From 9a33c25272200cf4a16b1bc08a89b5f87b4353db Mon Sep 17 00:00:00 2001
From: "a.croix" <croix.alexandre@gmail.com>
Date: Mon, 11 Mar 2019 17:44:12 +0100
Subject: [PATCH] Implementation of Point class + Roc class + Utils class +
RocCoordinates class
---
java-roc.iml | 21 +-
pom.xml | 210 ++++++++++++++++++
src/main/java/be/cylab/java/roc/Point.java | 42 ++++
src/main/java/be/cylab/java/roc/Roc.java | 91 ++++++++
.../be/cylab/java/roc/RocCoordinates.java | 36 +++
src/main/java/be/cylab/java/roc/Utils.java | 26 +++
6 files changed, 422 insertions(+), 4 deletions(-)
create mode 100644 pom.xml
create mode 100644 src/main/java/be/cylab/java/roc/Point.java
create mode 100644 src/main/java/be/cylab/java/roc/Roc.java
create mode 100644 src/main/java/be/cylab/java/roc/RocCoordinates.java
create mode 100644 src/main/java/be/cylab/java/roc/Utils.java
diff --git a/java-roc.iml b/java-roc.iml
index 8021953..cd80409 100644
--- a/java-roc.iml
+++ b/java-roc.iml
@@ -1,9 +1,22 @@
<?xml version="1.0" encoding="UTF-8"?>
-<module type="WEB_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="true">
- <exclude-output />
- <content url="file://$MODULE_DIR$" />
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" version="4">
+ <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
+ <output url="file://$MODULE_DIR$/target/classes" />
+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
+ <content url="file://$MODULE_DIR$">
+ <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.junit.jupiter:junit-jupiter-api:5.3.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.apiguardian:apiguardian-api:1.0.0" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.opentest4j:opentest4j:1.1.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.junit.platform:junit-platform-commons:1.3.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.junit.jupiter:junit-jupiter-params:5.3.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.junit.jupiter:junit-jupiter-engine:5.3.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.junit.platform:junit-platform-engine:1.3.1" level="project" />
</component>
</module>
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..ae47e60
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,210 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>be.cylab</groupId>
+ <artifactId>java-roc</artifactId>
+ <version>1.0-SNAPSHOT</version>
+
+ <name>${project.artifactId}</name>
+ <url>https://gitlab.cylab.be/cylab/java-roc</url>
+ <description>Java library to compute ROC curve and AUC</description>
+
+ <licenses>
+ <license>
+ <name>MIT License</name>
+ <url>http://www.opensource.org/licenses/mit-license.php</url>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <name>Alexandre Croix</name>
+ <email>alexandre.croix@rma.ac.be</email>
+ <organization>cylab.be</organization>
+ <organizationUrl>https://cylab.be</organizationUrl>
+ </developer>
+ </developers>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.junit.jupiter</groupId>
+ <artifactId>junit-jupiter-api</artifactId>
+ <version>5.3.1</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>org.junit.jupiter</groupId>
+ <artifactId>junit-jupiter-params</artifactId>
+ <version>5.3.1</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>org.junit.jupiter</groupId>
+ <artifactId>junit-jupiter-engine</artifactId>
+ <version>5.3.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <!-- leave this one first, to be sure we use this recent version -->
+ <plugin>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.22.1</version>
+ </plugin>
+
+ <!-- to deploy to sonatype maven repository -->
+ <plugin>
+ <groupId>org.sonatype.plugins</groupId>
+ <artifactId>nexus-staging-maven-plugin</artifactId>
+ <version>1.6.8</version>
+ <extensions>true</extensions>
+ <configuration>
+ <serverId>ossrh</serverId>
+ <nexusUrl>https://oss.sonatype.org/</nexusUrl>
+ <autoReleaseAfterClose>true</autoReleaseAfterClose>
+ </configuration>
+ </plugin>
+
+ <!-- to create a jar containing the sources -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-source-plugin</artifactId>
+ <version>3.0.1</version>
+ <executions>
+ <execution>
+ <id>attach-sources</id>
+ <goals>
+ <goal>jar-no-fork</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+
+ <!-- to create a jar containing the javadoc -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.9.1</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <id>attach-javadocs</id>
+ <goals>
+ <goal>jar</goal>
+ </goals>
+ <configuration>
+ <additionalparam>${javadoc.opts}</additionalparam>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ <!-- To tag the release in git repository -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-release-plugin</artifactId>
+ <version>2.5.3</version>
+ <configuration>
+ <tagNameFormat>v@{project.version}</tagNameFormat>
+ </configuration>
+ </plugin>
+
+ <!-- to sign the jars with a GPG key -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-gpg-plugin</artifactId>
+ <version>1.6</version>
+ <executions>
+ <execution>
+ <id>sign-artifacts</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>sign</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+
+ <!-- To check that there are no unused dependencies -->
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.10</version>
+ <executions>
+ <execution>
+ <id>dependency-analyze</id>
+ <phase>test</phase>
+ <configuration>
+ <failOnWarning>true</failOnWarning>
+ <ignoreNonCompile>false</ignoreNonCompile>
+ <ignoredDependencies>
+ <ignoreDependency>org.junit.jupiter:junit-jupiter-engine:*</ignoreDependency>
+ <ignoreDependency>org.junit.jupiter:junit-jupiter-params:*</ignoreDependency>
+ </ignoredDependencies>
+ </configuration>
+ <goals>
+ <goal>analyze-only</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+
+ <!-- To check that we don't use -SNAPSHOT dependencies -->
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-enforcer-plugin</artifactId>
+ <version>3.0.0-M1</version>
+ <executions>
+ <execution>
+ <id>enforce-no-snapshots</id>
+ <goals>
+ <goal>enforce</goal>
+ </goals>
+ <configuration>
+ <rules>
+ <requireReleaseDeps>
+ <message>No Snapshots Allowed!</message>
+ </requireReleaseDeps>
+ </rules>
+ <fail>true</fail>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-checkstyle-plugin</artifactId>
+ <version>2.16</version>
+ <executions>
+ <execution>
+ <id>validate</id>
+ <phase>verify</phase>
+ <configuration>
+ <configLocation>checkstyle.xml</configLocation>
+ <encoding>UTF-8</encoding>
+ <consoleOutput>true</consoleOutput>
+ <linkXRef>false</linkXRef>
+ </configuration>
+ <goals>
+ <goal>check</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <maven.compiler.source>1.8</maven.compiler.source>
+ <maven.compiler.target>1.8</maven.compiler.target>
+ </properties>
+
+
+
+</project>
\ No newline at end of file
diff --git a/src/main/java/be/cylab/java/roc/Point.java b/src/main/java/be/cylab/java/roc/Point.java
new file mode 100644
index 0000000..b475816
--- /dev/null
+++ b/src/main/java/be/cylab/java/roc/Point.java
@@ -0,0 +1,42 @@
+package be.cylab.java.roc;
+
+public class Point implements Comparable<Point>{
+
+ private double score;
+ private boolean true_alert;
+
+ public Point(final double score, final boolean true_alert) {
+ this.setScore(score);
+ this.setTrueAlert(true_alert);
+ }
+
+ @Override
+ public final int compareTo(final Point point) {
+ if (this.score > point.score) {
+ return -1;
+ } else if (this.score < point.score) {
+ return 1;
+ } else {
+ return 0;
+ }
+ }
+
+ public void setScore(double score) {
+ if (score < 0 || score > 1) {
+ throw new IllegalArgumentException("Score must be between 0 and 1");
+ }
+ this.score = score;
+ }
+
+ public void setTrueAlert(boolean true_alert) {
+ this.true_alert = true_alert;
+ }
+
+ public double getScore() {
+ return score;
+ }
+
+ public boolean isTrueAlert() {
+ return true_alert;
+ }
+}
diff --git a/src/main/java/be/cylab/java/roc/Roc.java b/src/main/java/be/cylab/java/roc/Roc.java
new file mode 100644
index 0000000..64e2eff
--- /dev/null
+++ b/src/main/java/be/cylab/java/roc/Roc.java
@@ -0,0 +1,91 @@
+package be.cylab.java.roc;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+public class Roc {
+
+ private List<Point> points;
+ private int positive_examples_number;
+ private int negative_examples_number;
+
+
+ public Roc(double[] score, boolean[] true_alert) {
+ if (score.length != true_alert.length) {
+ throw new IllegalStateException(
+ "Score array and true alert array must be the same size");
+ }
+ for (int i = 0; i < score.length; i++) {
+ Point point = new Point(score[i], true_alert[i]);
+ this.points.add(point);
+ }
+ Collections.sort(points);
+ positive_examples_number = Utils.countPositiveExamples(this.points);
+ negative_examples_number = Utils.countNegativeExamples(this.points);
+ }
+
+ public List<RocCoordinates> computeRocPoints() {
+ int true_positive = 0;
+ int false_positive = 0;
+ List<RocCoordinates> roc_points = new ArrayList<>();
+ double previous_score = Double.NEGATIVE_INFINITY;
+ for (Point point : this.points) {
+ if (point.getScore() != previous_score) {
+ double true_detection = true_positive / positive_examples_number;
+ double false_alarm = false_positive /negative_examples_number;
+ roc_points.add(new RocCoordinates(true_detection, false_alarm));
+ previous_score = point.getScore();
+ }
+ if (point.getScore() == 1) {
+ true_positive++;
+ } else {
+ false_positive++;
+ }
+ }
+ double true_detection = true_positive / positive_examples_number;
+ double false_alarm = false_positive /negative_examples_number;
+ roc_points.add(new RocCoordinates(true_detection, false_alarm));
+ return roc_points;
+ }
+
+
+ public double computeAUC() {
+ int false_positive = 0;
+ int true_positive = 0;
+ int previous_false_positive = 0;
+ int previous_true_positive = 0;
+ double area = 0;
+ double previous_score = Double.NEGATIVE_INFINITY;
+ for (Point point : this.points) {
+ if (point.getScore() != previous_score) {
+ area += this.trapezoidArea(
+ false_positive,
+ previous_false_positive,
+ true_positive,
+ previous_true_positive);
+ previous_score = point.getScore();
+ previous_false_positive = false_positive;
+ previous_true_positive = true_positive;
+ }
+ if (point.isTrueAlert()) {
+ true_positive++;
+ } else {
+ false_positive++;
+ }
+ area += this.trapezoidArea(
+ false_positive,
+ previous_false_positive,
+ true_positive,
+ previous_true_positive);
+ }
+ return (area / (positive_examples_number * negative_examples_number));
+ }
+
+ private double trapezoidArea(double x1, double x2, double y1, double y2) {
+ double base = Math.abs(x1 - x2);
+ double height_average = (y1 + y2) / 2;
+ return (base * height_average);
+ }
+
+}
diff --git a/src/main/java/be/cylab/java/roc/RocCoordinates.java b/src/main/java/be/cylab/java/roc/RocCoordinates.java
new file mode 100644
index 0000000..f037241
--- /dev/null
+++ b/src/main/java/be/cylab/java/roc/RocCoordinates.java
@@ -0,0 +1,36 @@
+package be.cylab.java.roc;
+
+public class RocCoordinates {
+
+ private double false_alarm;
+ private double true_detection;
+
+ public RocCoordinates(double false_alarm, double true_detection) {
+ this.setFalseAlarm(false_alarm);
+ this.setTrueDetection(true_detection);
+ }
+
+ public double getFalseAlarm() {
+ return false_alarm;
+ }
+
+ public void setFalseAlarm(double false_alarm) {
+ if (false_alarm < 0 || false_alarm > 1) {
+ throw new IllegalArgumentException("" +
+ "False alarm must be between 0 and 1");
+ }
+ this.false_alarm = false_alarm;
+ }
+
+ public double getTrueDetection() {
+ return true_detection;
+ }
+
+ public void setTrueDetection(double true_detection) {
+ if (true_detection < 0 || true_detection > 1) {
+ throw new IllegalArgumentException(
+ "True detection value must be between 0 and 1");
+ }
+ this.true_detection = true_detection;
+ }
+}
diff --git a/src/main/java/be/cylab/java/roc/Utils.java b/src/main/java/be/cylab/java/roc/Utils.java
new file mode 100644
index 0000000..06aa542
--- /dev/null
+++ b/src/main/java/be/cylab/java/roc/Utils.java
@@ -0,0 +1,26 @@
+package be.cylab.java.roc;
+
+import java.util.List;
+
+public class Utils {
+
+ public static int countPositiveExamples(final List<Point> points) {
+ int positive_examples = 0;
+ for (Point point : points) {
+ if (point.isTrueAlert()) {
+ positive_examples++;
+ }
+ }
+ return positive_examples;
+ }
+
+ public static int countNegativeExamples(final List<Point> points) {
+ int negative_examples = 0;
+ for (Point point : points) {
+ if (!point.isTrueAlert()) {
+ negative_examples++;
+ }
+ }
+ return negative_examples;
+ }
+}
--
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