From d46f209f3202b79488b8598d06d0c1d2cdf95816 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Tue, 2 Jul 2024 19:33:35 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 41 ++-
pom.xml | 6 +-
.../CanonicalProgramParameters.java | 3 +-
.../CanonicalSimplexProgram.java | 274 ++++++++++--------
.../LinearProgrammingICYPlugin.java | 18 +-
.../SimplexBLAND.java | 8 +-
.../SimplexLEXICO.java | 8 +-
.../SimplexMAX.java | 8 +-
.../TableauMinSlackObjective.java | 7 +-
.../TableauWithSlackVariables.java | 46 +--
src/main/resources/linear-programming.png | Bin 0 -> 3286 bytes
11 files changed, 251 insertions(+), 168 deletions(-)
create mode 100644 src/main/resources/linear-programming.png
diff --git a/.gitignore b/.gitignore
index b0a9905..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,41 @@
-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
+.factorypath
.project
-**/.DS_Store
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 18fcc24..4ae3a2f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>linear-programming</artifactId>
- <version>2.0.0</version>
+ <version>2.0.0-a.1</version>
<name>Linear Programming</name>
<description>
@@ -26,7 +26,7 @@
<repositories>
<repository>
<id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalProgramParameters.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalProgramParameters.java
index 2c85ae2..3ace13d 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalProgramParameters.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalProgramParameters.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -45,7 +45,6 @@ package plugins.nchenouard.linearprogrammingfullsimplex;
*
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
-
public class CanonicalProgramParameters {
/**
* The objective function coefficient: c'*x or sum_i c[i]*x[i] for the variable x.
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
index d54cfb9..64ddf5e 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,9 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
-import icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import java.io.*;
@@ -45,7 +47,6 @@ import java.io.*;
*
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
-
public abstract class CanonicalSimplexProgram {
/**
* Parameters defining the linear programming problem
@@ -86,7 +87,7 @@ public abstract class CanonicalSimplexProgram {
* @param equality indicates whether each constraint is an equality. Else it is
* <=.
*/
- public CanonicalSimplexProgram(final double[][] A, final double[] b, final double[] c, final boolean maximization, final boolean[] equality) {
+ public CanonicalSimplexProgram(final double[][] A, final double @NotNull [] b, final double @NotNull [] c, final boolean maximization, final boolean[] equality) {
this.parameters = new CanonicalProgramParameters();
this.parameters.A = A;
this.parameters.b = b;
@@ -102,7 +103,8 @@ public abstract class CanonicalSimplexProgram {
*
* @param p Parameters of the linear programming problem.
*/
- public CanonicalSimplexProgram(final CanonicalProgramParameters p) {
+ @Contract(pure = true)
+ public CanonicalSimplexProgram(final @NotNull CanonicalProgramParameters p) {
this.parameters = p;
this.numVariables = p.c.length;
this.numConstraints = p.b.length;
@@ -224,7 +226,7 @@ public abstract class CanonicalSimplexProgram {
// Canonical form: initial tableau is built by introducing unit vectors
solvePhaseICanonicalSimplex();
if (verbose) {
- System.out.println("Tableau after phase 1 :");
+ IcyLogger.trace(this.getClass(), "Tableau after phase 1: ");
tableau0.printTableau();
}
// Phase II: optimisation by Gauss-Jordan replacement of non-basic columns
@@ -269,7 +271,7 @@ public abstract class CanonicalSimplexProgram {
if (!success)
return false;
if (verbose) {
- System.out.println("Phase 1 ");
+ IcyLogger.trace(this.getClass(), "Phase 1 ");
tableau0.printTableau();
}
if (Math.abs(tableau0.scoreValue) < tol) // optimal score should be 0
@@ -337,22 +339,22 @@ public abstract class CanonicalSimplexProgram {
}
else {
if (verbose)
- System.out.println("replacement: row = " + rowIdx + ", column = " + colIdx);
+ IcyLogger.trace(this.getClass(), "replacement: row = " + rowIdx + ", column = " + colIdx);
tableau.pivot(colIdx, rowIdx);
}
}
if (verbose) {
- System.out.println("Tableau at iteration:");
+ IcyLogger.trace(this.getClass(), "Tableau at iteration: ");
tableau.printTableau();
}
}
if (verbose) {
- System.out.println("Final tableau:");
+ IcyLogger.trace(this.getClass(), "Final tableau: ");
tableau.printTableau();
}
if (!feasible) {
if (verbose)
- System.out.println("UNFEASIBLE problem");
+ IcyLogger.trace(this.getClass(), "UNFEASIBLE problem");
return false;
}
else {
@@ -404,7 +406,7 @@ public abstract class CanonicalSimplexProgram {
for (int j = 0; j < solution.length; j++) {
v += A0[i][j] * solution[j];
}
- System.out.println(v + "<?>" + b0[i]);
+ IcyLogger.info(this.getClass(), v + "<?>" + b0[i]);
}
}
}
@@ -465,36 +467,35 @@ public abstract class CanonicalSimplexProgram {
public void displayProblem() {
- System.out.println("Linear Programming problem max c'x st. Ax <= b, x >= 0 and some equality contraints defined by eq");
+ IcyLogger.info(this.getClass(), "Linear Programming problem max c'x st. Ax <= b, x >= 0 and some equality contraints defined by eq");
if (parameters.maximization)
- System.out.println("Maximization problem");
+ IcyLogger.info(this.getClass(), "Maximization problem");
else
- System.out.println("Minimization problem");
- System.out.print("c = [");
+ IcyLogger.info(this.getClass(), "Minimization problem");
+ IcyLogger.info(this.getClass(), "c = [");
for (int i = 0; i < parameters.c.length; i++)
- System.out.print(parameters.c[i] + ", ");
- System.out.println("]");
- System.out.print("b = [");
+ IcyLogger.info(this.getClass(), parameters.c[i] + ", ");
+ IcyLogger.info(this.getClass(), "]");
+ IcyLogger.info(this.getClass(), "b = [");
for (int i = 0; i < parameters.b.length; i++)
- System.out.print(parameters.b[i] + ", ");
- System.out.println("]");
- System.out.print("eq = [");
+ IcyLogger.info(this.getClass(), parameters.b[i] + ", ");
+ IcyLogger.info(this.getClass(), "]");
+ IcyLogger.info(this.getClass(), "eq = [");
for (int i = 0; i < parameters.equalityConstraints.length; i++)
- System.out.print(parameters.equalityConstraints[i] + ", ");
- System.out.println("]");
- System.out.print("A = [");
+ IcyLogger.info(this.getClass(), parameters.equalityConstraints[i] + ", ");
+ IcyLogger.info(this.getClass(), "]");
+ IcyLogger.info(this.getClass(), "A = [");
for (int i = 0; i < parameters.A.length; i++) {
- System.out.print("[");
+ IcyLogger.info(this.getClass(), "[");
for (int j = 0; j < parameters.A[i].length; j++)
- System.out.print(parameters.A[i][j] + ", ");
- System.out.println("],");
+ IcyLogger.info(this.getClass(), parameters.A[i][j] + ", ");
+ IcyLogger.info(this.getClass(), "],");
}
- System.out.println("]");
+ IcyLogger.info(this.getClass(), "]");
}
public void displayProblemTutorial() {
- System.out.println("Linear Programming problem:");
- System.out.println();
+ IcyLogger.info(this.getClass(), "Linear Programming problem:");
StringBuilder line = new StringBuilder();
if (parameters.maximization)
line.append("max_x");
@@ -507,10 +508,8 @@ public abstract class CanonicalSimplexProgram {
else
line.append(" - ").append(Math.abs(parameters.c[i])).append("*x[").append(i).append("]");
}
- System.out.println(line);
- System.out.println();
- System.out.println("Such that x >= 0 and:");
- System.out.println();
+ IcyLogger.info(this.getClass(), line.toString());
+ IcyLogger.info(this.getClass(), "Such that x >= 0 and:");
for (int i = 0; i < parameters.b.length; i++) {
line = new StringBuilder();
for (int j = 0; j < parameters.A[i].length; j++) {
@@ -524,7 +523,7 @@ public abstract class CanonicalSimplexProgram {
else
line.append(" <= ");
line.append(parameters.b[i]);
- System.out.println(line);
+ IcyLogger.info(this.getClass(), line.toString());
}
}
@@ -532,30 +531,31 @@ public abstract class CanonicalSimplexProgram {
* @return Manual of the library for stand-alone use through command line
*/
public static String getHelp() {
- return "Run the solver for example problems or for a user-defined system\n"
- + "Empty arguments to use the default example.\n"
- + "Enter an integer from 0 to 3 for different example scenarios.\n"
- + "Enter -1 for a user-defined scenario through text files.\n "
- + "For custom scenarios, enter filenames (text files) for different parameters of the problem preceded by the appropriate prefix:\n"
- + "-c for the objective function file.\n"
- + "-A for constraint matrix file.\n"
- + "-b for the constraint value file.\n"
- + "-e for the equality constraint file.\n"
- + "-max or -min to indicate a maximization or minimization problem, respectively. Default in minimization.\n"
- + "Example arguments: java -jar linearProgrammingICY.jar -c c.txt -A A.txt -b b.txt -e eq.txt -max -o solution.txt"
- + "Each text file must contain a series of double values separated by ',' in a single line, except for the constraint file which contains one line per constraint.\n"
- + "For the equality file '0' stands for 'false' and '1' for true.\n\n"
- + "Version 1.0. April 2014. Author: Nicolas Chenouard. nicolas.chenouard.dev@gmail.com. Licence GPL V3.0";
+ return """
+ Run the solver for example problems or for a user-defined system
+ Empty arguments to use the default example.
+ Enter an integer from 0 to 3 for different example scenarios.
+ Enter -1 for a user-defined scenario through text files.
+ For custom scenarios, enter filenames (text files) for different parameters of the problem preceded by the appropriate prefix:
+ -c for the objective function file.
+ -A for constraint matrix file.
+ -b for the constraint value file.
+ -e for the equality constraint file.
+ -max or -min to indicate a maximization or minimization problem, respectively. Default in minimization.
+ Example arguments: java -jar linearProgrammingICY.jar -c c.txt -A A.txt -b b.txt -e eq.txt -max -o solution.txt\
+ Each text file must contain a series of double values separated by ',' in a single line, except for the constraint file which contains one line per constraint.
+ For the equality file '0' stands for 'false' and '1' for true.
+
+ Version 1.0. April 2014. Author: Nicolas Chenouard. nicolas.chenouard.dev@gmail.com. Licence GPL V3.0""";
}
/**
* Display the manual of the library for stand-alone use through command line
*/
public static void displayHelp() {
- System.out.println(getHelp());
+ IcyLogger.info(CanonicalSimplexProgram.class, getHelp());
}
-
/**
* Run the solver for example problems or for a user-defined system
*
@@ -575,7 +575,7 @@ public abstract class CanonicalSimplexProgram {
* Each text file must contain a series of double values separated by ',' in a single line, except for the constraint file which contains one line per constraint.
* For the equality file '0' stands for 'false' and '1' for true.
*/
- public static void main(final String[] args) {
+ public static void main(final String @NotNull [] args) {
int scenario = 0;
if (args.length > 0) {
if (args[0].compareTo("-h") == 0 || args[0].compareTo("-help") == 0 || args[0].compareTo("--h") == 0 || args[0].compareTo("--help") == 0) {
@@ -587,20 +587,28 @@ public abstract class CanonicalSimplexProgram {
scenario = Integer.parseInt(args[0]);
}
catch (final NumberFormatException e) {
- System.out.println("Invalid input argument");
- System.out.println("Use input option -help to display the manual of the software");
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Invalid input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
}
}
else {
- System.out.println("Solving a default simple linear problem with the Simplex algorithm.");
- System.out.println("Enter -help for the manual explicating the customization options.");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "Solving a default simple linear problem with the Simplex algorithm.",
+ "Enter -help for the manual explicating the customization options."
+ );
}
if (scenario < -1 || scenario > 3) {
- System.out.println("Invalid input argument");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Invalid input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
boolean maximization = false;
@@ -633,8 +641,11 @@ public abstract class CanonicalSimplexProgram {
}
}
if (fileA == null) {
- System.out.println("Missing -A input argument");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Missing -A input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
String fileB = null;
@@ -645,8 +656,11 @@ public abstract class CanonicalSimplexProgram {
}
}
if (fileB == null) {
- System.out.println("Missing -b input argument");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Missing -b input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
@@ -658,8 +672,11 @@ public abstract class CanonicalSimplexProgram {
}
}
if (fileC == null) {
- System.out.println("Missing -c input argument");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Missing -c input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
for (int i = 0; i < args.length - 1; i++) {
@@ -676,8 +693,11 @@ public abstract class CanonicalSimplexProgram {
}
}
if (fileE == null) {
- System.out.println("Missing -e input argument");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Missing -e input argument",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
try {
@@ -738,15 +758,18 @@ public abstract class CanonicalSimplexProgram {
fis.close();
}
catch (final IOException e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(CanonicalSimplexProgram.class, e);
return;
}
break;
}
case 0: {
- System.out.println("Basic example with 3 pivots");
- System.out.println("Optimal is 6.5");
- System.out.println("Solution is [1.0, 1.0, 0.5, 0.0]");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "Basic example with 3 pivots",
+ "Optimal is 6.5",
+ "Solution is [1.0, 1.0, 0.5, 0.0]"
+ );
A = new double[][]{{2, 1, 0, 0},
{0, 1, 4, 1},
{1, 3, 0, 1}
@@ -758,9 +781,12 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 1: {
- System.out.println("Example that would cycle with Bland rule.");
- System.out.println("Optimal score is 1/20.");
- System.out.println("Solution is [1/25, 0, 1, 0].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "Example that would cycle with Bland rule.",
+ "Optimal score is 1/20.",
+ "Solution is [1/25, 0, 1, 0]."
+ );
A = new double[][]{{1d / 4, -60, -1d / 25, 9},
{1d / 2, -90, -1d / 50, 3},
{0, 0, 1, 0}
@@ -772,8 +798,11 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 2: {
- System.out.println("An example with equality constraints");
- System.out.println("Solution is [0, 4/7, 1 + 5/7, 0, 0].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "An example with equality constraints",
+ "Solution is [0, 4/7, 1 + 5/7, 0, 0]."
+ );
A = new double[][]
{{5, -4, 13, -2, 1},
{1, -1, 5, -1, 1},
@@ -785,9 +814,12 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 3: {
- System.out.println("An example with equality constraints and negative right-hand-side");
- System.out.println("Optimal score is -3 - 1/16.");
- System.out.println("Solution is [3/16, 1 + 1/4, 0, 5/16].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "An example with equality constraints and negative right-hand-side",
+ "Optimal score is -3 - 1/16.",
+ "Solution is [3/16, 1 + 1/4, 0, 5/16]."
+ );
A = new double[][]
{{1, 2, 1, 1},
{1, -2, 2, 1},
@@ -800,8 +832,11 @@ public abstract class CanonicalSimplexProgram {
}
}
if (A == null || b == null || c == null || equality == null) {
- System.out.println("Missing arguments");
- System.out.println("Use input option -help to display the manual of the software");
+ IcyLogger.error(
+ CanonicalSimplexProgram.class,
+ "Missing arguments",
+ "Use input option -help to display the manual of the software"
+ );
return;
}
final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
@@ -811,21 +846,21 @@ public abstract class CanonicalSimplexProgram {
if (program.solvePrimalSimplex()) {
final double[] solution = program.solution;
if (verbose) {
- System.out.print("Computed solution = [");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed solution = [");
for (final double value : solution)
- System.out.print(value + ", ");
- System.out.println("]");
- System.out.println("Computed score = " + program.tableau0.scoreValue);
- System.out.println("Computed constraint values:");
+ IcyLogger.trace(CanonicalSimplexProgram.class, value + ", ");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "]");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed score = " + program.tableau0.scoreValue);
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed constraint values:");
for (int i = 0; i < A.length; i++) {
double v = 0;
// compute the constraint
for (int j = 0; j < A[i].length; j++)
v += A[i][j] * solution[j];
if (equality[i])
- System.out.println(v + " == " + b[i]);
+ IcyLogger.trace(CanonicalSimplexProgram.class, v + " == " + b[i]);
else
- System.out.println(v + " <= " + b[i]);
+ IcyLogger.trace(CanonicalSimplexProgram.class, v + " <= " + b[i]);
}
}
if (outputFile != null) {
@@ -841,19 +876,18 @@ public abstract class CanonicalSimplexProgram {
out.close();
}
catch (final IOException e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(CanonicalSimplexProgram.class, e);
}
}
}
else {
- System.out.println("Solve simplex failed");
+ IcyLogger.error(CanonicalSimplexProgram.class, "Solve simplex failed");
}
}
public static void runExampleScenario(final int scenario) {
if (scenario < 0 || scenario > 3) {
- System.out.println("Invalid input argument");
- System.out.println("Scenario indices are: 0, 1, 2 and 3");
+ IcyLogger.error(CanonicalSimplexProgram.class, "Invalid input argument", "Scenario indices are: 0, 1, 2 and 3");
return;
}
boolean maximization = false;
@@ -864,9 +898,12 @@ public abstract class CanonicalSimplexProgram {
final boolean verbose = true;
switch (scenario) {
case 0: {
- System.out.println("Basic example with 3 pivots");
- System.out.println("Optimal score is 6.5");
- System.out.println("Solution is [1.0, 1.0, 0.5, 0.0]");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "Basic example with 3 pivots",
+ "Optimal score is 6.5",
+ "Solution is [1.0, 1.0, 0.5, 0.0]"
+ );
A = new double[][]{{2, 1, 0, 0},
{0, 1, 4, 1},
{1, 3, 0, 1}
@@ -878,9 +915,12 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 1: {
- System.out.println("Example that would cycle with Bland rule.");
- System.out.println("Optimal score is 1/20.");
- System.out.println("Solution is [1/25, 0, 1, 0].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "Example that would cycle with Bland rule.",
+ "Optimal score is 1/20.",
+ "Solution is [1/25, 0, 1, 0]."
+ );
A = new double[][]{{1d / 4, -60, -1d / 25, 9},
{1d / 2, -90, -1d / 50, 3},
{0, 0, 1, 0}
@@ -892,8 +932,11 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 2: {
- System.out.println("An example with equality constraints");
- System.out.println("Solution is [0, 4/7, 1 + 5/7, 0, 0].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "An example with equality constraints",
+ "Solution is [0, 4/7, 1 + 5/7, 0, 0]."
+ );
A = new double[][]
{{5, -4, 13, -2, 1},
{1, -1, 5, -1, 1},
@@ -905,9 +948,12 @@ public abstract class CanonicalSimplexProgram {
break;
}
case 3: {
- System.out.println("An example with equality constraints and negative right-hand-side");
- System.out.println("Optimal score is -3 - 1/16.");
- System.out.println("Solution is [3/16, 1 + 1/4, 0, 5/16].");
+ IcyLogger.info(
+ CanonicalSimplexProgram.class,
+ "An example with equality constraints and negative right-hand-side",
+ "Optimal score is -3 - 1/16.",
+ "Solution is [3/16, 1 + 1/4, 0, 5/16]."
+ );
A = new double[][]
{{1, 2, 1, 1},
{1, -2, 2, 1},
@@ -922,35 +968,31 @@ public abstract class CanonicalSimplexProgram {
}
final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
if (verbose) {
- System.out.println();
program.displayProblemTutorial();
}
if (program.solvePrimalSimplex()) {
final double[] solution = program.solution;
if (verbose) {
- System.out.println();
- System.out.print("Computed solution = [");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed solution = [");
for (final double value : solution)
- System.out.print(value + ", ");
- System.out.println("]");
- System.out.println();
- System.out.println("Computed score = " + program.tableau0.scoreValue);
- System.out.println();
- System.out.println("Computed constraint values:");
+ IcyLogger.trace(CanonicalSimplexProgram.class, value + ", ");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "]");
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed score = " + program.tableau0.scoreValue);
+ IcyLogger.trace(CanonicalSimplexProgram.class, "Computed constraint values:");
for (int i = 0; i < A.length; i++) {
double v = 0;
// compute the constraint
for (int j = 0; j < A[i].length; j++)
v += A[i][j] * solution[j];
if (equality[i])
- System.out.println(v + " == " + b[i]);
+ IcyLogger.trace(CanonicalSimplexProgram.class, v + " == " + b[i]);
else
- System.out.println(v + " <= " + b[i]);
+ IcyLogger.trace(CanonicalSimplexProgram.class, v + " <= " + b[i]);
}
}
}
else {
- System.out.println("Solve simplex failed");
+ IcyLogger.error(CanonicalSimplexProgram.class, "Solve simplex failed");
}
}
}
\ No newline at end of file
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
index 728b638..b3df71c 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,20 +18,22 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
-import icy.gui.frame.progress.AnnounceFrame;
-import icy.plugin.abstract_.PluginActionable;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.PluginActionable;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.gui.frame.progress.AnnounceFrame;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+@IcyPluginName("Linear Programming Example")
+@IcyPluginIcon(path = "/linear-programming.png")
public class LinearProgrammingICYPlugin extends PluginActionable {
@Override
public void run() {
new AnnounceFrame("It is now running a series of example optimization problems. See the console for the output.");
- new AnnounceFrame("This is a utility plugin, intended to be used by other ICY plugins.");
+ new AnnounceFrame("This is an utility plugin, intended to be used by other ICY plugins.");
for (int i = 0; i < 3; i++) {
- System.out.println();
- System.out.println("=== Linear Programming test scenario " + i + " ===");
- System.out.println();
+ IcyLogger.info(this.getClass(), "=== Linear Programming test scenario " + i + " ===");
CanonicalSimplexProgram.runExampleScenario(i);
}
}
-
}
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
index a92558a..79b2b28 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,14 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
+import org.jetbrains.annotations.NotNull;
+
/**
* Implements the Bland rule for pivoting for the Simplex algorithm.
* <p>
* Warning: this rule shows high probability of cycling.
* <p>
- * Part of the Linear Programming plugin for ICY http://icy.bioimageanalysis.org
+ * Part of the Linear Programming plugin for ICY <a href="https://icy.bioimageanalysis.org">https://icy.bioimageanalysis.org</a>
*
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
@@ -59,7 +61,7 @@ public class SimplexBLAND extends CanonicalSimplexProgram {
* @return the row index in the tableau
*/
@Override
- protected int getRowidx(final TableauWithSlackVariables tableau, final int colIdx) {
+ protected int getRowidx(final @NotNull TableauWithSlackVariables tableau, final int colIdx) {
boolean found = false;
double maxVal = -1;
int rowIdx = -1;
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
index 172848c..61f7840 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,14 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
+import org.jetbrains.annotations.NotNull;
+
import java.util.ArrayList;
/**
* Implements the lexicographic rule for pivoting for the Simplex algorithm.
* <p>
- * Part of the Linear Programming plugin for ICY http://icy.bioimageanalysis.org
+ * Part of the Linear Programming plugin for ICY <a href="https://icy.bioimageanalysis.org">https://icy.bioimageanalysis.org</a>
*
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
@@ -100,7 +102,7 @@ public class SimplexLEXICO extends CanonicalSimplexProgram {
* @return the row index in the tableau
*/
@Override
- protected int getRowidx(final TableauWithSlackVariables tableau, final int colIdx) {
+ protected int getRowidx(final @NotNull TableauWithSlackVariables tableau, final int colIdx) {
int rowIdx = -1;
int numBasicRow = 0;
final ArrayList<Integer> basicCols = new ArrayList<>();
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
index a65f066..e1a13e3 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,14 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
+import org.jetbrains.annotations.NotNull;
+
/**
* Implements the maximum score rule for pivoting for the Simplex algorithm.
* <p>
* Warning: this rule shows high probability of cycling.
* <p>
- * Part of the Linear Programming plugin for ICY http://icy.bioimageanalysis.org
+ * Part of the Linear Programming plugin for ICY <a href="https://icy.bioimageanalysis.org">https://icy.bioimageanalysis.org</a>
*
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
@@ -96,7 +98,7 @@ public class SimplexMAX extends CanonicalSimplexProgram {
* @return the row index in the tableau
*/
@Override
- protected int getRowidx(final TableauWithSlackVariables tableau, final int colIdx) {
+ protected int getRowidx(final @NotNull TableauWithSlackVariables tableau, final int colIdx) {
boolean found = false;
double maxVal = -1;
int rowIdx = -1;
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauMinSlackObjective.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauMinSlackObjective.java
index 55a2ac2..d386e2c 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauMinSlackObjective.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauMinSlackObjective.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,8 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
+import org.jetbrains.annotations.NotNull;
+
/**
* Tableau used for Gauss-Jordan elimination in which slack variables are given a 1 score depending on whether constraints are equalities.
* Slack variables are added to the set of column vectors in a leading position.
@@ -27,7 +29,6 @@ package plugins.nchenouard.linearprogrammingfullsimplex;
* @author Nicolas Chenouard (nicolas.chenouard.dev@gmail.com)
*/
public class TableauMinSlackObjective extends TableauWithSlackVariables {
-
/**
* Create the tableau based on a linear program. The scores in the tableau
* will not be initialized to their standard value but set to handle
@@ -35,7 +36,7 @@ public class TableauMinSlackObjective extends TableauWithSlackVariables {
*
* @param simplexProgram parameters defining the linear optimization problem.
*/
- public TableauMinSlackObjective(final CanonicalSimplexProgram simplexProgram) {
+ public TableauMinSlackObjective(final @NotNull CanonicalSimplexProgram simplexProgram) {
super(simplexProgram.parameters.A);
// now make the slacks feasible
xCol = simplexProgram.parameters.b.clone(); // equal to b since we start with unit vectors as initial left vectors
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauWithSlackVariables.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauWithSlackVariables.java
index 110f17d..f22c28d 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauWithSlackVariables.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/TableauWithSlackVariables.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,9 @@
package plugins.nchenouard.linearprogrammingfullsimplex;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
+
/**
* Tableau used for Gauss-Jordan elimination.
* Initial basis is built by using slack variables.
@@ -88,7 +91,7 @@ public class TableauWithSlackVariables {
*
* @param parameters parameters defining the linear optimization problem.
*/
- public TableauWithSlackVariables(final CanonicalProgramParameters parameters) {
+ public TableauWithSlackVariables(final @NotNull CanonicalProgramParameters parameters) {
createVectors(parameters.A); // constraint value column
xCol = parameters.b.clone(); // equal to b since we start with unit vectors as initial left vectors
// build the score row
@@ -141,7 +144,7 @@ public class TableauWithSlackVariables {
*
* @param A Constraint matrix. Each element A[i] defines a linear combination of the variable corresponding to a constraint.
*/
- protected void createVectors(final double[][] A) {
+ protected void createVectors(final double @NotNull [] @NotNull [] A) {
final int numConstraints = A.length;
numVariables = A[0].length;
numCol = numConstraints + numVariables;
@@ -174,42 +177,39 @@ public class TableauWithSlackVariables {
* Print the tableau
*/
public void printTableau() {
- System.out.println("Column vectors");
+ IcyLogger.trace(this.getClass(), "Column vectors");
for (int i = 0; i < columnVectors.length; i++) {
final double[] vector = columnVectors[i];
- System.out.print("a" + i + " = [");
+ IcyLogger.trace(this.getClass(), "a" + i + " = [");
for (final double v : vector)
- System.out.print(v + ", ");
- System.out.println("]'");
+ IcyLogger.trace(this.getClass(), v + ", ");
+ IcyLogger.trace(this.getClass(), "]'");
}
- System.out.println("Basis vectors");
+ IcyLogger.trace(this.getClass(), "Basis vectors");
for (int i = 0; i < leftVectorsIdx.length; i++) {
final double[] vector = columnVectors[leftVectorsIdx[i]];
- System.out.print("v" + i + " = [");
+ IcyLogger.trace(this.getClass(), "v" + i + " = [");
for (final double v : vector)
- System.out.print(v + ", ");
- System.out.println("]'");
+ IcyLogger.trace(this.getClass(), v + ", ");
+ IcyLogger.trace(this.getClass(), "]'");
}
- System.out.println("Tableau");
+ IcyLogger.trace(this.getClass(), "Tableau");
for (final double[] doubles : tableau) {
for (final double aDouble : doubles)
- System.out.print(aDouble + " ");
- System.out.println();
+ IcyLogger.trace(this.getClass(), aDouble + " ");
}
- System.out.println();
- System.out.print("x = [");
+ IcyLogger.trace(this.getClass(), "x = [");
for (final double v : xCol)
- System.out.print(v + ", ");
- System.out.println("]'");
+ IcyLogger.trace(this.getClass(), v + ", ");
+ IcyLogger.trace(this.getClass(), "]'");
- System.out.println();
- System.out.print("score row = [");
+ IcyLogger.trace(this.getClass(), "score row = [");
for (final double v : scoreRow)
- System.out.print(v + ", ");
- System.out.println("]'");
+ IcyLogger.trace(this.getClass(), v + ", ");
+ IcyLogger.trace(this.getClass(), "]'");
- System.out.println("Score = " + scoreValue);
+ IcyLogger.trace(this.getClass(), "Score = " + scoreValue);
}
/**
diff --git a/src/main/resources/linear-programming.png b/src/main/resources/linear-programming.png
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literal 0
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--
GitLab