From 041bfed0b09e201f7e40511c1c05d27f319f12f1 Mon Sep 17 00:00:00 2001
From: Alexandre <alexandre.perles@gmail.com>
Date: Fri, 6 Oct 2023 10:50:44 +0200
Subject: [PATCH] Structure code
---
.../groovy/TemperatureClustering.groovy | 6 +--
.../TwoDimensionsPointsClustering.groovy | 4 +-
.../java/fr/irit/smac/amas4dc/AMAS4DC.java | 5 ++-
.../fr/irit/smac/amas4dc/amas/AMASOption.java | 2 -
.../amas4dc/amas/DynamicClusteringAMAS.java | 2 +-
.../amas/DynamicClusteringEnvironment.java | 3 +-
.../irit/smac/amas4dc/amas/MASSettings.java | 6 ++-
.../smac/amas4dc/amas/agent/ClusterAgent.java | 38 ++++++-------------
.../amas4dc/amas/agent/DataPointAgent.java | 10 ++---
.../AMAS4DCCommandAndQueryHandler.java | 4 +-
.../command/NewDataPointCommand.java | 2 +-
.../amas/controller/query/ExtendedResult.java | 3 +-
.../amas4dc/amas/controller/query/Result.java | 2 +-
.../messages/EvaluatedDistanceMessage.java | 2 +-
.../messages/InformMostSimilarMessage.java | 3 +-
...estClusterDistanceToBeAbsorbedMessage.java | 2 +-
...tDataPointDistanceToBeAbsorbedMessage.java | 2 +-
.../fr/irit/smac/amas4dc/cluster/Cluster.java | 7 +---
.../smac/amas4dc/cluster/ExtendedCluster.java | 2 +-
.../cluster/{ => datapoint}/DataPoint.java | 2 +-
.../{ => datapoint}/DataPointDatabase.java | 4 +-
.../{ => datapoint}/DataPointFuser.java | 2 +-
.../distance}/ClusterDistance.java | 4 +-
.../{ => distance}/DistanceMethod.java | 4 +-
.../CalinskiHarabazIndex.java | 5 ++-
.../SilhouetteScoreCalculator.java | 4 +-
.../ExtendedClusterException.java | 2 +-
.../{ => exception}/FusionException.java | 2 +-
src/test/groovy/SimpleClusteringIT.groovy | 6 +--
.../smac/amas4dc/amas/ClusterAgentTest.groovy | 6 +--
30 files changed, 64 insertions(+), 82 deletions(-)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => datapoint}/DataPoint.java (61%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => datapoint}/DataPointDatabase.java (88%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => datapoint}/DataPointFuser.java (72%)
rename src/main/java/fr/irit/smac/amas4dc/{amas => cluster/distance}/ClusterDistance.java (57%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => distance}/DistanceMethod.java (55%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => evaluation}/CalinskiHarabazIndex.java (91%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => evaluation}/SilhouetteScoreCalculator.java (92%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => exception}/ExtendedClusterException.java (72%)
rename src/main/java/fr/irit/smac/amas4dc/cluster/{ => exception}/FusionException.java (71%)
diff --git a/src/experiments/groovy/TemperatureClustering.groovy b/src/experiments/groovy/TemperatureClustering.groovy
index 5f804ea..cecc709 100644
--- a/src/experiments/groovy/TemperatureClustering.groovy
+++ b/src/experiments/groovy/TemperatureClustering.groovy
@@ -2,9 +2,9 @@ import fr.irit.smac.amas4dc.AMAS4DC
import fr.irit.smac.amas4dc.amas.AMASOption
import fr.irit.smac.amas4dc.amas.MASSettings
import fr.irit.smac.amas4dc.cluster.Cluster
-import fr.irit.smac.amas4dc.cluster.DataPoint
-import fr.irit.smac.amas4dc.cluster.DataPointFuser
-import fr.irit.smac.amas4dc.cluster.DistanceMethod
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPointFuser
+import fr.irit.smac.amas4dc.cluster.distance.DistanceMethod
import fr.irit.smac.lxplot.LxPlot
import groovy.transform.ToString
diff --git a/src/experiments/groovy/TwoDimensionsPointsClustering.groovy b/src/experiments/groovy/TwoDimensionsPointsClustering.groovy
index 16ee07a..79eb2e4 100644
--- a/src/experiments/groovy/TwoDimensionsPointsClustering.groovy
+++ b/src/experiments/groovy/TwoDimensionsPointsClustering.groovy
@@ -2,8 +2,8 @@ import fr.irit.smac.amas4dc.AMAS4DC
import fr.irit.smac.amas4dc.amas.AMASOption
import fr.irit.smac.amas4dc.amas.MASSettings
import fr.irit.smac.amas4dc.cluster.Cluster
-import fr.irit.smac.amas4dc.cluster.DataPoint
-import fr.irit.smac.amas4dc.cluster.DistanceMethod
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint
+import fr.irit.smac.amas4dc.cluster.distance.DistanceMethod
import fr.irit.smac.lxplot.LxPlot
import fr.irit.smac.lxplot.commons.ChartType
import groovy.transform.ToString
diff --git a/src/main/java/fr/irit/smac/amas4dc/AMAS4DC.java b/src/main/java/fr/irit/smac/amas4dc/AMAS4DC.java
index 6433f9b..6dd9cfb 100644
--- a/src/main/java/fr/irit/smac/amas4dc/AMAS4DC.java
+++ b/src/main/java/fr/irit/smac/amas4dc/AMAS4DC.java
@@ -8,7 +8,7 @@ import fr.irit.smac.amas4dc.amas.controller.query.ExtendedResult;
import fr.irit.smac.amas4dc.amas.controller.query.Result;
import fr.irit.smac.amas4dc.amas.controller.query.RetrieveClustersExtendedResultQuery;
import fr.irit.smac.amas4dc.amas.controller.query.RetrieveClustersResultQuery;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.util.List;
@@ -18,13 +18,16 @@ public class AMAS4DC<T extends DataPoint> {
public AMAS4DC(MASSettings<T> masSettings) {
this.controller = new AMAS4DCCommandAndQueryHandler<T>(masSettings);
}
+
public void fit(List<T> data) {
controller.handle(new NewDataPointCommand<T>(data));
controller.handle(new SolveCommand());
}
+
public Result<T> retrieveClusters() {
return controller.handle(new RetrieveClustersResultQuery());
}
+
public ExtendedResult<T> retrieveExtendedClusters() {
return controller.handle(new RetrieveClustersExtendedResultQuery());
}
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/AMASOption.java b/src/main/java/fr/irit/smac/amas4dc/amas/AMASOption.java
index 943fd10..b9fec55 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/AMASOption.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/AMASOption.java
@@ -1,7 +1,5 @@
package fr.irit.smac.amas4dc.amas;
public enum AMASOption {
- @Deprecated
- Forget,
KeepAllDataPoints
}
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringAMAS.java b/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringAMAS.java
index 680929a..6819af7 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringAMAS.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringAMAS.java
@@ -3,7 +3,7 @@ package fr.irit.smac.amas4dc.amas;
import fr.irit.smac.amak.Amas;
import fr.irit.smac.amas4dc.amas.agent.ClusterAgent;
import fr.irit.smac.amas4dc.amas.agent.DataPointAgent;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import lombok.Setter;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringEnvironment.java b/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringEnvironment.java
index 83f61c6..24dcd28 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringEnvironment.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/DynamicClusteringEnvironment.java
@@ -2,7 +2,7 @@ package fr.irit.smac.amas4dc.amas;
import fr.irit.smac.amak.Environment;
import fr.irit.smac.amas4dc.amas.agent.ClusterAgent;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import java.util.*;
@@ -13,7 +13,6 @@ import java.util.logging.Logger;
public class DynamicClusteringEnvironment<T extends DataPoint> extends Environment {
private final Queue<T> pendingAdditionDataPoints = new ConcurrentLinkedQueue<>();
- private static final Logger logger = Logger.getLogger(DynamicClusteringEnvironment.class.getName());
@Getter
private T lastPolledPendingDataPoint = null;
private final Map<Integer, List<ClusterAgent<T>>> buckets = new ConcurrentHashMap<>();
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/MASSettings.java b/src/main/java/fr/irit/smac/amas4dc/amas/MASSettings.java
index 916cc21..fcedf34 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/MASSettings.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/MASSettings.java
@@ -1,7 +1,9 @@
package fr.irit.smac.amas4dc.amas;
-import fr.irit.smac.amak.event.EventStore;
-import fr.irit.smac.amas4dc.cluster.*;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPointDatabase;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPointFuser;
+import fr.irit.smac.amas4dc.cluster.distance.DistanceMethod;
import java.util.EnumSet;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/agent/ClusterAgent.java b/src/main/java/fr/irit/smac/amas4dc/amas/agent/ClusterAgent.java
index 96fdc46..a1e45e0 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/agent/ClusterAgent.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/agent/ClusterAgent.java
@@ -2,7 +2,7 @@ package fr.irit.smac.amas4dc.amas.agent;
import fr.irit.smac.amak.Agent;
import fr.irit.smac.amas4dc.amas.AMASOption;
-import fr.irit.smac.amas4dc.amas.ClusterDistance;
+import fr.irit.smac.amas4dc.cluster.distance.ClusterDistance;
import fr.irit.smac.amas4dc.amas.DynamicClusteringAMAS;
import fr.irit.smac.amas4dc.amas.DynamicClusteringEnvironment;
import fr.irit.smac.amas4dc.amas.messages.EvaluatedDistanceMessage;
@@ -10,7 +10,7 @@ import fr.irit.smac.amas4dc.amas.messages.InformMostSimilarMessage;
import fr.irit.smac.amas4dc.amas.messages.RequestDataPointDistanceToBeAbsorbedMessage;
import fr.irit.smac.amas4dc.amas.messages.RequestClusterDistanceToBeAbsorbedMessage;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import fr.irit.smac.amas4dc.cluster.ExtendedCluster;
import lombok.Getter;
@@ -20,22 +20,18 @@ import java.util.logging.Level;
import java.util.logging.Logger;
public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAMAS<T>, DynamicClusteringEnvironment<T>> {
+ private static final Logger logger = Logger.getLogger(ClusterAgent.class.getName());
@Getter
-
private final Cluster<T> cluster;
private State state = State.DORMANT;
- private State nextState = state;
private final Map<ClusterAgent<T>, ClusterDistance<T>> distancesReceived = new HashMap<>();
- //region Action variables
- //endregion
- private static final Logger logger = Logger.getLogger(ClusterAgent.class.getName());
private Optional<RequestDataPointDistanceToBeAbsorbedMessage> receivedRequestDataPointDistanceToBeAbsorbedMessage = Optional.empty();
private Optional<RequestClusterDistanceToBeAbsorbedMessage> receivedRequestClusterDistanceToBeAbsorbedMessage = Optional.empty();
private Optional<InformMostSimilarMessage> receivedInformMostSimilarClusterAgentsMessage = Optional.empty();
- private List<ClusterAgent<T>> requestDistanceMessageSentAgents = new ArrayList<>();
+ private final List<ClusterAgent<T>> requestDistanceMessageSentAgents = new ArrayList<>();
protected ClusterAgent(DynamicClusteringAMAS amas, T dataPoint) {
super(amas);
@@ -91,7 +87,6 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
if (receivedRequestClusterDistanceToBeAbsorbedMessage.isPresent()) {
if (logger.isLoggable(Level.INFO))
logger.info(this + " received a request for distance to be absorbed");
- return;
}
}
case WAITING_FOR_DISTANCE -> {
@@ -108,7 +103,7 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
private void clearDeadAgentsFromThoseWeExpectAnAnswerFrom() {
- requestDistanceMessageSentAgents.removeIf(a -> a.getState() == ClusterAgent.State.DEAD && !distancesReceived.keySet().contains(a));
+ requestDistanceMessageSentAgents.removeIf(a -> a.getState() == ClusterAgent.State.DEAD && !distancesReceived.containsKey(a));
for (var key :
distancesReceived.keySet()) {
if (!requestDistanceMessageSentAgents.contains(key))
@@ -118,6 +113,7 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
@Override
protected void onDecideAndAct() {
+ State nextState = null;
switch (state) {
case DORMANT -> {
if (receivedRequestDataPointDistanceToBeAbsorbedMessage.isPresent()) {
@@ -154,13 +150,6 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
} else {
nextState = State.DORMANT;
}
- } else if (amas.getMasSettings().amasOptions().contains(AMASOption.Forget)) {
- // TODO decide to die logic
- /*
- if (dieCondition()) {
- destroy();
- }
- */
}
}
case WAITING_FOR_DISTANCE -> {
@@ -197,19 +186,15 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
}
}
}
- applyNextState();
- }
-
-
- private void applyNextState() {
- state = nextState;
+ if (nextState != null)
+ state = nextState;
}
private void absorbDataPoint(T otherDataPoint) {
if (logger.isLoggable(Level.INFO))
logger.info(this + " absorbs the data point " + otherDataPoint);
- T newRepresentative = (T) amas.getMasSettings().dataPointFuser().apply(cluster.getRepresentative(), otherDataPoint);
+ amas.getMasSettings().dataPointFuser().apply(cluster.getRepresentative(), otherDataPoint);
cluster.addDataPoint(otherDataPoint);
}
@@ -218,8 +203,7 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
logger.info(this + " absorbs the cluster " + otherCluster);
amas.getMasSettings().dataPointFuser().apply(cluster.getRepresentative(), otherCluster.getRepresentative());
-
-
+
if (getAmas().getMasSettings().amasOptions().contains(AMASOption.KeepAllDataPoints))
((ExtendedCluster<T>) cluster).addClusterContent((ExtendedCluster<T>) otherCluster);
else
@@ -229,7 +213,7 @@ public class ClusterAgent<T extends DataPoint> extends Agent<DynamicClusteringAM
@Override
protected void onDestroy() {
- nextState = State.DEAD;
+ state = State.DEAD;
amas.getMasSettings().database().remove(cluster.getRepresentative());
getAmas().getEnvironment().removeFromBucket(cluster.getRepresentative().getBucketId(), this);
}
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/agent/DataPointAgent.java b/src/main/java/fr/irit/smac/amas4dc/amas/agent/DataPointAgent.java
index 87792ba..d525868 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/agent/DataPointAgent.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/agent/DataPointAgent.java
@@ -1,14 +1,13 @@
package fr.irit.smac.amas4dc.amas.agent;
import fr.irit.smac.amak.Agent;
-import fr.irit.smac.amas4dc.amas.ClusterDistance;
+import fr.irit.smac.amas4dc.cluster.distance.ClusterDistance;
import fr.irit.smac.amas4dc.amas.DynamicClusteringAMAS;
import fr.irit.smac.amas4dc.amas.DynamicClusteringEnvironment;
import fr.irit.smac.amas4dc.amas.messages.EvaluatedDistanceMessage;
import fr.irit.smac.amas4dc.amas.messages.InformMostSimilarMessage;
import fr.irit.smac.amas4dc.amas.messages.RequestDataPointDistanceToBeAbsorbedMessage;
-import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.text.MessageFormat;
import java.util.*;
@@ -16,11 +15,10 @@ import java.util.logging.Level;
import java.util.logging.Logger;
public class DataPointAgent<T extends DataPoint> extends Agent<DynamicClusteringAMAS<T>, DynamicClusteringEnvironment<T>> {
- private static final float FLOAT_COMPARISON_EPSILON = 0.000001f;
+ private static final Logger logger = Logger.getLogger(DataPointAgent.class.getName());
private final T dataPoint;
private final List<ClusterAgent<T>> requestDistanceMessageSentAgents = new ArrayList<>();
private final Map<ClusterAgent<T>, ClusterDistance<T>> distancesReceived = new HashMap<>();
- private static final Logger logger = Logger.getLogger(DataPointAgent.class.getName());
public DataPointAgent(DynamicClusteringAMAS<T> amas, T dataPoint) {
super(amas);
@@ -115,7 +113,7 @@ public class DataPointAgent<T extends DataPoint> extends Agent<DynamicClustering
}
private void clearDeadAgentsFromThoseWeExpectAnAnswerFrom() {
- requestDistanceMessageSentAgents.removeIf(a -> a.getState() == ClusterAgent.State.DEAD && !distancesReceived.keySet().contains(a));
+ requestDistanceMessageSentAgents.removeIf(a -> a.getState() == ClusterAgent.State.DEAD && !distancesReceived.containsKey(a));
for (var key :
distancesReceived.keySet()) {
if (!requestDistanceMessageSentAgents.contains(key))
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/controller/AMAS4DCCommandAndQueryHandler.java b/src/main/java/fr/irit/smac/amas4dc/amas/controller/AMAS4DCCommandAndQueryHandler.java
index f984f25..b33dfb9 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/controller/AMAS4DCCommandAndQueryHandler.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/controller/AMAS4DCCommandAndQueryHandler.java
@@ -10,9 +10,9 @@ import fr.irit.smac.amas4dc.amas.controller.query.ExtendedResult;
import fr.irit.smac.amas4dc.amas.controller.query.Result;
import fr.irit.smac.amas4dc.amas.controller.query.RetrieveClustersExtendedResultQuery;
import fr.irit.smac.amas4dc.amas.controller.query.RetrieveClustersResultQuery;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import fr.irit.smac.amas4dc.cluster.ExtendedCluster;
-import fr.irit.smac.amas4dc.cluster.SilhouetteScoreCalculator;
+import fr.irit.smac.amas4dc.cluster.evaluation.SilhouetteScoreCalculator;
import lombok.Getter;
import java.util.concurrent.Executors;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/controller/command/NewDataPointCommand.java b/src/main/java/fr/irit/smac/amas4dc/amas/controller/command/NewDataPointCommand.java
index 70c99e2..105ff84 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/controller/command/NewDataPointCommand.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/controller/command/NewDataPointCommand.java
@@ -1,6 +1,6 @@
package fr.irit.smac.amas4dc.amas.controller.command;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.util.List;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/ExtendedResult.java b/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/ExtendedResult.java
index 97ef4f1..5b42601 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/ExtendedResult.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/ExtendedResult.java
@@ -1,8 +1,7 @@
package fr.irit.smac.amas4dc.amas.controller.query;
import fr.irit.smac.amas4dc.amas.MASSettings;
-import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import fr.irit.smac.amas4dc.cluster.ExtendedCluster;
import java.util.List;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/Result.java b/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/Result.java
index 500d99e..2ee3487 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/Result.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/controller/query/Result.java
@@ -2,7 +2,7 @@ package fr.irit.smac.amas4dc.amas.controller.query;
import fr.irit.smac.amas4dc.amas.MASSettings;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.util.List;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/messages/EvaluatedDistanceMessage.java b/src/main/java/fr/irit/smac/amas4dc/amas/messages/EvaluatedDistanceMessage.java
index 18a885c..e813d5a 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/messages/EvaluatedDistanceMessage.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/messages/EvaluatedDistanceMessage.java
@@ -3,7 +3,7 @@ package fr.irit.smac.amas4dc.amas.messages;
import fr.irit.smac.amak.messaging.Message;
import fr.irit.smac.amas4dc.amas.agent.ClusterAgent;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import lombok.ToString;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/messages/InformMostSimilarMessage.java b/src/main/java/fr/irit/smac/amas4dc/amas/messages/InformMostSimilarMessage.java
index 5cf0d9b..c268633 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/messages/InformMostSimilarMessage.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/messages/InformMostSimilarMessage.java
@@ -3,9 +3,8 @@ package fr.irit.smac.amas4dc.amas.messages;
import fr.irit.smac.amak.Agent;
import fr.irit.smac.amak.messaging.Message;
import fr.irit.smac.amas4dc.amas.agent.ClusterAgent;
-import fr.irit.smac.amas4dc.amas.agent.DataPointAgent;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import java.util.List;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestClusterDistanceToBeAbsorbedMessage.java b/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestClusterDistanceToBeAbsorbedMessage.java
index af4c75a..dddbd42 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestClusterDistanceToBeAbsorbedMessage.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestClusterDistanceToBeAbsorbedMessage.java
@@ -3,7 +3,7 @@ package fr.irit.smac.amas4dc.amas.messages;
import fr.irit.smac.amak.messaging.Message;
import fr.irit.smac.amas4dc.amas.agent.ClusterAgent;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
public class RequestClusterDistanceToBeAbsorbedMessage<T extends DataPoint> extends Message<ClusterAgent<T>> {
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestDataPointDistanceToBeAbsorbedMessage.java b/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestDataPointDistanceToBeAbsorbedMessage.java
index 8610e88..273fefc 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestDataPointDistanceToBeAbsorbedMessage.java
+++ b/src/main/java/fr/irit/smac/amas4dc/amas/messages/RequestDataPointDistanceToBeAbsorbedMessage.java
@@ -2,7 +2,7 @@ package fr.irit.smac.amas4dc.amas.messages;
import fr.irit.smac.amak.messaging.Message;
import fr.irit.smac.amas4dc.amas.agent.DataPointAgent;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
public class RequestDataPointDistanceToBeAbsorbedMessage<T extends DataPoint> extends Message<DataPointAgent<T>> {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/Cluster.java b/src/main/java/fr/irit/smac/amas4dc/cluster/Cluster.java
index cb7330d..048d423 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/Cluster.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/Cluster.java
@@ -1,15 +1,10 @@
package fr.irit.smac.amas4dc.cluster;
-import fr.irit.smac.amas4dc.amas.controller.MissingDataPointsException;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import lombok.Setter;
import lombok.ToString;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.UUID;
-
@ToString
public class Cluster<T extends DataPoint> {
@Getter
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedCluster.java b/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedCluster.java
index fc4a7d4..5c5a116 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedCluster.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedCluster.java
@@ -1,9 +1,9 @@
package fr.irit.smac.amas4dc.cluster;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import lombok.Getter;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.List;
public class ExtendedCluster<T extends DataPoint> extends Cluster<T> {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPoint.java b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPoint.java
similarity index 61%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/DataPoint.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPoint.java
index ac62dcb..5199f76 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPoint.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPoint.java
@@ -1,4 +1,4 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.datapoint;
public interface DataPoint {
default int getBucketId() {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPointDatabase.java b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointDatabase.java
similarity index 88%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/DataPointDatabase.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointDatabase.java
index 0f8cb53..cb29e9b 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPointDatabase.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointDatabase.java
@@ -1,4 +1,4 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.datapoint;
import java.util.*;
import java.util.logging.Level;
@@ -6,7 +6,7 @@ import java.util.logging.Logger;
public class DataPointDatabase<T extends DataPoint> {
private static final Logger logger = Logger.getLogger(DataPointDatabase.class.getName());
- private Set<T> content = new HashSet<>();
+ private final Set<T> content = new HashSet<>();
private T lastModifiedDataPoint;
public void add(T newDataPoint) {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPointFuser.java b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointFuser.java
similarity index 72%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/DataPointFuser.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointFuser.java
index 9d833f0..90788b8 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/DataPointFuser.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/datapoint/DataPointFuser.java
@@ -1,4 +1,4 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.datapoint;
import java.util.function.BiFunction;
diff --git a/src/main/java/fr/irit/smac/amas4dc/amas/ClusterDistance.java b/src/main/java/fr/irit/smac/amas4dc/cluster/distance/ClusterDistance.java
similarity index 57%
rename from src/main/java/fr/irit/smac/amas4dc/amas/ClusterDistance.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/distance/ClusterDistance.java
index c454eb4..8165099 100644
--- a/src/main/java/fr/irit/smac/amas4dc/amas/ClusterDistance.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/distance/ClusterDistance.java
@@ -1,8 +1,8 @@
-package fr.irit.smac.amas4dc.amas;
+package fr.irit.smac.amas4dc.cluster.distance;
import fr.irit.smac.amas4dc.cluster.Cluster;
-import fr.irit.smac.amas4dc.cluster.DataPoint;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
public record ClusterDistance<T extends DataPoint>(Cluster<T> cluster, float distance) {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/DistanceMethod.java b/src/main/java/fr/irit/smac/amas4dc/cluster/distance/DistanceMethod.java
similarity index 55%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/DistanceMethod.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/distance/DistanceMethod.java
index 7d1f1bf..14046ee 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/DistanceMethod.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/distance/DistanceMethod.java
@@ -1,6 +1,8 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.distance;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
+
public interface DistanceMethod<T extends DataPoint> {
float apply(T dp1, T dp2);
boolean areRoughlySimilar(T dp1, T dp2);
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/CalinskiHarabazIndex.java b/src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/CalinskiHarabazIndex.java
similarity index 91%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/CalinskiHarabazIndex.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/CalinskiHarabazIndex.java
index 72bcbf1..9c95f33 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/CalinskiHarabazIndex.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/CalinskiHarabazIndex.java
@@ -1,6 +1,8 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.evaluation;
import fr.irit.smac.amas4dc.amas.MASSettings;
+import fr.irit.smac.amas4dc.cluster.ExtendedCluster;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.util.List;
@@ -11,7 +13,6 @@ public class CalinskiHarabazIndex<T extends DataPoint> {
var ssw = computeWithinClusterVariance(clusters, masSettings);
if (ssw == 0) {
- // Avoid division by zero
return Double.POSITIVE_INFINITY;
}
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/SilhouetteScoreCalculator.java b/src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/SilhouetteScoreCalculator.java
similarity index 92%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/SilhouetteScoreCalculator.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/SilhouetteScoreCalculator.java
index f389f58..065f4d6 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/SilhouetteScoreCalculator.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/evaluation/SilhouetteScoreCalculator.java
@@ -1,8 +1,10 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.evaluation;
import fr.irit.smac.amas4dc.amas.AMASOption;
import fr.irit.smac.amas4dc.amas.MASSettings;
import fr.irit.smac.amas4dc.amas.controller.MissingDataPointsException;
+import fr.irit.smac.amas4dc.cluster.ExtendedCluster;
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint;
import java.util.ArrayList;
import java.util.List;
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedClusterException.java b/src/main/java/fr/irit/smac/amas4dc/cluster/exception/ExtendedClusterException.java
similarity index 72%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedClusterException.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/exception/ExtendedClusterException.java
index 2ae326c..e005e93 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/ExtendedClusterException.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/exception/ExtendedClusterException.java
@@ -1,4 +1,4 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.exception;
public class ExtendedClusterException extends RuntimeException {
public ExtendedClusterException(String s) {
diff --git a/src/main/java/fr/irit/smac/amas4dc/cluster/FusionException.java b/src/main/java/fr/irit/smac/amas4dc/cluster/exception/FusionException.java
similarity index 71%
rename from src/main/java/fr/irit/smac/amas4dc/cluster/FusionException.java
rename to src/main/java/fr/irit/smac/amas4dc/cluster/exception/FusionException.java
index f81880e..542709b 100644
--- a/src/main/java/fr/irit/smac/amas4dc/cluster/FusionException.java
+++ b/src/main/java/fr/irit/smac/amas4dc/cluster/exception/FusionException.java
@@ -1,4 +1,4 @@
-package fr.irit.smac.amas4dc.cluster;
+package fr.irit.smac.amas4dc.cluster.exception;
public class FusionException extends RuntimeException {
public FusionException(String message) {
diff --git a/src/test/groovy/SimpleClusteringIT.groovy b/src/test/groovy/SimpleClusteringIT.groovy
index ba75ddc..fdbd112 100644
--- a/src/test/groovy/SimpleClusteringIT.groovy
+++ b/src/test/groovy/SimpleClusteringIT.groovy
@@ -1,9 +1,9 @@
import fr.irit.smac.amas4dc.AMAS4DC
import fr.irit.smac.amas4dc.amas.AMASOption
import fr.irit.smac.amas4dc.amas.MASSettings
-import fr.irit.smac.amas4dc.cluster.DataPoint
-import fr.irit.smac.amas4dc.cluster.DataPointDatabase
-import fr.irit.smac.amas4dc.cluster.DistanceMethod
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPointDatabase
+import fr.irit.smac.amas4dc.cluster.distance.DistanceMethod
import spock.lang.Specification
class SimpleClusteringIT extends Specification {
diff --git a/src/test/groovy/fr/irit/smac/amas4dc/amas/ClusterAgentTest.groovy b/src/test/groovy/fr/irit/smac/amas4dc/amas/ClusterAgentTest.groovy
index a485f34..842141c 100644
--- a/src/test/groovy/fr/irit/smac/amas4dc/amas/ClusterAgentTest.groovy
+++ b/src/test/groovy/fr/irit/smac/amas4dc/amas/ClusterAgentTest.groovy
@@ -8,9 +8,9 @@ import fr.irit.smac.amas4dc.amas.messages.EvaluatedDistanceMessage
import fr.irit.smac.amas4dc.amas.messages.RequestClusterDistanceToBeAbsorbedMessage
import fr.irit.smac.amas4dc.amas.messages.RequestDataPointDistanceToBeAbsorbedMessage
import fr.irit.smac.amas4dc.cluster.Cluster
-import fr.irit.smac.amas4dc.cluster.DataPoint
-import fr.irit.smac.amas4dc.cluster.DataPointFuser
-import fr.irit.smac.amas4dc.cluster.DistanceMethod
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPoint
+import fr.irit.smac.amas4dc.cluster.datapoint.DataPointFuser
+import fr.irit.smac.amas4dc.cluster.distance.DistanceMethod
import spock.lang.Specification
import spock.util.concurrent.BlockingVariable
--
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