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OrientationJ/src/orientationj/MeasureDialog.java
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MeasureDialog.java
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//==============================================================================
//
// Project: Directional Image Analysis - OrientationJ plugin
//
// Author: Daniel Sage
//
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Information:
// OrientationJ: http://bigwww.epfl.ch/demo/orientation/
// MonogenicJ: http://bigwww.epfl.ch/demo/monogenic/
//
//
// Reference on methods and plugin
// Z. Püspöki, M. Storath, D. Sage, M. Unser
// "Transforms and Operators for Directional Bioimage Analysis: A Survey,"
// Advances in Anatomy, Embryology and Cell Biology, vol. 219, Focus on Bio-Image Informatics,
// Springer International Publishing, ch. 3, pp. 69-93, May 21, 2016.
//
// Reference on applications
// E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Ruefenacht, N. Stergiopulos
// "Effect of Aging on Elastin Functionality in Human Cerebral Arteries,"
// Stroke, vol. 40, no. 7, pp. 2552-2556, July 2009.
//
// R. Rezakhaniha, A. Agianniotis, J.T.C. Schrauwen, A. Griffa, D. Sage, C.V.C. Bouten, F.N. van de Vosse, M. Unser, N. Stergiopulos
// "Experimental Investigation of Collagen Waviness and Orientation in the Arterial Adventitia Using Confocal Laser Scanning Microscopy,"
// Biomechanics and Modeling in Mechanobiology, vol. 11, no. 3-4, pp. 461-473, 2012.
// Conditions of use: You'll be free to use this software for research purposes,
// but you should not redistribute it without our consent. In addition, we
// expect you to include a citation or acknowledgment whenever you present or
// publish results that are based on it.
//
// History:
// - Updated (Daniel Sage, 24 January 2011)
// - Added the Vector field (Daniel Sage, 1 March 2017)
//
//==============================================================================
package orientationj;
import java.awt.Cursor;
import java.awt.Polygon;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JFrame;
import additionaluserinterface.GridPanel;
import additionaluserinterface.GridToolbar;
import additionaluserinterface.Settings;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.GUI;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.Roi;
import ij.gui.StackWindow;
import ij.process.ByteBlitter;
import ij.process.ByteProcessor;
import ij.process.ImageProcessor;
import orientation.Gradient;
import orientation.GroupImage;
import orientation.OrientationParameters;
import orientation.OrientationService;
import orientation.StructureTensor;
public class MeasureDialog extends JFrame implements ActionListener, Runnable {
private WalkBarOrientationJ walk = new WalkBarOrientationJ();
private Settings settings = new Settings("OrientationJ", IJ.getDirectory("plugins") + "OrientationJ.txt");
private Table table;
private MeasureCanvas canvas;
private ImageCanvas canvasSaved;
private JButton bnCopy = new JButton("Copy Results");
private JButton bnRemove = new JButton("Remove");
private JButton bnMeasure = new JButton("Measure");
private JButton bnMask = new JButton("Create Mask");
private JButton bnOptions = new JButton("Options");
private Thread thread;
private int countMeasure = 1;
OrientationParameters params = new OrientationParameters(OrientationService.ANALYSIS);
private ImagePlus imp;
private boolean log = false;
/**
*/
public MeasureDialog(ImagePlus imp, boolean log, double sigma) {
super("OrientationJ Measure [" + imp.getTitle() + "]");
canvasSaved = imp.getCanvas();
this.imp = imp;
this.log = log;
table = new Table();
params.sigmaLoG = sigma;
}
public void showDialog() {
GridToolbar bar = new GridToolbar(false, 0);
bar.place(0, 0, bnCopy);
bar.place(0, 1, bnRemove);
bnCopy.addActionListener(this);
bnRemove.addActionListener(this);
GridPanel controls = new GridPanel(false);
controls.place(0, 2, bnMask);
controls.place(0, 3, bnOptions);
controls.place(0, 4, bnMeasure);
walk.getButtonClose().addActionListener(this);
bnMask.addActionListener(this);
bnMeasure.addActionListener(this);
bnOptions.addActionListener(this);
GridPanel pnTable = new GridPanel(false, 0);
pnTable.place(0, 0, table);
pnTable.place(1, 0, bar);
GridPanel pn = new GridPanel(false);
pn.place(1, 0, 2, 1, controls);
pn.place(2, 0, 2, 1, pnTable);
pn.place(4, 0, bar);
pn.place(4, 1, walk);
params.load(settings);
add(pn);
pack();
setResizable(false);
GUI.center(this);
setVisible(true);
pack();
}
/**
* Implements the actionPerformed for the ActionListener.
*/
public synchronized void actionPerformed(ActionEvent e) {
if (e.getSource() == walk.getButtonClose()) {
if (imp != null) {
if (imp.getStack().getSize() > 1)
imp.setWindow(new StackWindow(imp, canvasSaved));
else
imp.setWindow(new ImageWindow(imp, canvasSaved));
}
params.store(settings);
dispose();
}
else if (e.getSource() == bnMask) {
int nx = imp.getWidth();
int ny = imp.getHeight();
ByteProcessor bp = new ByteProcessor(nx, ny);
bp.setColor(255);
bp.fill();
Vector<Measure> measures = table.getMeasures();
for(int i=0; i<measures.size(); i++) {
Measure measure = (Measure)measures.get(i);
bp.copyBits(measure.mask, measure.rect.x, measure.rect.y, ByteBlitter.MIN);
}
ImagePlus imp = new ImagePlus("Mask", bp);
imp.show();
}
else if (e.getSource() == bnOptions) {
new ShowingOptionsDialog(params);
canvas.repaint();
}
else if (e.getSource() == bnMeasure && imp != null) {
if (thread == null) {
thread = new Thread(this);
thread.setPriority(Thread.MIN_PRIORITY);
thread.start();
}
}
else if (e.getSource() == bnRemove) {
table.remove();
}
else if (e.getSource() == bnCopy) {
table.copy();
}
}
/**
*/
public void run() {
Roi roi = imp.getRoi();
if (roi==null) {
IJ.error("No ROI selected.");
thread = null;
return;
}
if (roi.getType() != Roi.RECTANGLE)
if (roi.getType() != Roi.OVAL)
if (roi.getType() != Roi.FREEROI)
if (roi.getType() != Roi.POLYGON)
if (roi.getType() != Roi.POINT) {
IJ.error("The ROI should be a Rectangle or Oval or FreeRoi or Polygon or Point.");
thread = null;
return;
}
Rectangle rect = roi.getBounds();
if (rect.width < 2) {
IJ.error("The width of the ROI should be greater than 2.");
thread = null;
return;
}
if (rect.height < 2) {
IJ.error("The height of the ROI should be greater than 2.");
thread = null;
return;
}
if (canvas == null) {
canvas = new MeasureCanvas(imp);
if (imp.getStack().getSize() > 1)
imp.setWindow(new StackWindow(imp, canvas));
else
imp.setWindow(new ImageWindow(imp, canvas));
canvas.repaint();
table.setCanvas(canvas);
}
Polygon polygon = roi.getPolygon();
ByteProcessor mask = (ByteProcessor)imp.getMask();
ByteProcessor bpmask = null;
int area = 0;
if (mask == null) {
bpmask = new ByteProcessor(rect.width, rect.height);
bpmask.setColor(countMeasure);
bpmask.fill();
area = rect.width * rect.height;
}
else {
bpmask = new ByteProcessor(mask.getWidth(), mask.getHeight());
for(int i=0; i<mask.getWidth(); i++)
for(int j=0; j<mask.getHeight(); j++) {
if (mask.getPixel(i, j) == 0)
bpmask.putPixel(i, j, 255);
else {
bpmask.putPixel(i, j, countMeasure);
area++;
}
}
}
Cursor cursor = getCursor();
setCursor(new Cursor(Cursor.WAIT_CURSOR));
int n = imp.getSlice();
walk.reset();
int nz = imp.getStack().getSize();
Vector<Measure> measures = table.getMeasures();
for(int z=1; z<=nz; z++) {
walk.progress("Frame:" + z, (z/(double)nz)*100.0);
imp.setSlice(z);
imp.setRoi(roi);
ImageProcessor ip = imp.getProcessor().crop();
GroupImage gim = new GroupImage(walk, ip, params);
(new Gradient(null, gim, params)).run();
Measure measure = (new StructureTensor(walk, gim, params)).measure(z, countMeasure, imp, area, rect, polygon, bpmask);
measures.add(measure);
if (log) {
IJ.log(measure.headings());
IJ.log(measure.toString());
}
table.add(measure);
canvas.setMeasures(measures, table, params);
}
walk.finish("Mesure");
countMeasure++;
if (canvas != null)
canvas.repaint();
setCursor(cursor);
imp.setSlice(n);
thread = null;
}
}
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