fix pom issues

.classpath

@@ -4,6 +4,7 @@
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" output="target/classes" path="src/main/java">
@@ -22,28 +23,8 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry exported="true" kind="src" path="/Preprocessing"/>
 	<classpathentry exported="true" kind="src" path="/PolynomialRansac"/>
 	<classpathentry exported="true" kind="src" path="/MasterPanels"/>
-	<classpathentry exported="true" kind="src" path="/imglib2-roi"/>
-	<classpathentry combineaccessrules="false" exported="true" kind="src" path="/varun-imglib2-algorithm"/>
-	<classpathentry kind="lib" path="/Users/aimachine/.m2/repository/loci/loci_plugins/4.4.9/loci_plugins-4.4.9.jar">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="maven.groupId" value="loci"/>
-			<attribute name="maven.artifactId" value="loci_plugins"/>
-			<attribute name="maven.version" value="4.4.9"/>
-			<attribute name="maven.scope" value="compile"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="/Users/aimachine/.m2/repository/net/imglib2/imglib2/5.8.0/imglib2-5.8.0.jar">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="maven.groupId" value="net.imglib2"/>
-			<attribute name="maven.artifactId" value="imglib2"/>
-			<attribute name="maven.version" value="5.8.0"/>
-			<attribute name="maven.scope" value="compile"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="src" path="/Covisto_"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.settings/org.eclipse.jdt.core.prefs

@@ -8,6 +8,9 @@ org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8

pom.xml

@@ -114,6 +114,7 @@
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
+			<version>5.8.0</version>
 		</dependency>
 
 		<dependency>
@@ -156,7 +157,15 @@
 			<artifactId>commons-io</artifactId>
 			<version>${commons-io.version}</version>
 		</dependency>
-
+<dependency>
+    <groupId>net.imglib2</groupId>
+    <artifactId>imglib2-algorithm</artifactId>
+</dependency>
+
+<dependency>
+    <groupId>net.imglib2</groupId>
+    <artifactId>imglib2-algorithm-gpl</artifactId>
+</dependency>
 
 
 

src/main/java/pluginTools/simplifiedio/SimplifiedIO.java

@@ -13,9 +13,6 @@
 import ij.plugin.ImagesToStack;
 import io.scif.SCIFIO;
 import loci.formats.FormatException;
-import loci.plugins.in.ImagePlusReader;
-import loci.plugins.in.ImportProcess;
-import loci.plugins.in.ImporterOptions;
 import net.imagej.Dataset;
 import net.imagej.ImgPlus;
 import net.imagej.axis.Axes;
@@ -82,26 +79,7 @@ static ImgPlus openImageWithSCIFIO( final String path ) {
 	 *
 	 * @see net.imagej.ImgPlus
 	 */
-	@SuppressWarnings( "rawtypes" )
-	static ImgPlus openImageWithBioFormats( final String path ) {
-		// package private to allow testing
-		try {
-			ImporterOptions options = new ImporterOptions();
-			if ( Macro.getOptions() == null ) {
-				options.loadOptions();
-			}
-			options.parseArg( path );
-			options.checkObsoleteOptions();
-			ImportProcess process = new ImportProcess( options );
-			process.execute();
-			ImagePlusReader reader = new ImagePlusReader( process );
-			ImagePlus[] imps = reader.openImagePlus();
-			ImagePlus finalImage = ImagesToStack.run( imps );
-			return ImagePlusAdapter.wrapImgPlus( finalImage );
-		} catch ( FormatException | IOException e ) {
-			throw new SimplifiedIOException( e );
-		}
-	}
+
 
 	/**
 	 * Loads an image into an ImgPlus object
@@ -125,11 +103,6 @@ public static ImgPlus openImage( final String path ) {
 			messages.add( "SCIFIO Exception: " + e.getMessage() );
 		}
 
-		try {
-			return SimplifiedIO.openImageWithBioFormats( path );
-		} catch ( Exception e ) {
-			messages.add( "BioFormats Exception: " + e.getMessage() );
-		}
 
 		if ( !new File( path ).exists() )
 			throw new SimplifiedIOException( "Image file doesn't exist: " + path );

src/main/java/utility/Listordereing.java

@@ -9,6 +9,7 @@
 import ellipsoidDetector.Intersectionobject;
 import ij.IJ;
 import kalmanForSegments.Segmentobject;
+import kalmanTracker.NNFlagsearchKDtree;
 import mpicbg.models.Point;
 import net.imglib2.KDTree;
 import net.imglib2.RealLocalizable;