diff --git a/.gitignore b/.gitignore
index 723e68cb800c3637bda99e5df67f2676154a0a7b..1bcf8c19407ea6b0366dfc86fc384718177188be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,7 @@
*.jar
.project
.classpath
-export.jardesc
\ No newline at end of file
+export.jardesc
+target/
+.idea/
+*.iml
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index a9c418c590a959481bcae5be9bc73fab20320c2f..eb846fb5d9b1e949959aff3759ba8c5988fdc779 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,8 +4,13 @@
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>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-nherve-matrix</artifactId>
+ <parent>
+ <artifactId>pom-icy</artifactId>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <version>1.0.4</version>
+ </parent>
+
+ <artifactId>nherve-matrix</artifactId>
<version>1.1</version>
<packaging>jar</packaging>
@@ -46,32 +51,4 @@
</plugin>
</plugins>
</build>
-
- <dependencies>
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>2.1.0</version>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
- </repository>
- </repositories>
-
- <distributionManagement>
- <snapshotRepository>
- <id>icy-dev</id>
- <name>icy-dev</name>
- <url>https://icy-nexus-dev.pasteur.cloud/repository/icy-core/</url>
- </snapshotRepository>
- <repository>
- <id>icy-prod</id>
- <name>icy-prod</name>
- <url>https://icy-nexus.pasteur.fr/repository/icy-core/</url>
- </repository>
- </distributionManagement>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/nherve/matrix/CholeskyDecomposition.java b/src/main/java/plugins/nherve/matrix/CholeskyDecomposition.java
index d8ccd0272519e70eea2916a888acd1ee33300a12..fc8b7ed11389a0c3459b890bd71afa0fa6cc7d04 100644
--- a/src/main/java/plugins/nherve/matrix/CholeskyDecomposition.java
+++ b/src/main/java/plugins/nherve/matrix/CholeskyDecomposition.java
@@ -39,8 +39,7 @@ public class CholeskyDecomposition implements java.io.Serializable {
* ------------------------ */
/** Cholesky algorithm for symmetric and positive definite matrix.
- @param A Square, symmetric matrix.
- @return Structure to access L and isspd flag.
+ @param Arg Square, symmetric matrix.
*/
public CholeskyDecomposition (Matrix Arg) {
diff --git a/src/main/java/plugins/nherve/matrix/EigenvalueDecomposition.java b/src/main/java/plugins/nherve/matrix/EigenvalueDecomposition.java
index 35cf0dd583998362389b003210e1cd552e7b3aab..de318325ed64a174a865c3355911e592ce0f762a 100644
--- a/src/main/java/plugins/nherve/matrix/EigenvalueDecomposition.java
+++ b/src/main/java/plugins/nherve/matrix/EigenvalueDecomposition.java
@@ -858,8 +858,7 @@ public class EigenvalueDecomposition implements java.io.Serializable {
* ------------------------ */
/** Check for symmetry, then construct the eigenvalue decomposition
- @param A Square matrix
- @return Structure to access D and V.
+ @param Arg Square matrix
*/
public EigenvalueDecomposition (Matrix Arg) {
diff --git a/src/main/java/plugins/nherve/matrix/LUDecomposition.java b/src/main/java/plugins/nherve/matrix/LUDecomposition.java
index b7b536f4fb4bdcb84388ea4a8090681c15cf85b3..e4b248527e661650f093e4ababc291caa42c9dba 100644
--- a/src/main/java/plugins/nherve/matrix/LUDecomposition.java
+++ b/src/main/java/plugins/nherve/matrix/LUDecomposition.java
@@ -3,10 +3,10 @@ package plugins.nherve.matrix;
/** LU Decomposition.
<P>
- For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
+ For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
unit lower triangular matrix L, an n-by-n upper triangular matrix U,
and a permutation vector piv of length m so that A(piv,:) = L*U.
- If m < n, then L is m-by-m and U is m-by-n.
+ If m < n, then L is m-by-m and U is m-by-n.
<P>
The LU decompostion with pivoting always exists, even if the matrix is
singular, so the constructor will never fail. The primary use of the
@@ -45,7 +45,6 @@ public class LUDecomposition implements java.io.Serializable {
/** LU Decomposition
@param A Rectangular matrix
- @return Structure to access L, U and piv.
*/
public LUDecomposition (Matrix A) {
diff --git a/src/main/java/plugins/nherve/matrix/Matrix.java b/src/main/java/plugins/nherve/matrix/Matrix.java
index b38d648064c411376609d4fd85e75a2aeaf421ab..ee62bedb44c68830749cd6995e45fc299cf908e2 100644
--- a/src/main/java/plugins/nherve/matrix/Matrix.java
+++ b/src/main/java/plugins/nherve/matrix/Matrix.java
@@ -26,13 +26,12 @@ import plugins.nherve.matrix.util.Maths;
* printing matrices are also included. All the operations in this version of
* the Matrix Class involve real matrices. Complex matrices may be handled in a
* future version.
- * <P>
+ *
* Five fundamental matrix decompositions, which consist of pairs or triples of
* matrices, permutation vectors, and the like, produce results in five
* decomposition classes. These decompositions are accessed by the Matrix class
* to compute solutions of simultaneous linear equations, determinants, inverses
* and other matrix functions. The five decompositions are:
- * <P>
* <UL>
* <LI>Cholesky Decomposition of symmetric, positive definite matrices.
* <LI>LU Decomposition of rectangular matrices.
@@ -43,9 +42,7 @@ import plugins.nherve.matrix.util.Maths;
* </UL>
* <DL>
* <DT><B>Example of use:</B></DT>
- * <P>
* <DD>Solve a linear system A x = b and compute the residual norm, ||b - A x||.
- * <P>
*
* <PRE>
* double[][] vals = { { 1., 2., 3 }, { 4., 5., 6. }, { 7., 8., 10. } };
@@ -202,7 +199,7 @@ public class Matrix implements Cloneable, java.io.Serializable {
*/
/**
- * Construct a matrix from a copy of a 2-D array.
+ * @return Construct a matrix from a copy of a 2-D array.
*
* @param A
* Two-dimensional array of doubles.
@@ -227,7 +224,7 @@ public class Matrix implements Cloneable, java.io.Serializable {
}
/**
- * Make a deep copy of a matrix
+ * @return Make a deep copy of a matrix
*/
public Matrix copy() {
@@ -335,7 +332,7 @@ public class Matrix implements Cloneable, java.io.Serializable {
* @param j
* Column index.
* @return A(i,j)
- * @exception ArrayIndexOutOfBoundsException
+ * @throws ArrayIndexOutOfBoundsException Array out of bounds
*/
public double get(int i, int j) {
@@ -434,9 +431,9 @@ public class Matrix implements Cloneable, java.io.Serializable {
*
* @param r
* Array of row indices.
- * @param i0
+ * @param j0
* Initial column index
- * @param i1
+ * @param j1
* Final column index
* @return A(r(:),j0:j1)
* @exception ArrayIndexOutOfBoundsException
@@ -467,7 +464,7 @@ public class Matrix implements Cloneable, java.io.Serializable {
* Column index.
* @param s
* A(i,j).
- * @exception ArrayIndexOutOfBoundsException
+ * @throws ArrayIndexOutOfBoundsException array out of bounds
*/
public void set(int i, int j, double s) {
@@ -1207,13 +1204,14 @@ public class Matrix implements Cloneable, java.io.Serializable {
}
/**
- * Read a matrix from a stream. The format is the same the print method, so
+ * @return Read a matrix from a stream. The format is the same the print method, so
* printed matrices can be read back in (provided they were printed using US
* Locale). Elements are separated by whitespace, all the elements for each
* row appear on a single line, the last row is followed by a blank line.
*
* @param input
* the input stream.
+ * @throws java.io.IOException IO Exception
*/
public static Matrix read(BufferedReader input) throws java.io.IOException {
diff --git a/src/main/java/plugins/nherve/matrix/QRDecomposition.java b/src/main/java/plugins/nherve/matrix/QRDecomposition.java
index fc79248bd2abebe0dc941a9f4ddddbe8367b6203..7188d08731abb8e3883a0d414c0ecf0850da715e 100644
--- a/src/main/java/plugins/nherve/matrix/QRDecomposition.java
+++ b/src/main/java/plugins/nherve/matrix/QRDecomposition.java
@@ -4,7 +4,7 @@ import plugins.nherve.matrix.util.Maths;
/** QR Decomposition.
<P>
- For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n
+ For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n
orthogonal matrix Q and an n-by-n upper triangular matrix R so that
A = Q*R.
<P>
@@ -45,7 +45,6 @@ public class QRDecomposition implements java.io.Serializable {
/** QR Decomposition, computed by Householder reflections.
@param A Rectangular matrix
- @return Structure to access R and the Householder vectors and compute Q.
*/
public QRDecomposition (Matrix A) {
diff --git a/src/main/java/plugins/nherve/matrix/SingularValueDecomposition.java b/src/main/java/plugins/nherve/matrix/SingularValueDecomposition.java
index 70d26c85db944e745fb7f49ad765e572dccb5c5c..58ba5723ea3954bcd524e2883da5a586e444bc28 100644
--- a/src/main/java/plugins/nherve/matrix/SingularValueDecomposition.java
+++ b/src/main/java/plugins/nherve/matrix/SingularValueDecomposition.java
@@ -4,12 +4,12 @@ import plugins.nherve.matrix.util.Maths;
/** Singular Value Decomposition.
<P>
- For an m-by-n matrix A with m >= n, the singular value decomposition is
+ For an m-by-n matrix A with m >= n, the singular value decomposition is
an m-by-n orthogonal matrix U, an n-by-n diagonal matrix S, and
an n-by-n orthogonal matrix V so that A = U*S*V'.
<P>
The singular values, sigma[k] = S[k][k], are ordered so that
- sigma[0] >= sigma[1] >= ... >= sigma[n-1].
+ sigma[0] >= sigma[1] >= ... >= sigma[n-1].
<P>
The singular value decompostion always exists, so the constructor will
never fail. The matrix condition number and the effective numerical
@@ -46,8 +46,7 @@ public class SingularValueDecomposition implements java.io.Serializable {
* ------------------------ */
/** Construct the singular value decomposition
- @param A Rectangular matrix
- @return Structure to access U, S and V.
+ @param Arg Rectangular matrix
*/
public SingularValueDecomposition (Matrix Arg) {
diff --git a/src/main/java/plugins/nherve/matrix/util/Maths.java b/src/main/java/plugins/nherve/matrix/util/Maths.java
index 46ff5b81b6033f646290f383d2ba7c07c60bd107..4e77dff75b0764eb0dff34c936f5187d8aee735d 100644
--- a/src/main/java/plugins/nherve/matrix/util/Maths.java
+++ b/src/main/java/plugins/nherve/matrix/util/Maths.java
@@ -1,20 +1 @@
-package plugins.nherve.matrix.util;
-
-public class Maths {
-
- /** sqrt(a^2 + b^2) without under/overflow. **/
-
- public static double hypot(double a, double b) {
- double r;
- if (Math.abs(a) > Math.abs(b)) {
- r = b/a;
- r = Math.abs(a)*Math.sqrt(1+r*r);
- } else if (b != 0) {
- r = a/b;
- r = Math.abs(b)*Math.sqrt(1+r*r);
- } else {
- r = 0.0;
- }
- return r;
- }
-}
+package plugins.nherve.matrix.util;
public class Maths {
/**
* @return sqrt(a^2 + b^2) without under/overflow.
* @param a double
* @param b double
* **/
public static double hypot(double a, double b) {
double r;
if (Math.abs(a) > Math.abs(b)) {
r = b/a;
r = Math.abs(a)*Math.sqrt(1+r*r);
} else if (b != 0) {
r = a/b;
r = Math.abs(b)*Math.sqrt(1+r*r);
} else {
r = 0.0;
}
return r;
}
}
\ No newline at end of file