# Enable/disable various approximate inference methods
-WITH_BP = true
-WITH_MF = true
-WITH_HAK = true
-WITH_LC = true
-WITH_TREEEP = true
-WITH_JTREE = true
-WITH_MR = true
+WITH_BP=true
+WITH_MF=true
+WITH_HAK=true
+WITH_LC=true
+WITH_TREEEP=true
+WITH_JTREE=true
+WITH_MR=true
# Build with debug info?
-DEBUG = true
+DEBUG=true
# Build matlab interface?
-WITH_MATLAB =
+WITH_MATLAB=
# New/old matlab version?
-NEW_MATLAB = true
+NEW_MATLAB=true
# Windows or linux (default)?
-WINDOWS =
+WINDOWS=
# Directories
-INC = include/dai
-SRC = src
-LIB = lib
+INC=include/dai
+SRC=src
+LIB=lib
+
+# Extensions (library, object, executable extensions)
+LE=.a
+OE=.o
+EE=
+
+# Libraries
+LIBS=-ldai
# We use the BOOST Program Options library
-BOOSTFLAGS = -lboost_program_options
+BOOSTLIBS=-lboost_program_options
# Compile using GNU C++ Compiler
-CC = g++
+CC=g++
# Flags for the C++ compiler
-CCFLAGS = -Wall -W -Wextra -fpic -I./include -Llib -O3 #-pg #-static #-DVERBOSE
+CCFLAGS=-Wall -W -Wextra -fpic -I./include -Llib -O3 #-pg #-static #-DVERBOSE
ifdef DEBUG
-CCFLAGS := $(CCFLAGS) -g -DDAI_DEBUG
-else
-CCFLAGS := $(CCFLAGS)
+CCFLAGS:=$(CCFLAGS) -g -DDAI_DEBUG
endif
+ifdef WINDOWS
+CCFLAGS=$(CCFLAGS) -DWINDOWS
+endif
+
+OBJECTS:=exactinf$(OE)
ifdef WITH_BP
-CCFLAGS := $(CCFLAGS) -DWITH_BP
-OBJECTS := $(OBJECTS) bp.o
+CCFLAGS:=$(CCFLAGS) -DWITH_BP
+OBJECTS:=$(OBJECTS) bp$(OE)
endif
ifdef WITH_MF
-CCFLAGS := $(CCFLAGS) -DWITH_MF
-OBJECTS := $(OBJECTS) mf.o
+CCFLAGS:=$(CCFLAGS) -DWITH_MF
+OBJECTS:=$(OBJECTS) mf$(OE)
endif
ifdef WITH_HAK
-CCFLAGS := $(CCFLAGS) -DWITH_HAK
-OBJECTS := $(OBJECTS) hak.o
+CCFLAGS:=$(CCFLAGS) -DWITH_HAK
+OBJECTS:=$(OBJECTS) hak$(OE)
endif
ifdef WITH_LC
-CCFLAGS := $(CCFLAGS) -DWITH_LC
-OBJECTS := $(OBJECTS) lc.o
+CCFLAGS:=$(CCFLAGS) -DWITH_LC
+OBJECTS:=$(OBJECTS) lc$(OE)
endif
ifdef WITH_TREEEP
-CCFLAGS := $(CCFLAGS) -DWITH_TREEEP
-OBJECTS := $(OBJECTS) treeep.o
+CCFLAGS:=$(CCFLAGS) -DWITH_TREEEP
+OBJECTS:=$(OBJECTS) treeep$(OE)
endif
ifdef WITH_JTREE
-CCFLAGS := $(CCFLAGS) -DWITH_JTREE
-OBJECTS := $(OBJECTS) jtree.o
+CCFLAGS:=$(CCFLAGS) -DWITH_JTREE
+OBJECTS:=$(OBJECTS) jtree$(OE)
endif
ifdef WITH_MR
-CCFLAGS := $(CCFLAGS) -DWITH_MR
-OBJECTS := $(OBJECTS) mr.o
+CCFLAGS:=$(CCFLAGS) -DWITH_MR
+OBJECTS:=$(OBJECTS) mr$(OE)
endif
ifdef WITH_MATLAB
# Replace the following by the directory where Matlab has been installed
-MATLABDIR = /opt/matlab/bin
+MATLABDIR=/opt/matlab/bin
# Replace the following with the extension of compiled MEX files on this platform, e.g. .mexglx for x86
-MEXEXT = .mexglx
-MEX = $(MATLABDIR)/mex
-MEXFLAGS = -I.
+ME=.mexglx
+MEX=$(MATLABDIR)/mex
+MEXFLAGS=-I.
ifdef DEBUG
-MEXFLAGS := $(MEXFLAGS) -g -DDAI_DEBUG
+MEXFLAGS:=$(MEXFLAGS) -g -DDAI_DEBUG
endif
ifdef NEW_MATLAB
-MEXFLAGS := $(MEXFLAGS) -largeArrayDims
+MEXFLAGS:=$(MEXFLAGS) -largeArrayDims
else
-MEXFLAGS := $(MEXFLAGS) -DSMALLMEM
+MEXFLAGS:=$(MEXFLAGS) -DSMALLMEM
endif
endif
-HEADERS = $(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h
+HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h
-TARGETS = tests utils $(LIB)/libdai.a example testregression doc
+TARGETS=tests utils $(LIB)/libdai$(LE) example$(EE) testregression doc
ifdef WITH_MATLAB
-TARGETS := $(TARGETS) matlabs
+TARGETS:=$(TARGETS) matlabs
endif
all : $(TARGETS)
echo -e "\a"
-matlabs : matlab/dai.$(MEXEXT) matlab/dai_readfg.$(MEXEXT) matlab/dai_writefg.$(MEXEXT) matlab/dai_potstrength.$(MEXEXT)
+matlabs : matlab/dai.$(ME) matlab/dai_readfg.$(ME) matlab/dai_writefg.$(ME) matlab/dai_potstrength.$(ME)
-$(LIB)/libdai.a : bipgraph.o daialg.o alldai.o clustergraph.o factorgraph.o properties.o regiongraph.o util.o weightedgraph.o x2x.o exceptions.o $(OBJECTS)
- ar rcs $(LIB)/libdai.a bipgraph.o daialg.o alldai.o clustergraph.o factorgraph.o properties.o regiongraph.o util.o weightedgraph.o x2x.o exceptions.o $(OBJECTS)
+$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)
+ ar rcus $(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)
-tests : tests/test
+tests : tests/test$(EE)
-utils : utils/createfg utils/fg2dot utils/fginfo
+utils : utils/createfg$(EE) utils/fg2dot$(EE) utils/fginfo$(EE)
testregression : tests/test
echo Testing...this can take a while...
doxygen doxygen.conf
clean :
- rm *.o example matlab/*.$(MEXEXT) matlab/*.o tests/test utils/fg2dot utils/createfg utils/fginfo $(LIB)/libdai.a; echo
+ rm *$(OE) example$(EE) matlab/*.$(ME) matlab/*$(OE) tests/test$(EE) utils/fg2dot$(EE) utils/createfg$(EE) utils/fginfo$(EE) $(LIB)/libdai$(LE); echo
rm -R doc; echo
-bipgraph.o : $(SRC)/bipgraph.cpp $(HEADERS)
+bipgraph$(OE) : $(SRC)/bipgraph.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/bipgraph.cpp
-daialg.o : $(SRC)/daialg.cpp $(HEADERS)
+daialg$(OE) : $(SRC)/daialg.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/daialg.cpp
-bp.o : $(SRC)/bp.cpp $(INC)/bp.h $(HEADERS)
+exactinf$(OE) : $(SRC)/exactinf.cpp $(INC)/exactinf.h $(HEADERS)
+ $(CC) $(CCFLAGS) -c $(SRC)/exactinf.cpp
+
+bp$(OE) : $(SRC)/bp.cpp $(INC)/bp.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/bp.cpp
-lc.o : $(SRC)/lc.cpp $(INC)/lc.h $(HEADERS)
+lc$(OE) : $(SRC)/lc.cpp $(INC)/lc.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/lc.cpp
-mf.o : $(SRC)/mf.cpp $(INC)/mf.h $(HEADERS)
+mf$(OE) : $(SRC)/mf.cpp $(INC)/mf.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/mf.cpp
-factorgraph.o : $(SRC)/factorgraph.cpp $(INC)/factorgraph.h $(HEADERS)
+factorgraph$(OE) : $(SRC)/factorgraph.cpp $(INC)/factorgraph.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/factorgraph.cpp
-util.o : $(SRC)/util.cpp $(INC)/util.h $(HEADERS)
+util$(OE) : $(SRC)/util.cpp $(INC)/util.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/util.cpp
-regiongraph.o : $(SRC)/regiongraph.cpp $(INC)/regiongraph.h $(HEADERS)
+regiongraph$(OE) : $(SRC)/regiongraph.cpp $(INC)/regiongraph.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/regiongraph.cpp
-hak.o : $(SRC)/hak.cpp $(INC)/hak.h $(HEADERS) $(INC)/regiongraph.h
+hak$(OE) : $(SRC)/hak.cpp $(INC)/hak.h $(HEADERS) $(INC)/regiongraph.h
$(CC) $(CCFLAGS) -c $(SRC)/hak.cpp
-clustergraph.o : $(SRC)/clustergraph.cpp $(INC)/clustergraph.h $(HEADERS)
+clustergraph$(OE) : $(SRC)/clustergraph.cpp $(INC)/clustergraph.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/clustergraph.cpp
-jtree.o : $(SRC)/jtree.cpp $(INC)/jtree.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h
+jtree$(OE) : $(SRC)/jtree.cpp $(INC)/jtree.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h
$(CC) $(CCFLAGS) -c $(SRC)/jtree.cpp
-treeep.o : $(SRC)/treeep.cpp $(INC)/treeep.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h $(INC)/jtree.h
+treeep$(OE) : $(SRC)/treeep.cpp $(INC)/treeep.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h $(INC)/jtree.h
$(CC) $(CCFLAGS) -c $(SRC)/treeep.cpp
-weightedgraph.o : $(SRC)/weightedgraph.cpp $(INC)/weightedgraph.h $(HEADERS)
+weightedgraph$(OE) : $(SRC)/weightedgraph.cpp $(INC)/weightedgraph.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/weightedgraph.cpp
-mr.o : $(SRC)/mr.cpp $(INC)/mr.h $(HEADERS)
+mr$(OE) : $(SRC)/mr.cpp $(INC)/mr.h $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/mr.cpp
-properties.o : $(SRC)/properties.cpp $(HEADERS)
+properties$(OE) : $(SRC)/properties.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/properties.cpp
-exceptions.o: $(SRC)/exceptions.cpp $(HEADERS)
+exceptions$(OE) : $(SRC)/exceptions.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/exceptions.cpp
-alldai.o : $(SRC)/alldai.cpp $(HEADERS)
+alldai$(OE) : $(SRC)/alldai.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/alldai.cpp
-x2x.o : $(SRC)/x2x.cpp $(HEADERS)
+x2x$(OE) : $(SRC)/x2x.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/x2x.cpp
+
# EXAMPLE
##########
-example : example.cpp $(HEADERS) $(LIB)/libdai.a
- $(CC) $(CCFLAGS) -o example example.cpp -ldai
+example$(EE) : example.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ $(CC) $(CCFLAGS) -o example$(EE) example.cpp $(LIBS)
# TESTS
########
-tests/test : tests/test.cpp $(HEADERS) $(LIB)/libdai.a
- $(CC) $(CCFLAGS) -o tests/test tests/test.cpp -ldai $(BOOSTFLAGS)
+tests/test$(EE) : tests/test.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ $(CC) $(CCFLAGS) -o tests/test$(EE) tests/test.cpp $(LIBS) $(BOOSTLIBS)
# MATLAB INTERFACE
###################
-matlab/dai.$(MEXEXT) : matlab/dai.cpp $(HEADERS) matlab/matlab.o $(LIB)/libdai.a
- $(MEX) $(MEXFLAGS) -o matlab/dai matlab/dai.cpp matlab/matlab.o $(LIB)/libdai.a
+matlab/dai.$(ME) : matlab/dai.cpp $(HEADERS) matlab/matlab$(OE) $(LIB)/libdai$(LE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai matlab/dai.cpp matlab/matlab$(OE) $(LIB)/libdai$(LE)
-matlab/dai_readfg.$(MEXEXT) : matlab/dai_readfg.cpp $(HEADERS) factorgraph.o matlab/matlab.o
- $(MEX) $(MEXFLAGS) -o matlab/dai_readfg matlab/dai_readfg.cpp factorgraph.o matlab/matlab.o
+matlab/dai_readfg.$(ME) : matlab/dai_readfg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_readfg matlab/dai_readfg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
-matlab/dai_writefg.$(MEXEXT) : matlab/dai_writefg.cpp $(HEADERS) factorgraph.o matlab/matlab.o
- $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph.o matlab/matlab.o
+matlab/dai_writefg.$(ME) : matlab/dai_writefg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)
-matlab/dai_potstrength.$(MEXEXT) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab.o
- $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab.o
+matlab/dai_potstrength.$(ME) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab$(OE) exceptions$(OE)
+ $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab$(OE) exceptions$(OE)
-matlab/matlab.o : matlab/matlab.cpp matlab/matlab.h $(HEADERS)
+matlab/matlab$(OE) : matlab/matlab.cpp matlab/matlab.h $(HEADERS)
$(MEX) $(MEXFLAGS) -outdir matlab -c matlab/matlab.cpp
# UTILS
########
-utils/createfg : utils/createfg.cpp $(HEADERS) factorgraph.o weightedgraph.o util.o bipgraph.o exceptions.o
- $(CC) $(CCFLAGS) -o utils/createfg utils/createfg.cpp factorgraph.o weightedgraph.o util.o bipgraph.o exceptions.o $(BOOSTFLAGS)
+utils/createfg$(EE) : utils/createfg.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ $(CC) $(CCFLAGS) -o utils/createfg utils/createfg.cpp $(LIBS) $(BOOSTLIBS)
-utils/fg2dot : utils/fg2dot.cpp $(HEADERS) factorgraph.o exceptions.o
- $(CC) $(CCFLAGS) -o utils/fg2dot utils/fg2dot.cpp factorgraph.o exceptions.o
+utils/fg2dot$(EE) : utils/fg2dot.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ $(CC) $(CCFLAGS) -o utils/fg2dot utils/fg2dot.cpp $(LIBS)
-utils/fginfo : utils/fginfo.cpp $(HEADERS) factorgraph.o bipgraph.o exceptions.o
- $(CC) $(CCFLAGS) -o utils/fginfo utils/fginfo.cpp factorgraph.o bipgraph.o exceptions.o
+utils/fginfo$(EE) : utils/fginfo.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ $(CC) $(CCFLAGS) -o utils/fginfo utils/fginfo.cpp $(LIBS)
SRC=src\r
LIB=lib\r
\r
-# For some reason, we have to set the library path, although it is in the environment\r
-LIBS=/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"\r
+# Extensions (library, object, executable extensions)\r
+LE=.lib\r
+OE=.obj\r
+EE=.exe\r
+\r
+# Libraries (for some reason, we have to add the VC library path, although it is in the environment)\r
+LIBS=/link $(LIB)/libdai$(LE) /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"\r
+\r
# We use the BOOST Program Options library\r
BOOSTLIBS=/LIBPATH:C:\boost_1_36_0\stage\lib\r
\r
# Compile using GNU C++ Compiler\r
CC=cl\r
-OBJEXT=obj\r
-LIBEXT=lib\r
\r
# Flags for the C++ compiler\r
CCFLAGS=/I./include /IC:\boost_1_36_0 /EHsc /Ox\r
!IFDEF DEBUG\r
CCFLAGS=$(CCFLAGS) /Zi /DDAI_DEBUG\r
-!ELSE\r
-CCFLAGS=$(CCFLAGS)\r
!ENDIF\r
\r
!IFDEF WINDOWS\r
CCFLAGS=$(CCFLAGS) /DWINDOWS\r
!ENDIF\r
\r
+OBJECTS=exactinf$(OE)\r
!IFDEF WITH_BP\r
CCFLAGS=$(CCFLAGS) /DWITH_BP\r
-OBJECTS=$(OBJECTS) bp.obj\r
+OBJECTS=$(OBJECTS) bp$(OE)\r
!ENDIF\r
!IFDEF WITH_MF\r
CCFLAGS=$(CCFLAGS) /DWITH_MF\r
-OBJECTS=$(OBJECTS) mf.obj\r
+OBJECTS=$(OBJECTS) mf$(OE)\r
!ENDIF\r
!IFDEF WITH_HAK\r
CCFLAGS=$(CCFLAGS) /DWITH_HAK\r
-OBJECTS=$(OBJECTS) hak.obj\r
+OBJECTS=$(OBJECTS) hak$(OE)\r
!ENDIF\r
!IFDEF WITH_LC\r
CCFLAGS=$(CCFLAGS) /DWITH_LC\r
-OBJECTS=$(OBJECTS) lc.obj\r
+OBJECTS=$(OBJECTS) lc$(OE)\r
!ENDIF\r
!IFDEF WITH_TREEEP\r
CCFLAGS=$(CCFLAGS) /DWITH_TREEEP\r
-OBJECTS=$(OBJECTS) treeep.obj\r
+OBJECTS=$(OBJECTS) treeep$(OE)\r
!ENDIF\r
!IFDEF WITH_JTREE\r
CCFLAGS=$(CCFLAGS) /DWITH_JTREE\r
-OBJECTS=$(OBJECTS) jtree.obj\r
+OBJECTS=$(OBJECTS) jtree$(OE)\r
!ENDIF\r
!IFDEF WITH_MR\r
CCFLAGS=$(CCFLAGS) /DWITH_MR\r
-OBJECTS=$(OBJECTS) mr.obj\r
+OBJECTS=$(OBJECTS) mr$(OE)\r
!ENDIF\r
\r
!IFDEF WITH_MATLAB\r
# Replace the following by the directory where Matlab has been installed\r
-MATLABDIR = /opt/matlab/bin\r
+MATLABDIR=/opt/matlab/bin\r
# Replace the following with the extension of compiled MEX files on this platform, e.g. .mexglx for x86\r
-MEXEXT = .mexglx\r
-MEX = $(MATLABDIR)/mex\r
-MEXFLAGS = -I.\r
+ME=.mexglx\r
+MEX=$(MATLABDIR)/mex\r
+MEXFLAGS=-I.\r
!IFDEF DEBUG\r
-MEXFLAGS = $(MEXFLAGS) -g /DDAI_DEBUG\r
+MEXFLAGS=$(MEXFLAGS) -g /DDAI_DEBUG\r
!ENDIF\r
!IFDEF NEW_MATLAB\r
-MEXFLAGS = $(MEXFLAGS) -largeArrayDims\r
+MEXFLAGS=$(MEXFLAGS) -largeArrayDims\r
!ELSE\r
-MEXFLAGS = $(MEXFLAGS) /DSMALLMEM\r
+MEXFLAGS=$(MEXFLAGS) /DSMALLMEM\r
!ENDIF\r
!ENDIF\r
\r
-HEADERS = $(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h\r
+HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h\r
\r
-TARGETS = tests utils $(LIB)/libdai.lib example.exe\r
-# testregression disabled, it uses sh and awk\r
+TARGETS=tests utils $(LIB)/libdai$(LE) example$(EE)\r
+# testregression disabled, it uses diff\r
# doc disabled, it uses doxygen\r
!IFDEF WITH_MATLAB\r
TARGETS = $(TARGETS) matlabs\r
!ENDIF\r
all : $(TARGETS)\r
\r
-matlabs : matlab/dai.$(MEXEXT) matlab/dai_readfg.$(MEXEXT) matlab/dai_writefg.$(MEXEXT) matlab/dai_removeshortloops.$(MEXEXT) matlab/dai_potstrength.$(MEXEXT)\r
+matlabs : matlab/dai.$(ME) matlab/dai_readfg.$(ME) matlab/dai_writefg.$(ME) matlab/dai_potstrength.$(ME)\r
\r
-$(LIB)/libdai.lib : bipgraph.obj daialg.obj alldai.obj clustergraph.obj factorgraph.obj properties.obj regiongraph.obj util.obj weightedgraph.obj x2x.obj exceptions.obj $(OBJECTS)\r
- lib /out:$(LIB)/libdai.lib bipgraph.obj daialg.obj alldai.obj clustergraph.obj factorgraph.obj properties.obj regiongraph.obj util.obj weightedgraph.obj x2x.obj exceptions.obj $(OBJECTS)\r
+$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)\r
+ lib /out:$(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)\r
\r
-tests : tests/test.exe\r
+tests : tests/test$(EE)\r
\r
-utils : utils/createfg.exe utils/fg2dot.exe utils/remove_short_loops.exe utils/fginfo.exe\r
+utils : utils/createfg$(EE) utils/fg2dot$(EE) utils/fginfo$(EE)\r
\r
testregression : tests/test\r
echo Testing...this can take a while...\r
doxygen doxygen.conf\r
\r
clean :\r
- del *.obj *.ilk *.pdb *.exe matlab\*.$(MEXEXT) matlab\*.obj tests\test.exe tests\*.pdb tests\*.ilk utils\*.exe utils\*.pdb utils\*.ilk $(LIB)\libdai.lib\r
+ del *$(OE) *.ilk *.pdb *$(EE) matlab\*.$(ME) matlab\*$(OE) tests\test$(EE) tests\*.pdb tests\*.ilk utils\*$(EE) utils\*.pdb utils\*.ilk $(LIB)\libdai$(LE)\r
\r
\r
-bipgraph.obj : $(SRC)/bipgraph.cpp $(HEADERS)\r
+bipgraph$(OE) : $(SRC)/bipgraph.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/bipgraph.cpp\r
\r
-daialg.obj : $(SRC)/daialg.cpp $(HEADERS)\r
+daialg$(OE) : $(SRC)/daialg.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/daialg.cpp\r
\r
-bp.obj : $(SRC)/bp.cpp $(INC)/bp.h $(HEADERS)\r
+exactinf$(OE) : $(SRC)/exactinf.cpp $(INC)/exactinf.h $(HEADERS)\r
+ $(CC) $(CCFLAGS) -c $(SRC)/exactinf.cpp\r
+\r
+bp$(OE) : $(SRC)/bp.cpp $(INC)/bp.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/bp.cpp\r
\r
-lc.obj : $(SRC)/lc.cpp $(INC)/lc.h $(HEADERS)\r
+lc$(OE) : $(SRC)/lc.cpp $(INC)/lc.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/lc.cpp\r
\r
-mf.obj : $(SRC)/mf.cpp $(INC)/mf.h $(HEADERS)\r
+mf$(OE) : $(SRC)/mf.cpp $(INC)/mf.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/mf.cpp\r
\r
-factorgraph.obj : $(SRC)/factorgraph.cpp $(INC)/factorgraph.h $(HEADERS)\r
+factorgraph$(OE) : $(SRC)/factorgraph.cpp $(INC)/factorgraph.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/factorgraph.cpp\r
\r
-util.obj : $(SRC)/util.cpp $(INC)/util.h $(HEADERS)\r
+util$(OE) : $(SRC)/util.cpp $(INC)/util.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/util.cpp\r
\r
-regiongraph.obj : $(SRC)/regiongraph.cpp $(INC)/regiongraph.h $(HEADERS)\r
+regiongraph$(OE) : $(SRC)/regiongraph.cpp $(INC)/regiongraph.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/regiongraph.cpp\r
\r
-hak.obj : $(SRC)/hak.cpp $(INC)/hak.h $(HEADERS) $(INC)/regiongraph.h\r
+hak$(OE) : $(SRC)/hak.cpp $(INC)/hak.h $(HEADERS) $(INC)/regiongraph.h\r
$(CC) $(CCFLAGS) -c $(SRC)/hak.cpp\r
\r
-clustergraph.obj : $(SRC)/clustergraph.cpp $(INC)/clustergraph.h $(HEADERS)\r
+clustergraph$(OE) : $(SRC)/clustergraph.cpp $(INC)/clustergraph.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/clustergraph.cpp\r
\r
-jtree.obj : $(SRC)/jtree.cpp $(INC)/jtree.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h\r
+jtree$(OE) : $(SRC)/jtree.cpp $(INC)/jtree.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h\r
$(CC) $(CCFLAGS) -c $(SRC)/jtree.cpp\r
\r
-treeep.obj : $(SRC)/treeep.cpp $(INC)/treeep.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h $(INC)/jtree.h\r
+treeep$(OE) : $(SRC)/treeep.cpp $(INC)/treeep.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h $(INC)/jtree.h\r
$(CC) $(CCFLAGS) -c $(SRC)/treeep.cpp\r
\r
-weightedgraph.obj : $(SRC)/weightedgraph.cpp $(INC)/weightedgraph.h $(HEADERS)\r
+weightedgraph$(OE) : $(SRC)/weightedgraph.cpp $(INC)/weightedgraph.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/weightedgraph.cpp\r
\r
-mr.obj : $(SRC)/mr.cpp $(INC)/mr.h $(HEADERS)\r
+mr$(OE) : $(SRC)/mr.cpp $(INC)/mr.h $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/mr.cpp\r
\r
-properties.obj : $(SRC)/properties.cpp $(HEADERS)\r
+properties$(OE) : $(SRC)/properties.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/properties.cpp\r
\r
-exceptions.obj : $(SRC)/exceptions.cpp $(HEADERS)\r
+exceptions$(OE) : $(SRC)/exceptions.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/exceptions.cpp\r
\r
-alldai.obj : $(SRC)/alldai.cpp $(HEADERS)\r
+alldai$(OE) : $(SRC)/alldai.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/alldai.cpp\r
\r
-x2x.obj : $(SRC)/x2x.cpp $(HEADERS)\r
+x2x$(OE) : $(SRC)/x2x.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/x2x.cpp\r
\r
\r
# EXAMPLE\r
##########\r
\r
-example.exe : example.cpp $(HEADERS) $(LIB)/libdai.lib\r
- $(CC) $(CCFLAGS) /Feexample example.cpp /link $(LIB)/libdai.lib $(LIBS)\r
+example$(EE) : example.cpp $(HEADERS) $(LIB)/libdai$(LE)\r
+ $(CC) $(CCFLAGS) /Feexample example.cpp $(LIBS)\r
\r
\r
# TESTS\r
########\r
\r
-tests/test.exe : tests/test.cpp $(HEADERS) $(LIB)/libdai.lib\r
- $(CC) $(CCFLAGS) /Fetests/test tests/test.cpp /link $(LIB)/libdai.lib $(LIBS) $(BOOSTLIBS)\r
+tests/test$(EE) : tests/test.cpp $(HEADERS) $(LIB)/libdai$(LE)\r
+ $(CC) $(CCFLAGS) /Fetests/test tests/test.cpp $(LIBS) $(BOOSTLIBS)\r
\r
\r
# MATLAB INTERFACE\r
###################\r
\r
-matlab/dai.$(MEXEXT) : matlab/dai.cpp $(HEADERS) matlab/matlab.obj $(LIB)/libdai.lib\r
- $(MEX) $(MEXFLAGS) -o matlab/dai matlab/dai.cpp matlab/matlab.obj $(LIB)/libdai.lib\r
-\r
-matlab/dai_readfg.$(MEXEXT) : matlab/dai_readfg.cpp $(HEADERS) factorgraph.obj matlab/matlab.obj\r
- $(MEX) $(MEXFLAGS) -o matlab/dai_readfg matlab/dai_readfg.cpp factorgraph.obj matlab/matlab.obj\r
+matlab/dai.$(ME) : matlab/dai.cpp $(HEADERS) matlab/matlab$(OE) $(LIB)/libdai$(LE)\r
+ $(MEX) $(MEXFLAGS) -o matlab/dai matlab/dai.cpp matlab/matlab$(OE) $(LIB)/libdai$(LE)\r
\r
-matlab/dai_writefg.$(MEXEXT) : matlab/dai_writefg.cpp $(HEADERS) factorgraph.obj matlab/matlab.obj\r
- $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph.obj matlab/matlab.obj\r
+matlab/dai_readfg.$(ME) : matlab/dai_readfg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)\r
+ $(MEX) $(MEXFLAGS) -o matlab/dai_readfg matlab/dai_readfg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)\r
\r
-matlab/dai_removeshortloops.$(MEXEXT) : matlab/dai_removeshortloops.cpp $(HEADERS) factorgraph.obj matlab/matlab.obj\r
- $(MEX) $(MEXFLAGS) -o matlab/dai_removeshortloops matlab/dai_removeshortloops.cpp factorgraph.obj matlab/matlab.obj\r
+matlab/dai_writefg.$(ME) : matlab/dai_writefg.cpp $(HEADERS) factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)\r
+ $(MEX) $(MEXFLAGS) -o matlab/dai_writefg matlab/dai_writefg.cpp factorgraph$(OE) matlab/matlab$(OE) exceptions$(OE)\r
\r
-matlab/dai_potstrength.$(MEXEXT) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab.obj\r
- $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab.obj\r
+matlab/dai_potstrength.$(ME) : matlab/dai_potstrength.cpp $(HEADERS) matlab/matlab$(OE) exceptions$(OE)\r
+ $(MEX) $(MEXFLAGS) -o matlab/dai_potstrength matlab/dai_potstrength.cpp matlab/matlab$(OE) exceptions$(OE)\r
\r
-matlab/matlab.obj : matlab/matlab.cpp matlab/matlab.h $(HEADERS)\r
+matlab/matlab$(OE) : matlab/matlab.cpp matlab/matlab.h $(HEADERS)\r
$(MEX) $(MEXFLAGS) -outdir matlab -c matlab/matlab.cpp\r
\r
\r
# UTILS\r
########\r
\r
-utils/createfg.exe : utils/createfg.cpp $(HEADERS) factorgraph.obj weightedgraph.obj util.obj bipgraph.obj exceptions.obj\r
- $(CC) $(CCFLAGS) /Feutils/createfg utils/createfg.cpp factorgraph.obj weightedgraph.obj util.obj bipgraph.obj exceptions.obj /link $(LIBS) $(BOOSTLIBS)\r
-\r
-utils/fg2dot.exe : utils/fg2dot.cpp $(HEADERS) factorgraph.obj exceptions.obj\r
- $(CC) $(CCFLAGS) /Feutils/fg2dot utils/fg2dot.cpp factorgraph.obj exceptions.obj /link $(LIBS)\r
+utils/createfg$(EE) : utils/createfg.cpp $(HEADERS) $(LIB)/libdai$(LE)\r
+ $(CC) $(CCFLAGS) /Feutils/createfg utils/createfg.cpp $(LIBS) $(BOOSTLIBS)\r
\r
-utils/remove_short_loops.exe : utils/remove_short_loops.cpp $(HEADERS) factorgraph.obj exceptions.obj\r
- $(CC) $(CCFLAGS) /Feutils/remove_short_loops utils/remove_short_loops.cpp factorgraph.obj exceptions.obj /link $(LIBS)\r
+utils/fg2dot$(EE) : utils/fg2dot.cpp $(HEADERS) $(LIB)/libdai$(LE)\r
+ $(CC) $(CCFLAGS) /Feutils/fg2dot utils/fg2dot.cpp $(LIBS)\r
\r
-utils/fginfo.exe : utils/fginfo.cpp $(HEADERS) factorgraph.obj bipgraph.obj exceptions.obj\r
- $(CC) $(CCFLAGS) /Feutils/fginfo utils/fginfo.cpp factorgraph.obj bipgraph.obj exceptions.obj /link $(LIBS)\r
+utils/fginfo$(EE) : utils/fginfo.cpp $(HEADERS) $(LIB)/libdai$(LE)\r
+ $(CC) $(CCFLAGS) /Feutils/fginfo utils/fginfo.cpp $(LIBS)\r
- Can the FactorGraph constructors be optimized further?
- Solve the proliferation of type checks for all different ENUM's in
properties.cpp
+- Remove x2x?
TODO FOR RELEASE:
- Test Visual C++ compatibility
- Figure out which libraries are required and document in README
boost headers, boost::program_options library, boost::graph library,
boost::math library (under Windows)
+- Change email address
-FILES IN SVN HEAD THAT ARE NO LONGER RELEVANT FOR GIT MASTER
+FILES IN SVN HEAD THAT ARE NO LONGER RELEVANT FOR GIT MASTER:
diffs.h
index.h
util.h
exceptions.h
exceptions.cpp
enum.h
+doxygen.conf
+example.cpp
+FILEFORMAT
+Makefile
+exact.h
+exact.cpp
+alldai.h
+alldai.cpp
+
+FILES IN SVN HEAD THAT ARE STILL RELEVANT:
+weightedgraph.cpp
+ChangeLog
+README
+TODO
+prob.h
+properties.h
+properties.cpp
+factor.h
+factor.cpp
+factorgraph.h
+factorgraph.cpp
+regiongraph.h
+regiongraph.cpp
+
+daialg.h
+daialg.cpp
+bp.h
+bp.cpp
+hak.h
+hak.cpp
+jtree.h
+jtree.cpp
+lc.h
+lc.cpp
+mf.h
+mf.cpp
+mr.h
+mr.cpp
+treeep.h
+treeep.cpp
+
+matlab/*
+tests/*
+utils/*
+
DOCUMENTATION READY:
- bipgraph.h, bipgraph.cpp
cout << "Error reading " << argv[1] << endl;
return 2;
} else {
- size_t maxiter = 1000;
+ size_t maxiter = 10000;
double tol = 1e-9;
size_t verb = 1;
jt.init();
jt.run();
+ BP bp(fg, opts("updates",string("SEQFIX"))("logdomain",false));
+ bp.init();
+ bp.run();
+
cout << "Exact single node marginals:" << endl;
for( size_t i = 0; i < fg.nrVars(); i++ )
cout << jt.belief(fg.var(i)) << endl;
- BP bp(fg, opts("updates",string("SEQMAX"))("logdomain",false));
- bp.init();
- bp.run();
-
cout << "Approximate (loopy belief propagation) single node marginals:" << endl;
for( size_t i = 0; i < fg.nrVars(); i++ )
cout << bp.belief(fg.var(i)) << endl;
+
+ cout << "Exact factor marginals:" << endl;
+ for( size_t I = 0; I < fg.nrFactors(); I++ )
+ cout << jt.belief(fg.factor(I).vars()) << endl;
+
+ cout << "Approximate (loopy belief propagation) factor marginals:" << endl;
+ for( size_t I = 0; I < fg.nrFactors(); I++ )
+ cout << bp.belief(fg.factor(I).vars()) << "=" << bp.beliefF(I) << endl;
+
+ cout << "Exact log partition sum: " << jt.logZ() << endl;
+ cout << "Approximate (loopy belief propagation) log partition sum: " << bp.logZ() << endl;
}
}
#include <string>
#include <dai/daialg.h>
#include <dai/properties.h>
+#include <dai/exactinf.h>
#ifdef WITH_BP
#include <dai/bp.h>
#endif
/// DAINames contains the names of all approximate inference algorithms
static const char* DAINames[] = {
+ ExactInf::Name,
#ifdef WITH_BP
BP::Name,
#endif
--- /dev/null
+/* Copyright (C) 2006-2008 Joris Mooij [j dot mooij at science dot ru dot nl]
+ Radboud University Nijmegen, The Netherlands
+
+ This file is part of libDAI.
+
+ libDAI is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+#ifndef __defined_libdai_exactinf_h
+#define __defined_libdai_exactinf_h
+
+
+#include <dai/daialg.h>
+#include <dai/properties.h>
+#include <dai/factorgraph.h>
+#include <dai/enum.h>
+
+
+namespace dai {
+
+
+class ExactInf : public DAIAlgFG {
+ public:
+ struct Properties {
+ size_t verbose;
+ } props;
+
+ private:
+ std::vector<Factor> _beliefsV;
+ std::vector<Factor> _beliefsF;
+ Real _logZ;
+
+ public:
+ /// Default constructor
+ ExactInf() : DAIAlgFG(), props(), _beliefsV(), _beliefsF(), _logZ(0) {}
+
+ /// Copy constructor
+ ExactInf( const ExactInf &x ) : DAIAlgFG(x), props(x.props), _beliefsV(x._beliefsV), _beliefsF(x._beliefsF), _logZ(x._logZ) {}
+
+ /// Clone (virtual copy constructor)
+ virtual ExactInf* clone() const {
+ return new ExactInf(*this);
+ }
+
+ /// Construct from FactorGraph fg and PropertySet opts
+ ExactInf( const FactorGraph &fg, const PropertySet &opts ) : DAIAlgFG(fg), props(), _beliefsV(), _beliefsF(), _logZ() {
+ setProperties( opts );
+ create();
+ }
+
+ /// Assignment operator
+ ExactInf& operator=( const ExactInf &x ) {
+ if( this != &x ) {
+ DAIAlgFG::operator=( x );
+ props = x.props;
+ _beliefsV = x._beliefsV;
+ _beliefsF = x._beliefsF;
+ _logZ = x._logZ;
+ }
+ return *this;
+ }
+
+/* /// Create (virtual constructor)
+ virtual ExactInf* create() const {
+ return new ExactInf();
+ }
+*/
+ /// Return maximum difference between single node
+ /// beliefs for two consecutive iterations
+ virtual double maxDiff() const {
+ DAI_THROW(NOT_IMPLEMENTED);
+ return 0.0;
+ }
+
+ /// Identifies itself for logging purposes
+ virtual std::string identify() const;
+
+ /// Get single node belief
+ virtual Factor belief( const Var &n ) const {
+ return beliefV( findVar( n ) );
+ }
+
+ /// Get general belief
+ virtual Factor belief( const VarSet &n ) const;
+
+ /// Get all beliefs
+ virtual std::vector<Factor> beliefs() const;
+
+ /// Get log partition sum
+ virtual Real logZ() const {
+ return _logZ;
+ }
+
+ /// Clear messages and beliefs
+ virtual void init();
+
+ /// Clear messages and beliefs corresponding to the nodes in ns
+ virtual void init( const VarSet &/*ns*/ ) {}
+
+ /// The actual approximate inference algorithm
+ virtual double run();
+
+ /// Name of this inference method
+ static const char *Name;
+
+ void create();
+ void undoProbs( const VarSet &ns ) { FactorGraph::undoProbs(ns); init(ns); }
+ void setProperties( const PropertySet &opts );
+ PropertySet getProperties() const;
+
+ Factor beliefV( size_t i ) const {
+ return _beliefsV[i];
+ }
+
+ Factor beliefF( size_t I ) const {
+ return _beliefsF[I];
+ }
+};
+
+
+} // end of namespace dai
+
+
+#endif
InfAlg *newInfAlg( const string &name, const FactorGraph &fg, const PropertySet &opts ) {
+ if( name == ExactInf::Name )
+ return new ExactInf (fg, opts);
#ifdef WITH_BP
if( name == BP::Name )
return new BP (fg, opts);
--- /dev/null
+/* Copyright (C) 2006-2008 Joris Mooij [j dot mooij at science dot ru dot nl]
+ Radboud University Nijmegen, The Netherlands
+
+ This file is part of libDAI.
+
+ libDAI is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ libDAI is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with libDAI; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+*/
+
+
+#include <dai/exactinf.h>
+#include <sstream>
+
+
+namespace dai {
+
+
+using namespace std;
+
+
+const char *ExactInf::Name = "EXACT";
+
+
+void ExactInf::setProperties( const PropertySet &opts ) {
+ assert( opts.hasKey("verbose") );
+
+ props.verbose = opts.getStringAs<size_t>("verbose");
+}
+
+
+PropertySet ExactInf::getProperties() const {
+ PropertySet opts;
+ opts.Set( "verbose", props.verbose );
+ return opts;
+}
+
+
+void ExactInf::create() {
+ // clear variable beliefs and reserve space
+ _beliefsV.clear();
+ _beliefsV.reserve( nrVars() );
+ for( size_t i = 0; i < nrVars(); i++ )
+ _beliefsV.push_back( Factor( var(i) ) );
+
+ // clear factor beliefs and reserve space
+ _beliefsF.clear();
+ _beliefsF.reserve( nrFactors() );
+ for( size_t I = 0; I < nrFactors(); I++ )
+ _beliefsF.push_back( Factor( factor(I).vars() ) );
+}
+
+
+void ExactInf::init() {
+ for( size_t i = 0; i < nrVars(); i++ )
+ _beliefsV[i].fill( 1.0 );
+ for( size_t I = 0; I < nrFactors(); I++ )
+ _beliefsF[I].fill( 1.0 );
+}
+
+
+double ExactInf::run() {
+ if( props.verbose >= 1 )
+ cout << "Starting " << identify() << "...";
+
+ Factor P;
+ for( size_t I = 0; I < nrFactors(); I++ )
+ P *= factor(I);
+
+ Real Z = P.totalSum();
+ _logZ = std::log(Z);
+ for( size_t i = 0; i < nrVars(); i++ )
+ _beliefsV[i] = P.marginal(var(i));
+ for( size_t I = 0; I < nrFactors(); I++ )
+ _beliefsF[I] = P.marginal(factor(I).vars());
+
+ if( props.verbose >= 1 )
+ cout << "finished" << endl;
+
+ return 0.0;
+}
+
+
+vector<Factor> ExactInf::beliefs() const {
+ vector<Factor> result = _beliefsV;
+ result.insert( result.end(), _beliefsF.begin(), _beliefsF.end() );
+ return result;
+}
+
+
+Factor ExactInf::belief( const VarSet &ns ) const {
+ if( ns.size() == 0 )
+ return Factor();
+ else if( ns.size() == 1 ) {
+ return belief( *(ns.begin()) );
+ } else {
+ size_t I;
+ for( I = 0; I < nrFactors(); I++ )
+ if( factor(I).vars() >> ns )
+ break;
+ assert( I != nrFactors() );
+ return beliefF(I).marginal(ns);
+ }
+}
+
+
+string ExactInf::identify() const {
+ stringstream result (stringstream::out);
+ result << Name << getProperties();
+ return result.str();
+}
+
+
+} // end of namespace dai
HAK_LOOP5: HAK[doubleloop=1,clusters=LOOP,loopdepth=5,tol=1e-9,maxiter=10000,verbose=0]
HAK_LOOP6: HAK[doubleloop=1,clusters=LOOP,loopdepth=6,tol=1e-9,maxiter=10000,verbose=0]
HAK_LOOP8: HAK[doubleloop=1,clusters=LOOP,loopdepth=8,tol=1e-9,maxiter=10000,verbose=0]
-
-#---------------------------------------------------------------
-#EXACT
-#
-#
-#} else if( method.substr(0,5) == "EXACT" ) { // EXACT
-# // Look if the network is small enough to do brute-force exact method
-# bool toolarge = false;
-# size_t total_statespace = 1;
-# for( size_t i = 0; i < fg.nrVars(); i++ ) {
-# total_statespace *= fg.var(i).states();
-# if( total_statespace > (1UL << 16) )
-# toolarge = true;
-# }
-#
-# if( !toolarge ) {
-# Factor piet;
-# for( size_t I = 0; I < fg.nrFactors(); I++ )
-# piet *= fg.factor( I );
-# for( size_t i = 0; i < fg.nrVars(); i++ )
-# q.push_back(piet.marginal(fg.var(i)));
-# time += toc() - tic;
-# logZ = fg.ExactlogZ();
-# } else
-# throw "Network too large for EXACT method";
double maxdiff;
double time;
bool has_logZ;
+ bool has_maxdiff;
TestAI( const FactorGraph &fg, const string &_name, const PropertySet &opts ) : obj(NULL), name(_name), err(), q(), logZ(0.0), maxdiff(0.0), time(0), has_logZ(true) {
double tic = toc();
obj = newInfAlg( name, fg, opts );
time += toc() - tic;
-/*
- } else if( method.substr(0,5) == "EXACT" ) { // EXACT
- // Look if the network is small enough to do brute-force exact method
- bool toolarge = false;
- size_t total_statespace = 1;
- for( size_t i = 0; i < fg.nrVars(); i++ ) {
- total_statespace *= fg.var(i).states();
- if( total_statespace > (1UL << 16) )
- toolarge = true;
- }
-
- if( !toolarge ) {
- Factor piet;
- for( size_t I = 0; I < fg.nrFactors(); I++ )
- piet *= fg.factor( I );
- for( size_t i = 0; i < fg.nrVars(); i++ )
- q.push_back(piet.marginal(fg.var(i)));
- time += toc() - tic;
- logZ = fg.ExactlogZ();
- } else
- throw "Network too large for EXACT method";
- }
-*/
}
~TestAI() {
void doAI() {
double tic = toc();
-// if( name == "EXACT" ) {
-// // calculation has already been done
-// }
if( obj != NULL ) {
obj->init();
obj->run();
} catch( Exception &e ) {
has_logZ = false;
}
- maxdiff = obj->maxDiff();
+ try {
+ maxdiff = obj->maxDiff();
+ has_maxdiff = true;
+ } catch( Exception &e ) {
+ has_maxdiff = false;
+ }
q = allBeliefs();
};
}
double tol;
size_t maxiter;
size_t verbose;
+ bool marginals = false;
bool report_time = true;
po::options_description opts_required("Required options");
("tol", po::value< double >(&tol), "Override tolerance")
("maxiter", po::value< size_t >(&maxiter), "Override maximum number of iterations")
("verbose", po::value< size_t >(&verbose), "Override verbosity")
+ ("marginals", po::value< bool >(&marginals), "Output single node marginals?")
("report-time", po::value< bool >(&report_time), "Report calculation time")
;
cout << "N/A ";
}
cout.width( 10 );
- double md = clipdouble( piet.maxdiff, 1e-9 );
- if( isnan( me ) )
- md = me;
- if( isnan( ae ) )
- md = ae;
- cout << md << endl;
+ if( piet.has_maxdiff ) {
+ double md = clipdouble( piet.maxdiff, 1e-9 );
+ if( isnan( me ) )
+ md = me;
+ if( isnan( ae ) )
+ md = ae;
+ cout << md << endl;
+ } else {
+ cout << "N/A ";
+ }
} else
cout << endl;
+
+ if( marginals ) {
+ for( size_t i = 0; i < piet.q.size(); i++ )
+ cout << "# " << piet.q[i] << endl;
+ }
}
}
} catch(const char *e) {
#!/bin/bash
-./test --report-time false --aliases aliases.conf --filename $1 --methods JTREE_HUGIN JTREE_SHSH BP_SEQFIX BP_SEQRND BP_SEQMAX BP_PARALL BP_SEQFIX_LOG BP_SEQRND_LOG BP_SEQMAX_LOG BP_PARALL_LOG MF_SEQRND TREEEP TREEEPWC GBP_MIN GBP_DELTA GBP_LOOP3 GBP_LOOP4 HAK_MIN HAK_DELTA HAK_LOOP3 HAK_LOOP4 MR_RESPPROP_FULL MR_CLAMPING_FULL MR_EXACT_FULL MR_RESPPROP_LINEAR MR_CLAMPING_LINEAR MR_EXACT_LINEAR LCBP_FULLCAV_SEQFIX LCBP_FULLCAVin_SEQFIX LCBP_FULLCAV_SEQRND LCBP_FULLCAVin_SEQRND LCBP_FULLCAV_NONE LCBP_FULLCAVin_NONE LCBP_PAIRCAV_SEQFIX LCBP_PAIRCAVin_SEQFIX LCBP_PAIRCAV_SEQRND LCBP_PAIRCAVin_SEQRND LCBP_PAIRCAV_NONE LCBP_PAIRCAVin_NONE LCBP_UNICAV_SEQFIX LCBP_UNICAV_SEQRND
+./test --report-time false --aliases aliases.conf --filename $1 --methods EXACT[verbose=0] JTREE_HUGIN JTREE_SHSH BP_SEQFIX BP_SEQRND BP_SEQMAX BP_PARALL BP_SEQFIX_LOG BP_SEQRND_LOG BP_SEQMAX_LOG BP_PARALL_LOG MF_SEQRND TREEEP TREEEPWC GBP_MIN GBP_DELTA GBP_LOOP3 GBP_LOOP4 HAK_MIN HAK_DELTA HAK_LOOP3 HAK_LOOP4 MR_RESPPROP_FULL MR_CLAMPING_FULL MR_EXACT_FULL MR_RESPPROP_LINEAR MR_CLAMPING_LINEAR MR_EXACT_LINEAR LCBP_FULLCAV_SEQFIX LCBP_FULLCAVin_SEQFIX LCBP_FULLCAV_SEQRND LCBP_FULLCAVin_SEQRND LCBP_FULLCAV_NONE LCBP_FULLCAVin_NONE LCBP_PAIRCAV_SEQFIX LCBP_PAIRCAVin_SEQFIX LCBP_PAIRCAV_SEQRND LCBP_PAIRCAVin_SEQRND LCBP_PAIRCAV_NONE LCBP_PAIRCAVin_NONE LCBP_UNICAV_SEQFIX LCBP_UNICAV_SEQRND
-test --report-time false --aliases aliases.conf --filename %1 --methods JTREE_HUGIN JTREE_SHSH BP_SEQFIX BP_SEQRND BP_SEQMAX BP_PARALL BP_SEQFIX_LOG BP_SEQRND_LOG BP_SEQMAX_LOG BP_PARALL_LOG MF_SEQRND TREEEP TREEEPWC GBP_MIN GBP_DELTA GBP_LOOP3 GBP_LOOP4 HAK_MIN HAK_DELTA HAK_LOOP3 HAK_LOOP4 MR_RESPPROP_FULL MR_CLAMPING_FULL MR_EXACT_FULL MR_RESPPROP_LINEAR MR_CLAMPING_LINEAR MR_EXACT_LINEAR LCBP_FULLCAV_SEQFIX LCBP_FULLCAVin_SEQFIX LCBP_FULLCAV_SEQRND LCBP_FULLCAVin_SEQRND LCBP_FULLCAV_NONE LCBP_FULLCAVin_NONE LCBP_PAIRCAV_SEQFIX LCBP_PAIRCAVin_SEQFIX LCBP_PAIRCAV_SEQRND LCBP_PAIRCAVin_SEQRND LCBP_PAIRCAV_NONE LCBP_PAIRCAVin_NONE LCBP_UNICAV_SEQFIX LCBP_UNICAV_SEQRND
+test --report-time false --aliases aliases.conf --filename %1 --methods EXACT[verbose=0] JTREE_HUGIN JTREE_SHSH BP_SEQFIX BP_SEQRND BP_SEQMAX BP_PARALL BP_SEQFIX_LOG BP_SEQRND_LOG BP_SEQMAX_LOG BP_PARALL_LOG MF_SEQRND TREEEP TREEEPWC GBP_MIN GBP_DELTA GBP_LOOP3 GBP_LOOP4 HAK_MIN HAK_DELTA HAK_LOOP3 HAK_LOOP4 MR_RESPPROP_FULL MR_CLAMPING_FULL MR_EXACT_FULL MR_RESPPROP_LINEAR MR_CLAMPING_LINEAR MR_EXACT_LINEAR LCBP_FULLCAV_SEQFIX LCBP_FULLCAVin_SEQFIX LCBP_FULLCAV_SEQRND LCBP_FULLCAVin_SEQRND LCBP_FULLCAV_NONE LCBP_FULLCAVin_NONE LCBP_PAIRCAV_SEQFIX LCBP_PAIRCAVin_SEQFIX LCBP_PAIRCAV_SEQRND LCBP_PAIRCAVin_SEQRND LCBP_PAIRCAV_NONE LCBP_PAIRCAVin_NONE LCBP_UNICAV_SEQFIX LCBP_UNICAV_SEQRND
# testfast.fg
# METHOD MAX ERROR AVG ERROR LOGZ ERROR MAXDIFF
-JTREE_HUGIN
+EXACT[verbose=0]
+JTREE_HUGIN 1.000e-09 1.000e-09 1.000e-09 1.000e-09
JTREE_SHSH 1.000e-09 1.000e-09 1.000e-09 1.000e-09
BP_SEQFIX 9.483e-02 3.078e-02 1.737e-02 1.000e-09
BP_SEQRND 9.483e-02 3.078e-02 1.737e-02 1.000e-09
projects / libdai.git / commitdiff