Merge branch 'edf'

Conflicts: .gitignore Fakefile Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
ivanmkc · Dec 24, 2010 · b05edaf · b05edaf
2 parents b8049b3 + d740405
commit b05edaf
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diff --git a/.gitignore b/.gitignore
@@ -210,3 +210,6 @@
 /plugins/Temporal_Color_Coder.jar
 /plugins/Samples_.jar
 /plugins/Lasso_and_Blow_Tool.jar
+/jars/wavelets.jar
+/jars/imageware.jar
+/plugins/Extended_Depth_Field.jar
diff --git a/Fakefile b/Fakefile
@@ -204,7 +204,10 @@ PLUGIN_TARGETS=plugins/Jython_Interpreter.jar \
 	plugins/Temporal_Color_Coder.jar \
 	plugins/Samples_.jar \
 	plugins/Lasso_and_Blow_Tool.jar \
-	jars/mij.jar
+	jars/mij.jar \
+	jars/wavelets.jar \
+	jars/imageware.jar \
+	plugins/Extended_Depth_Field.jar \
 
 all <- fiji $SUBMODULE_TARGETS $PLUGIN_TARGETS
 
@@ -396,6 +399,9 @@ CLASSPATH(plugins/Linear_Kuwahara.jar)=jars/ij.jar
 CLASSPATH(plugins/Thread_Killer.jar)=jars/ij.jar
 CLASSPATH(plugins/MosaicJ_.jar)=jars/ij.jar
 CLASSPATH(plugins/SheppLogan_.jar)=jars/ij.jar
+CLASSPATH(jars/wavelets.jar)=jars/ij.jar
+CLASSPATH(jars/imageware.jar)=jars/ij.jar
+CLASSPATH(plugins/Extended_Depth_Field.jar)=jars/ij.jar:jars/imageware.jar:jars/wavelets.jar
 
 # pre-Java5 generics ;-)
 

diff --git a/LICENSES b/LICENSES
@@ -32,6 +32,7 @@ Name					File					Author(s)						Contact								License
 * Color Histogram 			Color_Histogram.jar			Dimiter Prodanov 					dimiterpp@gmail.com 						GPL 2
 * Color Inspector 3D 			Color_Inspector_3D.jar			Kai Uwe Barthel 					k.barthel@fhtw-berlin.de 					PD
 * Differentials				Differentials_.jar			Philippe Thevenaz					http://bigwww.epfl.ch/thevenaz/differentials/			BIG (see below)
+* Extended Depth of Focus		Extended_Depth_Field.jar		Alex Prudencio, Daniel Sage et al			http://bigwww.epfl.ch/demo/edf/					BIG (see below)
 * FeatureJ	 			FeatureJ_.jar	 			Erik Meijering	 					http://www.imagescience.org/meijering/software/featurej/	imagescience (see below)
 * Fiji_Plugins.jar 			Fiji_Plugins.jar 			Various authors 					http://pacific.mpi-cbg.de/contributors 				PD,GPL
 * Fiji as a framework																							GPL

diff --git a/src-plugins/Extended_Depth_Field/Demo.java b/src-plugins/Extended_Depth_Field/Demo.java
@@ -0,0 +1,114 @@
+//==============================================================================
+//
+// Project: EDF - Extended Depth of Focus
+//
+// Author: Daniel Sage
+//
+// Organization: Biomedical Imaging Group (BIG)
+// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
+//
+// Information: http://bigwww.epfl.ch/demo/edf/
+//
+// Reference: B. Forster, D. Van De Ville, J. Berent, D. Sage, M. Unser
+// Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion
+// of Multichannel Microscopy Images, Microscopy Research and Techniques,
+// 65(1-2), pp. 33-42, September 2004.
+//
+// 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, 21 December 2010)
+//
+//==============================================================================
+
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.process.ColorProcessor;
+
+import java.applet.Applet;
+import java.awt.Dimension;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.Toolkit;
+import java.net.URL;
+
+/**
+ * This class is an applet demonstration of the EDF. It loads a image stack
+ * and present the easy dialog.
+ */
+public class Demo extends Applet {
+
+	private EDF_Easy_ edf;
+
+	/**
+	 * Initialization of the applet.
+	 * Load the image stack soudure.
+	 */
+	public void init() {
+		ImageStack stack = new ImageStack(512, 512);
+		for(int i=2; i<9; i++) {
+			ColorProcessor cp1 = (ColorProcessor)(new ImagePlus("",
+					loadImageFile("soudure/s000" + i + ".jpg"))).getProcessor();
+			stack.addSlice("", cp1);
+		}
+
+		ImagePlus imp = new ImagePlus("z-stack of images", stack);
+
+		imp.show();
+			Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+		Dimension window = imp.getWindow().getSize();
+		if (window.width==0)
+			return;
+		int left = screen.width/4-window.width/2;
+		int top = (screen.height-window.height)/4;
+		if (top<0) top = 0;
+		imp.getWindow().setLocation(left, top);
+
+		edf = new EDF_Easy_();
+		edf.run("applet");
+
+		edf.dl.setJSliderQuality(2);
+		edf.dl.setJSliderRegularization(4);
+		edf.dl.setJCheckBoxShow3D(true);
+		edf.dl.setJCheckBoxShowTopology(true);
+	}
+
+	/**
+	 * Load an image from a URL.
+	 */
+	public Image loadImageURL(String urltext) {
+		Image image = null;
+		try {
+			URL url = new URL(urltext);
+			MediaTracker mtracker = new MediaTracker(this);
+			image = getImage(url);
+			mtracker.addImage(image, 0);
+			mtracker.waitForAll();
+		}
+		catch  (Exception e) {
+			System.out.println("Exeception" + e);
+		}
+		return image;
+	}
+
+	/**
+	 * Load an image from a local file.
+	 */
+	public Image loadImageFile(String filename) {
+		Image image=null;
+		MediaTracker mtracker = new MediaTracker(this);
+		image = getImage(this.getDocumentBase(), filename);
+		mtracker.addImage(image, 0);
+		try {
+			mtracker.waitForAll();
+		}
+		catch (InterruptedException ie) {
+			System.out.println("Bad loading of an image.");
+		}
+		return image;
+	}
+
+}
diff --git a/src-plugins/Extended_Depth_Field/EDF-demo.txt b/src-plugins/Extended_Depth_Field/EDF-demo.txt
@@ -0,0 +1,37 @@
+// EDF Demo Macro
+//
+// http://bigwww.epfl.ch/demo/edf/
+//
+// Daniel Sage
+// Biomecial Imaging Group (BIG)
+// Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
+//
+// 14 June 2007
+//
+
+run("EDF Easy ", "quality='0' topology='1' show-topology='off' show-view='off'");
+
+//
+// Description of the arguments
+//
+// argument quality: Speed/Quality trade-off.
+//		0 for fast
+//		1 for intermediate speed
+//		2 for medium quality / medium speed
+//		3 for intermediate quality
+//		4 for high quality
+//
+// argument topology: Topology smoothness
+//		0 for no smoothing of the topology
+//		1 for weak smoothing
+//		2 for medium smoothing
+//		3 for strong smoothing
+//		4 for very strong smoothing
+//
+// argument show-topology: Show the topology map
+//		on
+//		off
+//
+// argument show-view: Show the 3D view
+//		on
+//		off
diff --git a/src-plugins/Extended_Depth_Field/EDF_Easy_.java b/src-plugins/Extended_Depth_Field/EDF_Easy_.java
@@ -0,0 +1,162 @@
+//==============================================================================
+//
+// Project: EDF - Extended Depth of Focus
+//
+// Author: Daniel Sage
+//
+// Organization: Biomedical Imaging Group (BIG)
+// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
+//
+// Information: http://bigwww.epfl.ch/demo/edf/
+//
+// Reference: B. Forster, D. Van De Ville, J. Berent, D. Sage, M. Unser
+// Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion
+// of Multichannel Microscopy Images, Microscopy Research and Techniques,
+// 65(1-2), pp. 33-42, September 2004.
+//
+// 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, 21 December 2010)
+//
+//==============================================================================
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.Macro;
+import ij.WindowManager;
+import ij.gui.GUI;
+import ij.plugin.PlugIn;
+
+import java.util.StringTokenizer;
+
+import edfgui.BasicDialog;
+
+/**
+ * This class is a plugin of ImageJ. It offers an easy dialog box to run
+ * the EDF program.
+ */
+public class EDF_Easy_ implements PlugIn {
+
+	public BasicDialog dl;
+
+	/**
+	 * Implements the run method of PlugIn.
+	 */
+	public void run(String args) {
+		// Check the ImageJ version
+		if (IJ.versionLessThan("1.21a"))
+			return;
+
+		// Check the presence of the image
+		ImagePlus imp = WindowManager.getCurrentImage();
+
+		if (imp == null) {
+			IJ.error("No stack of images open");
+			return;
+		}
+
+		// Check the size of the image
+		if (imp.getWidth() < 4) {
+			IJ.error("The image is too small (nx=" + imp.getWidth() + ")");
+			return;
+		}
+
+		if (imp.getHeight() < 4) {
+			IJ.error("The image is too small (ny=" + imp.getHeight() + ")");
+			return;
+		}
+
+		if (imp.getStackSize() < 2) {
+			IJ.error("The stack of images is too small (nz=" + imp.getStackSize() + ")");
+			return;
+		}
+
+		// Color or grayscale image
+		boolean color = false;
+		if (imp.getType() == ImagePlus.COLOR_RGB)
+			color = true;
+		else if (imp.getType() == ImagePlus.GRAY8)
+			color = false;
+		else if (imp.getType() == ImagePlus.GRAY16)
+			color = false;
+		else if (imp.getType() == ImagePlus.GRAY32)
+			color = false;
+		else {
+			IJ.error("Only process 8-bits, 16-bits, 32-bits and RGB images");
+			return;
+		}
+
+		if (Macro.getOptions() != null) {
+			dl = new BasicDialog(new int[]{imp.getWidth(), imp.getHeight()}, color, args.equals("applet"));
+
+			String params = Macro.getValue(Macro.getOptions(), "quality", "");
+			if (!params.equals("")) {
+				String arguments[] = split(params);
+				if (arguments.length != 1) {
+					IJ.error("The arguments of the quality are not valid. Correct example: quality='0'");
+					return;
+				}
+				int quality = (new Integer(arguments[0])).intValue();
+				dl.parameters.setQualitySettings(quality);
+			}
+
+			params = Macro.getValue(Macro.getOptions(), "topology", "");
+			if (!params.equals("")) {
+				String arguments[] = split(params);
+				if (arguments.length != 1) {
+					IJ.error("The arguments of the topology are not valid. Correct example: topology='0'");
+					return;
+				}
+				int topology = (new Integer(arguments[0])).intValue();
+				dl.parameters.setTopologySettings(topology);
+			}
+
+			params = Macro.getValue(Macro.getOptions(), "show-view", "");
+			if (!params.equals("")) {
+				String arguments[] = split(params);
+				if (arguments.length != 1) {
+					IJ.error("The arguments of the show-view are not valid. Correct example: show-view='on'");
+					return;
+				}
+				dl.parameters.show3dView = arguments[0].equals("on");
+			}
+
+			params = Macro.getValue(Macro.getOptions(), "show-topology", "");
+			if (!params.equals("")) {
+				String arguments[] = split(params);
+				if (arguments.length != 1) {
+					IJ.error("The arguments of the show-topology are not valid. Correct example: show-topology='on'");
+					return;
+				}
+				dl.parameters.showTopology = arguments[0].equals("on");
+			}
+
+			dl.process();
+		}
+		else {
+			dl = new BasicDialog(new int[]{imp.getWidth(), imp.getHeight()},color, args.equals("applet"));
+			dl.initialize();
+			dl.pack();
+			GUI.center(dl);
+			dl.setVisible(true);
+		}
+
+	}
+
+	/**
+	 * Split a macro options string.
+	 */
+	private String[] split(String s) {
+		StringTokenizer t = new StringTokenizer(s);
+		String[] items = new String[t.countTokens()];
+		for (int k = 0; (k < items.length); k++) {
+			items[k] = t.nextToken();
+		}
+		return(items);
+	}
+
+}