Finished release 0.2.4

diff --git a/AUTHORS b/AUTHORS
index 100492a..974aea3 100644 (file)
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,4 +1,4 @@
-The following people have contributed to libDAI (in order of importance):
+The following people have contributed to libDAI (in decreasing order of importance):

 
 Joris Mooij
 Martijn Leisink
 
 Joris Mooij
 Martijn Leisink


@@ -12,7 +12,8 @@ Claudio Lima
 Jiuxiang Hu
 Peter Gober
 Sebastian Nowozin
 Jiuxiang Hu
 Peter Gober
 Sebastian Nowozin

-Alexander Gerhard Schwing
+Alexander Schwing
+Alejandro Lage

 
 This work is part of the Interactive Collaborative Information Systems (ICIS) 
 project, supported by the Dutch Ministry of Economic Affairs, grant BSIK03024.
 
 This work is part of the Interactive Collaborative Information Systems (ICIS) 
 project, supported by the Dutch Ministry of Economic Affairs, grant BSIK03024.

diff --git a/ChangeLog b/ChangeLog
index f18a64a..fcf903d 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,18 +1,40 @@
-* Documented and cleaned up utils/createfg
+libDAI-0.2.4 (2010-02-11)
+-------------------------
+
+New features:
+* Implemented Tree-Reweighted BP
+* [Frederik Eaton] Implemented Fractional Belief Propagation
+
+Miscellaneous improvements:
+* Improved documentation
+* [Frederik Eaton] Added constructors for BBPCostFunction
+* [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
+* [Frederik Eaton] Added unary minus to TProb<>
+* [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
+* [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
+* tests/testdai option "marginals" now has three possible values: NONE
+  outputs no marginals, VAR only variable marginals, and ALL outputs all
+  marginals calculated by the algorithm.
+* Strengthened convergence criteria of various algorithms

 * Added GraphAL, an adjacency list implementation for graphs,
   similar to (but simpler than) BipartiteGraph
 * Added GraphAL, an adjacency list implementation for graphs,
   similar to (but simpler than) BipartiteGraph

-* Renamed Graph into GraphEL (for Graph, implemented as Edge List)

 * Added some functionality to create various standard factors
   (the functions whose names start with "createFactor")
 * Added some functionality to create various standard factors
   (the functions whose names start with "createFactor")

-* Renamed "Clamped BP" into "Conditioned BP"
-* Improved documentation
-* Documented tests/testdai
-* Moved platform independent build options into Makefile.ALL
-* Windows platform now needs boost 1.37 or higher
-* Implemented Tree-Reweighted BP
+* Added examples example_sprinkler_gibbs and example_sprinkler_em

 * Implemented various heuristics for choosing a variable elimination sequence 
   in JTree
 * Added BETHE method for GBP/HAK cluster choice
 * Implemented various heuristics for choosing a variable elimination sequence 
   in JTree
 * Added BETHE method for GBP/HAK cluster choice

+
+Build system:
+* Moved platform independent build options into Makefile.ALL
+* Windows platform now needs Boost 1.37 or higher
+
+Code cleanup:
+* Cleaned up utils/createfg and tests/testdai
+
+Interface changes (the old interface is marked obsolete and will be removed in the next release):
+* Removed obsolete/deprecated stuff
+* Renamed Graph into GraphEL (for Graph, implemented as Edge List)

 * Renamed some functions of BipartiteGraph:
     add1() -> addNode1()
     erase1() -> eraseNode1()
 * Renamed some functions of BipartiteGraph:
     add1() -> addNode1()
     erase1() -> eraseNode1()


@@ -20,27 +42,21 @@
     add2() -> addNode2()
     erase2() -> eraseNode2()
     nr2() -> nrNodes2()
     add2() -> addNode2()
     erase2() -> eraseNode2()
     nr2() -> nrNodes2()

-* Added examples example_sprinkler_gibbs and example_sprinkler_em
-* Strengthened convergence criteria of various algorithms
-* Implemented FBP::logZ()
-* Fixed bug in HAK for trivial region graphs (with only one outer region
-  and no inner regions), reported by Alejandro Lage.
-* tests/testdai option "marginals" now has three possible values: NONE
-  outputs no marginals, VAR only variable marginals, and ALL outputs all
-  marginals calculated by the algorithm.
-* [Frederik Eaton] Added Fractional Belief Propagation
-* [Alexander Gerhard Schwing] Fixed error in BP that occured with damping
-  and using log-domain updates
-* Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
-* [Frederik Eaton] Two small patches for src/jtree.cpp and utils/createfg.cpp
+* Renamed some functions in ClusterGraph:
+    ClusterGraph::eliminationCost() -> ::eliminationCost_MinFill() 
+    ClusterGraph::VarElim() -> ClusterGraph::VarElim( sequentialVariableElimination( ElimSeq ) ) 
+    ClusterGraph::VarElim_MinFill() -> ClusterGraph::VarElim( greedyVariableElimination( eliminationCost_MinFill ) )
+* Changed interface of one RegionGraph constructor
+* Renamed "Clamped BP" into "Conditioned BP"
+
+Bug fixes:

 * Fixed regression in scripts/regenerate-properties (now all errors are 
   gathered before throwing the exception, as used to be the case)
 * Fixed regression in scripts/regenerate-properties (now all errors are 
   gathered before throwing the exception, as used to be the case)

-* [Frederik Eaton] Added constructors for BBPCostFunction
-* [Frederik Eaton] Added accessor/mutator for the elements of a SmallSet<>
-* [Frederik Eaton] Added unary minus to TProb<>
-* [Frederik Eaton] Added Hellinger distance to TProb<>::DistType
-* Some small modifications to AUTHORS and main page of documentation
-* Removed obsolete/deprecated stuff
+* Fixed FTBFS errors on MACOSX (thanks to Sebastian Riedel for reporting this bug)
+* [Alexander Schwing] Fixed error in BP that occured with damping
+  and using log-domain updates
+* Fixed bug in HAK for trivial region graphs (with only one outer region
+  and no inner regions), reported by Alejandro Lage.

 
 
 libDAI-0.2.3 (2009-11-16)
 
 
 libDAI-0.2.3 (2009-11-16)

diff --git a/Makefile b/Makefile
index 447721a..e476c2a 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -15,8 +15,8 @@ include Makefile.ALL
 include Makefile.conf
 
 # Set version and date
 include Makefile.conf
 
 # Set version and date

-DAI_VERSION="git HEAD"
-DAI_DATE="February 4, 2010 - or later"
+DAI_VERSION="0.2.4"
+DAI_DATE="February 11, 2010"

 
 # Directories of libDAI sources
 # Location libDAI headers
 
 # Directories of libDAI sources
 # Location libDAI headers

diff --git a/Makefile.ALL b/Makefile.ALL
index b159a2f..a13c11c 100644 (file)
--- a/Makefile.ALL
+++ b/Makefile.ALL
@@ -33,7 +33,7 @@ WITH_GIBBS=true
 WITH_CBP=true
 
 # Build doxygen documentation?
 WITH_CBP=true
 
 # Build doxygen documentation?

-WITH_DOC=true
+WITH_DOC=

 
 # Build with debug info?
 DEBUG=true
 
 # Build with debug info?
 DEBUG=true

diff --git a/Makefile.WINDOWS b/Makefile.WINDOWS
index 5f7ae9e..c09be0c 100644 (file)
--- a/Makefile.WINDOWS
+++ b/Makefile.WINDOWS
@@ -40,13 +40,13 @@ CCDEBUGFLAGS=/Ox /Zi -DDAI_DEBUG
 # Flags to add in non-debugging mode (if DEBUG=false)
 CCNODEBUGFLAGS=/Ox
 # Standard include directories
 # Flags to add in non-debugging mode (if DEBUG=false)
 CCNODEBUGFLAGS=/Ox
 # Standard include directories

-CCINC=/Iinclude /IC:\boost_1_36_0
+CCINC=/Iinclude /IE:\boost_1_42_0

 
 # LINKER
 # Standard libraries to include
 LIBS=/link $(LIB)/libdai$(LE)
 # For linking with the BOOST Program Options library
 
 # LINKER
 # Standard libraries to include
 LIBS=/link $(LIB)/libdai$(LE)
 # For linking with the BOOST Program Options library

-BOOSTLIBS=/LIBPATH:C:\boost_1_36_0\stage\lib
+BOOSTLIBS=/LIBPATH:E:\boost_1_42_0\stage\lib

 # Additional library search paths for linker
 # (For some reason, we have to add the VC library path, although it is in the environment)
 CCLIB=/LIBPATH:"C:\Program Files\Microsoft Visual Studio 9.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files\Microsoft Visual Studio 9.0\VC\LIB" /LIBPATH:"C:\Program Files\Microsoft SDKs\Windows\v6.0A\lib"
 # Additional library search paths for linker
 # (For some reason, we have to add the VC library path, although it is in the environment)
 CCLIB=/LIBPATH:"C:\Program Files\Microsoft Visual Studio 9.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files\Microsoft Visual Studio 9.0\VC\LIB" /LIBPATH:"C:\Program Files\Microsoft SDKs\Windows\v6.0A\lib"


@@ -65,4 +65,4 @@ SWIG=swig
 # Location of Python header files
 INCLUDE_PYTHON=C:\python2.5
 # Location of Boost C++ library header files
 # Location of Python header files
 INCLUDE_PYTHON=C:\python2.5
 # Location of Boost C++ library header files

-INCLUDE_BOOST=C:\boost_1_36_0
+INCLUDE_BOOST=E:\boost_1_42_0

diff --git a/README b/README
index 7245cb8..5aaa74f 100644 (file)
--- a/README
+++ b/README
@@ -2,8 +2,8 @@ libDAI  -  A free/open source C++ library for Discrete Approximate Inference
 
 -------------------------------------------------------------------------------
 
 
 -------------------------------------------------------------------------------
 

-Version:  git HEAD
-Date:     February 4, 2010 - or later
+Version:  0.2.4
+Date:     February 11, 2010

 See also: http://www.libdai.org
 
 -------------------------------------------------------------------------------
 See also: http://www.libdai.org
 
 -------------------------------------------------------------------------------


@@ -34,12 +34,22 @@ of this program, please:
   * mention this software in the Acknowledgements section.
 
 An appropriate citation would be:
   * mention this software in the Acknowledgements section.
 
 An appropriate citation would be:

-J. M. Mooij (2009) "libDAI 0.2.3: A free/open source C++ library for Discrete
-Approximate Inference", http://www.libdai.org
+
+Joris M. Mooij et al. (2010) "libDAI 0.2.4: A free/open source C++ library for
+Discrete Approximate Inference", http://www.libdai.org
+
+or in BiBTeX format:
+
+  @misc{mooij2010libdai,
+    author = "Joris M. Mooij et al.",
+    title = "lib{DAI} 0.2.4: A free/open source {C}++ library for {D}iscrete {A}pproximate {I}nference",
+    howpublished = "http://www.libdai.org/",
+    year = 2010
+  }
+

 
 Moreover, as a personal note, I would appreciate it if you would email
 
 Moreover, as a personal note, I would appreciate it if you would email

-(citations of) papers referencing this work to joris dot mooij at libdai dot
-org.
+(citations of) papers referencing this work to joris dot mooij at libdai dot org.

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


@@ -141,11 +151,12 @@ Mailing list
 
 The Google group "libDAI" (http://groups.google.com/group/libdai) can be used
 for getting support and discussing development issues.
 
 The Google group "libDAI" (http://groups.google.com/group/libdai) can be used
 for getting support and discussing development issues.

-

 -------------------------------------------------------------------------------
 
 Building libDAI under UNIX variants (Linux / Cygwin / Mac OS X)
 
 -------------------------------------------------------------------------------
 
 Building libDAI under UNIX variants (Linux / Cygwin / Mac OS X)
 

+Preparations
+

 You need:
 
   * a recent version of gcc (at least version 3.4)
 You need:
 
   * a recent version of gcc (at least version 3.4)


@@ -180,6 +191,8 @@ http://www.boost.org/ and compile/install it with:
   make install
 
 
   make install
 
 

+Building libDAI
+

 To build the libDAI source, first copy a template Makefile.* to Makefile.conf
 (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). Then,
 edit the Makefile.conf template to adapt it to your local setup. Especially
 To build the libDAI source, first copy a template Makefile.* to Makefile.conf
 (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). Then,
 edit the Makefile.conf template to adapt it to your local setup. Especially


@@ -194,7 +207,7 @@ If the build is successful, you can test the example program:
 
   examples/example tests/alarm.fg
 
 
   examples/example tests/alarm.fg
 

-or the more elaborate test program:
+or the more extensive test program:

 
   tests/testdai --aliases tests/aliases.conf --filename tests/alarm.fg --methods JTREE_HUGIN BP_SEQMAX
 
 
   tests/testdai --aliases tests/aliases.conf --filename tests/alarm.fg --methods JTREE_HUGIN BP_SEQMAX
 


@@ -202,6 +215,8 @@ or the more elaborate test program:
 
 Building libDAI under Windows
 
 
 Building libDAI under Windows
 

+Preparations
+

 You need:
 
   * A recent version of MicroSoft Visual Studio (2008 is known to work)
 You need:
 
   * A recent version of MicroSoft Visual Studio (2008 is known to work)


@@ -212,6 +227,8 @@ For the regression test, you need:
 
   * GNU diff, GNU sed (can be obtained from http://gnuwin32.sourceforge.net)
 
 
   * GNU diff, GNU sed (can be obtained from http://gnuwin32.sourceforge.net)
 

+Building libDAI
+

 To build the source, copy Makefile.WINDOWS to Makefile.conf. Then, edit
 Makefile.conf to adapt it to your local setup. Platform independent build
 options can be set in Makefile.ALL. Finally, run (from the command line)
 To build the source, copy Makefile.WINDOWS to Makefile.conf. Then, edit
 Makefile.conf to adapt it to your local setup. Platform independent build
 options can be set in Makefile.ALL. Finally, run (from the command line)


@@ -224,7 +241,7 @@ If the build is successful, you can test the example program:
 
   examples\example tests\alarm.fg
 
 
   examples\example tests\alarm.fg
 

-or the more elaborate test program:
+or the more extensive test program:

 
   tests\testdai --aliases tests\aliases.conf --filename tests\alarm.fg --methods JTREE_HUGIN BP_SEQMAX
 
 
   tests\testdai --aliases tests\aliases.conf --filename tests\alarm.fg --methods JTREE_HUGIN BP_SEQMAX
 


@@ -282,4 +299,3 @@ Install doxygen, graphviz and a TeX distribution and use
 to build the documentation. If the documentation is not clear enough, feel free
 to send me an email (or even better, to improve the documentation and send a
 patch!). The documentation can also be browsed online at http://www.libdai.org.
 to build the documentation. If the documentation is not clear enough, feel free
 to send me an email (or even better, to improve the documentation and send a
 patch!). The documentation can also be browsed online at http://www.libdai.org.

-

diff --git a/include/dai/doc.h b/include/dai/doc.h
index 6d438f9..f750e84 100644 (file)
--- a/include/dai/doc.h
+++ b/include/dai/doc.h
@@ -40,9 +40,9 @@
 
 
 /** \mainpage Reference manual for libDAI - A free/open source C++ library for Discrete Approximate Inference methods
 
 
 /** \mainpage Reference manual for libDAI - A free/open source C++ library for Discrete Approximate Inference methods

- *  \author Joris Mooij
- *  \version git HEAD
- *  \date February 4, 2010 - or later
+ *  \author Joris Mooij, Frederik Eaton
+ *  \version 0.2.4
+ *  \date February 11, 2010

  *
  *  <hr size="1">
  *  \section about About libDAI
  *
  *  <hr size="1">
  *  \section about About libDAI


@@ -173,9 +173,21 @@
  *    - mention this software in the Acknowledgements section. 
  *
  *  An appropriate citation would be:\n
  *    - mention this software in the Acknowledgements section. 
  *
  *  An appropriate citation would be:\n

- *  J. M. Mooij (2009) "libDAI 0.2.3: A free/open source C++ library for Discrete 
+ *
+ *  Joris M. Mooij et al. (2010) "libDAI 0.2.4: A free/open source C++ library for Discrete 

  *  Approximate Inference", http://www.libdai.org
  *
  *  Approximate Inference", http://www.libdai.org
  *

+ *  or in BiBTeX format:
+ *  
+ *  <pre>
+ *  \@misc{mooij2010libdai,
+ *    author = "Joris M. Mooij et al.",
+ *    title = "lib{DAI} 0.2.4: A free/open source {C}++ library for {D}iscrete {A}pproximate {I}nference",
+ *    howpublished = "http://www.libdai.org/",
+ *    year = 2010
+ *  }
+ *  </pre>
+ *

  *  Moreover, as a personal note, I would appreciate it if you would email
  *  (citations of) papers referencing this work to joris dot mooij at libdai dot org.
  */
  *  Moreover, as a personal note, I would appreciate it if you would email
  *  (citations of) papers referencing this work to joris dot mooij at libdai dot org.
  */


@@ -192,6 +204,8 @@
  *  <hr size="1">
  *  \section build-unix Building libDAI under UNIX variants (Linux / Cygwin / Mac OS X)
  *
  *  <hr size="1">
  *  \section build-unix Building libDAI under UNIX variants (Linux / Cygwin / Mac OS X)
  *

+ *  \subsection build-unix-preparations Preparations
+ *

  *  You need:
  *    - a recent version of gcc (at least version 3.4)
  *    - GNU make
  *  You need:
  *    - a recent version of gcc (at least version 3.4)
  *    - GNU make


@@ -220,6 +234,8 @@
  *  make install
  *  </pre>
  *
  *  make install
  *  </pre>
  *

+ *  \subsection build-unix-libdai Building libDAI
+ *

  *  To build the libDAI source, first copy a template Makefile.* to Makefile.conf
  *  (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). 
  *  Then, edit the Makefile.conf template to adapt it to your local setup.
  *  To build the libDAI source, first copy a template Makefile.* to Makefile.conf
  *  (for example, copy Makefile.LINUX to Makefile.conf if you use GNU/Linux). 
  *  Then, edit the Makefile.conf template to adapt it to your local setup.


@@ -230,13 +246,15 @@
  *
  *  If the build is successful, you can test the example program:
  *  <pre>  examples/example tests/alarm.fg</pre>
  *
  *  If the build is successful, you can test the example program:
  *  <pre>  examples/example tests/alarm.fg</pre>

- *  or the more elaborate test program:
+ *  or the more extensive test program:

  *  <pre>  tests/testdai --aliases tests/aliases.conf --filename tests/alarm.fg --methods JTREE_HUGIN BP_SEQMAX</pre>
  *
  *
  *  <hr size="1">
  *  \section build-windows Building libDAI under Windows
  *
  *  <pre>  tests/testdai --aliases tests/aliases.conf --filename tests/alarm.fg --methods JTREE_HUGIN BP_SEQMAX</pre>
  *
  *
  *  <hr size="1">
  *  \section build-windows Building libDAI under Windows
  *

+ *  \subsection build-windows-preparations Preparations
+ *

  *  You need:
  *  - A recent version of MicroSoft Visual Studio (2008 is known to work)
  *  - recent boost C++ libraries (version 1.37 or higher)
  *  You need:
  *  - A recent version of MicroSoft Visual Studio (2008 is known to work)
  *  - recent boost C++ libraries (version 1.37 or higher)


@@ -245,6 +263,8 @@
  *  For the regression test, you need:
  *  - GNU diff, GNU sed (can be obtained from http://gnuwin32.sourceforge.net)
  *
  *  For the regression test, you need:
  *  - GNU diff, GNU sed (can be obtained from http://gnuwin32.sourceforge.net)
  *

+ *  \subsection build-windows-libdai Building libDAI
+ *

  *  To build the source, copy Makefile.WINDOWS to Makefile.conf. Then, edit 
  *  Makefile.conf to adapt it to your local setup. Platform independent 
  *  build options can be set in Makefile.ALL. Finally, run (from the command line)
  *  To build the source, copy Makefile.WINDOWS to Makefile.conf. Then, edit 
  *  Makefile.conf to adapt it to your local setup. Platform independent 
  *  build options can be set in Makefile.ALL. Finally, run (from the command line)


@@ -253,7 +273,7 @@
  *
  *  If the build is successful, you can test the example program:
  *  <pre>  examples\\example tests\\alarm.fg</pre>
  *
  *  If the build is successful, you can test the example program:
  *  <pre>  examples\\example tests\\alarm.fg</pre>

- *  or the more elaborate test program:
+ *  or the more extensive test program:

  *  <pre>  tests\\testdai --aliases tests\\aliases.conf --filename tests\\alarm.fg --methods JTREE_HUGIN BP_SEQMAX</pre>
  *
  *
  *  <pre>  tests\\testdai --aliases tests\\aliases.conf --filename tests\\alarm.fg --methods JTREE_HUGIN BP_SEQMAX</pre>
  *
  *

diff --git a/include/dai/weightedgraph.h b/include/dai/weightedgraph.h
index 0d543b5..d28e8c8 100644 (file)
--- a/include/dai/weightedgraph.h
+++ b/include/dai/weightedgraph.h
@@ -131,7 +131,7 @@ class GraphEL : public std::set<UEdge> {
 };
 
 
 };
 
 

-/// \deprecated Please use GraphEL instead.
+/// \deprecated Please use dai::GraphEL instead.

 typedef GraphEL Graph;
 
 
 typedef GraphEL Graph;
 
 

diff --git a/src/bipgraph.cpp b/src/bipgraph.cpp
index a6f1e6f..8dbe4c1 100644 (file)
--- a/src/bipgraph.cpp
+++ b/src/bipgraph.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/exactinf.cpp b/src/exactinf.cpp
index 8c7d1c7..875b728 100644 (file)
--- a/src/exactinf.cpp
+++ b/src/exactinf.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/gibbs.cpp b/src/gibbs.cpp
index b62cdf3..65e8603 100644 (file)
--- a/src/gibbs.cpp
+++ b/src/gibbs.cpp
@@ -5,6 +5,7 @@
  *  warranty. See the file COPYING for more details.
  *
  *  Copyright (C) 2008  Frederik Eaton  [frederik at ofb dot net]
  *  warranty. See the file COPYING for more details.
  *
  *  Copyright (C) 2008  Frederik Eaton  [frederik at ofb dot net]

+ *  Copyright (C) 2008-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  */
 
 
  */
 
 

diff --git a/src/jtree.cpp b/src/jtree.cpp
index b1d5edd..8b7fd75 100644 (file)
--- a/src/jtree.cpp
+++ b/src/jtree.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/lc.cpp b/src/lc.cpp
index 47c5da4..c8f3bbf 100644 (file)
--- a/src/lc.cpp
+++ b/src/lc.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/matlab/dai.cpp b/src/matlab/dai.cpp
index 3402854..5ef330d 100644 (file)
--- a/src/matlab/dai.cpp
+++ b/src/matlab/dai.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/mf.cpp b/src/mf.cpp
index b7119d2..227b11a 100644 (file)
--- a/src/mf.cpp
+++ b/src/mf.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/mr.cpp b/src/mr.cpp
index 29ade12..c23a6a8 100644 (file)
--- a/src/mr.cpp
+++ b/src/mr.cpp
@@ -5,7 +5,7 @@
  *  warranty. See the file COPYING for more details.
  *
  *  Copyright (C) 2007       Bastian Wemmenhove
  *  warranty. See the file COPYING for more details.
  *
  *  Copyright (C) 2007       Bastian Wemmenhove

- *  Copyright (C) 2007-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2007-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2007       Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2007       Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/regiongraph.cpp b/src/regiongraph.cpp
index 6df320e..4d68d2c 100644 (file)
--- a/src/regiongraph.cpp
+++ b/src/regiongraph.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/treeep.cpp b/src/treeep.cpp
index 2aa3106..5c9f369 100644 (file)
--- a/src/treeep.cpp
+++ b/src/treeep.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/src/weightedgraph.cpp b/src/weightedgraph.cpp
index e70e4bf..f51e982 100644 (file)
--- a/src/weightedgraph.cpp
+++ b/src/weightedgraph.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 

diff --git a/utils/fg2dot.cpp b/utils/fg2dot.cpp
index aefdf3d..727352d 100644 (file)
--- a/utils/fg2dot.cpp
+++ b/utils/fg2dot.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 


@@ -22,18 +22,20 @@ using namespace std;
 
 int main( int argc, char *argv[] ) {
     if( argc != 3 ) {
 
 int main( int argc, char *argv[] ) {
     if( argc != 3 ) {

-        cout << "Usage: " << argv[0] << " <in.fg> <out.dot>" << endl << endl;
-        cout << "Converts a .fg (FactorGraph) file to a .dot (GraphViz) file for" << endl;
-        cout << "visualization. The .dot file can be converted to .ps (PostScript) by" << endl;
+        // Display help message if number of command line arguments is incorrect
+        cout << "This program is part of libDAI - http://www.libdai.org/" << endl << endl;
+        cout << "Usage: ./fg2dot <in.fg> <out.dot>" << endl << endl;
+        cout << "Converts a libDAI factor graph file to a GraphViz .dot file for visualization." << endl;
+        cout << "The .dot file can be converted to .ps (PostScript) by" << endl;

         cout << "'neato -T ps out.dot > out.ps' or by 'dot -T ps out.dot > out.ps'" << endl << endl;
         return 1;
     } else {
         // Read factorgraph
         FactorGraph fg;
         char *infile = argv[1];
         cout << "'neato -T ps out.dot > out.ps' or by 'dot -T ps out.dot > out.ps'" << endl << endl;
         return 1;
     } else {
         // Read factorgraph
         FactorGraph fg;
         char *infile = argv[1];

-

         fg.ReadFromFile( infile );
 
         fg.ReadFromFile( infile );
 

+        // Open output file for writing (except if filename equals "-")

         ostream *os = &cout;
         ofstream outfile;
         if( string( argv[2] ) != "-" ) {
         ostream *os = &cout;
         ofstream outfile;
         if( string( argv[2] ) != "-" ) {


@@ -43,8 +45,9 @@ int main( int argc, char *argv[] ) {
                 return 1;
             }
             os = &outfile;
                 return 1;
             }
             os = &outfile;

-        }
+        } // else, write to cout

 
 

+        // Write the .dot file

         fg.printDot( *os );
 
         return 0;
         fg.printDot( *os );
 
         return 0;

diff --git a/utils/fginfo.cpp b/utils/fginfo.cpp
index e42cb9e..848eac5 100644 (file)
--- a/utils/fginfo.cpp
+++ b/utils/fginfo.cpp
@@ -4,7 +4,7 @@
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *
  *  2, or (at your option) any later version. libDAI is distributed without any
  *  warranty. See the file COPYING for more details.
  *

- *  Copyright (C) 2006-2009  Joris Mooij  [joris dot mooij at libdai dot org]
+ *  Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]

  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 
  *  Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
  */
 


@@ -73,8 +73,10 @@ bool hasNegatives( const std::vector<Factor> &P ) {
 
 int main( int argc, char *argv[] ) {
     if( argc != 3 ) {
 
 int main( int argc, char *argv[] ) {
     if( argc != 3 ) {

-        cout << "Usage: " << argv[0] << " <in.fg> <tw>" << endl << endl;
-        cout << "Reports some characteristics of the .fg network." << endl;
+        // Display help message if number of command line arguments is incorrect
+        cout << "This program is part of libDAI - http://www.libdai.org/" << endl << endl;
+        cout << "Usage: ./fginfo <in.fg> <tw>" << endl << endl;
+        cout << "Reports some detailed information about the factor graph <in.fg>." << endl;

         cout << "Also calculates treewidth (which may take some time) unless <tw> == 0." << endl;
         return 1;
     } else {
         cout << "Also calculates treewidth (which may take some time) unless <tw> == 0." << endl;
         return 1;
     } else {


@@ -84,6 +86,7 @@ int main( int argc, char *argv[] ) {
         int calc_tw = atoi(argv[2]);
         fg.ReadFromFile( infile );
 
         int calc_tw = atoi(argv[2]);
         fg.ReadFromFile( infile );
 

+        // Output various statistics

         cout << "Number of variables:   " << fg.nrVars() << endl;
         cout << "Number of factors:     " << fg.nrFactors() << endl;
         cout << "Connected:             " << fg.isConnected() << endl;
         cout << "Number of variables:   " << fg.nrVars() << endl;
         cout << "Number of factors:     " << fg.nrFactors() << endl;
         cout << "Connected:             " << fg.isConnected() << endl;


@@ -92,6 +95,7 @@ int main( int argc, char *argv[] ) {
         cout << "Has negatives:         " << hasNegatives(fg.factors()) << endl;
         cout << "Binary variables?      " << fg.isBinary() << endl;
         cout << "Pairwise interactions? " << fg.isPairwise() << endl;
         cout << "Has negatives:         " << hasNegatives(fg.factors()) << endl;
         cout << "Binary variables?      " << fg.isBinary() << endl;
         cout << "Pairwise interactions? " << fg.isPairwise() << endl;

+        // Calculate treewidth using various heuristics, if requested

         if( calc_tw ) {
             std::pair<size_t,size_t> tw;
             tw = boundTreewidth(fg, &eliminationCost_MinNeighbors);
         if( calc_tw ) {
             std::pair<size_t,size_t> tw;
             tw = boundTreewidth(fg, &eliminationCost_MinNeighbors);


@@ -103,11 +107,15 @@ int main( int argc, char *argv[] ) {
             tw = boundTreewidth(fg, &eliminationCost_WeightedMinFill);
             cout << "Treewidth (WeightedMinFill):  " << tw.first << " (" << tw.second << " states)" << endl;
         }
             tw = boundTreewidth(fg, &eliminationCost_WeightedMinFill);
             cout << "Treewidth (WeightedMinFill):  " << tw.first << " (" << tw.second << " states)" << endl;
         }

+        // Calculate total state space

         long double stsp = 1.0;
         for( size_t i = 0; i < fg.nrVars(); i++ )
             stsp *= fg.var(i).states();
         cout << "Total state space:   " << stsp << endl;
         long double stsp = 1.0;
         for( size_t i = 0; i < fg.nrVars(); i++ )
             stsp *= fg.var(i).states();
         cout << "Total state space:   " << stsp << endl;

+        // Output type of factor graph
+        cout << "Type: " << (fg.isPairwise() ? "pairwise" : "higher order") << " interactions, " << (fg.isBinary() ? "binary" : "nonbinary") << " variables" << endl;

 
 

+        // Calculate complexity for LCBP

         long double cavsum_lcbp = 0.0;
         long double cavsum_lcbp2 = 0.0;
         size_t max_Delta_size = 0;
         long double cavsum_lcbp = 0.0;
         long double cavsum_lcbp2 = 0.0;
         size_t max_Delta_size = 0;


@@ -133,8 +141,7 @@ int main( int argc, char *argv[] ) {
             cout << it->first << "(" << it->second << ") ";
         cout << endl;
 
             cout << it->first << "(" << it->second << ") ";
         cout << endl;
 

-        cout << "Type: " << (fg.isPairwise() ? "pairwise" : "higher order") << " interactions, " << (fg.isBinary() ? "binary" : "nonbinary") << " variables" << endl;
-
+        // Calculate girth and length of loops

         if( fg.isPairwise() ) {
             bool girth_reached = false;
             size_t loopdepth;
         if( fg.isPairwise() ) {
             bool girth_reached = false;
             size_t loopdepth;


@@ -150,6 +157,7 @@ int main( int argc, char *argv[] ) {
                 cout << "Girth: infinity" << endl;
         }
 
                 cout << "Girth: infinity" << endl;
         }
 

+        // Output factor state spaces

         map<size_t,size_t> facsizes;
         for( size_t I = 0; I < fg.nrFactors(); I++ ) {
             size_t Isize = fg.factor(I).vars().size();
         map<size_t,size_t> facsizes;
         for( size_t I = 0; I < fg.nrFactors(); I++ ) {
             size_t Isize = fg.factor(I).vars().size();