diff --git a/src/main/java/results/EasyDisplay.java b/src/main/java/results/EasyDisplay.java
index e870312..cd4c2c5 100644
--- a/src/main/java/results/EasyDisplay.java
+++ b/src/main/java/results/EasyDisplay.java
@@ -1,85 +1,90 @@
package results;
import algorithms.Histogram2D;
import gadgets.DataContainer;
import ij.IJ;
import ij.ImagePlus;
import ij.text.TextWindow;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.math.ImageStatistics;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.RealType;
public class EasyDisplay<T extends RealType<T>> implements ResultHandler<T> {
// the text window to present value and text results
protected static TextWindow textWindow;
/* the data container with general information about the
* source images that were processed by the algorithms.
*/
protected DataContainer<T> container;
public EasyDisplay(DataContainer<T> container) {
final int twWidth = 170;
final int twHeight = 250;
//test if the results windows is already there, if so use it.
if (textWindow == null || !textWindow.isVisible())
textWindow = new TextWindow("Results",
"Result\tValue\n", "", twWidth, twHeight);
else {
// set dimensions
textWindow.setSize(twWidth, twHeight);
}
// deactivate the window for now
textWindow.setVisible(false);
// save a reference to the data container
this.container = container;
}
public void handleImage(RandomAccessibleInterval<T> image, String name) {
ImagePlus imp = ImageJFunctions.wrapFloat( image, name );
double max = ImageStatistics.getImageMax( image ).getRealDouble();
showImage( imp, max );
}
public void handleHistogram(Histogram2D<T> histogram, String name) {
ImagePlus imp = ImageJFunctions.wrapFloat( histogram.getPlotImage(), name );
double max = ImageStatistics.getImageMax( histogram.getPlotImage() ).getRealDouble();
showImage( imp, max );
}
protected void showImage(ImagePlus imp, double max) {
// set the display range
imp.setDisplayRange(0.0, max);
imp.show();
}
public void handleWarning(Warning warning) {
// no warnings are shown in easy display
}
+ @Override
+ public void handleValue(String name, String value) {
+ textWindow.getTextPanel().appendLine(name + "\t"
+ + value + "\n");
+ }
+
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
public void handleValue(String name, double value, int decimals) {
- textWindow.getTextPanel().appendLine(name + "\t"
- + IJ.d2s(value, decimals) + "\n");
+ handleValue(name, IJ.d2s(value, decimals));
}
protected void printTextStatistics(DataContainer<T> container){
textWindow.getTextPanel().appendLine("Ch1 Mean\t" + container.getMeanCh1() + "\n");
textWindow.getTextPanel().appendLine("Ch2 Mean\t" + container.getMeanCh2() + "\n");
textWindow.getTextPanel().appendLine("Ch1 Min\t" + container.getMinCh1() + "\n");
textWindow.getTextPanel().appendLine("Ch2 Min\t" + container.getMinCh2() + "\n");
textWindow.getTextPanel().appendLine("Ch1 Max\t" + container.getMaxCh1() + "\n");
textWindow.getTextPanel().appendLine("Ch2 Max\t" + container.getMaxCh2() + "\n");
}
public void process() {
// print some general information about images
printTextStatistics(container);
// show the results
textWindow.setVisible(true);
IJ.selectWindow("Results");
}
}
diff --git a/src/main/java/results/PDFWriter.java b/src/main/java/results/PDFWriter.java
index 3db95cb..faa8e81 100644
--- a/src/main/java/results/PDFWriter.java
+++ b/src/main/java/results/PDFWriter.java
@@ -1,223 +1,229 @@
package results;
import algorithms.Histogram2D;
import com.itextpdf.text.BadElementException;
import com.itextpdf.text.Document;
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.PageSize;
import com.itextpdf.text.Paragraph;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfWriter;
import gadgets.DataContainer;
import gadgets.DataContainer.MaskType;
import ij.IJ;
import ij.ImagePlus;
import ij.io.SaveDialog;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.math.ImageStatistics;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
public class PDFWriter<T extends RealType<T>> implements ResultHandler<T> {
// indicates if we want to produce US letter or A4 size
boolean isLetter = false;
// indicates if the content is the first item on the page
boolean isFirst = true;
// show the name of the image
static boolean showName=true;
// a static counter for this sessions created PDFs
static int succeededPrints = 0;
// show the size in pixels of the image
static boolean showSize=true;
// a reference to the data container
DataContainer<T> container;
PdfWriter writer;
Document document;
// a list of the available result images, no matter what specific kinds
protected List<com.itextpdf.text.Image> listOfPDFImages
= new ArrayList<com.itextpdf.text.Image>();
protected List<Paragraph> listOfPDFTexts
= new ArrayList<Paragraph>();
/**
* Creates a new PDFWriter that can access the container.
*
* @param container The data container for source image data
*/
public PDFWriter(DataContainer<T> container) {
this.container = container;
}
public void handleImage(RandomAccessibleInterval<T> image, String name) {
ImagePlus imp = ImageJFunctions.wrapFloat( image, name );
// set the display range
double max = ImageStatistics.getImageMax(image).getRealDouble();
imp.setDisplayRange(0.0, max);
addImageToList(imp, name);
}
/**
* Handles a histogram the following way: create snapshot, log data, reset the
* display range, apply the Fire LUT and finally store it as an iText PDF image.
* Afterwards the image is reset to its orignal state again
*/
public void handleHistogram(Histogram2D<T> histogram, String name) {
RandomAccessibleInterval<LongType> image = histogram.getPlotImage();
ImagePlus imp = ImageJFunctions.wrapFloat( image, name );
// make a snapshot to be able to reset after modifications
imp.getProcessor().snapshot();
imp.getProcessor().log();
imp.updateAndDraw();
imp.getProcessor().resetMinAndMax();
IJ.run(imp,"Fire", null);
addImageToList(imp, name);
// reset the imp from the log scaling we applied earlier
imp.getProcessor().reset();
}
protected void addImageToList(ImagePlus imp, String name) {
java.awt.Image awtImage = imp.getImage();
try {
com.itextpdf.text.Image pdfImage = com.itextpdf.text.Image.getInstance(awtImage, null);
pdfImage.setAlt(name); // iText-1.3 setMarkupAttribute("name", name);
listOfPDFImages.add(pdfImage);
}
catch (BadElementException e) {
IJ.log("Could not convert image to correct format for PDF generation");
IJ.handleException(e);
}
catch (IOException e) {
IJ.log("Could not convert image to correct format for PDF generation");
IJ.handleException(e);
}
}
public void handleWarning(Warning warning) {
listOfPDFTexts.add(new Paragraph("Warning! " + warning.getShortMessage() + " - " + warning.getLongMessage()));
}
+ @Override
+ public void handleValue(String name, String value) {
+ // send (output parameter name, value) to IJ.log for scraping batch results
+ IJ.log(name + ", " + value);
+ listOfPDFTexts.add(new Paragraph(name + ": " + value));
+ }
+
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
public void handleValue(String name, double value, int decimals) {
//send (output parameter name, value) to IJ.log for scraping batch results
- IJ.log(name + ", "+ IJ.d2s(value, decimals));
- listOfPDFTexts.add(new Paragraph(name + ": " + IJ.d2s(value, decimals)));
+ handleValue(name, IJ.d2s(value, decimals));
}
/**
* Prints an image into the opened PDF.
* @param img The image to print.
* @param printName The name to print under the image.
*/
protected void addImage(com.itextpdf.text.Image image)
throws DocumentException, IOException {
if (! isFirst) {
document.add(new Paragraph("\n"));
float vertPos = writer.getVerticalPosition(true);
if (vertPos - document.bottom() < image.getHeight()) {
document.newPage();
} else {
PdfContentByte cb = writer.getDirectContent();
cb.setLineWidth(1f);
if (isLetter) {
cb.moveTo(PageSize.LETTER.getLeft(50), vertPos);
cb.lineTo(PageSize.LETTER.getRight(50), vertPos);
} else {
cb.moveTo(PageSize.A4.getLeft(50), vertPos);
cb.lineTo(PageSize.A4.getRight(50), vertPos);
}
cb.stroke();
}
}
if (showName) {
Paragraph paragraph = new Paragraph(image.getAlt()); // iText-1.3: getMarkupAttribute("name"));
paragraph.setAlignment(Paragraph.ALIGN_CENTER);
document.add(paragraph);
//spcNm = 40;
}
if (showSize) {
Paragraph paragraph = new Paragraph(image.getWidth() + " x " + image.getHeight());
paragraph.setAlignment(Paragraph.ALIGN_CENTER);
document.add(paragraph);
//spcSz = 40;
}
image.setAlignment(com.itextpdf.text.Image.ALIGN_CENTER);
document.add(image);
isFirst = false;
}
public void process() {
try {
// produce default name
String nameCh1 = container.getSourceImage1Name();
String nameCh2 = container.getSourceImage2Name();
////send names of the 2 images to IJ.log for scraping batch results
IJ.log("ImageNames" + ", " + nameCh1 + ", " + nameCh2);
String name = "coloc_" + nameCh1 + "_" + nameCh2;
/* If a mask is in use, add a counter
* information to the name.
*/
if (container.getMaskType() != MaskType.None) {
name += "_mask_"+ (succeededPrints + 1);
}
// get the path to the file we are about to create
SaveDialog sd = new SaveDialog("Save as PDF", name, ".pdf");
name = sd.getFileName();
String directory = sd.getDirectory();
// make sure we got what we need
if ((name == null) || (directory == null)) {
return;
}
String path = directory+name;
// create a new iText Document and add date and title
document = new Document(isLetter ? PageSize.LETTER : PageSize.A4);
document.addCreationDate();
document.addTitle(name);
// get a writer object to do the actual output
writer = PdfWriter.getInstance(document, new FileOutputStream(path));
document.open();
// iterate over all produced images
for (com.itextpdf.text.Image img : listOfPDFImages) {
addImage(img);
}
//send name of analysis job to IJ.log for scraping batch results
IJ.log("ColocAnalysisJobName" + ", " + name);
//iterate over all produced text objects
for (Paragraph p : listOfPDFTexts) {
document.add(p);
}
} catch(DocumentException de) {
IJ.showMessage("PDF Writer", de.getMessage());
} catch(IOException ioe) {
IJ.showMessage("PDF Writer", ioe.getMessage());
} finally {
if (document !=null) {
document.close();
succeededPrints++;
}
}
}
}
diff --git a/src/main/java/results/ResultHandler.java b/src/main/java/results/ResultHandler.java
index c2d2ac4..ae8b932 100644
--- a/src/main/java/results/ResultHandler.java
+++ b/src/main/java/results/ResultHandler.java
@@ -1,32 +1,34 @@
package results;
import algorithms.Histogram2D;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.numeric.RealType;
/**
* A result handler offers different methods to process results
* of algorithms. Algorithms get passed such a result handler and
* can let the handler process whatever information they like.
*
* @param <T> The source images value type
*/
public interface ResultHandler<T extends RealType<T>> {
void handleImage(RandomAccessibleInterval<T> image, String name);
void handleHistogram(Histogram2D<T> histogram, String name);
void handleWarning(Warning warning);
+ void handleValue(String name, String value);
+
void handleValue(String name, double value);
void handleValue(String name, double value, int decimals);
/**
* The process method should start the processing of the
* previously collected results. E.g. it could show some
* windows or produce a final zip file.
*/
void process();
}
diff --git a/src/main/java/results/SingleWindowDisplay.java b/src/main/java/results/SingleWindowDisplay.java
index b843dd8..68e7a93 100644
--- a/src/main/java/results/SingleWindowDisplay.java
+++ b/src/main/java/results/SingleWindowDisplay.java
@@ -1,637 +1,646 @@
package results;
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 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.JScrollPane;
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){
super("Colocalisation " + container.getSourceImage1Name() + " vs " +
container.getSourceImage2Name());
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() {
public void actionPerformed(ActionEvent e) {
showList();
}
});
buttons.add(listButton);
// add button for data copy of histograms
copyButton = new JButton("Copy");
copyButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
copyToClipboard();
}
});
buttons.add(copyButton);
// add button for PDF printing
JButton pdfButten = new JButton("PDF");
pdfButten.addActionListener(new ActionListener() {
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;
pane.add(imagePanel, c);
c.gridy++; c.weighty = 1;
pane.add(scrollPane, c);
c.weighty = 0; c.gridy++;
pane.add(buttons, c);
pack();
}
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() ) );
}
// create HTML table
makeHtmlText();
// set up the GUI
setup();
// display the first image available, if any
if (listOfImages.size() > 0) {
adjustDisplayedImage(listOfImages.get(0).object);
}
// show the GUI
this.setVisible(true);
}
public void handleImage(RandomAccessibleInterval<T> image, String name) {
listOfImages.add( new NamedContainer<RandomAccessibleInterval<? extends RealType<?>> >(
image, name ) );
}
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");
}
public void handleWarning(Warning warning) {
warnings.add( warning );
}
+ @Override
+ public void handleValue(String name, String value) {
+ valueResults.add( new ValueResult(name, value));
+ }
+
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
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");
}
/**
* Prints an HTML table entry onto the stream.
*/
protected void printTableRow(PrintWriter out, String name, double number) {
printTableRow(out, name, number, 3);
}
/**
* 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;}"
+ "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 occured</H1>");
}
// print out simple value results
out.print("<H1>Results</H1>");
// Print out the table
out.print("<TABLE><TR>");
out.print("<TH>Name</TH><TH>Result</TH></TR>");
for ( ValueResult vr : valueResults) {
- printTableRow(out, vr.name, vr.number, vr.decimals);
+ if (vr.isNumber) {
+ printTableRow(out, vr.name, vr.number, vr.decimals);
+ } else {
+ printTableRow(out, vr.name, vr.value);
+ }
}
out.println("</TABLE>");
// print some image statistics
out.print("<H1>Image statistics</H1>");
out.print("<TABLE>");
printTableRow(out, "Min channel 1", dataContainer.getMinCh1());
printTableRow(out, "Max channel 1", dataContainer.getMaxCh1());
printTableRow(out, "Mean channel 1", dataContainer.getMeanCh1());
printTableRow(out, "Min channel 2", dataContainer.getMinCh2());
printTableRow(out, "Max channel 2", dataContainer.getMaxCh2());
printTableRow(out, "Mean channel 2", dataContainer.getMeanCh2());
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();
}
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();
}
public void actionPerformed(ActionEvent e) {
if (e.getSource() == log) {
toggleLogarithmic(log.isSelected());
}
}
public void lostOwnership(Clipboard clipboard, Transferable contents) {
// nothing to do here
}
}
diff --git a/src/main/java/results/ValueResult.java b/src/main/java/results/ValueResult.java
index 75322cb..0148008 100644
--- a/src/main/java/results/ValueResult.java
+++ b/src/main/java/results/ValueResult.java
@@ -1,17 +1,26 @@
package results;
/**
* A small structure to keep decimal places information
- * with numbers along with a name.
+ * with numbers along with a name or a simple named text.
*/
public class ValueResult {
public String name;
public double number;
public int decimals;
+ public String value;
+ public boolean isNumber;
public ValueResult( String name, double number, int decimals ) {
this.name = name;
this.number = number;
this.decimals = decimals;
+ this.isNumber = true;
+ }
+
+ public ValueResult( String name, String value) {
+ this.name = name;
+ this.value = value;
+ this.isNumber = false;
}
}