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Posted to commits@commons.apache.org by er...@apache.org on 2021/05/19 13:34:52 UTC
[commons-math] branch modularized_master updated (9d1741b ->
9fca795)
This is an automated email from the ASF dual-hosted git repository.
erans pushed a change to branch modularized_master
in repository https://gitbox.apache.org/repos/asf/commons-math.git.
from 9d1741b Modularization.
new ac978e2 Typo.
new 1c4e414 Remove unused/outdated file.
new 9fca795 Set up module for example applications.
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.../LICENCE | 0
.../NOTICE | 0
.../examples-sofm}/LICENCE | 0
.../examples-sofm}/NOTICE | 0
.../examples-sofm/chinese-rings}/LICENCE | 0
.../examples-sofm/chinese-rings}/NOTICE | 0
.../examples-sofm/chinese-rings/pom.xml | 96 ++++++
.../examples/sofm/chineserings}/ChineseRings.java | 41 ++-
.../sofm/chineserings/ChineseRingsClassifier.java | 190 ++++++++++++
.../examples/sofm/chineserings/StandAlone.java | 118 ++++++++
commons-math-examples/examples-sofm/pom.xml | 57 ++++
.../examples/neuralnet/sofm/tsp/StandAlone.java | 27 +-
commons-math-examples/pom.xml | 119 ++++++++
commons-math-legacy/pom.xml | 2 +-
pom.xml | 13 +-
.../userguide/sofm/ChineseRingsClassifier.java | 337 ---------------------
test-jar.xml | 99 ------
17 files changed, 637 insertions(+), 462 deletions(-)
copy {commons-math-legacy => commons-math-examples}/LICENCE (100%)
copy {commons-math-legacy => commons-math-examples}/NOTICE (100%)
copy {commons-math-legacy => commons-math-examples/examples-sofm}/LICENCE (100%)
copy {commons-math-legacy => commons-math-examples/examples-sofm}/NOTICE (100%)
copy {commons-math-legacy => commons-math-examples/examples-sofm/chinese-rings}/LICENCE (100%)
copy {commons-math-legacy => commons-math-examples/examples-sofm/chinese-rings}/NOTICE (100%)
create mode 100644 commons-math-examples/examples-sofm/chinese-rings/pom.xml
rename {src/userguide/java/org/apache/commons/math4/userguide/sofm => commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings}/ChineseRings.java (80%)
create mode 100644 commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRingsClassifier.java
create mode 100644 commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/StandAlone.java
create mode 100644 commons-math-examples/examples-sofm/pom.xml
copy commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/fitting/leastsquares/ParameterValidator.java => commons-math-examples/examples-sofm/src/main/java/org/apache/commons/math4/examples/neuralnet/sofm/tsp/StandAlone.java (63%)
create mode 100644 commons-math-examples/pom.xml
delete mode 100644 src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRingsClassifier.java
delete mode 100644 test-jar.xml
[commons-math] 03/03: Set up module for example applications.
Posted by er...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
erans pushed a commit to branch modularized_master
in repository https://gitbox.apache.org/repos/asf/commons-math.git
commit 9fca795acfb74a5954229743780a71a7c0b16c76
Author: Gilles Sadowski <gi...@gmail.com>
AuthorDate: Wed May 19 15:28:59 2021 +0200
Set up module for example applications.
Moved "Chinese Rings" example into the new module.
---
commons-math-examples/LICENCE | 457 +++++++++++++++++++++
commons-math-examples/NOTICE | 9 +
commons-math-examples/examples-sofm/LICENCE | 457 +++++++++++++++++++++
commons-math-examples/examples-sofm/NOTICE | 9 +
.../examples-sofm/chinese-rings/LICENCE | 457 +++++++++++++++++++++
.../examples-sofm/chinese-rings/NOTICE | 9 +
.../examples-sofm/chinese-rings/pom.xml | 96 +++++
.../examples/sofm/chineserings}/ChineseRings.java | 41 +-
.../sofm/chineserings/ChineseRingsClassifier.java | 190 +++++++++
.../examples/sofm/chineserings/StandAlone.java | 118 ++++++
commons-math-examples/examples-sofm/pom.xml | 57 +++
.../examples/neuralnet/sofm/tsp/StandAlone.java | 41 ++
commons-math-examples/pom.xml | 119 ++++++
pom.xml | 13 +-
.../userguide/sofm/ChineseRingsClassifier.java | 337 ---------------
15 files changed, 2058 insertions(+), 352 deletions(-)
diff --git a/commons-math-examples/LICENCE b/commons-math-examples/LICENCE
new file mode 100644
index 0000000..d97b49a
--- /dev/null
+++ b/commons-math-examples/LICENCE
@@ -0,0 +1,457 @@
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+
+===============================================================================
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+
+-----------------------------------------------------------------------------
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+The initial commit of package "org.apache.commons.math3.ml.neuralnet" is
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+===============================================================================
+
+The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
+an adapted version of code translated from the netlib Fortran program, rjbesl
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+===============================================================================
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+and PowellOptimizer (package org.apache.commons.math3.optimization.general)
+classes are based on the Python code in module "optimize.py" (version 0.5)
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+===============================================================================
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diff --git a/commons-math-examples/NOTICE b/commons-math-examples/NOTICE
new file mode 100644
index 0000000..587cd7f
--- /dev/null
+++ b/commons-math-examples/NOTICE
@@ -0,0 +1,9 @@
+Apache Commons Math
+Copyright 2001-2020 The Apache Software Foundation
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+This product includes software developed at
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+This product includes software developed for Orekit by
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+Copyright 2010-2012 CS Systèmes d'Information
diff --git a/commons-math-examples/examples-sofm/LICENCE b/commons-math-examples/examples-sofm/LICENCE
new file mode 100644
index 0000000..d97b49a
--- /dev/null
+++ b/commons-math-examples/examples-sofm/LICENCE
@@ -0,0 +1,457 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+===============================================================================
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+ Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
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+ Redistribution and use in source and binary forms, with or without
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+
+===============================================================================
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+The initial code for shuffling an array (originally in class
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+a method in class "org.apache.commons.math3.util.MathArrays") was
+inspired from the algorithm description provided in
+"Algorithms", by Ian Craw and John Pulham (University of Aberdeen 1999).
+The textbook (containing a proof that the shuffle is uniformly random) is
+available here:
+ http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf
+
+===============================================================================
+License statement for the direction numbers in the resource files for Sobol sequences.
+
+-----------------------------------------------------------------------------
+Licence pertaining to sobol.cc and the accompanying sets of direction numbers
+
+-----------------------------------------------------------------------------
+Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
+All rights reserved.
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+Redistribution and use in source and binary forms, with or without
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+
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+ University of New South Wales and the University of Waikato
+ and its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
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+===============================================================================
+
+The initial commit of package "org.apache.commons.math3.ml.neuralnet" is
+an adapted version of code developed in the context of the Data Processing
+and Analysis Consortium (DPAC) of the "Gaia" project of the European Space
+Agency (ESA).
+===============================================================================
+
+The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
+an adapted version of code translated from the netlib Fortran program, rjbesl
+http://www.netlib.org/specfun/rjbesl by R.J. Cody at Argonne National
+Laboratory (USA). There is no license or copyright statement included with the
+original Fortran sources.
+===============================================================================
+
+
+The BracketFinder (package org.apache.commons.math3.optimization.univariate)
+and PowellOptimizer (package org.apache.commons.math3.optimization.general)
+classes are based on the Python code in module "optimize.py" (version 0.5)
+developed by Travis E. Oliphant for the SciPy library (http://www.scipy.org/)
+Copyright © 2003-2009 SciPy Developers.
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+Copyright © 2001, 2002 Enthought, Inc.
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+Redistribution and use in source and binary forms, with or without
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+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY
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+===============================================================================
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diff --git a/commons-math-examples/examples-sofm/NOTICE b/commons-math-examples/examples-sofm/NOTICE
new file mode 100644
index 0000000..587cd7f
--- /dev/null
+++ b/commons-math-examples/examples-sofm/NOTICE
@@ -0,0 +1,9 @@
+Apache Commons Math
+Copyright 2001-2020 The Apache Software Foundation
+
+This product includes software developed at
+The Apache Software Foundation (http://www.apache.org/).
+
+This product includes software developed for Orekit by
+CS Systèmes d'Information (http://www.c-s.fr/)
+Copyright 2010-2012 CS Systèmes d'Information
diff --git a/commons-math-examples/examples-sofm/chinese-rings/LICENCE b/commons-math-examples/examples-sofm/chinese-rings/LICENCE
new file mode 100644
index 0000000..d97b49a
--- /dev/null
+++ b/commons-math-examples/examples-sofm/chinese-rings/LICENCE
@@ -0,0 +1,457 @@
+ Apache License
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+ Unless required by applicable law or agreed to in writing, software
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+
+
+Apache Commons Math includes the following code provided to the ASF under the
+Apache License 2.0:
+
+ - The inverse error function implementation in the Erf class is based on CUDA
+ code developed by Mike Giles, Oxford-Man Institute of Quantitative Finance,
+ and published in GPU Computing Gems, volume 2, 2010 (grant received on
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+ - The LinearConstraint, LinearObjectiveFunction, LinearOptimizer,
+ RelationShip, SimplexSolver and SimplexTableau classes in package
+ org.apache.commons.math3.optimization.linear include software developed by
+ Benjamin McCann (http://www.benmccann.com) and distributed with
+ the following copyright: Copyright 2009 Google Inc. (grant received on
+ March 16th 2009)
+ - The class "org.apache.commons.math3.exception.util.LocalizedFormatsTest" which
+ is an adapted version of "OrekitMessagesTest" test class for the Orekit library
+ - The "org.apache.commons.math3.analysis.interpolation.HermiteInterpolator"
+ has been imported from the Orekit space flight dynamics library.
+
+===============================================================================
+
+
+
+APACHE COMMONS MATH DERIVATIVE WORKS:
+
+The Apache commons-math library includes a number of subcomponents
+whose implementation is derived from original sources written
+in C or Fortran. License terms of the original sources
+are reproduced below.
+
+===============================================================================
+For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in
+the LevenbergMarquardtOptimizer class in package
+org.apache.commons.math3.optimization.general
+Original source copyright and license statement:
+
+Minpack Copyright Notice (1999) University of Chicago. All rights reserved
+
+Redistribution and use in source and binary forms, with or
+without modification, are permitted provided that the
+following conditions are met:
+
+1. Redistributions of source code must retain the above
+copyright notice, this list of conditions and the following
+disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following
+disclaimer in the documentation and/or other materials
+provided with the distribution.
+
+3. The end-user documentation included with the
+redistribution, if any, must include the following
+acknowledgment:
+
+ "This product includes software developed by the
+ University of Chicago, as Operator of Argonne National
+ Laboratory.
+
+Alternately, this acknowledgment may appear in the software
+itself, if and wherever such third-party acknowledgments
+normally appear.
+
+4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS"
+WITHOUT WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE
+UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND
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+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
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+SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
+(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,
+EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
+POSSIBILITY OF SUCH LOSS OR DAMAGES.
+===============================================================================
+
+Copyright and license statement for the odex Fortran routine developed by
+E. Hairer and G. Wanner and translated in GraggBulirschStoerIntegrator class
+in package org.apache.commons.math3.ode.nonstiff:
+
+
+Copyright (c) 2004, Ernst Hairer
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+- Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+===============================================================================
+
+Copyright and license statement for the original Mersenne twister C
+routines translated in MersenneTwister class in package
+org.apache.commons.math3.random:
+
+ Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ 3. The names of its contributors may not be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+===============================================================================
+
+The initial code for shuffling an array (originally in class
+"org.apache.commons.math3.random.RandomDataGenerator", now replaced by
+a method in class "org.apache.commons.math3.util.MathArrays") was
+inspired from the algorithm description provided in
+"Algorithms", by Ian Craw and John Pulham (University of Aberdeen 1999).
+The textbook (containing a proof that the shuffle is uniformly random) is
+available here:
+ http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf
+
+===============================================================================
+License statement for the direction numbers in the resource files for Sobol sequences.
+
+-----------------------------------------------------------------------------
+Licence pertaining to sobol.cc and the accompanying sets of direction numbers
+
+-----------------------------------------------------------------------------
+Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ * Neither the names of the copyright holders nor the names of the
+ University of New South Wales and the University of Waikato
+ and its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+===============================================================================
+
+The initial commit of package "org.apache.commons.math3.ml.neuralnet" is
+an adapted version of code developed in the context of the Data Processing
+and Analysis Consortium (DPAC) of the "Gaia" project of the European Space
+Agency (ESA).
+===============================================================================
+
+The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
+an adapted version of code translated from the netlib Fortran program, rjbesl
+http://www.netlib.org/specfun/rjbesl by R.J. Cody at Argonne National
+Laboratory (USA). There is no license or copyright statement included with the
+original Fortran sources.
+===============================================================================
+
+
+The BracketFinder (package org.apache.commons.math3.optimization.univariate)
+and PowellOptimizer (package org.apache.commons.math3.optimization.general)
+classes are based on the Python code in module "optimize.py" (version 0.5)
+developed by Travis E. Oliphant for the SciPy library (http://www.scipy.org/)
+Copyright © 2003-2009 SciPy Developers.
+
+SciPy license
+Copyright © 2001, 2002 Enthought, Inc.
+All rights reserved.
+
+Copyright © 2003-2013 SciPy Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+ * Neither the name of Enthought nor the names of the SciPy Developers may
+ be used to endorse or promote products derived from this software without
+ specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+===============================================================================
+
diff --git a/commons-math-examples/examples-sofm/chinese-rings/NOTICE b/commons-math-examples/examples-sofm/chinese-rings/NOTICE
new file mode 100644
index 0000000..587cd7f
--- /dev/null
+++ b/commons-math-examples/examples-sofm/chinese-rings/NOTICE
@@ -0,0 +1,9 @@
+Apache Commons Math
+Copyright 2001-2020 The Apache Software Foundation
+
+This product includes software developed at
+The Apache Software Foundation (http://www.apache.org/).
+
+This product includes software developed for Orekit by
+CS Systèmes d'Information (http://www.c-s.fr/)
+Copyright 2010-2012 CS Systèmes d'Information
diff --git a/commons-math-examples/examples-sofm/chinese-rings/pom.xml b/commons-math-examples/examples-sofm/chinese-rings/pom.xml
new file mode 100644
index 0000000..86b170f
--- /dev/null
+++ b/commons-math-examples/examples-sofm/chinese-rings/pom.xml
@@ -0,0 +1,96 @@
+<?xml version="1.0"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<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>
+
+ <parent>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>examples-sofm</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>examples-sofm-chinese-rings</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ <!-- This name is used in the shaded jar to provide the application title for the version information. -->
+ <name>Chinese Rings</name>
+
+ <description>SOFM used for classification.</description>
+
+ <properties>
+ <maven.compiler.source>1.8</maven.compiler.source>
+ <maven.compiler.target>1.8</maven.compiler.target>
+
+ <!-- OSGi -->
+ <commons.osgi.symbolicName>org.apache.commons.math4.examples.sofm.chineserings</commons.osgi.symbolicName>
+ <commons.osgi.export>org.apache.commons.math4.examples.sofm.chineserings</commons.osgi.export>
+ <!-- Java 9+ -->
+ <commons.automatic.module.name>org.apache.commons.math4.examples.sofm.chineserings</commons.automatic.module.name>
+ <!-- Workaround to avoid duplicating config files. -->
+ <math.parent.dir>${basedir}/../../..</math.parent.dir>
+
+ <uberjar.name>examples-sofm-chineserings</uberjar.name>
+ <project.mainClass>org.apache.commons.math4.examples.sofm.chineserings.StandAlone</project.mainClass>
+ </properties>
+
+ <dependencies>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-geometry-euclidean</artifactId>
+ </dependency>
+
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ <configuration>
+ <finalName>${uberjar.name}</finalName>
+ <minimizeJar>true</minimizeJar>
+ <transformers>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <mainClass>${project.mainClass}</mainClass>
+ </transformer>
+ </transformers>
+ <filters>
+ <filter>
+ <!-- Shading signed JARs will fail without this. http://stackoverflow.com/questions/999489/invalid-signature-file-when-attempting-to-run-a-jar -->
+ <artifact>*:*</artifact>
+ <excludes>
+ <exclude>META-INF/*.SF</exclude>
+ <exclude>META-INF/*.DSA</exclude>
+ <exclude>META-INF/*.RSA</exclude>
+ </excludes>
+ </filter>
+ </filters>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
diff --git a/src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRings.java b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRings.java
similarity index 80%
rename from src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRings.java
rename to commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRings.java
index 01d5572..83e4e68 100644
--- a/src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRings.java
+++ b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRings.java
@@ -15,7 +15,9 @@
* limitations under the License.
*/
-package org.apache.commons.math4.userguide.sofm;
+package org.apache.commons.math4.examples.sofm.chineserings;
+
+import java.util.Iterator;
import org.apache.commons.rng.UniformRandomProvider;
import org.apache.commons.rng.simple.RandomSource;
@@ -27,10 +29,10 @@ import org.apache.commons.statistics.distribution.ContinuousDistribution;
import org.apache.commons.statistics.distribution.UniformContinuousDistribution;
/**
- * Class that creates two intertwined rings.
+ * Class that creates two intertwined rings in 3D-space.
* Each ring is composed of a cloud of points.
*/
-public class ChineseRings {
+class ChineseRings {
/** Points in the two rings. */
private final Vector3D[] points;
@@ -110,4 +112,37 @@ public class ChineseRings {
public Vector3D[] getPoints() {
return points.clone();
}
+
+ /**
+ * Creates an iterable that will present the points coordinates.
+ *
+ * @return the iterable.
+ */
+ public Iterable<double[]> createIterable() {
+ return new Iterable<double[]>() {
+ public Iterator<double[]> iterator() {
+ return new Iterator<double[]>() {
+ /** Data. */
+ final Vector3D[] points = getPoints();
+ /** Number of samples. */
+ private int n = 0;
+
+ /** {@inheritDoc} */
+ public boolean hasNext() {
+ return n < points.length;
+ }
+
+ /** {@inheritDoc} */
+ public double[] next() {
+ return points[n++].toArray();
+ }
+
+ /** {@inheritDoc} */
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+ };
+ }
}
diff --git a/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRingsClassifier.java b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRingsClassifier.java
new file mode 100644
index 0000000..f5343fb
--- /dev/null
+++ b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/ChineseRingsClassifier.java
@@ -0,0 +1,190 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math4.examples.sofm.chineserings;
+
+import java.util.Iterator;
+
+import org.apache.commons.rng.UniformRandomProvider;
+import org.apache.commons.rng.simple.RandomSource;
+import org.apache.commons.geometry.euclidean.threed.Vector3D;
+
+import org.apache.commons.math4.legacy.ml.neuralnet.SquareNeighbourhood;
+import org.apache.commons.math4.legacy.ml.neuralnet.FeatureInitializer;
+import org.apache.commons.math4.legacy.ml.neuralnet.FeatureInitializerFactory;
+import org.apache.commons.math4.legacy.ml.neuralnet.MapUtils;
+import org.apache.commons.math4.legacy.ml.neuralnet.twod.NeuronSquareMesh2D;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.LearningFactorFunction;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.LearningFactorFunctionFactory;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.NeighbourhoodSizeFunction;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.NeighbourhoodSizeFunctionFactory;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.KohonenUpdateAction;
+import org.apache.commons.math4.legacy.ml.neuralnet.sofm.KohonenTrainingTask;
+import org.apache.commons.math4.legacy.ml.distance.DistanceMeasure;
+import org.apache.commons.math4.legacy.ml.distance.EuclideanDistance;
+import org.apache.commons.math4.legacy.stat.descriptive.SummaryStatistics;
+
+/**
+ * SOFM for categorizing points that belong to each of two intertwined rings.
+ */
+class ChineseRingsClassifier {
+ /** SOFM. */
+ private final NeuronSquareMesh2D sofm;
+ /** Rings. */
+ private final ChineseRings rings;
+ /** Distance function. */
+ private final DistanceMeasure distance = new EuclideanDistance();
+
+ /**
+ * @param rings Training data.
+ * @param dim1 Number of rows of the SOFM.
+ * @param dim2 Number of columns of the SOFM.
+ */
+ public ChineseRingsClassifier(ChineseRings rings,
+ int dim1,
+ int dim2) {
+ this.rings = rings;
+ sofm = new NeuronSquareMesh2D(dim1, false,
+ dim2, false,
+ SquareNeighbourhood.MOORE,
+ makeInitializers());
+ }
+
+ /**
+ * Creates training tasks.
+ *
+ * @param numTasks Number of tasks to create.
+ * @param numSamplesPerTask Number of training samples per task.
+ * @return the created tasks.
+ */
+ public Runnable[] createParallelTasks(int numTasks,
+ long numSamplesPerTask) {
+ final Runnable[] tasks = new Runnable[numTasks];
+ final LearningFactorFunction learning
+ = LearningFactorFunctionFactory.exponentialDecay(1e-1,
+ 5e-2,
+ numSamplesPerTask / 2);
+ final double numNeurons = Math.sqrt(sofm.getNumberOfRows() * sofm.getNumberOfColumns());
+ final NeighbourhoodSizeFunction neighbourhood
+ = NeighbourhoodSizeFunctionFactory.exponentialDecay(0.5 * numNeurons,
+ 0.2 * numNeurons,
+ numSamplesPerTask / 2);
+
+ for (int i = 0; i < numTasks; i++) {
+ final KohonenUpdateAction action = new KohonenUpdateAction(distance,
+ learning,
+ neighbourhood);
+ tasks[i] = new KohonenTrainingTask(sofm.getNetwork(),
+ createRandomIterator(numSamplesPerTask),
+ action);
+ }
+
+ return tasks;
+ }
+
+ /**
+ * Creates a training task.
+ *
+ * @param numSamples Number of training samples.
+ * @return the created task.
+ */
+ public Runnable createSequentialTask(long numSamples) {
+ return createParallelTasks(1, numSamples)[0];
+ }
+
+ /**
+ * Computes various quality measures.
+ *
+ * @return the indicators.
+ */
+ public NeuronSquareMesh2D.DataVisualization computeQualityIndicators() {
+ return sofm.computeQualityIndicators(rings.createIterable());
+ }
+
+ /**
+ * Creates the features' initializers.
+ * They are sampled from a uniform distribution around the barycentre of
+ * the rings.
+ *
+ * @return an array containing the initializers for the x, y and
+ * z coordinates of the features array of the neurons.
+ */
+ private FeatureInitializer[] makeInitializers() {
+ final SummaryStatistics[] centre = new SummaryStatistics[] {
+ new SummaryStatistics(),
+ new SummaryStatistics(),
+ new SummaryStatistics()
+ };
+ for (Vector3D p : rings.getPoints()) {
+ centre[0].addValue(p.getX());
+ centre[1].addValue(p.getY());
+ centre[2].addValue(p.getZ());
+ }
+
+ final double[] mean = new double[] {
+ centre[0].getMean(),
+ centre[1].getMean(),
+ centre[2].getMean()
+ };
+ final double s = 0.1;
+ final double[] dev = new double[] {
+ s * centre[0].getStandardDeviation(),
+ s * centre[1].getStandardDeviation(),
+ s * centre[2].getStandardDeviation()
+ };
+
+ return new FeatureInitializer[] {
+ FeatureInitializerFactory.uniform(mean[0] - dev[0], mean[0] + dev[0]),
+ FeatureInitializerFactory.uniform(mean[1] - dev[1], mean[1] + dev[1]),
+ FeatureInitializerFactory.uniform(mean[2] - dev[2], mean[2] + dev[2])
+ };
+ }
+
+ /**
+ * Creates an iterator that will present a series of points coordinates in
+ * a random order.
+ *
+ * @param numSamples Number of samples.
+ * @return the iterator.
+ */
+ private Iterator<double[]> createRandomIterator(final long numSamples) {
+ return new Iterator<double[]>() {
+ /** Data. */
+ final Vector3D[] points = rings.getPoints();
+ /** RNG. */
+ final UniformRandomProvider rng = RandomSource.create(RandomSource.KISS);
+ /** Number of samples. */
+ private long n = 0;
+
+ /** {@inheritDoc} */
+ public boolean hasNext() {
+ return n < numSamples;
+ }
+
+ /** {@inheritDoc} */
+ public double[] next() {
+ ++n;
+ return points[rng.nextInt(points.length)].toArray();
+ }
+
+ /** {@inheritDoc} */
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+}
diff --git a/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/StandAlone.java b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/StandAlone.java
new file mode 100644
index 0000000..71f72a6
--- /dev/null
+++ b/commons-math-examples/examples-sofm/chinese-rings/src/main/java/org/apache/commons/math4/examples/sofm/chineserings/StandAlone.java
@@ -0,0 +1,118 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.commons.math4.examples.sofm.chineserings;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.concurrent.Callable;
+
+import picocli.CommandLine;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Command;
+
+import org.apache.commons.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math4.legacy.ml.neuralnet.twod.NeuronSquareMesh2D;
+
+/**
+ * Application class.
+ */
+@Command(description = "Run the application",
+ mixinStandardHelpOptions = true)
+public class StandAlone implements Callable<Void> {
+ @Option(names = { "-r" }, paramLabel = "numRows",
+ description = "Number of rows of the 2D SOFM (default: ${DEFAULT-VALUE}).")
+ private int _numRows = 15;
+ @Option(names = { "-c" }, paramLabel = "numCols",
+ description = "Number of columns of the 2D SOFM (default: ${DEFAULT-VALUE}).")
+ private int _numCols = 15;
+ @Option(names = { "-s" }, paramLabel = "numSamples",
+ description = "Number of samples for the training (default: ${DEFAULT-VALUE}).")
+ private long _numSamples = 100000;
+ @Option(names = { "-o" }, paramLabel = "outputFile", required = true,
+ description = "Output file name.")
+ private String _outputFile = null;
+
+ /**
+ * Program entry point. All solver parameters must be provided
+ * through a {@link java.util.Properties Properties} file.
+ *
+ * @param args Command line arguments and options.
+ */
+ public static void main(String[] args) {
+ CommandLine.call(new StandAlone(), args);
+ }
+
+ @Override
+ public Void call() throws Exception {
+ final ChineseRings rings = new ChineseRings(Vector3D.of(1, 2, 3),
+ 25, 2,
+ 20, 1,
+ 2000, 1500);
+
+ final ChineseRingsClassifier classifier = new ChineseRingsClassifier(rings, _numRows, _numCols);
+ classifier.createSequentialTask(_numSamples).run();
+ printResult(_outputFile, classifier);
+
+ return null;
+ }
+
+ /**
+ * Prints various quality measures of the map to files.
+ *
+ * @param fileName File name.
+ * @param sofm Classifier.
+ */
+ private static void printResult(String fileName,
+ ChineseRingsClassifier sofm) {
+ final NeuronSquareMesh2D.DataVisualization result = sofm.computeQualityIndicators();
+
+ try (final PrintWriter out = new PrintWriter(fileName)) {
+ out.println("# Number of samples: " + result.getNumberOfSamples());
+ out.println("# Quantization error: " + result.getMeanQuantizationError());
+ out.println("# Topographic error: " + result.getMeanTopographicError());
+ out.println();
+
+ printImage("Quantization error", result.getQuantizationError(), out);
+ printImage("Topographic error", result.getTopographicError(), out);
+ printImage("Normalized hits", result.getNormalizedHits(), out);
+ printImage("U-matrix", result.getUMatrix(), out);
+ } catch (IOException e) {
+ // Do nothing.
+ }
+ }
+
+ /**
+ * @param desc Data description.
+ * @param image Data.
+ * @param out Output stream.
+ */
+ private static void printImage(String desc,
+ double[][] image,
+ PrintWriter out) {
+ out.println("# " + desc);
+ final int nR = image.length;
+ final int nC = image[0].length;
+ for (int i = 0; i < nR; i++) {
+ for (int j = 0; j < nC; j++) {
+ out.print(image[i][j] + " ");
+ }
+ out.println();
+ }
+ out.println();
+ }
+}
diff --git a/commons-math-examples/examples-sofm/pom.xml b/commons-math-examples/examples-sofm/pom.xml
new file mode 100644
index 0000000..8c3befd
--- /dev/null
+++ b/commons-math-examples/examples-sofm/pom.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<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>
+
+ <parent>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math-examples</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>examples-sofm</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>SOFM</name>
+
+ <description>Self-organized feature map (ANN) sample codes.</description>
+
+ <properties>
+ <!-- Workaround to avoid duplicating config files. -->
+ <math.parent.dir>${basedir}/../..</math.parent.dir>
+ </properties>
+
+ <dependencies>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math4-legacy</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>info.picocli</groupId>
+ <artifactId>picocli</artifactId>
+ </dependency>
+
+ </dependencies>
+
+ <modules>
+ <module>chinese-rings</module>
+ </modules>
+
+</project>
diff --git a/commons-math-examples/examples-sofm/src/main/java/org/apache/commons/math4/examples/neuralnet/sofm/tsp/StandAlone.java b/commons-math-examples/examples-sofm/src/main/java/org/apache/commons/math4/examples/neuralnet/sofm/tsp/StandAlone.java
new file mode 100644
index 0000000..3fea193
--- /dev/null
+++ b/commons-math-examples/examples-sofm/src/main/java/org/apache/commons/math4/examples/neuralnet/sofm/tsp/StandAlone.java
@@ -0,0 +1,41 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.math3.examples.neuralnet.sofm.tsp;
+
+import org.apache.commons.rng.simple.RandomSource;
+
+/**
+ */
+public class StandAlone {
+ /**
+ * Program entry point.
+ *
+ * @param args Arguments.
+ * The order is as follows:
+ * <ol>
+ * <li>
+ * </li>
+ * <li>
+ * </li>
+ * </ol>
+ */
+ public static void main(String[] args) {
+ if (args.length != EXPECTED_ARGUMENTS) {
+ throw new IllegalStateException("Missing arguments");
+ }
+ }
+}
diff --git a/commons-math-examples/pom.xml b/commons-math-examples/pom.xml
new file mode 100644
index 0000000..3b663e9
--- /dev/null
+++ b/commons-math-examples/pom.xml
@@ -0,0 +1,119 @@
+<?xml version="1.0"?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+<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>
+
+ <parent>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math-parent</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>commons-math-examples</artifactId>
+ <version>4.0-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache Commons Math Examples</name>
+
+ <description>Examples of use of the "Commons Math" library.
+ Codes in this module and its sub-modules are not part of the public API.
+ </description>
+
+ <properties>
+ <maven.compiler.source>1.8</maven.compiler.source>
+ <maven.compiler.target>1.8</maven.compiler.target>
+
+ <!-- OSGi -->
+ <commons.osgi.symbolicName>org.apache.commons.math4.examples</commons.osgi.symbolicName>
+ <commons.osgi.export>org.apache.commons.math4.examples</commons.osgi.export>
+ <!-- Java 9+ -->
+ <commons.automatic.module.name>org.apache.commons.math4.examples</commons.automatic.module.name>
+ <!-- Workaround to avoid duplicating config files. -->
+ <math.parent.dir>${basedir}/..</math.parent.dir>
+
+ <math.version>4.0-SNAPSHOT</math.version>
+ <math.picocli.version>3.9.5</math.picocli.version>
+ <math.rng.version>1.3</math.rng.version>
+ <math.geometry.version>1.0-beta1</math.geometry.version>
+
+ <!-- Disable JApiCmp failures (but keep the report). The examples API is allowed to change. -->
+ <commons.japicmp.breakBuildOnBinaryIncompatibleModifications>false</commons.japicmp.breakBuildOnBinaryIncompatibleModifications>
+ <commons.japicmp.breakBuildOnSourceIncompatibleModifications>false</commons.japicmp.breakBuildOnSourceIncompatibleModifications>
+ <math.jira.component>examples</math.jira.component>
+ </properties>
+
+ <dependencyManagement>
+ <dependencies>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math4-neuralnet</artifactId>
+ <version>${math.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-math4-legacy</artifactId>
+ <version>${math.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-rng-client-api</artifactId>
+ <version>${math.rng.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-rng-simple</artifactId>
+ <version>${math.rng.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-geometry-euclidean</artifactId>
+ <version>${math.geometry.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>info.picocli</groupId>
+ <artifactId>picocli</artifactId>
+ <version>${math.picocli.version}</version>
+ </dependency>
+
+ </dependencies>
+ </dependencyManagement>
+
+ <build>
+ <pluginManagement>
+
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.6.0</version>
+ </plugin>
+ </plugins>
+
+ </pluginManagement>
+ </build>
+
+ <modules>
+ <module>examples-sofm</module>
+ </modules>
+
+</project>
diff --git a/pom.xml b/pom.xml
index 2a86fd8..0806bef 100644
--- a/pom.xml
+++ b/pom.xml
@@ -106,9 +106,7 @@
<modules>
<module>commons-math-legacy</module>
- <!-- <module>commons-math-core</module> -->
- <!-- <module>commons-math-ml-nn</module> -->
- <!-- <module>commons-math-ml-ga</module> -->
+ <module>commons-math-examples</module>
</modules>
<scm>
@@ -721,15 +719,6 @@
</plugins>
</build>
</profile>
- <!--
- Profiles for modules with special requirements.
- -->
- <profile>
- <id>commons-numbers-examples</id>
- <modules>
- <module>commons-numbers-examples</module>
- </modules>
- </profile>
</profiles>
<developers>
diff --git a/src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRingsClassifier.java b/src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRingsClassifier.java
deleted file mode 100644
index ce0f473..0000000
--- a/src/userguide/java/org/apache/commons/math4/userguide/sofm/ChineseRingsClassifier.java
+++ /dev/null
@@ -1,337 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.apache.commons.math4.userguide.sofm;
-
-import java.util.Iterator;
-import java.io.PrintWriter;
-import java.io.IOException;
-
-import org.apache.commons.rng.UniformRandomProvider;
-import org.apache.commons.rng.simple.RandomSource;
-import org.apache.commons.geometry.euclidean.threed.Vector3D;
-
-import org.apache.commons.math4.ml.neuralnet.SquareNeighbourhood;
-import org.apache.commons.math4.ml.neuralnet.FeatureInitializer;
-import org.apache.commons.math4.ml.neuralnet.FeatureInitializerFactory;
-import org.apache.commons.math4.ml.neuralnet.MapUtils;
-import org.apache.commons.math4.ml.neuralnet.twod.NeuronSquareMesh2D;
-import org.apache.commons.math4.ml.neuralnet.sofm.LearningFactorFunction;
-import org.apache.commons.math4.ml.neuralnet.sofm.LearningFactorFunctionFactory;
-import org.apache.commons.math4.ml.neuralnet.sofm.NeighbourhoodSizeFunction;
-import org.apache.commons.math4.ml.neuralnet.sofm.NeighbourhoodSizeFunctionFactory;
-import org.apache.commons.math4.ml.neuralnet.sofm.KohonenUpdateAction;
-import org.apache.commons.math4.ml.neuralnet.sofm.KohonenTrainingTask;
-import org.apache.commons.math4.ml.distance.DistanceMeasure;
-import org.apache.commons.math4.ml.distance.EuclideanDistance;
-import org.apache.commons.math4.stat.descriptive.SummaryStatistics;
-import org.apache.commons.math4.util.FastMath;
-import org.apache.commons.math4.exception.MathUnsupportedOperationException;
-
-/**
- * SOFM for categorizing points that belong to each of two intertwined rings.
- *
- * The output currently consists in 3 text files:
- * <ul>
- * <li>"before.chinese.U.seq.dat": U-matrix of the SOFM before training</li>
- * <li>"after.chinese.U.seq.dat": U-matrix of the SOFM after training</li>
- * <li>"after.chinese.hit.seq.dat": Hit histogram after training</li>
- * </ul>
- */
-public class ChineseRingsClassifier {
- /** SOFM. */
- private final NeuronSquareMesh2D sofm;
- /** Rings. */
- private final ChineseRings rings;
- /** Distance function. */
- private final DistanceMeasure distance = new EuclideanDistance();
-
- public static void main(String[] args) {
- final ChineseRings rings = new ChineseRings(Vector3D.of(1, 2, 3),
- 25, 2,
- 20, 1,
- 2000, 1500);
- final ChineseRingsClassifier classifier = new ChineseRingsClassifier(rings, 15, 15);
- printU("before.chinese.U.seq.dat", classifier);
- classifier.createSequentialTask(100000).run();
- printU("after.chinese.U.seq.dat", classifier);
- printHit("after.chinese.hit.seq.dat", classifier);
- }
-
- /**
- * @param rings Training data.
- * @param dim1 Number of rows of the SOFM.
- * @param dim2 Number of columns of the SOFM.
- */
- public ChineseRingsClassifier(ChineseRings rings,
- int dim1,
- int dim2) {
- this.rings = rings;
- sofm = new NeuronSquareMesh2D(dim1, false,
- dim2, false,
- SquareNeighbourhood.MOORE,
- makeInitializers());
- }
-
- /**
- * Creates training tasks.
- *
- * @param numTasks Number of tasks to create.
- * @param numSamplesPerTask Number of training samples per task.
- * @return the created tasks.
- */
- public Runnable[] createParallelTasks(int numTasks,
- long numSamplesPerTask) {
- final Runnable[] tasks = new Runnable[numTasks];
- final LearningFactorFunction learning
- = LearningFactorFunctionFactory.exponentialDecay(1e-1,
- 5e-2,
- numSamplesPerTask / 2);
- final double numNeurons = FastMath.sqrt(sofm.getNumberOfRows() * sofm.getNumberOfColumns());
- final NeighbourhoodSizeFunction neighbourhood
- = NeighbourhoodSizeFunctionFactory.exponentialDecay(0.5 * numNeurons,
- 0.2 * numNeurons,
- numSamplesPerTask / 2);
-
- for (int i = 0; i < numTasks; i++) {
- final KohonenUpdateAction action = new KohonenUpdateAction(distance,
- learning,
- neighbourhood);
- tasks[i] = new KohonenTrainingTask(sofm.getNetwork(),
- createRandomIterator(numSamplesPerTask),
- action);
- }
-
- return tasks;
- }
-
- /**
- * Creates a training task.
- *
- * @param numSamples Number of training samples.
- * @return the created task.
- */
- public Runnable createSequentialTask(long numSamples) {
- return createParallelTasks(1, numSamples)[0];
- }
-
- /**
- * Computes the U-matrix.
- *
- * @return the U-matrix of the network.
- */
- public double[][] computeU() {
- return MapUtils.computeU(sofm, distance);
- }
-
- /**
- * Computes the hit histogram.
- *
- * @return the histogram.
- */
- public int[][] computeHitHistogram() {
- return MapUtils.computeHitHistogram(createIterable(),
- sofm,
- distance);
- }
-
- /**
- * Computes the quantization error.
- *
- * @return the quantization error.
- */
- public double computeQuantizationError() {
- return MapUtils.computeQuantizationError(createIterable(),
- sofm.getNetwork(),
- distance);
- }
-
- /**
- * Computes the topographic error.
- *
- * @return the topographic error.
- */
- public double computeTopographicError() {
- return MapUtils.computeTopographicError(createIterable(),
- sofm.getNetwork(),
- distance);
- }
-
- /**
- * Creates the features' initializers.
- * They are sampled from a uniform distribution around the barycentre of
- * the rings.
- *
- * @return an array containing the initializers for the x, y and
- * z coordinates of the features array of the neurons.
- */
- private FeatureInitializer[] makeInitializers() {
- final SummaryStatistics[] centre = new SummaryStatistics[] {
- new SummaryStatistics(),
- new SummaryStatistics(),
- new SummaryStatistics()
- };
- for (Vector3D p : rings.getPoints()) {
- centre[0].addValue(p.getX());
- centre[1].addValue(p.getY());
- centre[2].addValue(p.getZ());
- }
-
- final double[] mean = new double[] {
- centre[0].getMean(),
- centre[1].getMean(),
- centre[2].getMean()
- };
- final double s = 0.1;
- final double[] dev = new double[] {
- s * centre[0].getStandardDeviation(),
- s * centre[1].getStandardDeviation(),
- s * centre[2].getStandardDeviation()
- };
-
- return new FeatureInitializer[] {
- FeatureInitializerFactory.uniform(mean[0] - dev[0], mean[0] + dev[0]),
- FeatureInitializerFactory.uniform(mean[1] - dev[1], mean[1] + dev[1]),
- FeatureInitializerFactory.uniform(mean[2] - dev[2], mean[2] + dev[2])
- };
- }
-
- /**
- * Creates an iterable that will present the points coordinates.
- *
- * @return the iterable.
- */
- private Iterable<double[]> createIterable() {
- return new Iterable<double[]>() {
- public Iterator<double[]> iterator() {
- return new Iterator<double[]>() {
- /** Data. */
- final Vector3D[] points = rings.getPoints();
- /** Number of samples. */
- private int n = 0;
-
- /** {@inheritDoc} */
- public boolean hasNext() {
- return n < points.length;
- }
-
- /** {@inheritDoc} */
- public double[] next() {
- return points[n++].toArray();
- }
-
- /** {@inheritDoc} */
- public void remove() {
- throw new MathUnsupportedOperationException();
- }
- };
- }
- };
- }
-
- /**
- * Creates an iterator that will present a series of points coordinates in
- * a random order.
- *
- * @param numSamples Number of samples.
- * @return the iterator.
- */
- private Iterator<double[]> createRandomIterator(final long numSamples) {
- return new Iterator<double[]>() {
- /** Data. */
- final Vector3D[] points = rings.getPoints();
- /** RNG. */
- final UniformRandomProvider rng = RandomSource.create(RandomSource.KISS);
- /** Number of samples. */
- private long n = 0;
-
- /** {@inheritDoc} */
- public boolean hasNext() {
- return n < numSamples;
- }
-
- /** {@inheritDoc} */
- public double[] next() {
- ++n;
- return points[rng.nextInt(points.length)].toArray();
- }
-
- /** {@inheritDoc} */
- public void remove() {
- throw new MathUnsupportedOperationException();
- }
- };
- }
-
- /**
- * Prints the U-matrix of the map to the given file name.
- *
- * @param fileName File.
- * @param sofm Classifier.
- */
- private static void printU(String fileName,
- ChineseRingsClassifier sofm) {
- PrintWriter out = null;
- try {
- out = new PrintWriter(fileName);
-
- final double[][] uMatrix = sofm.computeU();
- for (int i = 0; i < uMatrix.length; i++) {
- for (int j = 0; j < uMatrix[0].length; j++) {
- out.print(uMatrix[i][j] + " ");
- }
- out.println();
- }
- out.println("# Quantization error: " + sofm.computeQuantizationError());
- out.println("# Topographic error: " + sofm.computeTopographicError());
- } catch (IOException e) {
- // Do nothing.
- } finally {
- if (out != null) {
- out.close();
- }
- }
- }
-
- /**
- * Prints the hit histogram of the map to the given file name.
- *
- * @param fileName File.
- * @param sofm Classifier.
- */
- private static void printHit(String fileName,
- ChineseRingsClassifier sofm) {
- PrintWriter out = null;
- try {
- out = new PrintWriter(fileName);
-
- final int[][] histo = sofm.computeHitHistogram();
- for (int i = 0; i < histo.length; i++) {
- for (int j = 0; j < histo[0].length; j++) {
- out.print(histo[i][j] + " ");
- }
- out.println();
- }
- } catch (IOException e) {
- // Do nothing.
- } finally {
- if (out != null) {
- out.close();
- }
- }
- }
-}
[commons-math] 02/03: Remove unused/outdated file.
Posted by er...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
erans pushed a commit to branch modularized_master
in repository https://gitbox.apache.org/repos/asf/commons-math.git
commit 1c4e4146175720d28b6f76766fe9b64988db79cb
Author: Gilles Sadowski <gi...@gmail.com>
AuthorDate: Tue May 18 03:23:27 2021 +0200
Remove unused/outdated file.
---
test-jar.xml | 99 ------------------------------------------------------------
1 file changed, 99 deletions(-)
diff --git a/test-jar.xml b/test-jar.xml
deleted file mode 100644
index e5a20a5..0000000
--- a/test-jar.xml
+++ /dev/null
@@ -1,99 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--
- Licensed to the Apache Software Foundation (ASF) under one or more
- contributor license agreements. See the NOTICE file distributed with
- this work for additional information regarding copyright ownership.
- The ASF licenses this file to You under the Apache License, Version 2.0
- (the "License"); you may not use this file except in compliance with
- the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
--->
-
-<!--
- Compiles and runs unit tests against distribution jar(s). Use .antrc or the
- command line to control the jdk used to execute this build file.
-
- Assumes that the distribution jar to be tested is in the basedir/lib, along
- with any dependent jars (junit, hamcrest). Use the "libdir" property to specify
- the path to the directory containing these jars.
-
- The default target, "test," executes clean as a dependency.
--->
-
-<project default="test" name="commons-math" basedir=".">
- <property name="libdir" value="lib"/>
- <property name="testclassesdir" value="target/test-classes"/>
- <property name="testreportdir" value="target/test-reports"/>
- <property name="defaulttargetdir" value="target"/>
- <property name="test.resources" value="src/test/resources"/>
- <property name="build.home" value="target"/>
- <path id="build.classpath">
- <fileset dir="${libdir}">
- <include name="*.jar" />
- </fileset>
- </path>
- <target name="clean" description="o Clean up the generated directories">
- <delete dir="${defaulttargetdir}"/>
- </target>
- <target name="init" description="o Initializes some properties">
- <echo>
- JAVA ENVIRONMENT
- **************************Java runtime version*****************************
- ${java.runtime.version}
- **************************Java class path**********************************
- ${java.class.path}
- **************************Java home****************************************
- ${java.home}
- *************************Java library path*******************************
- Java library path: ${java.library.path}
- ===========================================================================
- </echo>
- </target>
- <target name="test" description="o Run the test cases" if="test.failure" depends="internal-test">
- <fail message="There were test failures.">
- </fail>
- </target>
- <target name="internal-test" depends="clean,compile-tests">
- <mkdir dir="${testreportdir}"/>
- <junit dir="./" failureproperty="test.failure" printSummary="yes"
- fork="true" haltonerror="true" showOutput="true">
- <sysproperty key="basedir" value="."/>
- <formatter type="brief"/>
- <classpath>
- <path refid="build.classpath"/>
- <pathelement path="${testclassesdir}"/>
- </classpath>
- <batchtest todir="${testreportdir}">
- <fileset dir="src/test/java">
- <include name="**/*Test.java"/>
- <exclude name="**/*AbstractTest.java"/>
- </fileset>
- </batchtest>
- </junit>
- </target>
- <target name="compile-tests" >
- <mkdir dir="${testclassesdir}"/>
- <javac destdir="${testclassesdir}" deprecation="true" debug="true"
- optimize="false" excludes="**/package.html">
- <src>
- <pathelement location="src/test"/>
- </src>
- <classpath>
- <path refid="build.classpath"/>
- </classpath>
- </javac>
- <copy todir="${build.home}/test-classes">
- <fileset dir="${test.resources}">
- </fileset>
- </copy>
- </target>
-</project>
-
[commons-math] 01/03: Typo.
Posted by er...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
erans pushed a commit to branch modularized_master
in repository https://gitbox.apache.org/repos/asf/commons-math.git
commit ac978e2c4c4f96b835fa7efc5d23f5c40eaea1b9
Author: Gilles Sadowski <gi...@gmail.com>
AuthorDate: Tue May 18 03:23:05 2021 +0200
Typo.
---
commons-math-legacy/pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/commons-math-legacy/pom.xml b/commons-math-legacy/pom.xml
index 8795be8..30fb6ef 100644
--- a/commons-math-legacy/pom.xml
+++ b/commons-math-legacy/pom.xml
@@ -26,7 +26,7 @@
<version>4.0-SNAPSHOT</version>
</parent>
- <artifactId>commons-math-legacy</artifactId>
+ <artifactId>commons-math4-legacy</artifactId>
<name>Apache Commons Math (Legacy)</name>
<description>Legacy codes that are either currently unsupported or not yet modularized.</description>