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

Example 51 with GenericDialog

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

the class About method installResource.

/**
	 * @param resource
	 * @param ijDirectory
	 * @param destinationName
	 * @param resourceTitle
	 * @param notes
	 * @param options
	 * @return -1 on error, 0 if installed, 1 if removed
	 */
private static int installResource(String resource, String ijDirectory, String destinationName, String resourceTitle, String notes, ConfigureOption... options) {
    Class<About> resourceClass = About.class;
    InputStream toolsetStream = resourceClass.getResourceAsStream(resource);
    if (toolsetStream == null)
        return -1;
    String dir = IJ.getDirectory(ijDirectory);
    if (dir == null) {
        IJ.error("Unable to locate " + ijDirectory + " directory");
        return -1;
    }
    EnumSet<ConfigureOption> opt = EnumSet.of(options[0], options);
    GenericDialog gd = new GenericDialog(TITLE);
    String filename = dir + destinationName;
    boolean fileExists = new File(filename).exists();
    StringBuilder sb = new StringBuilder();
    sb.append("Configure resource '").append(resourceTitle).append("' at:\n \n").append(filename);
    if (notes != null)
        sb.append("\n \n").append(XmlUtils.lineWrap(notes, 80, 0, null));
    gd.addMessage(sb.toString());
    // Configure the options
    String[] choices = new String[3];
    ConfigureOption[] optChoices = new ConfigureOption[choices.length];
    int count = 0;
    if (opt.contains(ConfigureOption.INSTALL)) {
        choices[count] = ConfigureOption.INSTALL.toString();
        if (fileExists)
            choices[count] += " (overwrite)";
        optChoices[count] = ConfigureOption.INSTALL;
        count++;
    }
    if (opt.contains(ConfigureOption.EDIT)) {
        choices[count] = ConfigureOption.EDIT.toString();
        if (fileExists)
            choices[count] += " (overwrite)";
        optChoices[count] = ConfigureOption.EDIT;
        count++;
    }
    if (opt.contains(ConfigureOption.REMOVE) && fileExists) {
        choices[count] = ConfigureOption.REMOVE.toString();
        optChoices[count] = ConfigureOption.REMOVE;
        count++;
    }
    if (count == 0)
        return -1;
    choices = Arrays.copyOf(choices, count);
    gd.addChoice("Option", choices, choices[0]);
    gd.showDialog();
    if (gd.wasCanceled())
        return -1;
    ConfigureOption choice = optChoices[gd.getNextChoiceIndex()];
    if (choice == ConfigureOption.REMOVE) {
        try {
            new File(filename).delete();
            return 1;
        } catch (SecurityException e) {
            IJ.error("Unable to remove existing file");
        }
        return -1;
    }
    // Read the file
    LinkedList<String> contents = new LinkedList<String>();
    BufferedReader input = null;
    try {
        // Read
        input = new BufferedReader(new UnicodeReader(toolsetStream, null));
        String line;
        while ((line = input.readLine()) != null) {
            contents.add(line);
        }
    } catch (IOException e) {
        IJ.error("Unable to install " + resourceTitle + ".\n \n" + e.getMessage());
        return -1;
    } finally {
        close(input);
    }
    if (choice == ConfigureOption.EDIT) {
        // Allow the user to edit the file contents
        gd = new GenericDialog(TITLE);
        gd.addMessage("Edit the file contents before install:");
        sb.setLength(0);
        for (String line : contents) sb.append(line).append("\n");
        gd.addTextAreas(sb.toString(), null, 20, 80);
        gd.showDialog();
        if (gd.wasOKed()) {
            contents.clear();
            String text = gd.getNextText();
            for (String line : text.split("\n")) contents.add(line);
        }
    }
    // Install the file
    BufferedWriter output = null;
    try {
        // Write
        FileOutputStream fos = new FileOutputStream(filename);
        output = new BufferedWriter(new OutputStreamWriter(fos, "UTF-8"));
        for (String content : contents) {
            output.write(content);
            output.newLine();
        }
    } catch (IOException e) {
        IJ.error("Unable to install " + resourceTitle + ".\n \n" + e.getMessage());
    } finally {
        close(output);
    }
    return 0;
}

Example 52 with GenericDialog

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

the class BatchPeakFit method showDialog.

/**
	 * Ask for parameters
	 * 
	 * @return True if not cancelled
	 */
private boolean showDialog() {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addStringField("Config_filename", configFilename);
    gd.addCheckbox("Create_config_file", false);
    if (Utils.isShowGenericDialog()) {
        configFilenameText = (TextField) gd.getStringFields().get(0);
        configFilenameText.setColumns(30);
        configFilenameText.addMouseListener(this);
        Checkbox cb = (Checkbox) gd.getCheckboxes().get(0);
        cb.addItemListener(this);
    }
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    configFilename = gd.getNextString().trim();
    return true;
}

Example 53 with GenericDialog

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

the class About method showAbout.

public static void showAbout() {
    // Locate the README.txt file and load that into the dialog. Include revision
    Class<About> resourceClass = About.class;
    InputStream readmeStream = resourceClass.getResourceAsStream("/gdsc/smlm/README.txt");
    StringBuilder msg = new StringBuilder();
    String helpURL = HELP_URL;
    String version = Version.getVersion();
    String buildDate = Version.getBuildDate();
    BufferedReader input = null;
    try {
        // Read the contents of the README file
        input = new BufferedReader(new UnicodeReader(readmeStream, null));
        String line;
        while ((line = input.readLine()) != null) {
            if (line.contains("http:")) {
                helpURL = line;
            } else {
                if (line.equals(""))
                    // Required to insert a line in the GenericDialog
                    line = " ";
                msg.append(line).append("\n");
            }
        }
    } catch (IOException e) {
        // Default message
        msg.append("GDSC SMLM Plugins for ImageJ\n");
        msg.append(" \n");
        msg.append("Copyright (C) ").append(YEAR).append(" Alex Herbert\n");
        msg.append("MRC Genome Damage and Stability Centre\n");
        msg.append("University of Sussex, UK\n");
    } finally {
        try {
            input.close();
        } catch (IOException e) {
        }
    }
    // Build final message
    msg = new StringBuilder(msg.toString().trim());
    if (version != Version.UNKNOWN || buildDate != Version.UNKNOWN)
        msg.append("\n \n");
    if (version != Version.UNKNOWN)
        msg.append("Version : ").append(version).append("\n");
    if (buildDate != Version.UNKNOWN)
        msg.append("Build Date : ").append(buildDate).append("\n");
    if (helpURL != null)
        msg.append("\n \n(Click help for more information)");
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage(msg.toString());
    gd.addHelp(helpURL);
    gd.hideCancelButton();
    gd.showDialog();
}

Example 54 with GenericDialog

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

the class BenchmarkFilterAnalysis method showIterationDialog.

private boolean showIterationDialog() {
    GenericDialog gd = new GenericDialog(TITLE);
    StringBuilder sb = new StringBuilder();
    sb.append("Iterate ").append(BenchmarkSpotFit.TITLE).append(" & ").append(TITLE).append(".\n");
    sb.append(BenchmarkSpotFit.TITLE).append(" will be run once interactively if results cannot be loaded.\n");
    sb.append(TITLE).append(" will be run once interactively to obtain settings.\n \n");
    sb.append("Configure the convergence criteria for iteration:");
    gd.addMessage(sb.toString());
    gd.addNumericField("Score_Tolerance", iterationScoreTolerance, -1);
    gd.addNumericField("Filter_Tolerance", iterationFilterTolerance, -1);
    gd.addCheckbox("Compare_Results", iterationCompareResults);
    gd.addNumericField("Compare_Distance", iterationCompareDistance, 2);
    gd.addNumericField("Iter_Max_Iterations", iterationMaxIterations, 0);
    gd.addMessage("Configure how the parameter range is updated per iteration:");
    gd.addSlider("Min_range_reduction", 0, 1, iterationMinRangeReduction);
    gd.addSlider("Min_range_reduction_iteration", 1, 10, iterationMinRangeReductionIteration);
    gd.addCheckbox("Converge_before_refit", iterationConvergeBeforeRefit);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    iterationScoreTolerance = gd.getNextNumber();
    iterationFilterTolerance = gd.getNextNumber();
    iterationCompareResults = gd.getNextBoolean();
    iterationCompareDistance = Math.abs(gd.getNextNumber());
    iterationMaxIterations = (int) gd.getNextNumber();
    iterationMinRangeReduction = Math.abs(gd.getNextNumber());
    iterationMinRangeReductionIteration = (int) Math.abs(gd.getNextNumber());
    iterationConvergeBeforeRefit = gd.getNextBoolean();
    return true;
}

Example 55 with GenericDialog

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

the class BenchmarkFilterAnalysis method showScoreDialog.

private boolean showScoreDialog() {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    addSimulationData(gd);
    // Get the last scored filter or default to the best filter
    getScoreFilter();
    gd.addSlider("Fail_count", 0, 20, scoreFailCount);
    if (BenchmarkSpotFit.computeDoublets)
        gd.addSlider("Residuals_threshold", 0.01, 1, scoreResidualsThreshold);
    gd.addNumericField("Duplicate_distance", scoreDuplicateDistance, 2);
    gd.addTextAreas(XmlUtils.convertQuotes(scoreFilter.toXML()), null, 6, 60);
    gd.addCheckbox("Reset_filter", false);
    //gd.addCheckbox("Show_table", showResultsTable);
    gd.addCheckbox("Show_summary", showSummaryTable);
    gd.addCheckbox("Clear_tables", clearTables);
    //gd.addSlider("Summary_top_n", 0, 20, summaryTopN);
    gd.addCheckbox("Save_best_filter", saveBestFilter);
    gd.addCheckbox("Save_template", saveTemplate);
    gd.addCheckbox("Calculate_sensitivity", calculateSensitivity);
    gd.addSlider("Delta", 0.01, 1, delta);
    if (!simulationParameters.fixedDepth)
        gd.addCheckbox("Depth_recall_analysis", depthRecallAnalysis);
    gd.addCheckbox("Score_analysis", scoreAnalysis);
    gd.addChoice("Component_analysis", COMPONENT_ANALYSIS, COMPONENT_ANALYSIS[componentAnalysis]);
    gd.addStringField("Title", resultsTitle, 20);
    String[] labels = { "Show_TP", "Show_FP", "Show_FN" };
    gd.addCheckboxGroup(1, 3, labels, new boolean[] { showTP, showFP, showFN });
    // Dialog to have a reset checkbox. This reverts back to the default.
    if (Utils.isShowGenericDialog()) {
        final Checkbox cb = (Checkbox) (gd.getCheckboxes().get(0));
        @SuppressWarnings("unchecked") final Vector<TextField> v = gd.getNumericFields();
        final TextArea ta = gd.getTextArea1();
        cb.addItemListener(new ItemListener() {

            public void itemStateChanged(ItemEvent e) {
                if (cb.getState()) {
                    scoreFilter = null;
                    getScoreFilter();
                    int i = 0;
                    v.get(i++).setText(Integer.toString(scoreFailCount));
                    if (BenchmarkSpotFit.computeDoublets)
                        v.get(i++).setText(Double.toString(scoreResidualsThreshold));
                    v.get(i++).setText(Double.toString(scoreDuplicateDistance));
                    ta.setText(XmlUtils.convertQuotes(scoreFilter.toXML()));
                }
            }
        });
    }
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    scoreFailCount = (int) Math.abs(gd.getNextNumber());
    if (BenchmarkSpotFit.computeDoublets)
        scoreResidualsThreshold = Math.abs(gd.getNextNumber());
    scoreDuplicateDistance = Math.abs(gd.getNextNumber());
    String xml = gd.getNextText();
    try {
        scoreFilter = (DirectFilter) DirectFilter.fromXML(xml);
    } catch (Exception e) {
        scoreFilter = null;
        getScoreFilter();
    }
    boolean reset = gd.getNextBoolean();
    if (reset) {
        scoreFilter = null;
        getScoreFilter();
    }
    //showResultsTable = gd.getNextBoolean();
    showSummaryTable = gd.getNextBoolean();
    clearTables = gd.getNextBoolean();
    //summaryTopN = (int) Math.abs(gd.getNextNumber());
    saveBestFilter = gd.getNextBoolean();
    saveTemplate = gd.getNextBoolean();
    calculateSensitivity = gd.getNextBoolean();
    delta = gd.getNextNumber();
    if (!simulationParameters.fixedDepth)
        depthRecallAnalysis = gd.getNextBoolean();
    scoreAnalysis = gd.getNextBoolean();
    componentAnalysis = gd.getNextChoiceIndex();
    resultsTitle = gd.getNextString();
    showTP = gd.getNextBoolean();
    showFP = gd.getNextBoolean();
    showFN = gd.getNextBoolean();
    if (gd.invalidNumber())
        return false;
    resultsPrefix = BenchmarkSpotFit.resultPrefix + "\t" + resultsTitle + "\t";
    createResultsPrefix2(scoreFailCount, scoreResidualsThreshold, scoreDuplicateDistance);
    // Check there is one output
    if (!showSummaryTable && !calculateSensitivity && !saveBestFilter && !saveTemplate) {
        IJ.error(TITLE, "No output selected");
        return false;
    }
    // Check arguments
    try {
        Parameters.isAboveZero("Delta", delta);
        Parameters.isBelow("Delta", delta, 1);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    if (!selectTableColumns())
        return false;
    return true;
}