diff --git a/pom.xml b/pom.xml
index 4ae3a2f216d7bc146d03cf00b8e70c077821bf81..2e59ad487129fa7b858a9faf302c5827f51138cd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>3.0.0-a.1</version>
+ <version>3.0.0-a.3</version>
</parent>
<artifactId>linear-programming</artifactId>
- <version>2.0.0-a.1</version>
+ <version>2.0.0-a.2</version>
<name>Linear Programming</name>
<description>
@@ -22,11 +22,4 @@
custom problems: java -jar linearProgrammingICY.jar -help for the manual.
Sources files are provided in the jar file.
</description>
-
- <repositories>
- <repository>
- <id>icy</id>
- <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/CanonicalSimplexProgram.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
index 64ddf5ec455e8e2123bff8a5228898339e8eb749..19d3bc0c53fbe0d586014827ad2abc89de22933e 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/CanonicalSimplexProgram.java
@@ -43,7 +43,7 @@ import java.io.*;
* A[i]*x <= b if equalityConstraints[i]
* <p>
* <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)
*/
@@ -266,7 +266,7 @@ public abstract class CanonicalSimplexProgram {
// for (int i = 0; i < numConstraints; i ++)
// if (parameters.equalityConstraints[i])
// c[i] = 1;//put weights to slack variables which correspond to equalities
- //// tableau0.solverWithLPSolve(c, b0, false);
+ // tableau0.solverWithLPSolve(c, b0, false);
// }
if (!success)
return false;
@@ -530,7 +530,8 @@ public abstract class CanonicalSimplexProgram {
/**
* @return Manual of the library for stand-alone use through command line
*/
- public static String getHelp() {
+ @Contract(pure = true)
+ public static @NotNull String getHelp() {
return """
Run the solver for example problems or for a user-defined system
Empty arguments to use the default example.
@@ -545,7 +546,7 @@ public abstract class CanonicalSimplexProgram {
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""";
}
@@ -904,7 +905,8 @@ public abstract class CanonicalSimplexProgram {
"Optimal score is 6.5",
"Solution is [1.0, 1.0, 0.5, 0.0]"
);
- A = new double[][]{{2, 1, 0, 0},
+ A = new double[][]{
+ {2, 1, 0, 0},
{0, 1, 4, 1},
{1, 3, 0, 1}
};
@@ -921,7 +923,8 @@ public abstract class CanonicalSimplexProgram {
"Optimal score is 1/20.",
"Solution is [1/25, 0, 1, 0]."
);
- A = new double[][]{{1d / 4, -60, -1d / 25, 9},
+ A = new double[][]{
+ {1d / 4, -60, -1d / 25, 9},
{1d / 2, -90, -1d / 50, 3},
{0, 0, 1, 0}
};
@@ -937,10 +940,10 @@ public abstract class CanonicalSimplexProgram {
"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},
- };
+ A = new double[][]{
+ {5, -4, 13, -2, 1},
+ {1, -1, 5, -1, 1},
+ };
b = new double[]{20, 8};
c = new double[]{1, 6, -7, 1, 5};
equality = new boolean[]{true, true};
@@ -954,11 +957,11 @@ public abstract class CanonicalSimplexProgram {
"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},
- {3, -1, 0, -1}
- };
+ A = new double[][]{
+ {1, 2, 1, 1},
+ {1, -2, 2, 1},
+ {3, -1, 0, -1}
+ };
b = new double[]{3, -2, -1};
c = new double[]{2, -3, 1, 1};
equality = new boolean[]{true, true, true};
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
index b3df71c62d5b2dff290f2bb7bb89777096af2cf3..0bbae89e38e274244b64ad001c8167622a6f9c44 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/LinearProgrammingICYPlugin.java
@@ -25,7 +25,7 @@ import org.bioimageanalysis.icy.gui.frame.progress.AnnounceFrame;
import org.bioimageanalysis.icy.system.logging.IcyLogger;
@IcyPluginName("Linear Programming Example")
-@IcyPluginIcon(path = "/linear-programming.png")
+@IcyPluginIcon(path = "/plugins/nchenouard/linearprogramming/linear-programming.png")
public class LinearProgrammingICYPlugin extends PluginActionable {
@Override
public void run() {
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
index 79b2b283c7b72b6dda76b6b3374f539e891453de..802671b2cbedc992ba0907f41947a0fe59c586ce 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexBLAND.java
@@ -93,24 +93,24 @@ public class SimplexBLAND extends CanonicalSimplexProgram {
*/
@Override
protected int getPivotColumn(final TableauWithSlackVariables tableau, final boolean max) {
+ int idx = -1;
+
if (max) {
- int idx = -1;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] < 0 && tableau.originalColOrder[i] >= 0) {
idx = i;
break;
}
- return idx;
}
else {
- int idx = -1;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] > 0 && tableau.originalColOrder[i] >= 0) {
idx = i;
break;
}
- return idx;
}
+
+ return idx;
}
/**
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
index 61f78404f3393822989e08502283a7892b7547da..925e7fbc63545c7ce0620d8ce4381922a4c8f68a 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexLEXICO.java
@@ -63,9 +63,10 @@ public class SimplexLEXICO extends CanonicalSimplexProgram {
@Override
protected int getPivotColumn(final TableauWithSlackVariables tableau, final boolean max) {
// max score choice strategy
+ int idx = -1;
+ double score = 0;
+
if (max) {
- int idx = -1;
- double score = 0;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] < score) {
if (tableau.originalColOrder[i] >= 0 || !parameters.equalityConstraints[i]) {
@@ -73,25 +74,20 @@ public class SimplexLEXICO extends CanonicalSimplexProgram {
idx = i;
}
}
- if (idx >= 0)
- return idx;
- else
- return -1;
}
else {
- int idx = -1;
- double score = 0;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] > score)
if (tableau.originalColOrder[i] >= 0 || !parameters.equalityConstraints[i]) {
score = tableau.scoreRow[i];
idx = i;
}
- if (idx >= 0)
- return idx;
- else
- return -1;
}
+
+ if (idx >= 0)
+ return idx;
+ else
+ return -1;
}
/**
diff --git a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
index e1a13e3eb06e3667892a562bf5f33b05d80f3d99..1f97090ddcbc47922cdd3f62edca3c4de6e49dc6 100644
--- a/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
+++ b/src/main/java/plugins/nchenouard/linearprogrammingfullsimplex/SimplexMAX.java
@@ -62,32 +62,28 @@ public class SimplexMAX extends CanonicalSimplexProgram {
*/
@Override
protected int getPivotColumn(final TableauWithSlackVariables tableau, final boolean max) {
+ int idx = -1;
+ double score = 0;
+
if (max) {
- int idx = -1;
- double score = 0;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] < score && tableau.originalColOrder[i] >= 0) {
score = tableau.scoreRow[i];
idx = i;
}
- if (idx >= 0)
- return idx;
- else
- return -1;
}
else {
- int idx = -1;
- double score = 0;
for (int i = 0; i < tableau.scoreRow.length; i++)
if (tableau.scoreRow[i] > score && tableau.originalColOrder[i] >= 0) {
score = tableau.scoreRow[i];
idx = i;
}
- if (idx >= 0)
- return idx;
- else
- return -1;
}
+
+ if (idx >= 0)
+ return idx;
+ else
+ return -1;
}
/**
diff --git a/src/main/resources/README.txt b/src/main/resources/plugins/nchenouard/linearprogramming/README.txt
similarity index 100%
rename from src/main/resources/README.txt
rename to src/main/resources/plugins/nchenouard/linearprogramming/README.txt
diff --git a/src/main/resources/linear-programming.png b/src/main/resources/plugins/nchenouard/linearprogramming/linear-programming.png
similarity index 100%
rename from src/main/resources/linear-programming.png
rename to src/main/resources/plugins/nchenouard/linearprogramming/linear-programming.png
diff --git a/src/test/java/plugins/nchenouard/linearprogrammingfullsimplex/TestCanonicalSimplexProgram.java b/src/test/java/plugins/nchenouard/linearprogrammingfullsimplex/TestCanonicalSimplexProgram.java
new file mode 100644
index 0000000000000000000000000000000000000000..5295bddc1fcec643f1dbd9aadc615318973e6ce0
--- /dev/null
+++ b/src/test/java/plugins/nchenouard/linearprogrammingfullsimplex/TestCanonicalSimplexProgram.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright (c) 2010-2024. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package plugins.nchenouard.linearprogrammingfullsimplex;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+public class TestCanonicalSimplexProgram {
+ @Test
+ void scenarioZero() {
+ final double[][] A = new double[][]{
+ {2, 1, 0, 0},
+ {0, 1, 4, 1},
+ {1, 3, 0, 1}
+ };
+ final double[] b = new double[]{3, 3, 4};
+ final double[] c = new double[]{2, 4, 1, 1};
+ final boolean[] equality = new boolean[b.length];
+ final boolean maximization = true;
+
+ final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
+
+ assertTrue(program.solvePrimalSimplex());
+ final double score = program.getScore();
+ final double[] solution = program.solution;
+
+ assertEquals(6.5d, score);
+ assertArrayEquals(new double[]{1.d, 1.d, .5d, .0d}, solution);
+ }
+
+ @Test
+ void scenarioOne() {
+ final double[][] A = new double[][]{
+ {1d / 4, -60, -1d / 25, 9},
+ {1d / 2, -90, -1d / 50, 3},
+ {0, 0, 1, 0}
+ };
+ final double[] b = new double[]{0, 0, 1};
+ final double[] c = new double[]{3d / 4, -150, 1d / 50, -6};
+ final boolean[] equality = new boolean[b.length];
+ final boolean maximization = true;
+
+ final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
+
+ assertTrue(program.solvePrimalSimplex());
+ final double score = program.getScore();
+ final double[] solution = program.solution;
+
+ assertEquals(1.d / 20.d, score);
+ assertArrayEquals(new double[]{1.d / 25.d, .0d, 1.d, .0d}, solution);
+ }
+
+ @Test
+ void scenarioTwo() {
+ final double[][] A = new double[][]{
+ {5, -4, 13, -2, 1},
+ {1, -1, 5, -1, 1},
+ };
+ final double[] b = new double[]{20, 8};
+ final double[] c = new double[]{1, 6, -7, 1, 5};
+ final boolean[] equality = new boolean[]{true, true};
+ final boolean maximization = false;
+
+ final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
+
+ assertTrue(program.solvePrimalSimplex());
+ final double[] solution = program.solution;
+
+ assertArrayEquals(new double[]{.0d, 4.d / 7.d, 1.d + (5.d / 7.d), .0d, .0d}, solution, .0001d);
+ }
+
+ @Test
+ void scenarioThree() {
+ final double[][] A = new double[][]{
+ {1, 2, 1, 1},
+ {1, -2, 2, 1},
+ {3, -1, 0, -1}
+ };
+ final double[] b = new double[]{3, -2, -1};
+ final double[] c = new double[]{2, -3, 1, 1};
+ final boolean[] equality = new boolean[]{true, true, true};
+ final boolean maximization = true;
+
+ final CanonicalSimplexProgram program = new SimplexLEXICO(A, b, c, maximization, equality);
+
+ assertTrue(program.solvePrimalSimplex());
+ final double score = program.getScore();
+ final double[] solution = program.solution;
+
+ assertEquals(-3.d - (1.d / 16.d), score, .0001d);
+ assertArrayEquals(new double[]{3.d / 16.d, 1.d + 1.d / 4.d, .0d, 5.d / 16.d}, solution, .0001d);
+ }
+}