be loaded");
            return DONE;
        }
        // Check for single frame
        singleFrame = results.getHead().getFrame();
        for (PeakResult result : results.getResults()) {
            if (singleFrame != result.getFrame()) {
                singleFrame = 0;
                break;
            }
        }
        imageSource = results.getSource();
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else if (runSeries) {
        imp = null;
        // Select input folder
        String inputDirectory;
        inputDirectory = IJ.getDirectory("Select image series ...");
        //inputDirectory = getInputDirectory("Select image series ...");
        if (inputDirectory == null)
            return DONE;
        // Load input series ...
        SeriesOpener series;
        if (extraOptions)
            series = new SeriesOpener(inputDirectory, true, numberOfThreads);
        else
            series = new SeriesOpener(inputDirectory);
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory);
            return DONE;
        }
        SeriesImageSource seriesImageSource = new SeriesImageSource(getName(series.getImageList()), series);
        seriesImageSource.setLogProgress(true);
        if (extraOptions) {
            numberOfThreads = Math.max(1, series.getNumberOfThreads());
            seriesImageSource.setNumberOfThreads(numberOfThreads);
        }
        imageSource = seriesImageSource;
        plugin_flags |= NO_IMAGE_REQUIRED;
    } else {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }
        // Check it is not a previous result
        if (imp.getTitle().endsWith(IJImagePeakResults.IMAGE_SUFFIX)) {
            IJImageSource tmpImageSource = null;
            // Check the image to see if it has an image source XML structure in the info property
            Object o = imp.getProperty("Info");
            Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL);
            Matcher match = pattern.matcher((o == null) ? "" : o.toString());
            if (match.find()) {
                ImageSource source = ImageSource.fromXML(match.group(1));
                if (source instanceof IJImageSource) {
                    tmpImageSource = (IJImageSource) source;
                    if (!tmpImageSource.open()) {
                        tmpImageSource = null;
                    } else {
                        imp = WindowManager.getImage(tmpImageSource.getName());
                    }
                }
            }
            if (tmpImageSource == null) {
                // Look for a parent using the title
                String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - IJImagePeakResults.IMAGE_SUFFIX.length() - 1);
                ImagePlus parentImp = WindowManager.getImage(parentTitle);
                if (parentImp != null) {
                    tmpImageSource = new IJImageSource(parentImp);
                    imp = parentImp;
                }
            }
            String message = "The selected image may be a previous fit result";
            if (tmpImageSource != null) {
                // are missing
                if (!Utils.isNullOrEmpty(tmpImageSource.getName()))
                    message += " of: \n \n" + tmpImageSource.getName();
                message += " \n \nFit the parent?";
            } else
                message += " \n \nDo you want to continue?";
            YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message);
            if (tmpImageSource == null) {
                if (!d.yesPressed())
                    return DONE;
            } else {
                if (d.yesPressed())
                    imageSource = tmpImageSource;
                if (d.cancelPressed())
                    return DONE;
            }
        }
        if (imageSource == null)
            imageSource = new IJImageSource(imp);
    }
    time = -1;
    if (!initialiseImage(imageSource, getBounds(imp), false)) {
        IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName());
        return DONE;
    }
    int flags = showDialog(imp);
    if ((flags & DONE) == 0) {
        // Repeat so that we pass in the selected option for ignoring the bounds.
        // This should not be necessary since it is set within the readDialog method.
        //if (ignoreBoundsForNoise)
        //	initialiseImage(imageSource, bounds, ignoreBoundsForNoise);
        initialiseFitting();
    }
    return flags;
}

Example 2 with YesNoCancelDialog

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

the class Configuration method refreshSettings.

private void refreshSettings(String newFilename) {
    if (newFilename != null && new File(newFilename).exists()) {
        YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), TITLE, "Reload settings from file");
        d.setVisible(true);
        if (d.yesPressed()) {
            // Reload the settings and update the GUI
            // XXX : This does not deal with loading settings into fields that are not displayed,
            // e.g. for configuring the Fit Solvers. This could be done by writing into
            // a class scope settings instance (loaded in showDialog()). However the user would not 
            // see all the changes that have been written, since the later dialogs are shown depending 
            // on what options are initially configured. 
            GlobalSettings settings = SettingsManager.unsafeLoadSettings(newFilename, false);
            if (settings == null)
                return;
            FitEngineConfiguration config = settings.getFitEngineConfiguration();
            FitConfiguration fitConfig = config.getFitConfiguration();
            Calibration calibration = settings.getCalibration();
            textNmPerPixel.setText("" + calibration.getNmPerPixel());
            textGain.setText("" + calibration.getGain());
            textEMCCD.setState(calibration.isEmCCD());
            textExposure.setText("" + calibration.getExposureTime());
            textInitialPeakStdDev0.setText("" + fitConfig.getInitialPeakStdDev0());
            textInitialPeakStdDev1.setText("" + fitConfig.getInitialPeakStdDev1());
            textInitialAngleD.setText("" + fitConfig.getInitialAngle());
            textDataFilterType.select(config.getDataFilterType().ordinal());
            textDataFilter.select(config.getDataFilter(0).ordinal());
            textSmooth.setText("" + config.getSmooth(0));
            textSearch.setText("" + config.getSearch());
            textBorder.setText("" + config.getBorder());
            textFitting.setText("" + config.getFitting());
            textFitSolver.select(fitConfig.getFitSolver().ordinal());
            textFitFunction.select(fitConfig.getFitFunction().ordinal());
            textFailuresLimit.setText("" + config.getFailuresLimit());
            textIncludeNeighbours.setState(config.isIncludeNeighbours());
            textNeighbourHeightThreshold.setText("" + config.getNeighbourHeightThreshold());
            textResidualsThreshold.setText("" + config.getResidualsThreshold());
            textDuplicateDistance.setText("" + fitConfig.getDuplicateDistance());
            textCoordinateShiftFactor.setText("" + fitConfig.getCoordinateShiftFactor());
            textSignalStrength.setText("" + fitConfig.getSignalStrength());
            textMinPhotons.setText("" + fitConfig.getMinPhotons());
            textMinWidthFactor.setText("" + fitConfig.getMinWidthFactor());
            textWidthFactor.setText("" + fitConfig.getWidthFactor());
            textPrecisionThreshold.setText("" + fitConfig.getPrecisionThreshold());
        }
    }
}

Example 3 with YesNoCancelDialog

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

the class ResultsManager method addFileResults.

private void addFileResults(PeakResultsList resultsList, boolean showDeviations, boolean showEndFrame, boolean showId) {
    if (resultsSettings.resultsFilename != null && resultsSettings.resultsFilename.length() > 0) {
        // Remove extension
        resultsSettings.resultsFilename = Utils.replaceExtension(resultsSettings.resultsFilename, resultsSettings.getResultsFileFormat().getExtension());
        if (fileInput && inputFilename.equals(resultsSettings.resultsFilename)) {
            IJ.log(TITLE + ": Input and output files are the same, skipping output ...");
            return;
        }
        // Check if file exists
        File file = new File(resultsSettings.resultsFilename);
        if (file.exists()) {
            YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), TITLE, "Overwrite existing file?\n" + resultsSettings.resultsFilename);
            if (!d.yesPressed())
                return;
        }
        File parent = file.getParentFile();
        if (parent != null && parent.exists()) {
            PeakResults r;
            switch(resultsSettings.getResultsFileFormat()) {
                case GDSC_BINARY:
                    r = new BinaryFilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case GDSC_TEXT:
                    r = new FilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case MALK:
                    r = new MALKFilePeakResults(resultsSettings.resultsFilename);
                    break;
                case TSF:
                    r = new TSFPeakResultsWriter(resultsSettings.resultsFilename);
                    break;
                default:
                    throw new RuntimeException("Unsupported file format: " + resultsSettings.getResultsFileFormat());
            }
            if (r instanceof FilePeakResults) {
                FilePeakResults fr = (FilePeakResults) r;
                fr.setPeakIdColumnName("Frame");
            }
            resultsList.addOutput(r);
        }
    }
}