Copyright and license information for third-party code or libraries used in MIPAV


Binary libraries

Apache License 2.0

axiom-api-*.jar, axiom-dom-*.jar, axiom-impl-*.jar, commons-logging-*.jar, xstx-asl-*.jar, axis2-kernel-*.jar, commons-codec-*.jar, commons-httpclient-*.jar, commons-lang3-*.jar neethi-*.jar, XmlSchema-*.jar, rampart-core-ndar-*.jar, rampart-policy-*.jar, rampart-trust-*.jar, wss4j-*.jar, xmlsec-*.jar, fontbox-*.jar, jempbox-*.jar, pdfbox-*.jar

See http://www.apache.org/licenses/LICENSE-2.0.html.


LGPL 3 + copyright notice

jj2kpack.jar

See http://code.google.com/p/jj2000/. LGPL 3 available here.

Original copyright notice:

This software module was originally developed by Rapha?l Grosbois and
Diego Santa Cruz (Swiss Federal Institute of Technology-EPFL); Joel
Askel?f (Ericsson Radio Systems AB); and Bertrand Berthelot, David
Bouchard, F?lix Henry, Gerard Mozelle and Patrice Onno (Canon Research
Centre France S.A) in the course of development of the JPEG2000
standard as specified by ISO/IEC 15444 (JPEG 2000 Standard). This
software module is an implementation of a part of the JPEG 2000
Standard. Swiss Federal Institute of Technology-EPFL, Ericsson Radio
Systems AB and Canon Research Centre France S.A (collectively JJ2000
Partners) agree not to assert against ISO/IEC and users of the JPEG
2000 Standard (Users) any of their rights under the copyright, not
including other intellectual property rights, for this software module
with respect to the usage by ISO/IEC and Users of this software module
or modifications thereof for use in hardware or software products
claiming conformance to the JPEG 2000 Standard. Those intending to use
this software module in hardware or software products are advised that
their use may infringe existing patents. The original developers of
this software module, JJ2000 Partners and ISO/IEC assume no liability
for use of this software module or modifications thereof. No license
or right to this software module is granted for non JPEG 2000 Standard
conforming products. JJ2000 Partners have full right to use this
software module for his/her own purpose, assign or donate this
software module to any third party and to inhibit third parties from
using this software module for non JPEG 2000 Standard conforming
products. This copyright notice must be included in all copies or
derivative works of this software module.

Copyright (c) 1999/2000 JJ2000 Partners.


LGPL 2.1

hyperapplet.jar

LGPL 2.1 available here.


Clearthought Software License 2.0

TableLayout-*.jar

Unmodified binary redistribution fine with no restrictions. See this debian discussion thread for more information.

/*
 * ====================================================================
 *
 * The Clearthought Software License, Version 2.0
 *
 * Copyright (c) 2001 Daniel Barbalace.  All rights reserved.
 *
 * Project maintained at https://tablelayout.dev.java.net
 *
 * I. Terms for redistribution of original source and binaries
 *
 * Redistribution and use of unmodified source and/or binaries are
 * permitted provided that the following condition is met:
 *
 * 1. Redistributions of original source code must retain the above
 *    copyright notice and license.  You are not required to redistribute
 *    the original source; you may choose to redistribute only the
 *    binaries.
 *
 * Basically, if you distribute unmodified source, you meet
 * automatically comply with the license with no additional effort on
 * your part.
 *
 * II. Terms for distribution of derived works via subclassing and/or
 *     composition.
 *
 * You may generate derived works by means of subclassing and/or
 * composition (e.g., the Adaptor Pattern), provided that the following
 * conditions are met:
 *
 * 1. Redistributions of original source code must retain the above
 *    copyright notice and license.  You are not required to redistribute
 *    the original source; you may choose to redistribute only the
 *    binaries.
 *
 * 2. The original software is not altered.
 *
 * 3. Derived works are not contained in the info.clearthought
 *    namespace/package or any subpackage of info.clearthought.
 *
 * 4. Derived works do not use the class or interface names from the
 *    info.clearthought... packages
 *
 * For example, you may define a class with the following full name:
 *    org.nameOfMyOrganization.layouts.RowMajorTableLayout
 *
 * However, you may not define a class with the either of the
 * following full names:
 *    info.clearthought.layout.RowMajorTableLayout
 *    org.nameOfMyOrganization.layouts.TableLayout
 *
 * III. Terms for redistribution of source modified via patch files.
 *
 * You may generate derived works by means of patch files provided
 * that the following conditions are met:
 *
 * 1. Redistributions of original source code must retain the above
 *    copyright notice and license.  You are not required to
 *    redistribute the original source; you may choose to redistribute
 *    only the binaries resulting from the patch files.
 *
 * 2. The original source files are not altered.  All alteration is
 *    done in patch files.
 *
 * 3. Derived works are not contained in the info.clearthought
 *    namespace/package or any subpackage of info.clearthought.  This
 *    means that your patch files must change the namespace/package
 *    for the derived work.  See section II for examples.
 *
 * 4. Derived works do not use the class or interface names from the
 *    info.clearthought... packages.  This means your patch files
 *    must change the names of the interfaces and classes they alter.
 *    See section II for examples.
 *
 * 5. Derived works must include the following disclaimer.
 *    "This work is derived from Clearthought's TableLayout,
 *     https://tablelayout.dev.java.net, by means of patch files
 *     rather than subclassing or composition.  Therefore, this work
 *     might not contain the latest fixes and features of TableLayout."
 *
 * IV. Terms for repackaging, transcoding, and compiling of binaries.
 *
 * You may do any of the following with the binaries of the
 * original software.
 *
 * 1. You may move binaries (.class files) from the original .jar file
 *    to your own .jar file.
 *
 * 2. You may move binaries from the original .jar file to other
 *    resource containing files, including but not limited to .zip,
 *    .gz, .tar, .dll, .exe files.
 *
 * 3. You may backend compile the binaries to any platform, including
 *    but not limited to Win32, Win64, MAC OS, Linux, Palm OS, any
 *    handheld or embedded platform.
 *
 * 4. You may transcribe the binaries to other virtual machine byte
 *    code protocols, including but not limited to .NET.
 *
 * V. License Disclaimer.
 *
 * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 AUTHOR, AFFILATED BUSINESSES,
 * OR ANYONE ELSE 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.
 * ====================================================================
 */


Sun Binary Code License Agreement, with Supplement

jmf.jar, mediaplayer.jar

Sun Binary Code License Agreement, with Supplement. See the full license here by clicking to the 'Download' page.


Sun Binary Code License Agreement, with Supplement

jhall.jar

Sun Binary Code License Agreement, with Supplement. See the full license here by clicking to the 'Download' page.


Apache-style w/o required attribution.

jdom.jar

Apache-style w/o required attribution. See more information here.

/*-- 

 $Id: LICENSE.txt,v 1.11 2004/02/06 09:32:57 jhunter Exp $

 Copyright (C) 2000-2004 Jason Hunter & Brett McLaughlin.
 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 disclaimer that follows 
    these conditions in the documentation and/or other materials 
    provided with the distribution.

 3. The name "JDOM" must not be used to endorse or promote products
    derived from this software without prior written permission.  For
    written permission, please contact <request_AT_jdom_DOT_org>.
 
 4. Products derived from this software may not be called "JDOM", nor
    may "JDOM" appear in their name, without prior written permission
    from the JDOM Project Management <request_AT_jdom_DOT_org>.
 
 In addition, we request (but do not require) that you include in the 
 end-user documentation provided with the redistribution and/or in the 
 software itself an acknowledgement equivalent to the following:
     "This product includes software developed by the
      JDOM Project (http://www.jdom.org/)."
 Alternatively, the acknowledgment may be graphical using the logos 
 available at http://www.jdom.org/images/logos.

 THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 JDOM AUTHORS OR THE PROJECT
 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.

 This software consists of voluntary contributions made by many 
 individuals on behalf of the JDOM Project and was originally 
 created by Jason Hunter <jhunter_AT_jdom_DOT_org> and
 Brett McLaughlin <brett_AT_jdom_DOT_org>.  For more information
 on the JDOM Project, please see <http://www.jdom.org/>. 

 */


MIT license adaptation

bcprov-*.jar

MIT license adaptation. See the license here.


Sun Microsystems Inc. Software License Agreement

jax-qname.jar, dom.jar, sax.jar, xalan.jar, xercesImpl.jar

Sun Microsystems Inc. Software License Agreement


Sun Binary Code License Agreement, with Supplement

JimiProClasses.jar

Sun Binary Code License Agreement, with Supplement from here.


Public domain

tar.jar

Released to the public domain by Timothy Gerard Endres, time@gjt.org with no warranty.


Attribution required

jaxen-*.jar

Attribution required for distribution:

/*
 $Id: LICENSE.txt,v 1.5 2006/02/05 21:49:04 elharo Exp $

 Copyright 2003-2006 The Werken Company. 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 the Jaxen Project nor the names of 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 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.
 
 */


BSD license

jTEM.jar

All jTEM projects are licensed under the FreeBSD license or 2-clause BSD license (see http://www.opensource.org/licenses/bsd-license.php).

Copyright (c) 2006-2010, Technische Universität Berlin, jTEM
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.
 
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 HOLDER 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.

Common Public License 1.0

wsdl4j-*.jar, junit-*.jar

See this and this for more information.


Acknowledgement in publications required

jhdf5.jar, jhdf5obj.jar, jhdfobj.jar, hdf5.dll/.so files included in JREs

Attribution/acknowledgement required in publications mentioning use of the libraries.

License:

HDF Java Products
Copyright 2006-2010 by The HDF Group.

NCSA HDF Java Products
Copyright 1988-2006 by the Board of Trustees of the University of Illinois.

All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted for any purpose (including commercial purposes)
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 materials provided with the distribution.

3. In addition, redistributions of modified forms of the source or binary
   code must carry prominent notices stating that the original code was
   changed and the date of the change.

4. All publications or advertising materials mentioning features or use of 
   this software are asked, but not required, to acknowledge that it was 
   developed by The HDF Group and by the National Center for Supercomputing 
   Applications at the University of Illinois at Urbana-Champaign and 
   credit the contributors.

5. Neither the name of The HDF Group, the name of the University, nor the 
   name of any Contributor may be used to endorse or promote products derived 
   from this software without specific prior written permission from The HDF 
   Group, the University, or the Contributor, respectively.

DISCLAIMER: 
THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS "AS IS" 
WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event 
shall The HDF Group or the Contributors be liable for any damages suffered 
by the users arising out of the use of this software, even if advised of 
the possibility of such damage. 

--------------------------------------------------------------------------
--------------------------------------------------------------------------

Contributors: National Center for Supercomputing Applications (NCSA) at 
the University of Illinois, Lawrence Livermore National Laboratory (LLNL), 
Sandia National Laboratories (SNL), Los Alamos National Laboratory (LANL), 
Fortner Software, Unidata Program Center (netCDF), The Independent JPEG 
Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), and Digital Equipment 
Corporation (DEC). 

--------------------------------------------------------------------------

Portions of the HDF Java Products were developed with support from the 
University of California, Lawrence Livermore National Laboratory (UC LLNL).
The following statement applies to those portions of the product
and must be retained in any redistribution of source code, binaries,
documentation, and/or accompanying materials:

    This work was partially produced at the University of California,
    Lawrence Livermore National Laboratory (UC LLNL) under contract no.
    W-7405-ENG-48 (Contract 48) between the U.S. Department of Energy 
    (DOE) and The Regents of the University of California (University) 
    for the operation of UC LLNL.

    DISCLAIMER:
    This work was prepared as an account of work sponsored by an agency 
    of the United States Government.  Neither the United States 
    Government nor the University of California nor any of their 
    employees, makes any warranty, express or implied, or assumes any 
    liability or responsibility for the accuracy, completeness, or 
    usefulness of any information, apparatus, product, or process 
    disclosed, or represents that its use would not infringe privately-
    owned rights.  Reference herein to any specific commercial products, 
    process, or service by trade name, trademark, manufacturer, or 
    otherwise, does not necessarily constitute or imply its endorsement, 
    recommendation, or favoring by the United States Government or the 
    University of California.  The views and opinions of authors 
    expressed herein do not necessarily state or reflect those of the 
    United States Government or the University of California, and shall 
    not be used for advertising or product endorsement purposes.


BSD license

InsightToolkit/*

From the ITK license for versions 3.6 to 3.20:

Copyright (c) 1999-2008 Insight Software Consortium All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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.


Public domain, no warranty

ij.jar

Developed by Wayne Rasband of NIH. http://rsbweb.nih.gov/ij/disclaimer.html:

ImageJ is being developed at the National Institutes of Health by an employee of the Federal Government in the course of his official duties. Pursuant to Title 17, Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. ImageJ is an experimental system. NIH assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Artistic License 2.0

camino.jar

The Software is made available for use under the Open Source-approved Artistic Licence 2.0. The Owner draws your attention to the fact that the Software has been developed for and is intended for use in a research environment only. No endorsement can be given for other use including, but not limited to, use in a clinical environment.

http://www.perlfoundation.org/artistic_license_2_0

The copyright in this software and its associated electronic documentation (together "the Software") is owned by University College London of Gower Street, London WC1E 7HN [change this to Camino explanation] ("the Owner"). By proceeding to use the Software you (an individual or legal entity) agree with the Owner to be bound by the terms of this Agreement which will govern your use of the Software.

The Software is made available for use under the Open Source-approved Artistic Licence 2.0, the terms of which are displayed below. The Owner draws your attention to the fact that the Software has been developed for and is intended for use in a research environment only. No endorsement can be given for other use including, but not limited to, use in a clinical environment.

Artistic License 2.0

Copyright (c) 2000-2006, The Perl Foundation.

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Preamble

This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software.

You are always permitted to make arrangements wholly outside of this license directly with the Copyright Holder of a given Package. If the terms of this license do not permit the full use that you propose to make of the Package, you should contact the Copyright Holder and seek a different licensing arrangement. Definitions

"Copyright Holder" means the individual(s) or organization(s) named in the copyright notice for the entire Package.

"Contributor" means any party that has contributed code or other material to the Package, in accordance with the Copyright Holder's procedures.

"You" and "your" means any person who would like to copy, distribute, or modify the Package.

"Package" means the collection of files distributed by the Copyright Holder, and derivatives of that collection and/or of those files. A given Package may consist of either the Standard Version, or a Modified Version.

"Distribute" means providing a copy of the Package or making it accessible to anyone else, or in the case of a company or organization, to others outside of your company or organization.

"Distributor Fee" means any fee that you charge for Distributing this Package or providing support for this Package to another party. It does not mean licensing fees.

"Standard Version" refers to the Package if it has not been modified, or has been modified only in ways explicitly requested by the Copyright Holder.

"Modified Version" means the Package, if it has been changed, and such changes were not explicitly requested by the Copyright Holder.

"Original License" means this Artistic License as Distributed with the Standard Version of the Package, in its current version or as it may be modified by The Perl Foundation in the future.

"Source" form means the source code, documentation source, and configuration files for the Package.

"Compiled" form means the compiled bytecode, object code, binary, or any other form resulting from mechanical transformation or translation of the Source form.

Permission for Use and Modification Without Distribution

(1) You are permitted to use the Standard Version and create and use Modified Versions for any purpose without restriction, provided that you do not Distribute the Modified Version.

Permissions for Redistribution of the Standard Version

(2) You may Distribute verbatim copies of the Source form of the Standard Version of this Package in any medium without restriction, either gratis or for a Distributor Fee, provided that you duplicate all of the original copyright notices and associated disclaimers. At your discretion, such verbatim copies may or may not include a Compiled form of the Package.

(3) You may apply any bug fixes, portability changes, and other modifications made available from the Copyright Holder. The resulting Package will still be considered the Standard Version, and as such will be subject to the Original License.

Distribution of Modified Versions of the Package as Source

(4) You may Distribute your Modified Version as Source (either gratis or for a Distributor Fee, and with or without a Compiled form of the Modified Version) provided that you clearly document how it differs from the Standard Version, including, but not limited to, documenting any non-standard features, executables, or modules, and provided that you do at least ONE of the following:

(a) make the Modified Version available to the Copyright Holder of the Standard Version, under the Original License, so that the Copyright Holder may include your modifications in the Standard Version.

(b) ensure that installation of your Modified Version does not prevent the user installing or running the Standard Version. In addition, the Modified Version must bear a name that is different from the name of the Standard Version.

(c) allow anyone who receives a copy of the Modified Version to make the Source form of the Modified Version available to others under

(i) the Original License or

(ii) a license that permits the licensee to freely copy, modify and redistribute the Modified Version using the same licensing terms that apply to the copy that the licensee received, and requires that the Source form of the Modified Version, and of any works derived from it, be made freely available in that license fees are prohibited but Distributor Fees are allowed.

Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source

(5) You may Distribute Compiled forms of the Standard Version without the Source, provided that you include complete instructions on how to get the Source of the Standard Version. Such instructions must be valid at the time of your distribution. If these instructions, at any time while you are carrying out such distribution, become invalid, you must provide new instructions on demand or cease further distribution. If you provide valid instructions or cease distribution within thirty days after you become aware that the instructions are invalid, then you do not forfeit any of your rights under this license.

(6) You may Distribute a Modified Version in Compiled form without the Source, provided that you comply with Section 4 with respect to the Source of the Modified Version.

Aggregating or Linking the Package

(7) You may aggregate the Package (either the Standard Version or Modified Version) with other packages and Distribute the resulting aggregation provided that you do not charge a licensing fee for the Package. Distributor Fees are permitted, and licensing fees for other components in the aggregation are permitted. The terms of this license apply to the use and Distribution of the Standard or Modified Versions as included in the aggregation.

(8) You are permitted to link Modified and Standard Versions with other works, to embed the Package in a larger work of your own, or to build stand-alone binary or bytecode versions of applications that include the Package, and Distribute the result without restriction, provided the result does not expose a direct interface to the Package.

Items That are Not Considered Part of a Modified Version

(9) Works (including, but not limited to, modules and scripts) that merely extend or make use of the Package, do not, by themselves, cause the Package to be a Modified Version. In addition, such works are not considered parts of the Package itself, and are not subject to the terms of this license.

General Provisions

(10) Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

(11) If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

(12) This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

(13) This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

(14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


Third-party source code

gov.nih.mipav.model.dicomcomm

Loosely based on Java Dicom Package (zdicom) library, originally.

Java Dicom Package (com.zmed.dicom)

Copyright (c) 1996-1997 Z Medical Imaging Systems, Inc.

This software is provided, as is, for non-commercial educational
purposes only.   Use or incorporation of this software or derivative
works in commercial applications requires written consent from
Z Medical Imaging Systems, Inc.
   
Z MEDICAL IMAGING SYSTEMS MAKES NO REPRESENTATIONS OR WARRANTIES ABOUT
THE SUITABILITY OF THE SOFTWARE, EITHER EXPRESS OR IMPLIED, INCLUDING
BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, OR CONFORMANCE TO ANY
SPECIFICATION OR STANDARD.  Z MEDICAL IMAGING SYSTEMS SHALL NOT BE
LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING OR
MODIFYING THIS SOFTWARE OR ITS DERIVATIVES.

This software package is implemented similarly to the UC Davis public domain C++ DICOM implementation which contains the following copyright notice:

Copyright (C) 1995, University of California, Davis

THIS SOFTWARE IS MADE AVAILABLE, AS IS, AND THE UNIVERSITY
OF CALIFORNIA DOES NOT MAKE ANY WARRANTY ABOUT THE SOFTWARE, ITS
PERFORMANCE, ITS MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR
USE, FREEDOM FROM ANY COMPUTER DISEASES OR ITS CONFORMITY TO ANY
SPECIFICATION. THE ENTIRE RISK AS TO QUALITY AND PERFORMANCE OF
THE SOFTWARE IS WITH THE USER.

Copyright of the software and supporting documentation is
owned by the University of California, and free access
is hereby granted as a license to use this software, copy this
software and prepare derivative works based upon this software.
However, any distribution of this software source code or
supporting documentation or derivative works (source code and
supporting documentation) must include this copyright notice.

The UC Davis C++ source code is publicly available from the following anonymous ftp site:

ftp://imrad.ucdmc.ucdavis.edu/pub/dicom/UCDMC/

gov.nih.mipav.model.file

BZip2Constants, CBZip2InputStream, CBZip2OutputStream, CRC

Code distributed under the Apache Software License, version 1.1.

See http://apache.org/licenses/LICENSE-1.1


FileDicomJPEG

Ported from code from Cornell, UC Berkeley and IJC.

 Copyright (c) 1993 Cornell University, Kongji Huang
 All rights reserved.
 
 Permission to use, copy, modify, and distribute this software and its
 documentation for research purposes, without fee, and without written
 agreement is hereby granted, provided that the above copyright notice
 and the following two paragraphs appear in all copies of this
 software.
 
 IN NO EVENT SHALL THE CORNELL UNIVERSITY BE LIABLE TO ANY PARTY FOR
 DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING
 OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE
 UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGE.
 
 THE CORNELL UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE SOFTWARE
 PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 ENHANCEMENTS, OR MODIFICATIONS.
 
---

 Copyright (c) 1993 The Regents of the University of California, Brian
 C. Smith All rights reserved.
 
 Permission to use, copy, modify, and distribute this software and its
 documentation for any purpose, without fee, and without written
 agreement is hereby granted, provided that the above copyright notice
 and the following two paragraphs appear in all copies of this
 software.
 
 IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
 THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
 SUCH DAMAGE.
 
 THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE SOFTWARE
 PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 ENHANCEMENTS, OR MODIFICATIONS.

--- 

 IJG Copyright
 
 The authors make NO WARRANTY or representation, either express or
 implied, with respect to this software, its quality, accuracy,
 merchantability, or fitness for a particular purpose.  This software is
 provided "AS IS", and you, its user, assume the entire risk as to its
 quality and accuracy.
 
 This software is copyright (C) 1991, 1992, Thomas G. Lane.  All Rights
 Reserved except as specified below.
 
 Permission is hereby granted to use, copy, modify, and distribute this
 software (or portions thereof) for any purpose, without fee, subject to
 these conditions:  (1) If any part of the source code for this software
 is distributed, then this README file must be included, with this
 copyright and no-warranty notice unaltered; and any additions,
 deletions, or changes to the original files must be clearly indicated
 in accompanying documentation.  (2) If only executable code is
 distributed, then the accompanying documentation must state that "this
 software is based in part on the work of the Independent JPEG Group".
 (3) Permission for use of this software is granted only if the user
 accepts full responsibility for any undesirable consequences; the
 authors accept NO LIABILITY for damages of any kind.
 
 Permission is NOT granted for the use of any IJG author's name or
 company name in advertising or publicity relating to this software or
 products derived from it.  This software may be referred to only as
 "the Independent JPEG Group's software".
 
 We specifically permit and encourage the use of this software as the
 basis of commercial products, provided that all warranty or liability
 claims are assumed by the product vendor.

FileDM3, FileFits

Contains some code from ImageJ.

ImageJ disclaimer:

ImageJ is being developed at the National Institutes of Health by an employee of the Federal Government in the course of his official duties. Pursuant to Title 17, Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. ImageJ is an experimental system. NIH assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.


TIFFLZWDecoder

Taken from Sun example code.

Copyright (c) 2001 Sun Microsystems, Inc. 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.

-Redistribution in binary form must reproduct 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 Sun Microsystems, Inc. or the names of contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.

This software is provided "AS IS," without a warranty of any kind. ALL
EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY
IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR
NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND ITS LICENSORS SHALL NOT BE
LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING
OR DISTRIBUTING THE SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR DIRECT,
INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER
CAUSED AND REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF THE USE OF
OR INABILITY TO USE SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.

You acknowledge that Software is not designed,licensed or intended for use in
the design, construction, operation or maintenance of any nuclear facility.

gov.nih.mipav.model.algorithms

AlgorithmAAM, AlgorithmASM

Ported from MATLAB code distributed under a BSD-style license.

Copyright (c) 2010, Dirk-Jan Kroon
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
      
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.

AlgorithmColocalizationEM

EM algorithm derived from code by Ismet Bayraktaroglu (ismet@bayraktaroglu.org).

Permission received from Ismet Bayraktaroglu for distribution under BSD license with MIPAV.


AlgorithmEllipsoidFit

The part of the code up to the derivation of v[0] through v[9] for the 3D ellipsoid model comes from the port of MATLAB code provided by Lecturer Qingde Li Department of Computer Science, University of Hull, Hull HU6 7RX, UK [q.li@hull.ac.uk] Reference: "Least Squares Ellipsoid Specific Fitting" by Qingde Li and John G. Griffiths, Proceedings of the Geometric Modeling and Processing 2004, IEEE Computer Society.

Use allowed by the author with the inclusion of the above statement.


AlgorithmIHN3Correction

Port of N3 correction code from MNI by John G. Sled.

Copyright 1996, John G. Sled
McConnell Brain Imaging Centre,
Montreal Neurological Institute, McGill University.

Permission to use, copy, modify, and distribute this software and its
documentation for any purpose and without fee is hereby granted,
provided that the above copyright notice appear in all copies.  The
author and McGill University make no representations about the
suitability of this software for any purpose.  It is provided "as is"
without express or implied warranty.


AlgorithmKernelRegression

This is a port of MATLAB routines contained in kernelRegressionBasedImageProcessingToolBox_ver1-2beta written by Hiroyuki Takeda, Sina Farsiu, and Peyman Milanfar. http://users.soe.ucsc.edu/~htakeda/KernelToolBox.htm

This is experimental software. It is provided for noncommercial research purposes only. Use at your own risk. No warranty is implied by this distribution. Copyright © 2007 by University of California.


AlgorithmNLNoiseReduction

Based on code from http://users.fmrib.ox.ac.uk/~steve/susan/. Non-commercial restriction. Had a patent, but it appears to be lapsed.

Note: the program is (c) Copyright 1995-1999, Defence and Evaluation Research Agency, UK. DERA has now become QinetiQ, who until recently held the patent on SUSAN, which now now lapsed.

  SUSAN Version 2l by Stephen Smith
  Oxford Centre for Functional Magnetic Resonance Imaging of the Brain,
  Department of Clinical Neurology, Oxford University, Oxford, UK
  (Previously in Computer Vision and Image Processing Group - now
  Computer Vision and Electro Optics Group - DERA Chertsey, UK)
  Email:    steve@fmrib.ox.ac.uk
  WWW:      http://www.fmrib.ox.ac.uk/~steve

  (C) Crown Copyright (1995-1999), Defence Evaluation and Research Agency,
  Farnborough, Hampshire, GU14 6TD, UK
  DERA WWW site:
  http://www.dera.gov.uk/
  DERA Computer Vision and Electro Optics Group WWW site:
  http://www.dera.gov.uk/imageprocessing/dera/group_home.html
  DERA Computer Vision and Electro Optics Group point of contact:
  Dr. John Savage, jtsavage@dera.gov.uk, +44 1344 633203

  A UK patent has been granted: "Method for digitally processing
  images to determine the position of edges and/or corners therein for
  guidance of unmanned vehicle", UK Patent 2272285. Proprietor:
  Secretary of State for Defence, UK. 15 January 1997

  This code is issued for research purposes only and remains the
  property of the UK Secretary of State for Defence. This code must
  not be passed on without this header information being kept
  intact. This code must not be sold.

AlgorithmRegionGrow

Port of fuzzy connectedness code from ITK.

Versions of ITK previous to ITK 3.6 are still distributed under the original license:

Copyright (c) 1999-2008 Insight Software Consortium All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER 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 AUTHORS 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.


AlgorithmWaveletThreshold

Ported from Numerical Recipes in C wavelet methods, which are in the public domain (see http://www.nr.com/public-domain.html).


Bessel, InverseLaplace2, NL2sol

Ported from ACM code.

ACM Software License Agreement

All software, both binary and source published by the Association for Computing Machinery (hereafter, Software) is copyrighted by the Association (hereafter, ACM) and ownership of all right, title and interest in and to the Software remains with ACM. By using or copying the Software, User agrees to abide by the terms of this Agreement.

Noncommercial Use

The ACM grants to you (hereafter, User) a royalty-free, nonexclusive right to execute, copy, modify and distribute both the binary and source code solely for academic, research and other similar noncommercial uses, subject to the following conditions:

Commercial Use

Any User wishing to make a commercial use of the Software must contact ACM at permissions@acm.org to arrange an appropriate license. Commercial use includes (1) integrating or incorporating all or part of the source code into a product for sale or license by, or on behalf of, User to third parties, or (2) distribution of the binary or source code to third parties for use with a commercial product sold or licensed by, or on behalf of, User.

Revised 6/98


ConfluentHypergeometric

Contains ports of code from ACM and Computation of Special Functions by Shanjie Zhang and Jianming Jin.

ACM Software License Agreement

All software, both binary and source published by the Association for Computing Machinery (hereafter, Software) is copyrighted by the Association (hereafter, ACM) and ownership of all right, title and interest in and to the Software remains with ACM. By using or copying the Software, User agrees to abide by the terms of this Agreement.

Noncommercial Use

The ACM grants to you (hereafter, User) a royalty-free, nonexclusive right to execute, copy, modify and distribute both the binary and source code solely for academic, research and other similar noncommercial uses, subject to the following conditions:

  1. User acknowledges that the Software is still in the development stage and that it is being supplied "as is," without any support services from ACM. Neither ACM nor the author makes any representations or warranties, express or implied, including, without limitation, any representations or warranties of the merchantability or fitness for any particular purpose, or that the application of the software, will not infringe on any patents or other proprietary rights of others.
  2. ACM shall not be held liable for direct, indirect, incidental or consequential damages arising from any claim by User or any third party with respect to uses allowed under this Agreement, or from any use of the Software.
  3. User agrees to fully indemnify and hold harmless ACM and/or the author(s) of the original work from and against any and all claims, demands, suits, losses, damages, costs and expenses arising out of the User's use of the Software, including, without limitation, arising out of the User's modification of the Software.
  4. User may modify the Software and distribute that modified work to third parties provided that: (a) if posted separately, it clearly acknowledges that it contains material copyrighted by ACM (b) no charge is associated with such copies, (c) User agrees to notify ACM and the Author(s) of the distribution, and (d) User clearly notifies secondary users that such modified work is not the original Software.
  5. User agrees that ACM, the authors of the original work and others may enjoy a royalty-free, non-exclusive license to use, copy, modify and redistribute these modifications to the Software made by the User and distributed to third parties as a derivative work under this agreement.
  6. This agreement will terminate immediately upon User's breach of, or non-compliance with, any of its terms. User may be held liable for any copyright infringement or the infringement of any other proprietary rights in the Software that is caused or facilitated by the User's failure to abide by the terms of this agreement.
  7. This agreement will be construed and enforced in accordance with the law of the state of New York applicable to contracts performed entirely within the State. The parties irrevocably consent to the exclusive jurisdiction of the state or federal courts located in the City of New York for all disputes concerning this agreement.

Commercial Use

Any User wishing to make a commercial use of the Software must contact ACM at permissions@acm.org to arrange an appropriate license. Commercial use includes (1) integrating or incorporating all or part of the source code into a product for sale or license by, or on behalf of, User to third parties, or (2) distribution of the binary or source code to third parties for use with a commercial product sold or licensed by, or on behalf of, User.

Revised 6/98

--

Excerpt from Appendix C of Computation of Special Functions by Shanjie Zhang and Jianming Jin:

All the programs and subroutines contained in this diskette are copyrighted. However, we give permission to the reader who purchases this book to incorporate any of these programs into his or her programs provided that the copyright is acknowledged.

...

DISCLAIMER OF WARRANTY

Although we have made a great effort to test and validate the computer programs, we make no warranties, express or implied, that these programs are free of error, or are consistent with any particular standard of merchantability, or that they will meet your requirements for any particular application. They should not be relied on for solving problems whose incorrect solution could result in injury to a person or loss of property. If you do use the programs in such a manner, it is at your own risk. The authors and publisher disclaim all liability for direct or consequential damages resulting from your use of the programs.


FFTUtility, FFTUtilityEP

This class is based on the Fortran/C code for R. C. Singleton's mixed radix FFT algorithm, released under the below license by Mark Olesen on NETLIB (netlib.org).

Copyright(c)1995,97 Mark Olesen <olesen@me.QueensU.CA>
    	Queen's Univ at Kingston (Canada)

Permission to use, copy, modify, and distribute this software for
any purpose without fee is hereby granted, provided that this
entire notice is included in all copies of any software which is
or includes a copy or modification of this software and in all
copies of the supporting documentation for such software.

THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR
IMPLIED WARRANTY.  IN PARTICULAR, NEITHER THE AUTHOR NOR QUEEN'S
UNIVERSITY AT KINGSTON MAKES ANY REPRESENTATION OR WARRANTY OF ANY
KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS
FITNESS FOR ANY PARTICULAR PURPOSE.

All of which is to say that you can do what you like with this
source code provided you don't try to sell it as your own and you
include an unaltered copy of this message (including the
copyright).

It is also implicitly understood that bug fixes and improvements
should make their way back to the general Internet community so
that everyone benefits.

Gamma, Hypergeometric, JacobianElliptic, Psi

Ported from FORTRAN code from Computation of Special Functions by Shanjie Zhang and Jianming Jin.

The FORTRAN code this class is based upon is by Shanjie Zhang and Jianming Jin and copyright 1996 John Wiley & Sons, Inc.

Excerpt from Appendix C:

All the programs and subroutines contained in this diskette are copyrighted. However, we give permission to the reader who purchases this book to incorporate any of these programs into his or her programs provided that the copyright is acknowledged.

...

DISCLAIMER OF WARRANTY

Although we have made a great effort to test and validate the computer programs, we make no warranties, express or implied, that these programs are free of error, or are consistent with any particular standard of merchantability, or that they will meet your requirements for any particular application. They should not be relied on for solving problems whose incorrect solution could result in injury to a person or loss of property. If you do use the programs in such a manner, it is at your own risk. The authors and publisher disclaim all liability for direct or consequential damages resulting from your use of the programs.


GeneralizedEigenvalue, GeneralizedInverse

Port of FORTRAN LAPACK 3.0 and 3.1 methods.

Copyright (c) 1992-2007 The University of Tennessee. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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


Integration2, Integration2EP

Based on FORTRAN numerical integration routines in QUADPACK.

This is a port of FORTRAN numerical integration routines in QUADPACK found at http://www.netlib.org/quadpack

Reference: R. Piessens, E. deDoncker-Kapenga, C. Uberhuber, D. Kahaner Quadpack: a Subroutine Package for Automatic Integration Springer Verlag, 1983. Series in Computational Mathematics v. 1

The original dqage, dqagie, dqagpe, dqagse, dqawce, dqawfe, dqawoe, adn dqawse routines were written by Robert Piessens and Elise de Doncker.

The original dqng routine was written by Robert Piessens and Elise de Doncker and modified by David Kahaner.

The original dqc25c, dqc25f, dqc25s, dqcheb, dqelg, dqk15, dqk15i, dqk15w, dqk21, dqk31, dqk41, dqk51, dqk61, dqmomo, dqpsrt, dqwgtc, dqwgtf, and dqwgts routines were written by Robert Piessens and Elise de Doncker.

The simple contents of dqwgtc, dqwgtf, and dqwgts are incorporated into dqk15w.

The linpack routine dgtsl was written by Jack Dongarra of the Argonne National Laboratory.

Self tests 1 to 15 come from quadpack_prb.f90 by John Burkardt.

Porting was performed by William Gandler.

The QUADPACK code is made freely available, with the following restrictions:

Re-distributions of the source code should credit Quadpack and retain the notice with the names of the original authors; the names of the copyright holders or contributors may not be used to endorse or promote any derived software without prior permission; the Quadpack software is provided "as is", without warranties; Quadpack and the authors deny any liability for situations resulting from the use of this software.


InverseLaplaceqd

This is a port of niltqd.m, a fast numerical inverse Laplace transform based on FFT and quotient-difference algorithm by Lubomir Brancik, 2001, Brno University of Technology.

Use allowed by the author with inclusion of the above acknowledgement.


InverseLaplace

Ported from MATLAB INVLAP.M by Karl Hollenbeck.

From the original MATLAB file:

Copyright: Karl Hollenbeck
Department of Hydrodynamics and Water Resources
Technical University of Denmark, DK-2800 Lyngby
email: karl@isv16.isva.dtu.dk

22 Nov 1996, MATLAB 5 version 27 Jun 1997 updated 1 Oct 1998

IF YOU PUBLISH WORK BENEFITING FROM THIS M-FILE, PLEASE CITE IT AS:
Hollenbeck, K. J. (1998) INVLAP.M: A matlab function for numerical
inversion of Laplace transforms by the de Hoog algorithm,
http://www.isva.dtu.dk/staff/karl/invlap.htm

Lmmin

Freely available under the below license.

lmfit is released under the LMFIT-BEER-WARE licence:

In writing this software, I borrowed heavily from the public domain,
especially from work by Burton S. Garbow, Kenneth E. Hillstrom,
Jorge J. More`, Steve Moshier, and the authors of lapack. To avoid
unneccessary complications, I put my additions and amendments also
into the public domain. Please retain this notice. Otherwise feel
free to do whatever you want with this stuff. If we meet some day,
and you think this work is worth it, you can buy me a beer in return.

NLConstrainedEngine, NLConstrainedEngineEP, AlgorithmConstELSUNCOpt3D, AlgorithmELSUNCOpt2D, AlgorithmELSUNCOpt3D

Port of ELSUNC algorithm.

Use allowed by the author with acknowledgement: Gauss-Newton Based Algorithms For Constrained Nonlinear Least Squares Problems by Per Lindstrom and Per-Ake Wedin, Institute of Information Processing, University of Umea, S-901 87 Umea, Sweden This can be downleaded from http://www.cs.umu.se/~perl/reports/alg.ps.gz


gov.nih.mipav.model.structures

TableSorter

Taken from Sun example code.

Copyright (c) 1995 - 2008 Sun Microsystems, Inc.  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 Sun Microsystems nor the names of 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 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.

VOIContour

2D convex hull algorithm based on C code by Ken Clarkson.

/*
 * Ken Clarkson wrote this.  Copyright (c) 1996 by AT&T..
 * Permission to use, copy, modify, and distribute this software for any
 * purpose without fee is hereby granted, provided that this entire notice
 * is included in all copies of any software which is or includes a copy
 * or modification of this software and in all copies of the supporting
 * documentation for such software.
 * THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
 * WARRANTY.  IN PARTICULAR, NEITHER THE AUTHORS NOR AT&T MAKE ANY
 * REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY
 * OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
 */

gov.nih.mipav.util

DoubleDouble

Based on DoubleDouble class written by Martin Davis and distributed under the BSD license.

Copyright © 2008-2012 Martin Davis. 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 name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY Martin Davis "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 AUTHOR 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.


Jama

Classes taken from the public domain Jama project.

This software is a cooperative product of The MathWorks and the National Institute of Standards and Technology (NIST) which has been released to the public domain. Neither The MathWorks nor NIST assumes any responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Releasing software into the public domain means that the authors are relinquishing any rights that they have to the software. It can be used for any purpose by anyone. No strings attached.