ij.text.TextWindow Java Examples

/**
 * Iterates on the list of TextWindows, and keeps only the ones containing a
 * non-null ResultsTable
 * 
 * @return an array containing the list of open TextWindows
 */
public static final TextWindow[] getTableWindows() 
{
    Frame[] frames = WindowManager.getNonImageWindows();
    
    ArrayList<TextWindow> windows = new ArrayList<TextWindow>(frames.length);
    
    for (Frame frame : frames) 
    {
        if (frame instanceof TextWindow) 
        {
            TextWindow tw = (TextWindow) frame;
            if (tw.getTextPanel().getResultsTable() != null) 
            {
                windows.add(tw);
            }
        }
    }
    
    return windows.toArray(new TextWindow[0]);
}
 

/**
 * Iterates on the list of TextWindows, and keeps only the ones containing a
 * non-null ResultsTable
 */
private static final TextWindow[] getTableWindows() 
{
	Frame[] frames = WindowManager.getNonImageWindows();
	
	ArrayList<TextWindow> windows = new ArrayList<TextWindow>(frames.length);
	
	for (Frame frame : frames) 
	{
		if (frame instanceof TextWindow) 
		{
			TextWindow tw = (TextWindow) frame;
			if (tw.getTextPanel().getResultsTable() != null) 
			{
				windows.add(tw);
			}
		}
	}
	
	return windows.toArray(new TextWindow[0]);
}
 

@Override
public void run(String arg0) 
{
	// Work on current image, and exit if no one is open
	this.targetImagePlus = IJ.getImage();

	// Check that a table window is open
	TextWindow[] textWindows = IJUtils.getTableWindows();
       if (textWindows.length == 0)
       {
           IJ.error("Requires at least one Table window");
           return;
       }
 		
	// Opens dialog to choose options
	createDialog();
	this.gd.showDialog();
	
	// parse dialog
	if (gd.wasCanceled())
		return;
	parseDialogOptions();
	saveDialogOptions();
	
	drawValues(this.targetImagePlus);
}
 

/**
 * analyse dialog, and setup inner fields of the class.
 */
private void parseDialogOptions() 
{
    // select the result table from its name
	String tableName = this.gd.getNextChoice();
	Frame tableFrame = WindowManager.getFrame(tableName);
	this.table = ((TextWindow) tableFrame).getTextPanel().getResultsTable();

       this.calibratedPosition = this.gd.getNextBoolean();
       this.xPosHeaderName = this.gd.getNextChoice();
       this.yPosHeaderName = this.gd.getNextChoice();
       this.xOffset = (int) this.gd.getNextNumber();
       this.yOffset = (int) this.gd.getNextNumber();
       this.valueHeaderName = this.gd.getNextChoice();
       this.pattern = this.gd.getNextString();
}
 

/**
 * If the currently selected ImageResult is an HistrogramResult, a table of
 * x-values, y-values and the counts.
 */
protected void showList() {
	/*
	 * check if we are dealing with an histogram result or a generic image
	 * result
	 */
	if (isHistogram(currentlyDisplayedImageResult)) {
		Histogram2D<T> hr = mapOf2DHistograms.get(currentlyDisplayedImageResult);
		double xBinWidth = 1.0 / hr.getXBinWidth();
		double yBinWidth = 1.0 / hr.getYBinWidth();
		// check if we have bins of size one or other ones
		boolean xBinWidthIsOne = Math.abs(xBinWidth - 1.0) < 0.00001;
		boolean yBinWidthIsOne = Math.abs(yBinWidth - 1.0) < 0.00001;
		// configure table headings accordingly
		String vHeadingX = xBinWidthIsOne ? "X value" : "X bin start";
		String vHeadingY = yBinWidthIsOne ? "Y value" : "Y bin start";
		// get the actual histogram data
		String histogramData = hr.getData();

		TextWindow tw = new TextWindow(getTitle(), vHeadingX + "\t" + vHeadingY + "\tcount", histogramData, 250,
				400);
		tw.setVisible(true);
	}
}
 

private GenericDialog createDialog()
	{
		// Get the list of windows containing tables
		TextWindow[] textWindows = getTableWindows();
		if (textWindows.length == 0)
		{
			IJ.error("Requires at least one Table window");
			return null;
		}
		String[] tableNames = new String[textWindows.length];
		for (int i = 0; i < textWindows.length; i++) {
			tableNames[i] = textWindows[i].getTitle();
//			IJ.log("Found table: " + tableNames[i]);
		}
		
		// Choose current table
		TextPanel tp = textWindows[0].getTextPanel();
		ResultsTable table = tp.getResultsTable();
		this.table = table;
		
		// Choose current heading
		String[] headings = table.getHeadings();
		String defaultHeading = headings[0];
		if (defaultHeading.equals("Label") && headings.length > 1)
		{
			defaultHeading = headings[1];
		}

		double[] extent = computeColumnExtent(table, defaultHeading);

		this.gd = new GenericDialog("Assign Measure to Label");
		gd.addChoice("Results Table:", tableNames, tableNames[0]);
		gd.addChoice("Column:", headings, defaultHeading);
		gd.addNumericField("Min Value", extent[0], this.nDigits, 10, null);
		gd.addNumericField("Max Value", extent[1], this.nDigits, 10, null);
		gd.addDialogListener(this);
		
		return gd;
	}
 

/**
 * analyse dialog, and setup inner fields of the class.
 */
private void parseDialogOptions() 
{
	String tableName = this.gd.getNextChoice();
	Frame tableFrame = WindowManager.getFrame(tableName);
	this.table = ((TextWindow) tableFrame).getTextPanel().getResultsTable();
	
	this.selectedHeaderName = this.gd.getNextChoice();
	
	this.minValue = this.gd.getNextNumber();
	this.maxValue = this.gd.getNextNumber();
}
 

@Override
public boolean dialogItemChanged(GenericDialog gd, AWTEvent evt) 
{
	if (gd.wasCanceled() || gd.wasOKed()) 
	{
		return true;
	}
	
	@SuppressWarnings({ "unchecked" })
       Vector<Choice> choices = gd.getChoices();
	if (choices == null) 
	{
		IJ.log("empty choices array...");
		return false;
	}
	
	// Change of the data table
       if (evt.getSource() == choices.get(0)) 
	{
		String tableName = ((Choice) evt.getSource()).getSelectedItem();
		Frame tableFrame = WindowManager.getFrame(tableName);
		this.table = ((TextWindow) tableFrame).getTextPanel().getResultsTable();
		
		// Choose current headings
		String[] headings = this.table.getHeadings();		
		replaceStrings(choices.get(1), headings, chooseDefaultHeading(headings, xPosHeaderName));
           replaceStrings(choices.get(2), headings, chooseDefaultHeading(headings, yPosHeaderName));
           replaceStrings(choices.get(3), headings, chooseDefaultHeading(headings, valueHeaderName));
	}
	
	return true;
}
 

@Override
public void run() {
    int stacksize = imp.getStack().getSize();

    if (imp.getStack().getSize() == 1) {
        IJ.error("You need a stack of images");
        return;
    }

    // Converter
    ImagePlusMatVectorConverter isc = new ImagePlusMatVectorConverter();
    opencv_core.MatVector mvec = isc.convert(imp,opencv_core.MatVector.class);

    if (!showDialog()) {
        return;
    }

    double[][] comparison = new double[4][stacksize * (stacksize - 1) / 2];

    opencv_core.Mat mask = new opencv_core.Mat();
    IntPointer intPtrChannels = new IntPointer(0, 1, 2);
    IntPointer intPtrHistSize = new IntPointer(hueBins, saturationBins, valueBins);
    FloatPointer fltPtrRanges = new FloatPointer(0.0f, 179.0f, 0.0f, 255.0f, 0.0f, 255.0f);
    PointerPointer ptptranges = new PointerPointer(fltPtrRanges, fltPtrRanges, fltPtrRanges);

    opencv_core.Mat hist1 = new opencv_core.Mat();
    opencv_core.Mat hist2 = new opencv_core.Mat();
    int n = 0;
    
    Mat hsv = new Mat();
    for (int i = 0; i < mvec.size() - 1; i++) {
        calcHist(mvec.get(i), 1, intPtrChannels, mask, hist1, 3, intPtrHistSize, ptptranges, true, false);
        opencv_core.normalize(hist1, hist1);
        for (int j = i + 1; j < mvec.size(); j++) {
            opencv_imgproc.cvtColor(mvec.get(j),hsv,opencv_imgproc.COLOR_BGR2HSV);
            calcHist(hsv, 1, intPtrChannels, mask, hist2, 3, intPtrHistSize, ptptranges, true, false);
            opencv_core.normalize(hist2, hist2);
            comparison[0][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CORREL);
            comparison[1][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CHISQR);
            comparison[2][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_INTERSECT);
            comparison[3][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_BHATTACHARYYA);
            n++;
        }
    }

    String headings = "Method\t";
    for (int i = 0; i < mvec.size() - 1; i++) {
        for (int j = i + 1; j < mvec.size(); j++) {
            headings = headings + (i + 1) + "-" + (j + 1) + "\t";
        }
    }
    headings = headings.substring(0, headings.lastIndexOf("\t"));
    ArrayList list = new ArrayList();

    String row1 = "Correlation\t";
    String row2 = "CHI Square\t";
    String row3 = "Intersection\t";
    String row4 = "BHATTACHARYYA\t";
    for (int i = 0; i < comparison[0].length - 1; i++) {
        row1 = row1 + comparison[0][i] + "\t";
        row2 = row2 + comparison[1][i] + "\t";
        row3 = row3 + comparison[2][i] + "\t";
        row4 = row4 + comparison[3][i] + "\t";

    }
    row1 = row1 + comparison[0][comparison[0].length - 1] ;
    row2 = row2 + comparison[1][comparison[0].length - 1];
    row3 = row3 + comparison[2][comparison[0].length - 1];
    row4 = row4 + comparison[3][comparison[0].length - 1];
    
    list.add(row1);
    list.add(row2);
    list.add(row3);
    list.add(row4);

    TextWindow textWindow = new TextWindow("Similarity Table", headings, list, 600, 400);
    textWindow.setVisible(true);

}
 

@Override
public void run() {
    int stacksize = imp.getStack().getSize();

    if (imp.getStack().getSize() == 1) {
        IJ.error("You need a stack of images");
        return;
    }

    // Converter
    ImagePlusMatVectorConverter isc = new ImagePlusMatVectorConverter();
    opencv_core.MatVector mvec = isc.convert(imp,MatVector.class);

    if (!showDialog()) {
        return;
    }

    double[][] comparison = new double[4][stacksize * (stacksize - 1) / 2];

    opencv_core.Mat mask = new opencv_core.Mat();
    IntPointer intPtrChannels = new IntPointer(0, 1, 2);
    IntPointer intPtrHistSize = new IntPointer(blueBins, greenBins, redBins);
    FloatPointer fltPtrRanges = new FloatPointer(0.0f, 255.0f, 0.0f, 255.0f, 0.0f, 255.0f);
    PointerPointer ptptranges = new PointerPointer(fltPtrRanges, fltPtrRanges, fltPtrRanges);

    opencv_core.Mat hist1 = new opencv_core.Mat();
    opencv_core.Mat hist2 = new opencv_core.Mat();
    int n = 0;
    for (int i = 0; i < mvec.size() - 1; i++) {
        calcHist(mvec.get(i), 1, intPtrChannels, mask, hist1, 3, intPtrHistSize, ptptranges, true, false);
        opencv_core.normalize(hist1, hist1);
        for (int j = i + 1; j < mvec.size(); j++) {
            calcHist(mvec.get(j), 1, intPtrChannels, mask, hist2, 3, intPtrHistSize, ptptranges, true, false);
            opencv_core.normalize(hist2, hist2);
            comparison[0][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CORREL);
            comparison[1][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_CHISQR);
            comparison[2][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_INTERSECT);
            comparison[3][n] = opencv_imgproc.compareHist(hist1, hist2, opencv_imgproc.CV_COMP_BHATTACHARYYA);
            n++;
        }
    }

    String headings = "Method\t";
    for (int i = 0; i < mvec.size() - 1; i++) {
        for (int j = i + 1; j < mvec.size(); j++) {
            headings = headings + (i + 1) + "-" + (j + 1) + "\t";
        }
    }
    headings = headings.substring(0, headings.lastIndexOf("\t"));
    ArrayList list = new ArrayList();

    String row1 = "Correlation\t";
    String row2 = "CHI Square\t";
    String row3 = "Intersection\t";
    String row4 = "BHATTACHARYYA\t";
    for (int i = 0; i < comparison[0].length - 1; i++) {
        row1 = row1 + comparison[0][i] + "\t";
        row2 = row2 + comparison[1][i] + "\t";
        row3 = row3 + comparison[2][i] + "\t";
        row4 = row4 + comparison[3][i] + "\t";

    }
    row1 = row1 + comparison[0][comparison[0].length - 1] ;
    row2 = row2 + comparison[1][comparison[0].length - 1];
    row3 = row3 + comparison[2][comparison[0].length - 1];
    row4 = row4 + comparison[3][comparison[0].length - 1];
    
    list.add(row1);
    list.add(row2);
    list.add(row3);
    list.add(row4);

    TextWindow textWindow = new TextWindow("Similarity Table", headings, list, 600, 400);
    textWindow.setVisible(true);

}
 

@Override
public void run() {
    int stacksize = imp.getStack().getSize();

    if (imp.getStack().getSize() == 1) {
        IJ.error("You need a stack of images");
        return;
    }

    // Converters
    ImagePlusMatVectorConverter isc = new ImagePlusMatVectorConverter();

    opencv_core.MatVector mvec = isc.convert(imp, MatVector.class);

    if (!showDialog()) {
        return;
    }

    // feature data
    FloatPointer featuresData = new FloatPointer((int) mvec.size() * 512);

    // Compute the histograms
    Mat mask = new Mat();
    IntPointer intPtrChannels = new IntPointer(0, 1, 2);
    IntPointer intPtrHistSize = new IntPointer(8, 8, 8);
    FloatPointer fltPtrRanges = new FloatPointer(0.0f, 255.0f, 0.0f, 255.0f, 0.0f, 255.0f);
    PointerPointer ptptranges = new PointerPointer(fltPtrRanges, fltPtrRanges, fltPtrRanges);

    Mat hist1 = new Mat();
    int n = 0;
    for (int i = 0; i < mvec.size(); i++) {
        calcHist(mvec.get(i), 1, intPtrChannels, mask, hist1, 3, intPtrHistSize, ptptranges, true, false);
        opencv_core.normalize(hist1, hist1);
        for (int j = 0; j < 512; j++) {
            featuresData.put(n, hist1.getFloatBuffer().get(j));
            n++;
        }

    }

    Mat data = new Mat((int) mvec.size(), 512, CV_32F, featuresData);

    Mat labels = new Mat();
    Mat centers = new Mat();

    opencv_core.TermCriteria tc = new opencv_core.TermCriteria(opencv_core.TermCriteria.EPS + opencv_core.TermCriteria.COUNT, 10, 1.0);

    kmeans(data, nclusters, labels, tc, 1, KMEANS_PP_CENTERS);

    String headings = "Image\t Cluster";
    ArrayList list = new ArrayList();

    String row = "";

    for (int i = 0; i < labels.rows(); i++) {
        row = imp.getStack().getSliceLabel(i + 1) + "\t" + labels.getIntBuffer().get(i);
        list.add(row);

    }

    TextWindow textWindow = new TextWindow("Clustering Table", headings, list, 600, 400);
    textWindow.setVisible(true);

}
 

@Override
public void run(String arg0) 
{
	// Work on current image, and exit if no one is open
	this.labelImagePlus = IJ.getImage();

	// Check that a table window is open
	TextWindow[] textWindows = getTableWindows();
       if (textWindows.length == 0)
       {
           IJ.error("Requires at least one Table window");
           return;
       }
       
	// Create empty result image
	initResultImage();
	
	// Opens dialog to choose options
	createDialog();
	this.gd.showDialog();
	
	// parse dialog
	if (gd.wasCanceled())
		return;
	parseDialogOptions();
	
	ImagePlus resultPlus = computeResultImage();
	if( null == resultPlus )
		return;
	
	this.resultPlus.copyScale(this.labelImagePlus);

	String newName = this.labelImagePlus.getShortTitle() + "-" + selectedHeaderName;
	resultPlus.setTitle(newName);
	resultPlus.show();
	
	// set up display 
	if (labelImagePlus.getStackSize() > 1) 
	{
		resultPlus.setSlice(labelImagePlus.getCurrentSlice());
	}
}
 

@Override
public boolean dialogItemChanged(GenericDialog gd, AWTEvent evt) 
{
	if (gd.wasCanceled() || gd.wasOKed()) 
	{
		return true;
	}
	
	@SuppressWarnings("rawtypes")
	Vector choices = gd.getChoices();
	if (choices == null) 
	{
		IJ.log("empty choices array...");
		return false;
	}
	
	// Change of the data table
       if (evt.getSource() == choices.get(0)) 
	{
		String tableName = ((Choice) evt.getSource()).getSelectedItem();
		Frame tableFrame = WindowManager.getFrame(tableName);
		this.table = ((TextWindow) tableFrame).getTextPanel().getResultsTable();
		
		// Choose current heading
		String[] headings = this.table.getHeadings();
		String defaultHeading = headings[0];
		if (defaultHeading.equals("Label") && headings.length > 1) 
		{
			defaultHeading = headings[1];
		}
		
		Choice headingChoice = (Choice) choices.get(1);
		headingChoice.removeAll();
		for (String heading : headings) 
		{
			headingChoice.add(heading);
		}
		headingChoice.select(defaultHeading);

		changeColumnHeader(defaultHeading);
	}
	
	// Change of the column heading
	if (evt.getSource() == choices.get(1)) 
	{
		String headerName = ((Choice) evt.getSource()).getSelectedItem();
           changeColumnHeader(headerName);
	}
	
	return true;
}
 

private GenericDialog createDialog()
{
	// Get the list of windows containing tables
	TextWindow[] textWindows = IJUtils.getTableWindows();
	if (textWindows.length == 0)
	{
		IJ.error("Requires at least one Table window");
		return null;
	}
	String[] tableNames = new String[textWindows.length];
	for (int i = 0; i < textWindows.length; i++) {
		tableNames[i] = textWindows[i].getTitle();
	}
	
	// Choose current table
	TextPanel tp = textWindows[0].getTextPanel();
	ResultsTable table = tp.getResultsTable();
	this.table = table;
	
	// Choose current heading
	String[] headings = table.getHeadings();
	String defaultHeading = headings[0];
	if (defaultHeading.equals("Label") && headings.length > 1)
	{
		defaultHeading = headings[1];
	}

	this.gd = new GenericDialog("Draw Text from Column");
	gd.addChoice("Results Table:", tableNames, tableNames[0]);
       gd.addCheckbox("Calibrated Position:", false);
       gd.addChoice("X-Position:", headings, defaultHeading);
       gd.addChoice("Y-Position:", headings, defaultHeading);
       gd.addNumericField("X-Offset:", this.xOffset, 0, 5, "pixels");
       gd.addNumericField("Y-Offset:", this.yOffset, 0, 5, "pixels");
       gd.addChoice("Values:", headings, defaultHeading);
       gd.addStringField("Pattern:", "%5.2f", 10);
       
       @SuppressWarnings("unchecked")
       Vector<Choice> choices = gd.getChoices();
       replaceStrings(choices.get(1), headings, chooseDefaultHeading(headings, xPosHeaderName));
       replaceStrings(choices.get(2), headings, chooseDefaultHeading(headings, yPosHeaderName));
       replaceStrings(choices.get(3), headings, chooseDefaultHeading(headings, valueHeaderName));

       gd.addDialogListener(this);
	
	return gd;
}
 

/**
 * Opens a tab or comma delimited text file.
 *
 * @param path
 *            The absolute pathname string of the file. A file open dialog
 *            is displayed if path is {@code null} or an empty string.
 * @param title
 *            The title of the window in which data is displayed. The
 *            filename is used if title is null or an empty string. To avoid
 *            windows with duplicated titles, title is made unique by
 *            {@link WindowManager} .
 * @param listener
 *            The {@link WindowListener} to be added to the window
 *            containing data if retrieval was successful. It is ignored
 *            when {@code null}.
 * @throws IOException
 *             if file could not be opened
 * @return A reference to the opened {link ResultsTable} or {@code null} if
 *         table was empty.
 *
 * @see #getTable()
 * @see ij.io.Opener#openTable(String)
 */
public static ResultsTable openAndDisplayTable(final String path, final String title, final WindowListener listener)
		throws IOException {
	ResultsTable rt = null;
	rt = ResultsTable.open(path);
	if (rt == null || rt.getCounter() == 0) // nothing to be displayed
		return null;
	rt.showRowNumbers(false);
	String rtTitle = (title != null && !title.isEmpty()) ? title : OpenDialog.getLastName();
	rtTitle = WindowManager.makeUniqueName(rtTitle);
	rt.show(rtTitle);
	final TextWindow rtWindow = (TextWindow) WindowManager.getFrame(rtTitle);
	if (rtWindow != null && listener != null)
		rtWindow.addWindowListener(listener);
	return rt;
}