69 image based hyperbolic navigator (#73)

Co-authored-by: samypr100 <[email protected]>
trinity-xai · Sep 21, 2024 · 6ac4c0e · 6ac4c0e
1 parent 338307f
commit 6ac4c0e
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diff --git a/.idea/runConfigurations/trinity__versions_display_dependency_updates_.xml b/.idea/runConfigurations/trinity__versions_display_dependency_updates_.xml
diff --git a/.idea/runConfigurations/trinity__versions_display_property_updates_.xml b/.idea/runConfigurations/trinity__versions_display_property_updates_.xml
diff --git a/nb-configuration.xml b/nb-configuration.xml
@@ -8,6 +8,8 @@ Without this configuration present, some functionality in the IDE may be limited
 -->
     <config-data xmlns="http://www.netbeans.org/ns/maven-config-data/1">
         <configurations>
+            <configuration id="http" profiles=""/>
+            <configuration id="ZeroMQ" profiles=""/>
             <configuration id="OutRun" profiles=""/>
             <configuration id="DalleWalle" profiles=""/>
             <configuration id="GraalVM" profiles=""/>
@@ -16,7 +18,7 @@ Without this configuration present, some functionality in the IDE may be limited
     </config-data>
     <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
         <!--
-Properties that influence various parts of the IDE, especially code formatting and the like. 
+Properties that influence various parts of the IDE, especially code formatting and the like.
 You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
 That way multiple projects can share the same settings (useful for formatting rules for example).
 Any value defined here will override the pom.xml file value but is only applicable to the current project.

diff --git a/nbactions-4kMemory.xml b/nbactions-4kMemory.xml
@@ -7,7 +7,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
@@ -23,7 +23,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G -Dprism.poolstats=true -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
@@ -40,7 +40,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>

diff --git a/nbactions-DalleWalle.xml b/nbactions-DalleWalle.xml
@@ -7,7 +7,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
@@ -24,7 +24,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
@@ -43,7 +43,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>

diff --git a/nbactions-GraalVM.xml b/nbactions-GraalVM.xml
@@ -2,14 +2,14 @@
 <actions>
         <action>
             <actionName>build</actionName>
-            <goals> 
+            <goals>
                 <goal>clean</goal>
                 <goal>gluonfx:compile</goal>
                 <goal>gluonfx:link</goal>
             </goals>
             <properties>
-                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>                
-            </properties>            
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+            </properties>
         </action>
         <action>
             <actionName>run</actionName>
@@ -22,7 +22,7 @@
             <properties>
                 <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>--outrun=true --matrix=true</exec.appArgs>                
+                <exec.appArgs>--outrun=true --matrix=true</exec.appArgs>
                 <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
                 <exec.executable>java</exec.executable>
             </properties>
@@ -34,7 +34,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
@@ -45,5 +45,5 @@
                 <jpda.listen>true</jpda.listen>
             </properties>
         </action>
-    
+
     </actions>
diff --git a/nbactions-OutRun.xml b/nbactions-OutRun.xml
@@ -7,7 +7,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
@@ -25,7 +25,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
@@ -44,7 +44,7 @@
             </packagings>
             <goals>
                 <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
             </goals>
             <properties>
                 <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>

diff --git a/nbactions-ZeroMQ.xml b/nbactions-ZeroMQ.xml
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+        <action>
+            <actionName>run</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--zeromq=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+        <action>
+            <actionName>debug</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--zeromq=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+                <jpda.listen>true</jpda.listen>
+            </properties>
+        </action>
+        <action>
+            <actionName>profile</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--zeromq=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+    </actions>
diff --git a/nbactions-http.xml b/nbactions-http.xml
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+        <action>
+            <actionName>run</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--http=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+        <action>
+            <actionName>debug</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--http=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+                <jpda.listen>true</jpda.listen>
+            </properties>
+        </action>
+        <action>
+            <actionName>profile</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>process-classes</goal>
+                <goal>org.codehaus.mojo:exec-maven-plugin:3.4.1:exec</goal>
+            </goals>
+            <properties>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+                <exec.appArgs>--http=true</exec.appArgs>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+                <exec.executable>java</exec.executable>
+            </properties>
+        </action>
+    </actions>
diff --git a/src/main/java/com/clust4j/Clust4j.java b/src/main/java/com/clust4j/Clust4j.java
@@ -20,14 +20,15 @@
 import java.io.IOException;
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
+import java.io.Serializable;
 
 /**
  * The absolute super type for all clust4j objects (models and datasets)
  * that should be able to commonly serialize their data.
  *
  * @author Taylor G Smith
  */
-public abstract class Clust4j implements java.io.Serializable {
+public abstract class Clust4j implements Serializable {
     private static final long serialVersionUID = -4522135376738501625L;
 
     /**

diff --git a/src/main/java/com/clust4j/algo/AbstractCentroidClusterer.java b/src/main/java/com/clust4j/algo/AbstractCentroidClusterer.java
@@ -27,6 +27,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Random;
@@ -95,7 +96,7 @@ static interface Initializer {
         int[] getInitialCentroidSeeds(AbstractCentroidClusterer model, double[][] X, int k, final Random seed);
     }
 
-    public static enum InitializationStrategy implements java.io.Serializable, Initializer, NamedEntity {
+    public static enum InitializationStrategy implements Serializable, Initializer, NamedEntity {
         AUTO {
             @Override
             public int[] getInitialCentroidSeeds(AbstractCentroidClusterer model, double[][] X, int k, final Random seed) {

diff --git a/src/main/java/com/clust4j/algo/AbstractClusterer.java b/src/main/java/com/clust4j/algo/AbstractClusterer.java
@@ -35,6 +35,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -50,7 +51,7 @@
  */
 public abstract class AbstractClusterer
     extends BaseModel
-    implements Loggable, NamedEntity, java.io.Serializable, MetricValidator {
+    implements Loggable, NamedEntity, Serializable, MetricValidator {
 
     private static final long serialVersionUID = -3623527903903305017L;
 

diff --git a/src/main/java/com/clust4j/algo/AffinityPropagation.java b/src/main/java/com/clust4j/algo/AffinityPropagation.java
@@ -17,6 +17,7 @@
 
 import com.clust4j.GlobalState;
 import com.clust4j.except.ModelNotFitException;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.metrics.pairwise.GeometricallySeparable;
@@ -291,7 +292,7 @@ public String getName() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.AFFINITY_PROP;
+        return Log.Tag.Algo.AFFINITY_PROP;
     }
 
     /**

diff --git a/src/main/java/com/clust4j/algo/BaseClassifier.java b/src/main/java/com/clust4j/algo/BaseClassifier.java
@@ -19,14 +19,16 @@
 import com.clust4j.metrics.scoring.UnsupervisedMetric;
 import org.apache.commons.math3.linear.RealMatrix;
 
+import java.io.Serializable;
+
 import static com.clust4j.metrics.scoring.UnsupervisedMetric.SILHOUETTE;
 
 /**
  * An interface for classifiers, both supervised and unsupervised.
  *
  * @author Taylor G Smith
  */
-public interface BaseClassifier extends java.io.Serializable {
+public interface BaseClassifier extends Serializable {
     public final static SupervisedMetric DEF_SUPERVISED_METRIC = SupervisedMetric.BINOMIAL_ACCURACY;
     public final static UnsupervisedMetric DEF_UNSUPERVISED_METRIC = SILHOUETTE;
 

diff --git a/src/main/java/com/clust4j/algo/BaseModel.java b/src/main/java/com/clust4j/algo/BaseModel.java
@@ -19,9 +19,10 @@
 import com.clust4j.utils.SynchronicityLock;
 import com.clust4j.utils.TableFormatter;
 
+import java.io.Serializable;
 import java.text.NumberFormat;
 
-abstract public class BaseModel extends Clust4j implements java.io.Serializable {
+abstract public class BaseModel extends Clust4j implements Serializable {
     private static final long serialVersionUID = 4707757741169405063L;
     public final static TableFormatter formatter;
 

diff --git a/src/main/java/com/clust4j/algo/BoruvkaAlgorithm.java b/src/main/java/com/clust4j/algo/BoruvkaAlgorithm.java
@@ -24,6 +24,8 @@
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
+
 /**
  * A graph traversal algorithm used in identifying the minimum spanning tree
  * in a graph for which all edge weights are distinct. Used in conjunction with
@@ -32,7 +34,7 @@
  * @author Taylor G Smith
  * @see <a href="https://en.wikipedia.org/wiki/Bor%C5%AFvka%27s_algorithm">Boruvka's algorithm</a>
  */
-class BoruvkaAlgorithm implements java.io.Serializable {
+class BoruvkaAlgorithm implements Serializable {
     private static final long serialVersionUID = 3935595821188876442L;
 
     // the initialization reorganizes the trees