diff --git a/src/main/java/results/SingleWindowDisplay.java b/src/main/java/results/SingleWindowDisplay.java
index 5c83bf0..7f79514 100644
--- a/src/main/java/results/SingleWindowDisplay.java
+++ b/src/main/java/results/SingleWindowDisplay.java
@@ -1,677 +1,677 @@
package results;
import java.awt.BorderLayout;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Panel;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.ClipboardOwner;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingConstants;
import javax.swing.border.EmptyBorder;
import algorithms.AutoThresholdRegression;
import algorithms.Histogram2D;
import fiji.util.gui.JImagePanel;
import gadgets.DataContainer;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.gui.Line;
import ij.gui.Overlay;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
/**
* This class displays the container contents in one single window and offers
* features like the use of different LUTs.
*
*/
public class SingleWindowDisplay<T extends RealType<T>> extends JFrame
implements ResultHandler<T>, ItemListener, ActionListener, ClipboardOwner, MouseMotionListener {
private static final long serialVersionUID = -5642321584354176878L;
protected static final int WIN_WIDTH = 350;
protected static final int WIN_HEIGHT = 600;
// a static list for keeping track of all other SingleWindowDisplays
protected static ArrayList<SingleWindowDisplay<?>> displays = new ArrayList<SingleWindowDisplay<?>>();
// indicates if original images should be displayed or not
protected boolean displayOriginalImages = false;
// this is the image currently selected by the drop down menu
protected RandomAccessibleInterval<? extends RealType<?>> currentlyDisplayedImageResult;
// a list of the available result images, no matter what specific kinds
protected List<NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>> listOfImages = new ArrayList<NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>>();
protected Map<RandomAccessibleInterval<LongType>, Histogram2D<T>> mapOf2DHistograms = new HashMap<RandomAccessibleInterval<LongType>, Histogram2D<T>>();
// a list of warnings
protected List<Warning> warnings = new ArrayList<Warning>();
// a list of named values, collected from algorithms
protected List<ValueResult> valueResults = new ArrayList<ValueResult>();
/*
* a map of images and corresponding LUTs. When an image is not in there no
* LUT should be applied.
*/
protected Map<Object, String> listOfLUTs = new HashMap<Object, String>();
// make a cursor so we can get pixel values from the image
protected RandomAccess<? extends RealType<?>> pixelAccessCursor;
// A PDF writer to call if user wants PDF print
protected PDFWriter<T> pdfWriter;
// The current image
protected ImagePlus imp;
// GUI elements
protected JImagePanel imagePanel;
protected JButton listButton, copyButton;
protected JCheckBox log;
/*
* The data container with general information about source images
*/
protected DataContainer<T> dataContainer = null;
public SingleWindowDisplay(DataContainer<T> container, PDFWriter<T> pdfWriter) {
// Show job name in title bar
super(container.getJobName());
setPreferredSize(new Dimension(WIN_WIDTH, WIN_HEIGHT));
// save a reference to the container
dataContainer = container;
this.pdfWriter = pdfWriter;
// don't show ourself on instantiation
this.setVisible(false);
// add ourself to the list of single window displays
displays.add(this);
}
public void setup() {
JComboBox dropDownList = new JComboBox();
for (NamedContainer<RandomAccessibleInterval<? extends RealType<?>>> img : listOfImages) {
dropDownList
.addItem(new NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>(img.object, img.name));
}
dropDownList.addItemListener(this);
imagePanel = new JImagePanel(ij.IJ.createImage("dummy", "8-bit", 10, 10, 1));
imagePanel.addMouseMotionListener(this);
// Create something to display it in
final JEditorPane editor = new JEditorPane();
editor.setEditable(false); // we're browsing not editing
editor.setContentType("text/html"); // must specify HTML text
editor.setText(makeHtmlText()); // specify the text to display
// Put the JEditorPane in a scrolling window and add it
JScrollPane scrollPane = new JScrollPane(editor);
scrollPane.setPreferredSize(new Dimension(256, 150));
Panel buttons = new Panel();
buttons.setLayout(new FlowLayout(FlowLayout.RIGHT));
// add button for data display of histograms
listButton = new JButton("List");
listButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
showList();
}
});
buttons.add(listButton);
// add button for data copy of histograms
copyButton = new JButton("Copy");
copyButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
copyToClipboard();
}
});
buttons.add(copyButton);
// add button for PDF printing
JButton pdfButten = new JButton("PDF");
pdfButten.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
pdfWriter.process();
}
});
buttons.add(pdfButten);
/*
* We want the image to be log scale by default so the user can see
* something.
*/
log = new JCheckBox("Log");
log.setSelected(true);
log.addActionListener(this);
buttons.add(log);
final GridBagLayout layout = new GridBagLayout();
final Container pane = getContentPane();
getContentPane().setLayout(layout);
final GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.BOTH;
c.weightx = 1;
c.gridwidth = GridBagConstraints.BOTH;
c.gridy++;
pane.add(dropDownList, c);
c.gridy++;
c.weighty = 1;
// code to include axis labels
JPanel imageAndLabelPanel = new JPanel();
imageAndLabelPanel.setLayout(new BorderLayout());
imageAndLabelPanel.add(imagePanel, BorderLayout.CENTER);
JLabel yAxisLabel = new JLabel(labelName(2, dataContainer.getSourceCh2Name()));
yAxisLabel.setHorizontalAlignment(SwingConstants.RIGHT);
yAxisLabel.setBorder(new EmptyBorder(0, 15, 0, 0));
imageAndLabelPanel.add(yAxisLabel, BorderLayout.WEST);
JLabel xAxisLabel = new JLabel(labelName(1, dataContainer.getSourceCh1Name()));
xAxisLabel.setHorizontalAlignment(SwingConstants.CENTER);
xAxisLabel.setBorder(new EmptyBorder(0, 0, 15, 0));
imageAndLabelPanel.add(xAxisLabel, BorderLayout.SOUTH);
pane.add(imageAndLabelPanel, c);
c.gridy++;
c.weighty = 1;
pane.add(scrollPane, c);
c.weighty = 0;
c.gridy++;
pane.add(buttons, c);
pack();
}
private String labelName(int ch, String s) {
final int maxLen = 30;
final String shortName = s.length() > maxLen ? //
s.substring(0, maxLen - 3) + "..." : s;
return "<html><center>Channel " + ch + "<br>(" + shortName + ")</center>";
}
@Override
public void process() {
// if wanted, display source images
if (displayOriginalImages) {
listOfImages.add(new NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>(
dataContainer.getSourceImage1(), dataContainer.getSourceImage1Name()));
listOfImages.add(new NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>(
dataContainer.getSourceImage2(), dataContainer.getSourceImage2Name()));
}
// set up the GUI, which runs makeHtmlText() for the value results
// formatting.
setup();
// display the first image available, if any
if (listOfImages.size() > 0) {
adjustDisplayedImage(listOfImages.get(0).object);
}
// show the GUI
this.setVisible(true);
}
@Override
public void handleImage(RandomAccessibleInterval<T> image, String name) {
listOfImages.add(new NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>(image, name));
}
@Override
public void handleHistogram(Histogram2D<T> histogram, String name) {
listOfImages.add(
new NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>(histogram.getPlotImage(), name));
mapOf2DHistograms.put(histogram.getPlotImage(), histogram);
// link the histogram to a LUT
listOfLUTs.put(histogram.getPlotImage(), "Fire");
}
@Override
public void handleWarning(Warning warning) {
warnings.add(warning);
}
@Override
public void handleValue(String name, String value) {
valueResults.add(new ValueResult(name, value));
}
@Override
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
@Override
public void handleValue(String name, double value, int decimals) {
valueResults.add(new ValueResult(name, value, decimals));
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, String text) {
- out.print("<TR><TD>" + name + "</TD><TD>" + text + "</TD></TR");
+ out.print("<TR><TD>" + name + "</TD><TD>" + text + "</TD></TR>");
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, double number, int decimalPlaces) {
printTableRow(out, name, IJ.d2s(number, decimalPlaces));
}
/**
* This method creates CSS formatted HTML source out of the results stored
* in the member variables and adds some image statistics found in the data
* container.
*
* @return The HTML source to display
*/
protected String makeHtmlText() {
StringWriter sout = new StringWriter();
PrintWriter out = new PrintWriter(sout);
out.print("<html><head>");
// add some style information
out.print("<style type=\"text/css\">" + "body {font-size: 9px; font-family: sans-serif;}"
+ "h1 {color: black; font-weight: bold; font-size: 10px;}" + "h1.warn {color: red;}"
+ "h1.nowarn {color: green;}" + "h1.results {color: black;}" + "table {width: auto;}"
+ "td { border-width:1px; border-style: solid; vertical-align:top; overflow:hidden;}" + "</style>");
out.print("</head>");
// print out warnings, if any
if (warnings.size() > 0) {
out.print("<H1 class=\"warn\">Warnings</H1>");
// Print out the table
out.print("<TABLE class=\"warn\"><TR>");
out.print("<TH>Type</TH><TH>Message</TH></TR>");
for (Warning w : warnings) {
printTableRow(out, w.getShortMessage(), w.getLongMessage());
}
out.println("</TABLE>");
} else {
out.print("<H1 class=\"nowarn\">No warnings occurred.</H1>");
}
// Spit warnings to the IJ log
IJ.log("!!! WARNINGS !!!");
for (Warning war : warnings) {
IJ.log("Warning! " + war.getShortMessage() + " - " + war.getLongMessage());
}
// print out simple value results
out.print("<H1 class=\"results\">Results</H1>");
// Print out the table
// out.print("<TABLE><TR>");
out.print("<TABLE class=\"results\"><TR>");
out.print("<TH>Name</TH><TH>Result</TH></TR>");
// Print table rows and spit results to the IJ log.
IJ.log("RESULTS:");
for (ValueResult vr : valueResults) {
if (vr.isNumber) {
printTableRow(out, vr.name, vr.number, vr.decimals);
IJ.log(vr.name + ", " + IJ.d2s(vr.number, vr.decimals));
} else {
printTableRow(out, vr.name, vr.value);
IJ.log(vr.name + ", " + vr.value);
}
}
out.println("</TABLE>");
out.print("</html>");
out.close();
// Get the string of HTML from the StringWriter and return it.
return sout.toString();
}
/**
* 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);
}
}
/**
* If the currently selected ImageResult is an HistogramRestult, this method
* copies its data into to the clipboard.
*/
protected void copyToClipboard() {
/*
* check if we are dealing with an histogram result or a generic image
* result
*/
if (isHistogram(currentlyDisplayedImageResult)) {
/*
* try to get the system clipboard and return if we can't get it
*/
Clipboard systemClipboard = null;
try {
systemClipboard = getToolkit().getSystemClipboard();
} catch (Exception e) {
systemClipboard = null;
}
if (systemClipboard == null) {
IJ.error("Unable to copy to Clipboard.");
return;
}
// copy histogram values
IJ.showStatus("Copying histogram values...");
String text = mapOf2DHistograms.get(currentlyDisplayedImageResult).getData();
StringSelection contents = new StringSelection(text);
systemClipboard.setContents(contents, this);
IJ.showStatus(text.length() + " characters copied to Clipboard");
}
}
@Override
public void mouseDragged(MouseEvent e) {
// nothing to do here
}
@Override
public void mouseMoved(MouseEvent e) {
if (e.getSource().equals(imagePanel)) {
/*
* calculate the mouse position relative to the upper left corner of
* the displayed image.
*/
final int imgWidth = imagePanel.getSrcRect().width;
final int imgHeight = imagePanel.getSrcRect().height;
int displayWidth = (int) (imgWidth * imagePanel.getMagnification());
int displayHeight = (int) (imgHeight * imagePanel.getMagnification());
int offsetX = (imagePanel.getWidth() - displayWidth) / 2;
int offsetY = (imagePanel.getHeight() - displayHeight) / 2;
int onImageX = imagePanel.screenX(e.getX() - offsetX);
int onImageY = imagePanel.screenY(e.getY() - offsetY);
// make sure we stay within the image boundaries
if (onImageX >= 0 && onImageX < imgWidth && onImageY >= 0 && onImageY < imgHeight) {
mouseMoved(onImageX, onImageY);
} else {
IJ.showStatus("");
}
}
}
/**
* Displays information about the pixel below the mouse cursor of the
* currently displayed image result. The coordinates passed are expected to
* be within the image boundaries.
*
* @param x
* @param y
*/
public void mouseMoved(int x, int y) {
final ImageJ ij = IJ.getInstance();
if (ij != null && currentlyDisplayedImageResult != null) {
/*
* If Alt key is not pressed, display the calibrated data. If not,
* display image positions and data. Non log image intensity from
* original image or 2D histogram result is always shown in status
* bar, not the log intensity that might actually be displayed in
* the image.
*/
if (!IJ.altKeyDown()) {
// the alt key is not pressed use x and y values that are bin
// widths or calibrated intensities not the x y image
// coordinates.
if (isHistogram(currentlyDisplayedImageResult)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(currentlyDisplayedImageResult);
synchronized (pixelAccessCursor) {
// set position of output cursor
pixelAccessCursor.setPosition(x, 0);
pixelAccessCursor.setPosition(y, 1);
// for a histogram coordinate display we need to invert
// the Y axis
y = (int) currentlyDisplayedImageResult.dimension(1) - 1 - y;
// get current value at position
RandomAccess<LongType> cursor = (RandomAccess<LongType>) pixelAccessCursor;
long val = cursor.get().getIntegerLong();
double calibratedXBinBottom = histogram.getXMin() + x / histogram.getXBinWidth();
double calibratedXBinTop = histogram.getXMin() + (x + 1) / histogram.getXBinWidth();
double calibratedYBinBottom = histogram.getYMin() + y / histogram.getYBinWidth();
double calibratedYBinTop = histogram.getYMin() + (y + 1) / histogram.getYBinWidth();
IJ.showStatus("x = " + IJ.d2s(calibratedXBinBottom) + " to " + IJ.d2s(calibratedXBinTop)
+ ", y = " + IJ.d2s(calibratedYBinBottom) + " to " + IJ.d2s(calibratedYBinTop)
+ ", value = " + val);
}
} else {
RandomAccessibleInterval<T> img = (RandomAccessibleInterval<T>) currentlyDisplayedImageResult;
ImagePlus imp = ImageJFunctions.wrapFloat(img, "TODO");
imp.mouseMoved(x, y);
}
} else {
// alt key is down, so show the image coordinates for x y in
// status bar.
RandomAccessibleInterval<T> img = (RandomAccessibleInterval<T>) currentlyDisplayedImageResult;
ImagePlus imp = ImageJFunctions.wrapFloat(img, "TODO");
imp.mouseMoved(x, y);
}
}
}
/**
* Draws the passed ImageResult on the ImagePlus of this class. If the image
* is part of a CompositeImageResult then contained lines will also be drawn
*/
protected void drawImage(RandomAccessibleInterval<? extends RealType<?>> img) {
// get ImgLib image as ImageJ image
imp = ImageJFunctions.wrapFloat((RandomAccessibleInterval<T>) img, "TODO");
imagePanel.updateImage(imp);
// set the display range
// check if a LUT should be applied
if (listOfLUTs.containsKey(img)) {
// select linked look up table
IJ.run(imp, listOfLUTs.get(img), null);
}
imp.getProcessor().resetMinAndMax();
boolean overlayModified = false;
Overlay overlay = new Overlay();
// if it is the 2d histogram, we want to show the regression line
if (isHistogram(img)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(img);
/*
* check if we should draw a regression line for the current
* histogram.
*/
if (histogram.getDrawingSettings().contains(Histogram2D.DrawingFlags.RegressionLine)) {
AutoThresholdRegression<T> autoThreshold = dataContainer.getAutoThreshold();
if (histogram != null && autoThreshold != null) {
if (img == histogram.getPlotImage()) {
drawLine(overlay, img, autoThreshold.getAutoThresholdSlope(),
autoThreshold.getAutoThresholdIntercept());
overlayModified = true;
}
}
}
}
if (overlayModified) {
overlay.setStrokeColor(java.awt.Color.WHITE);
imp.setOverlay(overlay);
}
imagePanel.repaint();
}
/**
* Tests whether the given image is a histogram or not.
*
* @param img
* The image to test
* @return true if histogram, false otherwise
*/
protected boolean isHistogram(RandomAccessibleInterval<? extends RealType<?>> img) {
return mapOf2DHistograms.containsKey(img);
}
/**
* Draws the line on the overlay.
*/
protected void drawLine(Overlay overlay, RandomAccessibleInterval<? extends RealType<?>> img, double slope,
double intercept) {
double startX, startY, endX, endY;
long imgWidth = img.dimension(0);
long imgHeight = img.dimension(1);
/*
* since we want to draw the line over the whole image we can directly
* use screen coordinates for x values.
*/
startX = 0.0;
endX = imgWidth;
// check if we can get some exta information for drawing
if (isHistogram(img)) {
Histogram2D<T> histogram = mapOf2DHistograms.get(img);
// get calibrated start y coordinates
double calibratedStartY = slope * histogram.getXMin() + intercept;
double calibratedEndY = slope * histogram.getXMax() + intercept;
// convert calibrated coordinates to screen coordinates
startY = calibratedStartY * histogram.getYBinWidth();
endY = calibratedEndY * histogram.getYBinWidth();
} else {
startY = slope * startX + intercept;
endY = slope * endX + intercept;
}
/*
* since the screen origin is in the top left of the image, we need to
* x-mirror our line
*/
startY = (imgHeight - 1) - startY;
endY = (imgHeight - 1) - endY;
// create the line ROI and add it to the overlay
Line lineROI = new Line(startX, startY, endX, endY);
/*
* Set drawing width of line to one, in case it has been changed
* globally.
*/
lineROI.setStrokeWidth(1.0f);
overlay.add(lineROI);
}
protected void adjustDisplayedImage(RandomAccessibleInterval<? extends RealType<?>> img) {
/*
* when changing the result image to display need to set the image we
* were looking at back to not log scale, so we don't log it twice if
* its reselected.
*/
if (log.isSelected())
toggleLogarithmic(false);
currentlyDisplayedImageResult = img;
pixelAccessCursor = img.randomAccess();
// Currently disabled, due to lag of non-histograms :-)
// disable list and copy button if it is no histogram result
listButton.setEnabled(isHistogram(img));
copyButton.setEnabled(isHistogram(img));
drawImage(img);
toggleLogarithmic(log.isSelected());
// ensure a valid layout, we changed the image
getContentPane().validate();
getContentPane().repaint();
}
@Override
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.SELECTED) {
RandomAccessibleInterval<? extends RealType<?>> img = ((NamedContainer<RandomAccessibleInterval<? extends RealType<?>>>) (e
.getItem())).getObject();
adjustDisplayedImage(img);
}
}
protected void toggleLogarithmic(boolean enabled) {
if (imp == null)
return;
ImageProcessor ip = imp.getProcessor();
if (enabled) {
ip.snapshot();
ip.log();
ip.resetMinAndMax();
} else
ip.reset();
imagePanel.repaint();
}
@Override
public void actionPerformed(ActionEvent e) {
if (e.getSource() == log) {
toggleLogarithmic(log.isSelected());
}
}
@Override
public void lostOwnership(Clipboard clipboard, Transferable contents) {
// nothing to do here
}
}