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 <gillese...@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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http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf
+
+===============================================================================
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sequences.
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+===============================================================================
+
+The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
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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
+
+This product includes software developed at
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+
+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/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/
+
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+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
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+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
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+
+ Copyright [yyyy] [name of copyright owner]
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+ Licensed 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
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+
+ 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.
+
+
+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
+ March 23th 2013)
+ - 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
+THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE
+OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY
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+
+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
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+ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,
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+ANY KIND OR NATURE, INCLUDING BUT NOT LIMITED TO LOSS OF
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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/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
+ 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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+ "Work" shall mean the work of authorship, whether in Source or
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+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
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+ the Work and Derivative Works thereof.
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+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
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+ means any form of electronic, verbal, or written communication sent
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+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
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+ 2. Grant of Copyright License. Subject to the terms and conditions of
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+ copyright license to reproduce, prepare Derivative Works of,
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+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
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+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
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+ Contribution(s) alone or by combination of their Contribution(s)
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+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed 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.
+
+
+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
+ March 23th 2013)
+ - 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
+THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE
+OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY
+OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
+USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF
+THE SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4)
+DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
+UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL
+BE CORRECTED.
+
+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
+HOLDER, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF
+ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,
+INCIDENTAL, CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF
+ANY KIND OR NATURE, INCLUDING BUT NOT LIMITED TO LOSS OF
+PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, WHETHER
+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();
- }
- }
- }
-}
