identified bug in the classification when parallelized... runs serial…

… for now and also added support for other image types e.g. tiff, png, psd, pdf, tga, ico, sgi

.classpath

@@ -1,9 +1,30 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path=""/>
-	<classpathentry exported="true" kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="lib" path="commons-math-2.1.jar"/>
-	<classpathentry kind="lib" path="itext-1.4.8.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
+	<classpathentry kind="lib" path="executable/lib/commons-math-2.1.jar"/>
+	<classpathentry kind="lib" path="executable/lib/itext-1.4.8.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-common-image-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-common-io-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-common-lang-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-bmp-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-clippath-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-core-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-hdr-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-icns-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-iff-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-jpeg-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-metadata-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-pcx-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-pdf-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-pict-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-pnm-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-psd-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-reference-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-sgi-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-tga-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-thumbsdb-3.3-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="executable/lib/twelvemonkeys-imageio-tiff-3.3-SNAPSHOT.jar"/>
 	<classpathentry kind="output" path=""/>
 </classpath>

GemIdentCentroidFinding/PostProcess.java

@@ -49,7 +49,6 @@
 import GemIdentImageSets.ImageAndScoresBank;
 import GemIdentImageSets.ImageSetInterface;
 import GemIdentImageSets.NonGlobalImageSet;
-import GemIdentImageSets.RegularSubImage;
 import GemIdentImageSets.Nuance.NuanceImageListInterface;
 import GemIdentOperations.FindErrorRateViaReconcilation;
 import GemIdentOperations.Run;

GemIdentClassificationEngine/Classify.java

@@ -103,13 +103,16 @@ private void BeginClassification() {
 		progress.StartTimer();
 		Run.it.imageset.LOG_AddToHistory("begun classification of " + filenames.size() + " images");
 
-		classifyPool=Executors.newFixedThreadPool(Run.it.num_threads);
+/*		classifyPool=Executors.newFixedThreadPool(Run.it.num_threads);
 		for (String filename:filenames)
 	    	classifyPool.execute(new SingleImageClassifier(filename));
 		classifyPool.shutdown();
 		try {	         
 	         classifyPool.awaitTermination(Long.MAX_VALUE,TimeUnit.SECONDS); //effectively infinity
-	    } catch (InterruptedException ignored){}
+	    } catch (InterruptedException ignored){}*/
+
+		for (String filename:filenames)
+			new SingleImageClassifier(filename).run();
 		progress.RemoveClassifyBars();
 	}
 	/**
@@ -212,8 +215,10 @@ public void run(){
 			System.out.println("done classifying pixels in image "+filename);
 			if (!stop){
 				progress.WritingImages(threadName);
-				for (String phenotype:Run.it.getPhenotyeNamesSaveNONAndFindPixels())
+				for (String phenotype:Run.it.getPhenotyeNamesSaveNONAndFindPixels()){
+					System.out.println("about to write ismatrix for file " + filename + " and phenotype " + phenotype + " and is matrix " + is.get(phenotype).toString());
 					IOTools.WriteIsMatrix(GetIsName(filename,phenotype),is.get(phenotype));
+				}
 
 				if (!(Run.it.imageset instanceof NuanceImageListInterface)){ //too complicated to do this if its Nuance
 					MarkIntermediatePixels();
@@ -296,10 +301,9 @@ private void MarkIntermediatePixels(){
 					HashMap<String,Boolean> isij=new HashMap<String,Boolean>(Run.it.numPhenotypes());
 					for (String phenotype:Run.it.getPhenotyeNamesSaveNON())
 						isij.put(phenotype,is.get(phenotype).get(i,j));
-					int T=0;
+
 					for (String phenotype:Run.it.getPhenotyeNamesSaveNON()){
 						if (isij.get(phenotype)){
-							T++;
 							actualImageInter.MarkPheno(i,j,phenotype);
 						}	
 					}

GemIdentImageSets/ImageAndScoresBank.java

@@ -158,7 +158,7 @@ public static BufferedImage getOrAddIs(String filename,String dir){
 		DataImage dataImage=isImages.get(filename);
 		if (dataImage == null){
 			dataImage=new RegularSubImage(filename,false);
-//			isImages.put(filename,dataImage);
+			isImages.put(filename,dataImage);
 		}
 		if (isImages.size() > IS_IMAGES_MAX_SIZE)
 			isImages.flushToSize(IS_IMAGES_MAX_SIZE);

GemIdentImageSets/Nuance/SuperNuanceImage.java

@@ -75,4 +75,9 @@ public DataImage getCenterImage(){
 	public Point AdjustPointForSuper(Point t){
 		return new Point(t.x+c,t.y+c);
 	}
+
+	@Override
+	public String filename() {
+		return filename;
+	}	
 }

GemIdentImageSets/SuperImage.java

@@ -66,4 +66,6 @@ public interface SuperImage {
 	 */
 	public BufferedImage getAsBufferedImage();
 
+	public String filename();
+
 }

GemIdentImageSets/SuperRegularImage.java

@@ -244,4 +244,9 @@ public Point AdjustPointForSuper(Point t){
 	public SuperRegularImage(String filename, BufferedImage clone, boolean crop) {
 		super(filename, clone, crop);
 	}
+
+	@Override
+	public String filename() {
+		return filename;
+	}
 }

GemIdentOperations/Run.java

@@ -88,16 +88,12 @@ public static void main(String[] args){
 
 	/** Prints the source code license to the terminal */
 	private static void ShowGplMessage() {
-		System.out.println("GemIdent v1.2b");
+		System.out.println("GemIdent v1.3b --- http://gemident.com");
 		System.out.println("Interactive Image Segmentation Software via Supervised Statistical Learning");
-		System.out.println("http://gemident.com");
-		System.out.println("");
-		System.out.println("For GemIdent to be used in tandem with the global labor force of Mechanical Turk, see DistributeEyes");
-		System.out.println("http://distributeeyes.com");
 		System.out.println("");		
-		System.out.println("Copyright (C) 2014");
-		System.out.println("Professor Susan Holmes, Stanford University &");
-		System.out.println("Adam Kapelner, The Wharton School of the University of Pennsylvania");
+		System.out.println("Copyright (C) 2016");
+		System.out.println("Adam Kapelner, Queens College, City University of New York and");
+		System.out.println("Professor Susan Holmes, Stanford University");
 		System.out.println("");
 		System.out.println("GemIdent comes with ABSOLUTELY NO WARRANTY. This is free software, and you are ");
 		System.out.println("welcome to redistribute it under certain conditions. Please see the GPL v2");
@@ -110,7 +106,7 @@ private static void ShowGplMessage() {
 	/** the program title */
 	private static final String ProgramName = "GemIdent";
 	/** the string to be used when building the window title (<b>GemIdent</b> is still in beta on the first release) */
-	private static final String VER = "1.2b";
+	private static final String VER = "1.3b";
 	/** The title of the program */
 	public static final String Title = ProgramName + " v" + VER + " - ";	
 

GemIdentTools/Thumbnails.java

@@ -109,7 +109,8 @@ public static ArrayList<String> GetImageListAsCollection(String dir){
 	}
 	/**
 	 * This {@link java.io.FilenameFilter file filter} returns
-	 * only image files of type "jpg", "tif", "tiff, and "bmp"
+	 * only image files of type listed below 
+	 * (thanks to TwelveMonkeys ImageIO extensions).
 	 *
 	 */
 	public static class ImageFileFilter implements FilenameFilter{
@@ -124,7 +125,18 @@ public boolean accept(File dir, String name) {
 			String[] fileparts=name.split("\\.");
 			if (fileparts.length >= 2){
 				String ext=fileparts[fileparts.length - 1].toLowerCase();
-				if (ext.equals("jpg") || ext.equals("tif") || ext.equals("tiff") || ext.equals("TIFF") || ext.equals("bmp") || ext.equals("png"))
+				if (ext.equals("jpg") || 
+						ext.equals("jpeg") || 
+						ext.equals("tif") || 
+						ext.equals("tiff") || 
+						ext.equals("bmp") || 
+						ext.equals("png") ||
+						ext.equals("ico") ||
+						ext.equals("pcx") ||
+						ext.equals("pnm") ||
+						ext.equals("psd") ||
+						ext.equals("sgi") ||
+						ext.equals("tga"))
 					return true;
 				else 
 					return false;

GemIdentView/AlphaSlider.java

@@ -116,8 +116,6 @@ public void stateChanged(ChangeEvent e){
 	}
 	/** sets up a mask for an is-pixel image - loads it from the hard disk, creates the 32-bit alpha image, and displays it */
 	private void SetUpIs(){
-//		String name=imagePanel.displayImage.getFilename();
-//		String name2=phenotype.getName();
 		String isName=Classify.GetIsName(imagePanel.displayImage.getFilename(),phenotype.getName());
 		if (IOTools.FileExists(isName)){
 			BufferedImage raw=ImageAndScoresBank.getOrAddIs(isName,null);

GemIdentView/KFrame.java

@@ -430,6 +430,7 @@ public void KillAnalysisTab(){
 		tabs.remove(analysisPanel);		
 	}
 	public void SwitchToAnalysisTab(){
+		System.out.println("SwitchToAnalysisTab analysisPanel:" + analysisPanel);
 		tabs.setSelectedComponent(analysisPanel);
 	}
 	public ConsoleParser getParser(){

MANIFEST.MF

@@ -1,3 +1,3 @@
 Manifest-Version: 1.0
 Main-Class: GemIdentOperations.Run
-Class-Path: itext-1.4.8.jar commons-math-2.1.jar
+Class-Path: itext-1.4.8.jar commons-math-2.1.jar twelvemonkeys*.jar

README → README.Md

@@ -1,26 +1,20 @@
 GemIdent --- Interactive Image Segmentation Software via Supervised Statistical Learning
 http://gemident.com
 
-Copyright (C) 2015
+Copyright (C) 2016
 --
 Adam Kapelner, Queens College, CUNY 
-http://kapelner.com
-& 
+http://kapelner.com &
+
 Professor Susan Holmes, Stanford University 
 http://statweb.stanford.edu/~susan/
 
-For GemIdent to be used in tandem with the global labor force of Mechanical Turk, see DistributeEyes
-http://distributeeyes.com
-
-For GemIdent to be used to track objects in videos see GemVident 
-https://github.com/kapelner/GemVident
+To download the software:
+https://github.com/kapelner/GemIdent/blob/master/gemident_executable.zip?raw=true
 
 For the publication see:
 http://www.jstatsoft.org/v30/i10
 
-To download the software:
-https://github.com/kapelner/GemIdent/blob/master/gemident_executable.zip?raw=true
-
 For the software manual:
 https://github.com/kapelner/GemIdent/raw/master/GemManualv2.pdf
 
@@ -44,6 +38,9 @@ https://www.youtube.com/watch?v=ZSveLYzhjQU
 For a presentation on GemIdent, see:
 https://github.com/kapelner/GemIdent/blob/master/gemident_presentation.pdf?raw=true
 
+For GemIdent to be used to track objects in videos see GemVident 
+https://github.com/kapelner/GemVident
+
 GemIdent is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

build.xml

@@ -25,10 +25,35 @@
 
     <!-- This creates the JAR file -->        	
 	<target name="distribute_as_jar" depends="compile_java_code" description="generate the jar file" >
-	    <jar destfile="executable/gemident_v1.2.jar" basedir="bin" excludes="executable/**,GemIdentManual/**,examples_image_sets/**,r_scripts/**,*.pdf,*.MF,README,build.xml,.project,.classpath,*.jar">
+	    <jar destfile="executable/gemident_v1.3.jar" 
+	    	basedir="bin" 
+	    	excludes="executable/**,GemIdentManual/**,examples_image_sets/**,r_scripts/**,.settings/**,*.pdf,*.MF,README.Md, *.zip, gpl*.txt ,build.xml,.project,.classpath,*.jar">
             <manifest>
                 <attribute name="Main-Class" value="GemIdentOperations.Run"/>
-                <attribute name="Class-Path" value="lib/itext-1.4.8.jar lib/commons-math-2.1.jar"/>
+                <attribute name="Class-Path" value="
+                	lib/itext-1.4.8.jar 
+                	lib/commons-math-2.1.jar 
+                	lib/twelvemonkeys-common-image-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-common-io-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-common-lang-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-bmp-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-clippath-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-core-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-hdr-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-icns-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-iff-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-jpeg-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-metadata-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-pcx-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-pdf-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-pict-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-pnm-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-psd-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-reference-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-sgi-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-tga-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-thumbsdb-3.3-SNAPSHOT.jar
+                	lib/twelvemonkeys-imageio-tiff-3.3-SNAPSHOT.jar"/>
             </manifest>
 		</jar>
 	</target> 

executable/run_gemident_mac_unix_linux

@@ -1 +1 @@
-java -Xmx1000m -Xss2m -Xoss2m -jar gemident_v1.2.jar
+java -Xmx3000m -Xss2m -Xoss2m -jar gemident_v1.3.jar

executable/run_gemident_windows.bat

@@ -1 +1 @@
-java -Xmx1000m -Xss2m -Xoss2m -jar gemident_v1.2.jar
+java -Xmx3000m -Xss2m -Xoss2m -jar gemident_v1.3.jar