Re-organization: moving all files.

I re-organized into original cpp directory and 4 additional directories: base, geometry, slam, and tests.
cpp will be further renamed/sub-divided and contains the core library.
I wanted it not depend on geometry or slam, which necessitated moving complicated tests to a dedicated directory.

CppUnitLite/Makefile

@@ -1,35 +0,0 @@
-# Makefile to compile the unit test library, will end up in $(LIBDIR)
-
-.PHONY: all install clean
-
-all: libCppUnitLite.a
-
-CC ?= gcc
-CXX ?= g++
-CPP ?= cpp
-CXXFLAGS += -O2
-
-sources = $(shell ls *.cpp)
-objects = $(sources:.cpp=.o)
-
-library = libCppUnitLite.a
-
-$(library): $(objects) 
-	ar crsv $@ $(objects) 
-	ranlib $(library)
-
-clean:
-	rm -f *.o *.*~ $(library)
-
-check:
-	echo 'no check for CppUnitLite'
-
-distdir:
-
-# Richard: added the following dependencies so that recursive make works:
-
-install: all
-
-distclean: clean
-
-check: all

CppUnitLite/Makefile.am

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CppUnitLite/Makefile.in

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LICENSE

@@ -1 +1,12 @@
 The GTSAM library has not been licensed yet. See also COPYING
+
+
+GTSAM depends on the following packages that are built locally:
+
+UFconfig
+Copyright (c) 2006-2009, Timothy A. Davis. Distributed under the GNU LGPL license.
+
+CCOLAMD
+Copyright (c) 1998-2007, University of Florida. Author: Timothy A. Davis, Siva Rajamanickam, 
+and Stefan Larimore. The COLAMD algorithm was developed in collaboration Esmond Ng and John Gilbert.
+Distributed under the GNU LGPL license.

Makefile.am

@@ -1,46 +1,49 @@
+#----------------------------------------------------------------------------------------------------
+# GTSAM top-level automake file
+#----------------------------------------------------------------------------------------------------
+
 #The option -I m4 tells Autoconf to look for additional Autoconf macros in the m4 subdirectory.
 ACLOCAL_AMFLAGS = -I m4
 
 # make automake install some standard but missing files
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = colamd CppUnitLite ldl spqr_mini cpp wrap
 
-# install the matlab toolbox
+# All the sub-directories that need to be built
+SUBDIRS = CppUnitLite colamd ldl spqr_mini base cpp geometry slam . tests wrap  
+
+# And the corresponding libraries produced
+SUBLIBS = colamd/libcolamd.la ldl/libldl.la \
+          base/libbase.la cpp/libcpp.la geometry/libgeometry.la slam/libslam.la
+
+if USE_LAPACK
+SUBLIBS += spqr_mini/libspqr_mini.la
+endif
+
+EXTRA_DIST = autogen.sh configure.ac THANKS 
+
+# The following lines specify the actual shared library to be built with libtool
+lib_LTLIBRARIES = libgtsam.la
+libgtsam_la_SOURCES =
+libgtsam_la_LIBADD = $(SUBLIBS)
+libgtsam_la_LDFLAGS = -version-info 0:0:0
+
+# TODO: UFconfig, CCOLAMD, and LDL automake magic without adding or touching any file
+# in those directories as to not invalidate the LGPL license
+# See some possibilities in
+# http://www.gnu.org/software/hello/manual/automake/Third_002dParty-Makefiles.html
+
+# install the headers and matlab toolbox
 install-exec-hook:
 	install -d ${toolbox}/gtsam && \
 	cp -rf toolbox/* ${toolbox}/gtsam && \
 	install -d ${prefix}/include/wrap && \
-	cp -f wrap/wrap-matlab.h  ${prefix}/include/wrap/matlab.h && \
+	cp -f wrap/wrap-matlab.h  ${prefix}/include/wrap/matlab.h
-	install -d $(prefix)/include && \
-	install -d $(prefix)/include/colamd && \
-	cp -f colamd/colamd.h $(prefix)/include/colamd/ && \
-	cp -f colamd/ccolamd.h $(prefix)/include/colamd/ && \
-	cp -f colamd/UFconfig.h $(prefix)/include/colamd/ && \
-	cp -f colamd/libcolamd.a $(prefix)/lib/ && \
-	install -d $(prefix)/include/ldl && \
-	cp -f ldl/ldl.h $(prefix)/include/ldl/ && \
-	cp -f ldl/UFconfig.h $(prefix)/include/ldl/ && \
-	cp -f ldl/libldl.a $(prefix)/lib/
 
+# Todo: Also do CppUnitLite with automake 
 dist-hook:
-	mkdir $(distdir)/CppUnitLite
+	mkdir $(distdir)/config
-	cp -p $(srcdir)/CppUnitLite/Makefile $(distdir)/CppUnitLite
-	cp -p $(srcdir)/CppUnitLite/*.h $(distdir)/CppUnitLite
-	cp -p $(srcdir)/CppUnitLite/*.cpp $(distdir)/CppUnitLite
-	mkdir $(distdir)/colamd
-	cp -p $(srcdir)/colamd/Makefile $(distdir)/colamd
-	cp -p $(srcdir)/colamd/*.h $(distdir)/colamd
-	cp -p $(srcdir)/colamd/*.c $(distdir)/colamd
-	cp -p $(srcdir)/colamd/*.cpp $(distdir)/colamd
-	mkdir $(distdir)/ldl
-	cp -p $(srcdir)/ldl/Makefile $(distdir)/ldl
-	cp -p $(srcdir)/ldl/*.h $(distdir)/ldl
-	cp -p $(srcdir)/ldl/*.c $(distdir)/ldl
-	cp -p $(srcdir)/ldl/*.cpp $(distdir)/ldl
-	mkdir $(distdir)/spqr_mini
-	cp -p $(srcdir)/spqr_mini/Makefile $(distdir)/spqr_mini
-	cp -p $(srcdir)/spqr_mini/*.h $(distdir)/spqr_mini
-	cp -p $(srcdir)/spqr_mini/*.c $(distdir)/spqr_mini
-	cp -p $(srcdir)/spqr_mini/*.cpp $(distdir)/spqr_mini
 	mkdir $(distdir)/matlab
 	cp -p $(srcdir)/matlab/*.m $(distdir)/matlab
+	cp -r $(srcdir)/wrap/expected $(distdir)/wrap
+
+

THANKS

@@ -0,0 +1,18 @@
+GTSAM was made possible by the efforts of many collaborators at Georgia Tech
+
+Doru Balcan
+Alex Cunningham
+Alireza Fathi
+Eohan George
+Viorela Ila
+Yong-Dian Jian
+Michael Kaess
+Kai Ni
+Carlos Nieto
+Manohar Paluri
+Christian Potthast
+Richard Roberts
+Grant Schindler
+
+Many thanks for your hard work!!!!
+Frank Dellaert

base/DSF.h

@@ -20,8 +20,6 @@
 
 namespace gtsam {
 
-	class Symbol;
-
 	template <class Key>
 	class DSF : protected BTree<Key, Key> {
 
@@ -153,6 +151,5 @@ namespace gtsam {
 
 	// shortcuts
 	typedef DSF<int> DSFInt;
-	typedef DSF<Symbol> DSFSymbol;
 
 } // namespace gtsam

base/Makefile.am

@@ -0,0 +1,86 @@
+#----------------------------------------------------------------------------------------------------
+# GTSAM base
+# provides some base Math and data structures, as well as test-related utilities
+#----------------------------------------------------------------------------------------------------
+
+headers =
+sources = 
+check_PROGRAMS = 
+
+# base Math
+sources += Vector.cpp svdcmp.cpp Matrix.cpp
+check_PROGRAMS += testVector testMatrix
+
+if USE_LAPACK
+sources += SPQRUtil.cpp
+check_PROGRAMS += testSPQRUtil
+endif
+
+# Testing
+headers += Testable.h numericalDerivative.h 
+
+# Lie Groups
+headers += Lie.h Lie-inl.h
+
+# Data structures
+headers += BTree.h DSF.h
+sources += DSFVector.cpp
+check_PROGRAMS += testBTree testDSF testDSFVector
+
+# Timing tests
+noinst_PROGRAMS = timeMatrix
+
+#----------------------------------------------------------------------------------------------------
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+# The headers are installed in $(includedir)/gtsam: 
+#----------------------------------------------------------------------------------------------------
+headers += $(sources:.cpp=.h)
+pkginclude_HEADERS = $(headers)
+noinst_LTLIBRARIES = libbase.la
+libbase_la_SOURCES = $(sources)
+
+AM_CPPFLAGS = -I$(boost)
+
+if USE_BLAS
+AM_CPPFLAGS += -DGT_USE_CBLAS
+endif
+
+if USE_LAPACK
+AM_CPPFLAGS += -DGT_USE_LAPACK
+endif
+
+# On Mac, we compile using the BLAS/LAPACK headers in the Accelerate framework 
+if USE_ACCELERATE_MACOS
+AM_CPPFLAGS += -F Accelerate
+endif
+
+#----------------------------------------------------------------------------------------------------
+# rules to build local programs
+#----------------------------------------------------------------------------------------------------
+TESTS = $(check_PROGRAMS)
+AM_DEFAULT_SOURCE_EXT = .cpp
+AM_LDFLAGS = $(BOOST_LDFLAGS) $(boost_serialization)
+LDADD = libbase.la ../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a 
+
+if USE_BLAS_LINUX
+AM_LDFLAGS += -lcblas -latlas  
+endif
+
+if USE_LAPACK
+LDADD += ../spqr_mini/libspqr_mini.la
+endif
+
+if USE_LAPACK_LINUX
+AM_LDFLAGS += -llapack
+endif
+
+if USE_ACCELERATE_MACOS
+AM_LDFLAGS += -framework Accelerate  
+endif
+
+# rule to run an executable
+%.run: % $(LDADD)
+	./$^
+
+#----------------------------------------------------------------------------------------------------

base/Makefile.in

@@ -0,0 +1,777 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+#----------------------------------------------------------------------------------------------------
+# GTSAM base
+# provides some base Math and data structures, as well as test-related utilities
+#----------------------------------------------------------------------------------------------------
+
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+check_PROGRAMS = testVector$(EXEEXT) testMatrix$(EXEEXT) \
+	$(am__EXEEXT_1) testBTree$(EXEEXT) testDSF$(EXEEXT) \
+	testDSFVector$(EXEEXT)
+@USE_LAPACK_TRUE@am__append_1 = SPQRUtil.cpp
+@USE_LAPACK_TRUE@am__append_2 = testSPQRUtil
+noinst_PROGRAMS = timeMatrix$(EXEEXT)
+@USE_BLAS_TRUE@am__append_3 = -DGT_USE_CBLAS
+@USE_LAPACK_TRUE@am__append_4 = -DGT_USE_LAPACK
+
+# On Mac, we compile using the BLAS/LAPACK headers in the Accelerate framework 
+@USE_ACCELERATE_MACOS_TRUE@am__append_5 = -F Accelerate
+@USE_BLAS_LINUX_TRUE@am__append_6 = -lcblas -latlas  
+@USE_LAPACK_TRUE@am__append_7 = ../spqr_mini/libspqr_mini.la
+@USE_LAPACK_LINUX_TRUE@am__append_8 = -llapack
+@USE_ACCELERATE_MACOS_TRUE@am__append_9 = -framework Accelerate  
+subdir = base
+DIST_COMMON = $(am__pkginclude_HEADERS_DIST) $(srcdir)/Makefile.am \
+	$(srcdir)/Makefile.in
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+	$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
+	$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \
+	$(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
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+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+LTLIBRARIES = $(noinst_LTLIBRARIES)
+libbase_la_LIBADD =
+am__libbase_la_SOURCES_DIST = Vector.cpp svdcmp.cpp Matrix.cpp \
+	SPQRUtil.cpp DSFVector.cpp
+@USE_LAPACK_TRUE@am__objects_1 = SPQRUtil.lo
+am__objects_2 = Vector.lo svdcmp.lo Matrix.lo $(am__objects_1) \
+	DSFVector.lo
+am_libbase_la_OBJECTS = $(am__objects_2)
+libbase_la_OBJECTS = $(am_libbase_la_OBJECTS)
+@USE_LAPACK_TRUE@am__EXEEXT_1 = testSPQRUtil$(EXEEXT)
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+testBTree_LDADD = $(LDADD)
+testBTree_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+testDSF_SOURCES = testDSF.cpp
+testDSF_OBJECTS = testDSF.$(OBJEXT)
+testDSF_LDADD = $(LDADD)
+testDSF_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+testDSFVector_SOURCES = testDSFVector.cpp
+testDSFVector_OBJECTS = testDSFVector.$(OBJEXT)
+testDSFVector_LDADD = $(LDADD)
+testDSFVector_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+testMatrix_SOURCES = testMatrix.cpp
+testMatrix_OBJECTS = testMatrix.$(OBJEXT)
+testMatrix_LDADD = $(LDADD)
+testMatrix_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+testSPQRUtil_SOURCES = testSPQRUtil.cpp
+testSPQRUtil_OBJECTS = testSPQRUtil.$(OBJEXT)
+testSPQRUtil_LDADD = $(LDADD)
+testSPQRUtil_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+testVector_SOURCES = testVector.cpp
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+testVector_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
+timeMatrix_SOURCES = timeMatrix.cpp
+timeMatrix_OBJECTS = timeMatrix.$(OBJEXT)
+timeMatrix_LDADD = $(LDADD)
+timeMatrix_DEPENDENCIES = libbase.la ../ldl/libldl.la \
+	../CppUnitLite/libCppUnitLite.a $(am__append_7)
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+LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
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+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+	--mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
+	$(LDFLAGS) -o $@
+SOURCES = $(libbase_la_SOURCES) testBTree.cpp testDSF.cpp \
+	testDSFVector.cpp testMatrix.cpp testSPQRUtil.cpp \
+	testVector.cpp timeMatrix.cpp
+DIST_SOURCES = $(am__libbase_la_SOURCES_DIST) testBTree.cpp \
+	testDSF.cpp testDSFVector.cpp testMatrix.cpp testSPQRUtil.cpp \
+	testVector.cpp timeMatrix.cpp
+am__pkginclude_HEADERS_DIST = Testable.h numericalDerivative.h Lie.h \
+	Lie-inl.h BTree.h DSF.h Vector.h svdcmp.h Matrix.h SPQRUtil.h \
+	DSFVector.h
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
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+    *) f=$$p;; \
+  esac;
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+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
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+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
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+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
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+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+toolbox = @toolbox@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+# Testing
+
+# Lie Groups
+
+# Data structures
+
+#----------------------------------------------------------------------------------------------------
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+# The headers are installed in $(includedir)/gtsam: 
+#----------------------------------------------------------------------------------------------------
+headers = Testable.h numericalDerivative.h Lie.h Lie-inl.h BTree.h \
+	DSF.h $(sources:.cpp=.h)
+
+# base Math
+sources = Vector.cpp svdcmp.cpp Matrix.cpp $(am__append_1) \
+	DSFVector.cpp
+pkginclude_HEADERS = $(headers)
+noinst_LTLIBRARIES = libbase.la
+libbase_la_SOURCES = $(sources)
+AM_CPPFLAGS = -I$(boost) $(am__append_3) $(am__append_4) \
+	$(am__append_5)
+
+#----------------------------------------------------------------------------------------------------
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+	$(am__append_8) $(am__append_9)
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+	$(am__append_7)
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .cpp .lo .o .obj
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+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
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+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu base/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu base/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
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+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+
+clean-noinstLTLIBRARIES:
+	-test -z "$(noinst_LTLIBRARIES)" || rm -f $(noinst_LTLIBRARIES)
+	@list='$(noinst_LTLIBRARIES)'; for p in $$list; do \
+	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
+	  test "$$dir" != "$$p" || dir=.; \
+	  echo "rm -f \"$${dir}/so_locations\""; \
+	  rm -f "$${dir}/so_locations"; \
+	done
+libbase.la: $(libbase_la_OBJECTS) $(libbase_la_DEPENDENCIES) 
+	$(CXXLINK)  $(libbase_la_OBJECTS) $(libbase_la_LIBADD) $(LIBS)
+
+clean-checkPROGRAMS:
+	@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
+	echo " rm -f" $$list; \
+	rm -f $$list || exit $$?; \
+	test -n "$(EXEEXT)" || exit 0; \
+	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+	echo " rm -f" $$list; \
+	rm -f $$list
+
+clean-noinstPROGRAMS:
+	@list='$(noinst_PROGRAMS)'; test -n "$$list" || exit 0; \
+	echo " rm -f" $$list; \
+	rm -f $$list || exit $$?; \
+	test -n "$(EXEEXT)" || exit 0; \
+	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+	echo " rm -f" $$list; \
+	rm -f $$list
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+	@rm -f testBTree$(EXEEXT)
+	$(CXXLINK) $(testBTree_OBJECTS) $(testBTree_LDADD) $(LIBS)
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+	@rm -f testDSF$(EXEEXT)
+	$(CXXLINK) $(testDSF_OBJECTS) $(testDSF_LDADD) $(LIBS)
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+	@rm -f testDSFVector$(EXEEXT)
+	$(CXXLINK) $(testDSFVector_OBJECTS) $(testDSFVector_LDADD) $(LIBS)
+testMatrix$(EXEEXT): $(testMatrix_OBJECTS) $(testMatrix_DEPENDENCIES) 
+	@rm -f testMatrix$(EXEEXT)
+	$(CXXLINK) $(testMatrix_OBJECTS) $(testMatrix_LDADD) $(LIBS)
+testSPQRUtil$(EXEEXT): $(testSPQRUtil_OBJECTS) $(testSPQRUtil_DEPENDENCIES) 
+	@rm -f testSPQRUtil$(EXEEXT)
+	$(CXXLINK) $(testSPQRUtil_OBJECTS) $(testSPQRUtil_LDADD) $(LIBS)
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+	@rm -f testVector$(EXEEXT)
+	$(CXXLINK) $(testVector_OBJECTS) $(testVector_LDADD) $(LIBS)
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+	@rm -f timeMatrix$(EXEEXT)
+	$(CXXLINK) $(timeMatrix_OBJECTS) $(timeMatrix_LDADD) $(LIBS)
+
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+	-rm -f *.$(OBJEXT)
+
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+	@$(NORMAL_INSTALL)
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+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(pkgincludedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(pkgincludedir)" || exit $$?; \
+	done
+
+uninstall-pkgincludeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
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+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(pkgincludedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(pkgincludedir)" && rm -f $$files
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+	  done | \
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+	mkid -fID $$unique
+tags: TAGS
+
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+	here=`pwd`; \
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+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
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+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
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+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
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+		$(TAGS_FILES) $(LISP)
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+	     $$unique
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+	here=`$(am__cd) $(top_builddir) && pwd` \
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+
+check-TESTS: $(TESTS)
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+	srcdir=$(srcdir); export srcdir; \
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+		col=$$grn; res=PASS; \
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+	      *[\ \	]$$tst[\ \	]*) \
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+	      col=$$blu; res=SKIP; \
+	    fi; \
+	    echo "$${col}$$res$${std}: $$tst"; \
+	  done; \
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+	    tests="test"; \
+	    All=""; \
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+	    tests="tests"; \
+	    All="All "; \
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+	  if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
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+	      dashes="$$report"; \
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+	    echo "$$grn$$dashes"; \
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+	    echo "$$red$$dashes"; \
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+	  test -z "$$report" || echo "$$report"; \
+	  echo "$$dashes$$std"; \
+	  test "$$failed" -eq 0; \
+	else :; fi
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+distdir: $(DISTFILES)
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+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
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+	$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS)
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+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
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+	clean-noinstLTLIBRARIES clean-noinstPROGRAMS mostlyclean-am
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+	clean-noinstLTLIBRARIES clean-noinstPROGRAMS ctags distclean \
+	distclean-compile distclean-generic distclean-libtool \
+	distclean-tags distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
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+
+# rule to run an executable
+%.run: % $(LDADD)
+	./$^
+
+#----------------------------------------------------------------------------------------------------
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

base/Matrix.cpp

@@ -11,19 +11,16 @@
 #include <fstream>
 
 #ifdef GT_USE_CBLAS
-	#ifdef YA_BLAS
+extern "C" {
-#include <vecLib/cblas.h>
-	#else
 #include <cblas.h>
-	#endif
+}
 #endif
 
 #ifdef GT_USE_LAPACK
-  #ifdef YA_BLAS
+extern "C" {
-#include <vecLib/clapack.h>
+#include <cblas.h>
-  #else
 #include <clapack.h>
-  #endif
+}
 #endif
 
 #include <boost/numeric/ublas/matrix_proxy.hpp>
@@ -190,7 +187,7 @@ void multiplyAdd(double alpha, const Matrix& A, const Vector& x, Vector& e) {
 
 	// fill in parameters
 	const double beta = 1.0;
-	const int incx = 1, incy = 1, ida = n;
+	const size_t incx = 1, incy = 1, ida = n;
 
 	// execute blas call
 	cblas_dgemv(CblasRowMajor, CblasNoTrans, m, n, alpha, Aptr, ida, Xptr, incx, beta, Eptr, incy);
@@ -201,9 +198,9 @@ void multiplyAdd(double alpha, const Matrix& A, const Vector& x, Vector& e) {
   size_t m = A.size1(), n = A.size2();
 	double * ei = e.data().begin();
 	const double * aij = A.data().begin();
-	for (int i = 0; i < m; i++, ei++) {
+	for(size_t i = 0; i < m; i++, ei++) {
 		const double * xj = x.data().begin();
-		for (int j = 0; j < n; j++, aij++, xj++)
+		for(size_t j = 0; j < n; j++, aij++, xj++)
 			(*ei) += alpha * (*aij) * (*xj);
 	}
 #endif
@@ -218,9 +215,9 @@ void multiplyAdd(const Matrix& A, const Vector& x, Vector& e) {
   size_t m = A.size1(), n = A.size2();
 	double * ei = e.data().begin();
 	const double * aij = A.data().begin();
-	for (int i = 0; i < m; i++, ei++) {
+	for(size_t i = 0; i < m; i++, ei++) {
 		const double * xj = x.data().begin();
-		for (int j = 0; j < n; j++, aij++, xj++)
+		for(size_t j = 0; j < n; j++, aij++, xj++)
 			(*ei) += (*aij) * (*xj);
 	}
 #endif
@@ -249,7 +246,7 @@ void transposeMultiplyAdd(double alpha, const Matrix& A, const Vector& e, Vector
 
 	// fill in parameters
 	const double beta = 1.0;
-	const int incx = 1, incy = 1, ida = n;
+	const size_t incx = 1, incy = 1, ida = n;
 
 	// execute blas call
 	cblas_dgemv(CblasRowMajor, CblasTrans, m, n, alpha, Aptr, ida, Eptr, incx, beta, Xptr, incy);
@@ -259,10 +256,10 @@ void transposeMultiplyAdd(double alpha, const Matrix& A, const Vector& e, Vector
 	// TODO: use BLAS
   size_t m = A.size1(), n = A.size2();
 	double * xj = x.data().begin();
-	for (int j = 0; j < n; j++,xj++) {
+	for(size_t j = 0; j < n; j++,xj++) {
 		const double * ei = e.data().begin();
 		const double * aij = A.data().begin() + j;
-		for (int i = 0; i < m; i++, aij+=n, ei++)
+		for(size_t i = 0; i < m; i++, aij+=n, ei++)
 			(*xj) += alpha * (*aij) * (*ei);
 	}
 #endif
@@ -276,10 +273,10 @@ void transposeMultiplyAdd(const Matrix& A, const Vector& e, Vector& x) {
 #else
   size_t m = A.size1(), n = A.size2();
 	double * xj = x.data().begin();
-	for (int j = 0; j < n; j++,xj++) {
+	for(size_t j = 0; j < n; j++,xj++) {
 		const double * ei = e.data().begin();
 		const double * aij = A.data().begin() + j;
-		for (int i = 0; i < m; i++, aij+=n, ei++)
+		for(size_t i = 0; i < m; i++, aij+=n, ei++)
 			(*xj) += (*aij) * (*ei);
 	}
 #endif
@@ -397,7 +394,7 @@ void solve(Matrix& A, Matrix& B)
 	pmatrix pm(A_.size1());
 
 	// perform LU-factorization
-	int res = lu_factorize(A_,pm);
+	size_t res = lu_factorize(A_,pm);
 	if( res != 0 ) throw runtime_error ("Matrix::solve: lu_factorize failed!");
 
 	// backsubstitute to get the inverse
@@ -462,7 +459,7 @@ pair<Matrix,Matrix> qr(const Matrix& A) {
  * on a number of different matrices for which all columns change.
  */
 /* ************************************************************************* */
-inline void householder_update_manual(Matrix &A, int j, double beta, const Vector& vjm) {
+inline void householder_update_manual(Matrix &A, size_t j, double beta, const Vector& vjm) {
 	const size_t m = A.size1(), n = A.size2();
 	// w = beta*transpose(A(j:m,:))*v(j:m)
 	Vector w(n);
@@ -486,7 +483,7 @@ inline void householder_update_manual(Matrix &A, int j, double beta, const Vecto
 	}
 }
 
-void householder_update(Matrix &A, int j, double beta, const Vector& vjm) {
+void householder_update(Matrix &A, size_t j, double beta, const Vector& vjm) {
 #if defined GT_USE_CBLAS
 
 	// CBLAS version not working, using manual approach
@@ -551,7 +548,7 @@ void householder_update(Matrix &A, int j, double beta, const Vector& vjm) {
 // update A, b
 // A' \define A_{S}-ar and b'\define b-ad
 // __attribute__ ((noinline))	// uncomment to prevent inlining when profiling
-inline void updateAb_manual(Matrix& A, Vector& b, int j, const Vector& a,
+inline void updateAb_manual(Matrix& A, Vector& b, size_t j, const Vector& a,
 		const Vector& r, double d) {
 	const size_t m = A.size1(), n = A.size2();
 	for (size_t i = 0; i < m; i++) { // update all rows
@@ -568,7 +565,7 @@ inline void updateAb_manual(Matrix& A, Vector& b, int j, const Vector& a,
 /**
  * Perform updates of system matrices
  */
-static void updateAb(Matrix& A, Vector& b, int j, const Vector& a,
+static void updateAb(Matrix& A, Vector& b, size_t j, const Vector& a,
 		const Vector& r, double d) {
 	// TODO: reimplement using BLAS
 	updateAb_manual(A,b,j,a,r,d);
@@ -682,9 +679,9 @@ void householder(Matrix &A) {
 	__CLPK_integer n = A.size2();
 
 	// convert from row major to column major
-	double a[m*n]; int k = 0;
+	double a[m*n]; size_t k = 0;
-	for(int j=0; j<n; j++)
+	for(size_t j=0; j<n; j++)
-		for(int i=0; i<m; i++, k++)
+		for(size_t i=0; i<m; i++, k++)
 			a[k] = A(i,j);
 
 	double tau[n];
@@ -696,13 +693,13 @@ void householder(Matrix &A) {
 	lwork = (__CLPK_integer)work_optimal_size;
 	double work[lwork];
 	dgeqrf_(&m, &n, a, &m, tau, work, &lwork, &info);
-	int k0 = 0;
+	size_t k0 = 0;
-	int j0;
+	size_t j0;
 	memset(A.data().begin(), 0, m*n*sizeof(double));
-	for(int j=0; j<n; j++, k0+=m) {
+	for(size_t j=0; j<n; j++, k0+=m) {
 		k = k0;
 		j0 = j+1<m?j+1:m;
-		for(int i=0; i<j0; i++, k++)
+		for(size_t i=0; i<j0; i++, k++)
 			A(i,j) = a[k];
 	}
 }
@@ -952,13 +949,13 @@ Matrix RtR(const Matrix &A)
 /* ************************************************************************* */
 Vector solve_ldl(const Matrix& M, const Vector& rhs) {
 
-	unsigned int N = M.size1(); // size of the matrix
+	int N = M.size1(); // size of the matrix
 
 	// count the nonzero entries above diagonal
 	double thresh = 1e-9;
-	unsigned int nrANZ = 0; // # of nonzeros on diagonal and upper triangular part of A
+	int nrANZ = 0; // # of nonzeros on diagonal and upper triangular part of A
-	for (size_t i=0; i<N; ++i) // rows
+	for (int i=0; i<N; ++i) // rows
-			for (size_t j=i; j<N; ++j) // columns
+			for (int j=i; j<N; ++j) // columns
 				if (fabs(M(i,j)) > thresh)
 					++nrANZ;
 
@@ -972,10 +969,10 @@ Vector solve_ldl(const Matrix& M, const Vector& rhs) {
 	Ap[N] = nrANZ;
 
 	// copy in the full A matrix to compressed column form
-	size_t t = 0; // count the elements added
+	int t = 0; // count the elements added
-	for (size_t j=0; j<N; ++j) { // columns
+	for (int j=0; j<N; ++j) { // columns
 		Ap[j] = t;   // add to the column indices
-		for (size_t i=0; i<=j; ++i) { // rows
+		for (int i=0; i<=j; ++i) { // rows
 			const double& m = M(i,j);
 			if (fabs(m) > thresh) {
 				Ai[t] = i;
@@ -985,7 +982,7 @@ Vector solve_ldl(const Matrix& M, const Vector& rhs) {
 	}
 
 	// copy in RHS
-	for (size_t i = 0; i < N; ++i)
+	for (int i = 0; i < N; ++i)
 		b[i] = rhs(i);
 
 	// workspace variables
@@ -1000,13 +997,13 @@ Vector solve_ldl(const Matrix& M, const Vector& rhs) {
     // factorize A into LDL' (P and Pinv not used)
     LDL_symbolic (N, Ap, Ai, Lp, Parent, Lnz, Flag, NULL, NULL);
 
-    size_t nrLNZ = Lp[N]; // # of nonzeros below the diagonal of L
+    int nrLNZ = Lp[N]; // # of nonzeros below the diagonal of L
 
     // after getting size of L, initialize storage arrays
 	double * Lx = new double[nrLNZ];
 	int * Li = new int [nrLNZ];
 
-    size_t d = LDL_numeric (N, Ap, Ai, Ax, Lp, Parent, Lnz, Li, Lx, D, Y, Pattern,
+    int d = LDL_numeric (N, Ap, Ai, Ax, Lp, Parent, Lnz, Li, Lx, D, Y, Pattern,
     		Flag, NULL, NULL);
 
     if (d == N) {
@@ -1138,9 +1135,9 @@ Matrix square_root_positive(const Matrix& A) {
 }
 
 /* ************************************************************************* */
-Matrix expm(const Matrix& A, int K) {
+Matrix expm(const Matrix& A, size_t K) {
 	Matrix E = eye(A.size1()), A_k = eye(4);
-	for (int k=1;k<=K;k++) {
+	for(size_t k=1;k<=K;k++) {
 		A_k = A_k*A/k;
 		E = E + A_k;
 	}

base/Matrix.h

@@ -226,7 +226,7 @@ std::pair<Matrix,Matrix> qr(const Matrix& A);
 /**
  * Imperative version of Householder rank 1 update
  */
-void householder_update(Matrix &A, int j, double beta, const Vector& vjm);
+void householder_update(Matrix &A, size_t j, double beta, const Vector& vjm);
 
 /**
  * Imperative algorithm for in-place full elimination with
@@ -383,7 +383,7 @@ Vector solve_ldl(const Matrix& A, const Vector& b);
  * @param A matrix to exponentiate
  * @param K number of iterations
  */
-Matrix expm(const Matrix& A, int K=7);
+Matrix expm(const Matrix& A, size_t K=7);
 
 // macro for unit tests
 #define EQUALITY(expected,actual)\

base/testBTree.cpp

@@ -12,31 +12,30 @@
 using namespace boost::assign;
 
 #include <CppUnitLite/TestHarness.h>
-#include "Key.h"
 #include "BTree.h"
 
 using namespace std;
 using namespace gtsam;
 
 typedef pair<size_t, size_t> Range;
-typedef BTree<Symbol, Range> RangeTree;
+typedef BTree<string, Range> RangeTree;
-typedef BTree<Symbol, int> IntTree;
+typedef BTree<string, int> IntTree;
 
 static std::stringstream ss;
-static Symbol x1('x', 1), x2('x', 2), x3('x', 3), x4('x', 4), x5('x', 5);
+static string x1("x1"), x2("x2"), x3("x3"), x4("x4"), x5("x5");
-typedef pair<Symbol, int> KeyInt;
+typedef pair<string, int> KeyInt;
 KeyInt p1(x1, 1), p2(x2, 2), p3(x3, 3), p4(x4, 4), p5(x5, 5);
 
 /* ************************************************************************* */
-int f(const Symbol& key, const Range& range) {
+int f(const string& key, const Range& range) {
 	return range.first;
 }
 
-void g(const Symbol& key, int i) {
+void g(const string& key, int i) {
 	ss << (string) key;
 }
 
-int add(const Symbol& k, int v, int a) {
+int add(const string& k, int v, int a) {
 	return v + a;
 }
 
@@ -122,7 +121,7 @@ TEST( BTree, iterating )
 	LONGS_EQUAL(25,tree.fold<int>(add,10))
 
 	// test iterator
-	BTree<Symbol, int>::const_iterator it = tree.begin(), it2 = tree.begin();
+	BTree<string, int>::const_iterator it = tree.begin(), it2 = tree.begin();
 	CHECK(it==it2)
 	CHECK(*it == p1)
 	CHECK(it->first == x1)
@@ -168,7 +167,7 @@ TEST( BTree, stress )
 	list<RangeTree::value_type> expected;
 	int N = 128;
 	for (int i = 1; i <= N; i++) {
-		Symbol key('a', i);
+		string key('a', i);
 		Range value(i - 1, i);
 		tree = tree.add(key, value);
 		LONGS_EQUAL(i,tree.size())
@@ -186,7 +185,7 @@ TEST( BTree, stress )
 
 	// deconstruct the tree
 	for (int i = N; i >= N; i--) {
-		Symbol key('a', i);
+		string key('a', i);
 		tree = tree.remove(key);
 		LONGS_EQUAL(i-1,tree.size())
 		CHECK(!tree.mem(key))

base/testDSF.cpp

@@ -13,7 +13,6 @@ using namespace boost::assign;
 #include <CppUnitLite/TestHarness.h>
 
 #include "DSF.h"
-#include "Key.h"
 
 using namespace std;
 using namespace gtsam;
@@ -249,17 +248,16 @@ TEST(DSF, flatten) {
 
 /* ************************************************************************* */
 TEST(DSF, flatten2) {
-	Symbol x1('x',1);
+	static string x1("x1"), x2("x2"), x3("x3"), x4("x4");
-	Symbol x2('x',2), x3('x',3), x4('x',4);
+	list<string> keys; keys += x1,x2,x3,x4;
-	list<Symbol> keys; keys += x1,x2,x3,x4;
+	DSF<string> dsf(keys);
-	DSFSymbol dsf(keys);
 	dsf = dsf.makeUnion(x1,x2);
 	dsf = dsf.makeUnion(x3,x4);
 	dsf = dsf.makeUnion(x1,x3);
 
 	CHECK(dsf != dsf.flatten());
 
-	DSFSymbol expected2;
+	DSF<string> expected2;
 	expected2 = expected2.makePair(x1, x2);
 	expected2 = expected2.makePair(x1, x3);
 	expected2 = expected2.makePair(x1, x4);

base/testDSFVector.cpp

@@ -13,7 +13,6 @@ using namespace boost::assign;
 #include <CppUnitLite/TestHarness.h>
 
 #include "DSFVector.h"
-#include "Key.h"
 
 using namespace std;
 using namespace gtsam;

colamd/Makefile

@@ -1,38 +0,0 @@
-# Makefile to compile the unit test library, will end up in $(LIBDIR)
-
-.PHONY: all install clean
-
-all: libcolamd.a
-
-CC ?= gcc
-CFLAGS += -O2
-CFLAGS += -fPIC
-
-
-sources = $(shell ls *.c)
-
-library = libcolamd.a
-
-#Note: hack was added to ensure that flags are acutally used for compilation 
-# This should probably be fixed, but will work for 64 bit machines now
-
-$(library): colamd.o colamd_global.o ccolamd.o ccolamd_global.o
-	$(CC) $(CFLAGS) -c -DDLONG -o colamd_l.o colamd.c
-	ar crsv $@ $^ colamd_l.o
-	ranlib $(library)
-
-clean:
-	rm -f *.o *.*~ $(library)
-
-check:
-	echo 'no check for colamd'
-
-distdir:
-
-# Richard: added the following dependencies so that recursive make works:
-
-install: all
-
-distclean: clean
-
-check: all

colamd/Makefile.am

@@ -0,0 +1,15 @@
+#----------------------------------------------------------------------------------------------------
+# colamd
+# replaced Makefile with automake for easy linking
+#----------------------------------------------------------------------------------------------------
+
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+noinst_LTLIBRARIES = libcolamd.la
+
+# We normally would not install these headers
+# but they are included in the templated class FactorGraph-inl.h so we need them
+pkginclude_HEADERS = colamd.h ccolamd.h UFconfig.h 
+
+# These are the sources for the library:
+libcolamd_la_SOURCES = colamd.c colamd_global.c ccolamd.c ccolamd_global.c

colamd/Makefile.in

@@ -0,0 +1,541 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+#----------------------------------------------------------------------------------------------------
+# colamd
+# replaced Makefile with automake for easy linking
+#----------------------------------------------------------------------------------------------------
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
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+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = colamd
+DIST_COMMON = $(pkginclude_HEADERS) $(srcdir)/Makefile.am \
+	$(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
+	$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
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+	$(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+LTLIBRARIES = $(noinst_LTLIBRARIES)
+libcolamd_la_LIBADD =
+am_libcolamd_la_OBJECTS = colamd.lo colamd_global.lo ccolamd.lo \
+	ccolamd_global.lo
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+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+	--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
+	$(LDFLAGS) -o $@
+SOURCES = $(libcolamd_la_SOURCES)
+DIST_SOURCES = $(libcolamd_la_SOURCES)
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
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+    *) f=$$p;; \
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+am__install_max = 40
+am__nobase_strip_setup = \
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+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
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+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
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+host_vendor = @host_vendor@
+htmldir = @htmldir@
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+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
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+lt_ECHO = @lt_ECHO@
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+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
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+program_transform_name = @program_transform_name@
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+srcdir = @srcdir@
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+target_alias = @target_alias@
+toolbox = @toolbox@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+noinst_LTLIBRARIES = libcolamd.la
+
+# We normally would not install these headers
+# but they are included in the templated class FactorGraph-inl.h so we need them
+pkginclude_HEADERS = colamd.h ccolamd.h UFconfig.h 
+
+# These are the sources for the library:
+libcolamd_la_SOURCES = colamd.c colamd_global.c ccolamd.c ccolamd_global.c
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .c .lo .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu colamd/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu colamd/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+
+clean-noinstLTLIBRARIES:
+	-test -z "$(noinst_LTLIBRARIES)" || rm -f $(noinst_LTLIBRARIES)
+	@list='$(noinst_LTLIBRARIES)'; for p in $$list; do \
+	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
+	  test "$$dir" != "$$p" || dir=.; \
+	  echo "rm -f \"$${dir}/so_locations\""; \
+	  rm -f "$${dir}/so_locations"; \
+	done
+libcolamd.la: $(libcolamd_la_OBJECTS) $(libcolamd_la_DEPENDENCIES) 
+	$(LINK)  $(libcolamd_la_OBJECTS) $(libcolamd_la_LIBADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ccolamd.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ccolamd_global.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/colamd.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/colamd_global.Plo@am__quote@
+
+.c.o:
+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+@am__fastdepCC_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(COMPILE) -c $<
+
+.c.obj:
+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+@am__fastdepCC_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(COMPILE) -c `$(CYGPATH_W) '$<'`
+
+.c.lo:
+@am__fastdepCC_TRUE@	$(LTCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+@am__fastdepCC_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(LTCOMPILE) -c -o $@ $<
+
+mostlyclean-libtool:
+	-rm -f *.lo
+
+clean-libtool:
+	-rm -rf .libs _libs
+install-pkgincludeHEADERS: $(pkginclude_HEADERS)
+	@$(NORMAL_INSTALL)
+	test -z "$(pkgincludedir)" || $(MKDIR_P) "$(DESTDIR)$(pkgincludedir)"
+	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(pkgincludedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(pkgincludedir)" || exit $$?; \
+	done
+
+uninstall-pkgincludeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(pkgincludedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(pkgincludedir)" && rm -f $$files
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
+	  dist_files=`for file in $$list; do echo $$file; done | \
+	  sed -e "s|^$$srcdirstrip/||;t" \
+	      -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+	case $$dist_files in \
+	  */*) $(MKDIR_P) `echo "$$dist_files" | \
+			   sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+			   sort -u` ;; \
+	esac; \
+	for file in $$dist_files; do \
+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+	  if test -d $$d/$$file; then \
+	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(LTLIBRARIES) $(HEADERS)
+installdirs:
+	for dir in "$(DESTDIR)$(pkgincludedir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic clean-libtool clean-noinstLTLIBRARIES \
+	mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-pkgincludeHEADERS
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+	mostlyclean-libtool
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-pkgincludeHEADERS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
+	clean-libtool clean-noinstLTLIBRARIES ctags distclean \
+	distclean-compile distclean-generic distclean-libtool \
+	distclean-tags distdir dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am install-html \
+	install-html-am install-info install-info-am install-man \
+	install-pdf install-pdf-am install-pkgincludeHEADERS \
+	install-ps install-ps-am install-strip installcheck \
+	installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+	tags uninstall uninstall-am uninstall-pkgincludeHEADERS
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

config.h.in

@@ -0,0 +1,89 @@
+/* config.h.in.  Generated from configure.ac by autoheader.  */
+
+/* boost serialization flag */
+#undef HAVE_BOOST_SERIALIZATION
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#undef HAVE_DLFCN_H
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the `pow' function. */
+#undef HAVE_POW
+
+/* Define to 1 if you have the `sqrt' function. */
+#undef HAVE_SQRT
+
+/* Define to 1 if stdbool.h conforms to C99. */
+#undef HAVE_STDBOOL_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to 1 if the system has the type `_Bool'. */
+#undef HAVE__BOOL
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+   */
+#undef LT_OBJDIR
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Version number of package */
+#undef VERSION
+
+/* Define to empty if `const' does not conform to ANSI C. */
+#undef const
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+   calls it, or to nothing if 'inline' is not supported under any name.  */
+#ifndef __cplusplus
+#undef inline
+#endif
+
+/* Define to `unsigned int' if <sys/types.h> does not define. */
+#undef size_t

configure.ac

@@ -4,12 +4,19 @@
 AC_PREREQ(2.59)
 AC_INIT(gtsam, 0.0.0, dellaert@cc.gatech.edu)
 AM_INIT_AUTOMAKE(gtsam, 0.0.0)
-AC_OUTPUT(Makefile spqr_mini/Makefile cpp/Makefile wrap/Makefile)
+AC_OUTPUT(Makefile CppUnitLite/Makefile colamd/Makefile ldl/Makefile spqr_mini/Makefile base/Makefile geometry/Makefile cpp/Makefile slam/Makefile tests/Makefile wrap/Makefile)
 AC_CONFIG_MACRO_DIR([m4])
-AC_CONFIG_SRCDIR([cpp/cal3_S2.cpp])
+AC_CONFIG_HEADER([config.h])
-AC_CONFIG_HEADER([cpp/config.h])
+AC_CONFIG_SRCDIR([CppUnitLite/Test.cpp])
-AC_CONFIG_SRCDIR([wrap/wrap.cpp])
+AC_CONFIG_SRCDIR([colamd/colamd.c])
+AC_CONFIG_SRCDIR([ldl/ldl.cpp])
 AC_CONFIG_SRCDIR([spqr_mini/spqr_front.cpp])
+AC_CONFIG_SRCDIR([base/DSFVector.cpp])
+AC_CONFIG_SRCDIR([geometry/Cal3_S2.cpp])
+AC_CONFIG_SRCDIR([cpp/GaussianFactor.cpp])
+AC_CONFIG_SRCDIR([slam/pose2SLAM.cpp])
+AC_CONFIG_SRCDIR([tests/testSQP.cpp])
+AC_CONFIG_SRCDIR([wrap/wrap.cpp])
 
 # Check for OS
 AC_CANONICAL_HOST    # needs to be called at some point earlier
@@ -52,6 +59,7 @@ AC_ARG_ENABLE([blas],
        *) AC_MSG_ERROR([bad value ${enableval} for --enable-blas]) ;;
      esac],[blas=false])
 
+AM_CONDITIONAL([USE_BLAS], test x$blas = xtrue)
 AM_CONDITIONAL([USE_BLAS_MACOS], [test x$blas = xtrue && test x$ISMAC = xtrue])
 AM_CONDITIONAL([USE_BLAS_LINUX], [test x$blas = xtrue && test x$ISMAC = xfalse])
 
@@ -64,12 +72,14 @@ AC_ARG_ENABLE([lapack],
        *) AC_MSG_ERROR([bad value ${enableval} for --enable-lapack]) ;;
      esac],[lapack=false])
 
+AM_CONDITIONAL([USE_LAPACK], test x$lapack = xtrue)
 AM_CONDITIONAL([USE_LAPACK_MACOS], [test x$lapack = xtrue && test x$ISMAC = xtrue])
 AM_CONDITIONAL([USE_LAPACK_LINUX], [test x$lapack = xtrue && test x$ISMAC = xfalse])
-AM_CONDITIONAL([USE_LAPACK], test x$lapack = xtrue)
-AM_CONDITIONAL([USE_VECLIB_MACOS], [(test x$lapack = xtrue || test x$blas = xtrue) && test x$ISMAC = xtrue])
 
-#enabgle SparseQR for linear solving
+# On Mac, we use the Accelerate framework for BLAS/LAPACK
+AM_CONDITIONAL([USE_ACCELERATE_MACOS], [(test x$lapack = xtrue || test x$blas = xtrue) && test x$ISMAC = xtrue])
+
+#enable SparseQR for linear solving
 AC_ARG_ENABLE([spqr],
      [  --enable-spqr    Enable SparseQR library support],
      [case "${enableval}" in

cpp/FactorGraph-inl.h

@@ -16,21 +16,17 @@
 #include <stdexcept>
 #include <functional>
 
-extern "C" {
-#include <colamd/colamd.h>
-#include <colamd/ccolamd.h>
-}
-
 #include <boost/foreach.hpp>
 #include <boost/tuple/tuple.hpp>
 #include <boost/format.hpp>
 #include <boost/graph/prim_minimum_spanning_tree.hpp>
-#include <colamd/colamd.h>
+#include "ccolamd.h"
 #include "Ordering.h"
 #include "FactorGraph.h"
 #include "graph-inl.h"
 #include "DSF.h"
 
+
 #define INSTANTIATE_FACTOR_GRAPH(F) \
   template class FactorGraph<F>; \
   /*template boost::shared_ptr<F> removeAndCombineFactors(FactorGraph<F>&, const std::string&);*/ \
@@ -189,7 +185,6 @@ void colamd(int n_col, int n_row, int nrNonZeros, const map<Key, vector<int> >&
 		Ordering& ordering, const set<Symbol>& lastKeys) {
 
 	// Convert to compressed column major format colamd wants it in (== MATLAB format!)
-	vector<Key> initialOrder;
 	int Alen = ccolamd_recommended(nrNonZeros, n_row, n_col);     /* colamd arg 3: size of the array A */
 	int * A = new int[Alen];      /* colamd arg 4: row indices of A, of size Alen */
 	int * p = new int[n_col + 1]; /* colamd arg 5: column pointers of A, of size n_col+1 */
@@ -200,6 +195,7 @@ void colamd(int n_col, int n_row, int nrNonZeros, const map<Key, vector<int> >&
 	int count = 0;
 	typedef typename map<Key, vector<int> >::const_iterator iterator;
 	bool front_exists = false;
+	vector<Key> initialOrder;
 	for(iterator it = columns.begin(); it != columns.end(); it++) {
 		const Key& key = it->first;
 		const vector<int>& column = it->second;
@@ -220,7 +216,7 @@ void colamd(int n_col, int n_row, int nrNonZeros, const map<Key, vector<int> >&
 	}
 
 	double* knobs = NULL;    /* colamd arg 6: parameters (uses defaults if NULL) */
-	int stats[COLAMD_STATS]; /* colamd arg 7: colamd output statistics and error codes */
+	int stats[CCOLAMD_STATS]; /* colamd arg 7: colamd output statistics and error codes */
 
 	// call colamd, result will be in p *************************************************
 	/* TODO: returns (1) if successful, (0) otherwise*/

cpp/ISAM2-inl.h

@@ -279,6 +279,7 @@ namespace gtsam {
 
 	}
 
+	/*
 	template<class Conditional, class Config>
 	void ISAM2<Conditional, Config>::linear_update(const FactorGraph<GaussianFactor>& newFactors) {
 
@@ -329,8 +330,8 @@ namespace gtsam {
 		}
 
 		// Output: BayesTree(this)
-
 	}
+	*/
 
 	template<class Conditional, class Config>
 	void ISAM2<Conditional, Config>::fluid_relinearization(double relinearize_threshold) {

cpp/Makefile.am

@@ -1,69 +1,24 @@
+#----------------------------------------------------------------------------------------------------
+# GTSAM core functionality: discrete, linear, and non-linear
+#----------------------------------------------------------------------------------------------------
 
-# the install destination
+headers =
-includedir = ${prefix}/include/gtsam
+sources = 
-libdir = ${exec_prefix}/lib
+check_PROGRAMS = 
 
-# library version
+#----------------------------------------------------------------------------------------------------
-current = 0  # The most recent interface number that this library implements. 
+# base
-revision = 0 # The implementation number of the current interface 
+#----------------------------------------------------------------------------------------------------
-age = 0 # The difference between the newest and oldest interfaces that	\
-this library implements. In other words, the library implements all	\
-the interface numbers in the range from number current - age to		\
-current.
 
-# from libtool manual:
+# GTSAM core
-# Here are a set of rules to help you update your library version information:
+headers += Factor.h Conditional.h Ordering.h IndexTable.h 
-#   Start with version information of ‘0:0:0’ for each libtool library.
+sources += Ordering.cpp 
-#   - Update the version information only immediately before a public
+check_PROGRAMS += testOrdering 
-#   release of your software.
-#   - If the library source code has changed at all since the last
-#   update, then increment revision
-#   - If any interfaces have been added, removed, or changed since the
-#   last update, increment current, and set revision to 0.
-#   - If any interfaces have been added since the last public release,
-#   then increment age.
-#   - If any interfaces have been removed since the last public release,
-#   then set age to 0.
-version = $(current):$(revision):$(age)
-
-# we specify the library in levels
-
-# basic Math
-sources = Vector.cpp svdcmp.cpp Matrix.cpp SPQRUtil.cpp
-check_PROGRAMS = testVector testMatrix testSPQRUtil
-testVector_SOURCES = testVector.cpp
-testVector_LDADD   = libgtsam.la
-testMatrix_SOURCES = testMatrix.cpp
-testMatrix_LDADD   = libgtsam.la
-testSPQRUtil_SOURCES = testSPQRUtil.cpp
-testSPQRUtil_LDADD   = libgtsam.la
-
-# GTSAM basics
-# The header files will be installed in ~/include/gtsam
-headers = gtsam.h Value.h Testable.h Factor.h Conditional.h 
-headers += Ordering.h IndexTable.h numericalDerivative.h
-headers += BTree.h DSF.h DSFVector.h
-sources += Ordering.cpp smallExample.cpp DSFVector.cpp
-check_PROGRAMS += testOrdering testBTree testDSF testDSFVector
-testOrdering_SOURCES = testOrdering.cpp
-testOrdering_LDADD   = libgtsam.la
-testBTree_SOURCES    = testBTree.cpp
-testBTree_LDADD		   = libgtsam.la
-testDSF_SOURCES    = testDSF.cpp
-testDSF_LDADD      = libgtsam.la
-testDSFVector_SOURCES    = testDSFVector.cpp
-testDSFVector_LDADD      = libgtsam.la
 
 # Symbolic Inference
 headers += SymbolicConditional.h
 sources += SymbolicFactor.cpp SymbolicFactorGraph.cpp SymbolicBayesNet.cpp
 check_PROGRAMS += testSymbolicFactor testSymbolicFactorGraph testSymbolicBayesNet  
-testSymbolicFactor_SOURCES      = testSymbolicFactor.cpp
-testSymbolicFactor_LDADD        = libgtsam.la
-testSymbolicFactorGraph_SOURCES = testSymbolicFactorGraph.cpp
-testSymbolicFactorGraph_LDADD   = libgtsam.la
-testSymbolicBayesNet_SOURCES    = testSymbolicBayesNet.cpp
-testSymbolicBayesNet_LDADD      = libgtsam.la
 
 # Inference
 headers += inference.h inference-inl.h
@@ -73,231 +28,91 @@ headers += JunctionTree.h JunctionTree-inl.h
 headers += BayesNet.h BayesNet-inl.h
 headers += BayesTree.h BayesTree-inl.h
 headers += ISAM.h ISAM-inl.h GaussianISAM.h
-headers += ISAM2.h ISAM2-inl.h GaussianISAM2.h
+headers += ISAM2.h ISAM2-inl.h
-sources += GaussianISAM.cpp GaussianISAM2.cpp
+sources += GaussianISAM.cpp
-check_PROGRAMS += testGraph testFactorGraph testJunctionTree testInference testOrdering
+check_PROGRAMS += testFactorGraph testJunctionTree testOrdering
-check_PROGRAMS += testBayesTree testISAM testGaussianISAM testGaussianISAM2
+check_PROGRAMS += testBayesTree testISAM
-testGraph_SOURCES              = testGraph.cpp
+
-testGraph_LDADD                = libgtsam.la
+#----------------------------------------------------------------------------------------------------
-testFactorGraph_SOURCES        = testFactorgraph.cpp
+# discrete
-testFactorGraph_LDADD          = libgtsam.la
+#----------------------------------------------------------------------------------------------------
-testJunctionTree_SOURCES       = testJunctionTree.cpp
-testJunctionTree_LDADD         = libgtsam.la
-testInference_SOURCES          = testInference.cpp
-testInference_LDADD            = libgtsam.la
-testBayesTree_SOURCES          = testBayesTree.cpp
-testBayesTree_LDADD            = libgtsam.la
-testGaussianISAM_SOURCES       = testGaussianISAM.cpp
-testGaussianISAM_LDADD         = libgtsam.la
-testGaussianISAM2_SOURCES      = testGaussianISAM2.cpp
-testGaussianISAM2_LDADD        = libgtsam.la
-testISAM_SOURCES               = testISAM.cpp
-testISAM_LDADD                 = libgtsam.la
 
 # Binary Inference
 headers += BinaryConditional.h
 check_PROGRAMS += testBinaryBayesNet
-testBinaryBayesNet_SOURCES    = testBinaryBayesNet.cpp
+
-testBinaryBayesNet_LDADD      = libgtsam.la 
+#----------------------------------------------------------------------------------------------------
+# linear
+#----------------------------------------------------------------------------------------------------
 
 # Gaussian inference 
 headers += GaussianFactorSet.h SharedGaussian.h SharedDiagonal.h VectorConfig.h Factorization.h
 sources += NoiseModel.cpp Errors.cpp VectorMap.cpp VectorBTree.cpp GaussianFactor.cpp 
 sources += GaussianFactorGraph.cpp GaussianConditional.cpp GaussianBayesNet.cpp
-check_PROGRAMS += testVectorMap testVectorBTree testGaussianFactor testGaussianFactorGraph 
+check_PROGRAMS += testVectorMap testVectorBTree testGaussianFactor 
-check_PROGRAMS += testGaussianConditional testGaussianBayesNet testNoiseModel testErrors
+check_PROGRAMS += testGaussianConditional testNoiseModel testErrors
-testVectorMap_SOURCES           = testVectorMap.cpp
-testVectorMap_LDADD             = libgtsam.la
-testVectorBTree_SOURCES         = testVectorBTree.cpp
-testVectorBTree_LDADD           = libgtsam.la
-testGaussianFactor_SOURCES      = testGaussianFactor.cpp
-testGaussianFactor_LDADD        = libgtsam.la
-testGaussianFactorGraph_SOURCES = testGaussianFactorGraph.cpp
-testGaussianFactorGraph_LDADD   = libgtsam.la
-testGaussianConditional_SOURCES = testGaussianConditional.cpp
-testGaussianConditional_LDADD   = libgtsam.la
-testGaussianBayesNet_SOURCES    = testGaussianBayesNet.cpp
-testGaussianBayesNet_LDADD      = libgtsam.la
-testNoiseModel_SOURCES          = testNoiseModel.cpp
-testNoiseModel_LDADD            = libgtsam.la
-testErrors_SOURCES              = testErrors.cpp
-testErrors_LDADD                = libgtsam.la
 
 # Iterative Methods
 headers += iterative-inl.h SubgraphSolver.h SubgraphSolver-inl.h
 sources += iterative.cpp BayesNetPreconditioner.cpp SubgraphPreconditioner.cpp
-check_PROGRAMS += testIterative testBayesNetPreconditioner testSubgraphPreconditioner
+check_PROGRAMS += testBayesNetPreconditioner
-testIterative_SOURCES              = testIterative.cpp
+
-testIterative_LDADD                = libgtsam.la
+# Timing tests
-testBayesNetPreconditioner_SOURCES = testBayesNetPreconditioner.cpp
+noinst_PROGRAMS = timeGaussianFactor timeSymbolMaps timeVectorConfig
-testBayesNetPreconditioner_LDADD   = libgtsam.la
+
-testSubgraphPreconditioner_SOURCES = testSubgraphPreconditioner.cpp
+#----------------------------------------------------------------------------------------------------
-testSubgraphPreconditioner_LDADD   = libgtsam.la
+# nonlinear
+#----------------------------------------------------------------------------------------------------
+
+# Lie Groups
+headers += LieConfig.h LieConfig-inl.h TupleConfig.h TupleConfig-inl.h
+check_PROGRAMS += testLieConfig 
 
 # Nonlinear inference 
 headers += Key.h SymbolMap.h NonlinearFactorGraph.h NonlinearFactorGraph-inl.h
 headers += NonlinearOptimizer.h NonlinearOptimizer-inl.h 
 headers += NonlinearFactor.h
-check_PROGRAMS += testNonlinearFactor testNonlinearFactorGraph testNonlinearOptimizer testKey
+check_PROGRAMS += testKey
-testNonlinearFactor_SOURCES      = testNonlinearFactor.cpp
-testNonlinearFactor_LDADD        = libgtsam.la
-testNonlinearFactorGraph_SOURCES = testNonlinearFactorGraph.cpp
-testNonlinearFactorGraph_LDADD   = libgtsam.la
-testNonlinearOptimizer_SOURCES   = testNonlinearOptimizer.cpp
-testNonlinearOptimizer_LDADD     = libgtsam.la
-testKey_SOURCES   				 = testKey.cpp
-testKey_LDADD     				 = libgtsam.la
 
 # Nonlinear constraints 
 headers += NonlinearConstraint.h NonlinearConstraint-inl.h
 headers += NonlinearEquality.h
-check_PROGRAMS += testNonlinearConstraint testNonlinearEquality 
+check_PROGRAMS += testNonlinearConstraint  
-testNonlinearConstraint_SOURCES = testNonlinearConstraint.cpp
-testNonlinearConstraint_LDADD   = libgtsam.la
-testNonlinearEquality_SOURCES   = testNonlinearEquality.cpp
-testNonlinearEquality_LDADD     = libgtsam.la
 
 # SQP
-headers += ConstraintOptimizer.h
 sources += ConstraintOptimizer.cpp
-check_PROGRAMS += testSQP testConstraintOptimizer
+check_PROGRAMS += testConstraintOptimizer
-testSQP_SOURCES                 = $(example) testSQP.cpp
-testSQP_LDADD                   = libgtsam.la
-testConstraintOptimizer_SOURCES = $(example) testConstraintOptimizer.cpp
-testConstraintOptimizer_LDADD   = libgtsam.la
-
-# geometry
-headers += Lie.h Lie-inl.h
-sources += Point2.cpp Rot2.cpp Pose2.cpp Point3.cpp Rot3.cpp Pose3.cpp Cal3_S2.cpp
-check_PROGRAMS += testPoint2 testRot2 testPose2 testPoint3 testRot3 testPose3 testCal3_S2 testLieConfig testTupleConfig
-testPoint2_SOURCES  = testPoint2.cpp
-testRot2_SOURCES    = testRot2.cpp
-testPose2_SOURCES   = testPose2.cpp
-testPoint3_SOURCES  = testPoint3.cpp
-testRot3_SOURCES    = testRot3.cpp
-testPose3_SOURCES   = testPose3.cpp
-testCal3_S2_SOURCES = testCal3_S2.cpp
-testLieConfig_SOURCES = testLieConfig.cpp               
-testTupleConfig_SOURCES = testTupleConfig.cpp               
-
-testPoint2_LDADD    = libgtsam.la
-testRot2_LDADD      = libgtsam.la
-testPose2_LDADD     = libgtsam.la
-testPoint3_LDADD    = libgtsam.la
-testRot3_LDADD      = libgtsam.la
-testPose3_LDADD     = libgtsam.la
-testCal3_S2_LDADD   = libgtsam.la
-testLieConfig_LDADD = libgtsam.la
-testTupleConfig_LDADD = libgtsam.la
-
-# simulated2D example
-headers += simulated2D.h simulated2DOriented.h
-headers += Simulated2DConfig.h Simulated2DOrientedConfig.h
-headers += Simulated2DPosePrior.h Simulated2DPointPrior.h Simulated2DOrientedPosePrior.h
-headers += Simulated2DOdometry.h Simulated2DMeasurement.h Simulated2DOrientedOdometry.h
-sources += simulated2D.cpp simulated2DOriented.cpp 
-testSimulated2D_SOURCES = testSimulated2D.cpp
-testSimulated2D_LDADD = libgtsam.la
-testSimulated2DOriented_SOURCES = testSimulated2DOriented.cpp
-testSimulated2DOriented_LDADD = libgtsam.la
-check_PROGRAMS += testSimulated2D testSimulated2DOriented
-
-# simulated3D example
-sources += Simulated3D.cpp 
-testSimulated3D_SOURCES = testSimulated3D.cpp
-testSimulated3D_LDADD = libgtsam.la
-check_PROGRAMS += testSimulated3D 
-
-# Pose SLAM headers
-headers += BetweenFactor.h PriorFactor.h 
-headers += LieConfig.h LieConfig-inl.h TupleConfig.h TupleConfig-inl.h
-
-# 2D Pose SLAM
-headers +=  
-sources += pose2SLAM.cpp Pose2SLAMOptimizer.cpp dataset.cpp
-check_PROGRAMS += testPose2Factor testPose2Config testPose2SLAM testPose2Prior
-testPose2Prior_SOURCES  = testPose2Prior.cpp
-testPose2Prior_LDADD    = libgtsam.la
-testPose2Factor_SOURCES = testPose2Factor.cpp
-testPose2Factor_LDADD   = libgtsam.la
-testPose2Config_SOURCES = testPose2Config.cpp
-testPose2Config_LDADD   = libgtsam.la
-testPose2SLAM_SOURCES  = testPose2SLAM.cpp
-testPose2SLAM_LDADD    = libgtsam.la
-
-# 2D SLAM using Bearing and Range
-headers += BearingFactor.h RangeFactor.h BearingRangeFactor.h
-sources += planarSLAM.cpp
-check_PROGRAMS += testPlanarSLAM
-testPlanarSLAM_SOURCES = testPlanarSLAM.cpp
-testPlanarSLAM_LDADD   = libgtsam.la
-
-# 3D Pose constraints
-headers +=   
-sources += pose3SLAM.cpp 
-check_PROGRAMS += testPose3Factor testPose3Config testPose3SLAM 
-testPose3Factor_SOURCES = testPose3Factor.cpp
-testPose3Factor_LDADD   = libgtsam.la
-testPose3Config_SOURCES = testPose3Config.cpp
-testPose3Config_LDADD   = libgtsam.la
-testPose3SLAM_SOURCES  = testPose3SLAM.cpp
-testPose3SLAM_LDADD    = libgtsam.la
-
-# Cameras
-sources += CalibratedCamera.cpp SimpleCamera.cpp
-check_PROGRAMS += testCalibratedCamera testSimpleCamera
-testCalibratedCamera_SOURCES = testCalibratedCamera.cpp
-testCalibratedCamera_LDADD = libgtsam.la
-testSimpleCamera_SOURCES = testSimpleCamera.cpp
-testSimpleCamera_LDADD = libgtsam.la
-
-# Tensors
-headers += tensors.h Tensor1.h Tensor2.h Tensor3.h Tensor4.h Tensor5.h
-headers += Tensor1Expression.h Tensor2Expression.h Tensor3Expression.h Tensor5Expression.h
-headers += projectiveGeometry.h tensorInterface.h 
-sources += projectiveGeometry.cpp tensorInterface.cpp
-check_PROGRAMS += testTensors testHomography2 testTrifocal
-testHomography2_SOURCES = testHomography2.cpp
-testHomography2_LDADD = libgtsam.la
-testTensors_SOURCES = testTensors.cpp
-testTensors_LDADD = libgtsam.la
-testTrifocal_SOURCES = testTrifocal.cpp
-testTrifocal_LDADD = libgtsam.la
-
-# Visual SLAM
-sources += visualSLAM.cpp
-check_PROGRAMS += testVSLAMFactor testVSLAMGraph testVSLAMConfig
-testVSLAMFactor_SOURCES = testVSLAMFactor.cpp
-testVSLAMFactor_LDADD = libgtsam.la
-testVSLAMGraph_SOURCES = testVSLAMGraph.cpp
-testVSLAMGraph_LDADD = libgtsam.la
-testVSLAMConfig_SOURCES = testVSLAMConfig.cpp
-testVSLAMConfig_LDADD = libgtsam.la
 
+#----------------------------------------------------------------------------------------------------
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+# The headers are installed in $(includedir)/gtsam: 
+#----------------------------------------------------------------------------------------------------
 headers += $(sources:.cpp=.h)
+pkginclude_HEADERS = $(headers)
+noinst_HEADERS = gtsam.h
+noinst_LTLIBRARIES = libcpp.la
+libcpp_la_SOURCES = $(sources)
+AM_CPPFLAGS = -I$(boost) -I../colamd -I../base 
 
-# Timing tests
+#----------------------------------------------------------------------------------------------------
-noinst_PROGRAMS = timeGaussianFactor timeGaussianFactorGraph timeRot3 timeMatrix timeSymbolMaps timeVectorConfig
+# rules to build local programs
-timeRot3_SOURCES = timeRot3.cpp
+#----------------------------------------------------------------------------------------------------
-timeRot3_LDADD   = libgtsam.la
+TESTS = $(check_PROGRAMS)
-timeGaussianFactor_SOURCES = timeGaussianFactor.cpp
+AM_LDFLAGS = $(BOOST_LDFLAGS) $(boost_serialization) 
-timeGaussianFactor_LDADD   = libgtsam.la 
+LDADD = libcpp.la ../base/libbase.la 
-timeGaussianFactorGraph_SOURCES = timeGaussianFactorGraph.cpp
+LDADD += ../CppUnitLite/libCppUnitLite.a ../colamd/libcolamd.la ../ldl/libldl.la 
-timeGaussianFactorGraph_LDADD   = libgtsam.la
+AM_DEFAULT_SOURCE_EXT = .cpp
-timeMatrix_SOURCES 			 = timeMatrix.cpp 
-timeMatrix_LDADD 			   = libgtsam.la
-timeSymbolMaps_SOURCES   = timeSymbolMaps.cpp
-timeSymbolMaps_LDADD     = libgtsam.la
-timeVectorConfig_SOURCES = timeVectorConfig.cpp 
-timeVectorConfig_LDADD 	 = libgtsam.la
 
-# create both dynamic and static libraries
+# rule to run an executable
-AM_CXXFLAGS = -I$(boost) -fPIC
+%.run: % $(LDADD)
-AM_LDFLAGS =
+	./$^
-lib_LTLIBRARIES = libgtsam.la
+
-libgtsam_la_SOURCES = $(sources)
+#----------------------------------------------------------------------------------------------------
-libgtsam_la_CPPFLAGS = $(AM_CXXFLAGS)
+# OLD, need to figure where these go!
-libgtsam_la_LDFLAGS = -version-info $(version) -L../colamd -lcolamd -L../ldl -lldl  
+#----------------------------------------------------------------------------------------------------
+
+AM_CXXFLAGS = 
 
 # enable debug if --enable-debug is set in configure
 if DEBUG
@@ -306,56 +121,11 @@ endif
 
 if USE_PROFILING
 AM_CXXFLAGS += -pg
-libgtsam_la_CPPFLAGS += -pg
 AM_LDFLAGS += -pg
-libgtsam_la_LDFLAGS += -pg
-endif
-
-# install the header files
-include_HEADERS = $(headers)
-
-AM_CXXFLAGS += -I.. 
-AM_LDFLAGS += -L../CppUnitLite -lCppUnitLite $(BOOST_LDFLAGS) $(boost_serialization) 
-
-# adding cblas implementation - split into a default linux version using the 
-# autotools script, and a mac version that is hardcoded 
-# NOTE: the GT_USE_CBLAS is just used as a means of detecting when blas is available
-if USE_BLAS_LINUX
-AM_CXXFLAGS += -DGT_USE_CBLAS
-libgtsam_la_CPPFLAGS += -DGT_USE_CBLAS
-AM_LDFLAGS += -lcblas -latlas           # If getting from script: $(BLAS_LIBS) $(LIBS) $(FLIBS)  
-libgtsam_la_LDFLAGS += -lcblas -latlas  # $(BLAS_LIBS) $(LIBS) $(FLIBS) 
-endif
-
-if USE_BLAS_MACOS
-AM_CXXFLAGS += -DGT_USE_CBLAS
-endif
-
-if USE_LAPACK_LINUX
-AM_CXXFLAGS += -I/usr/include
-AM_LDFLAGS += -llapack
-libgtsam_la_LDFLAGS += -llapack
 endif
 
 if USE_LAPACK
-AM_LDFLAGS += -L../spqr_mini -lspqr_mini
-libgtsam_la_LDFLAGS += -L../spqr_mini -lspqr_mini
 AM_CXXFLAGS += -DGT_USE_LAPACK
+LDADD += ../spqr_mini/libspqr_mini.la
 endif
 
-if USE_VECLIB_MACOS
-AM_CXXFLAGS += -DYA_BLAS -DYA_LAPACK -DYA_BLASMULT -I/System/Library/Frameworks/vecLib.framework/Headers 
-libgtsam_la_CPPFLAGS += -DGT_USE_CBLAS -DYA_BLAS -DYA_LAPACK -DYA_BLASMULT -I/System/Library/Frameworks/vecLib.framework/Headers 
-AM_LDFLAGS += -lcblas -latlas 
-libgtsam_la_LDFLAGS += -framework vecLib -lcblas -latlas
-endif
-
-TESTS = $(check_PROGRAMS)
-CXXLINK = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link \
-	$(CXXLD) -g $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-	-o $@ # CXXLINK is only used for unit tests
-
-# rule to run an executable
-%.run: % libgtsam.la
-	./$^
-

cpp/SymbolicFactorGraph.cpp

@@ -9,7 +9,6 @@
 #include <fstream>
 #include <boost/format.hpp>
 #include <boost/foreach.hpp>
-#include "Point2.h"
 #include "Ordering.h"
 #include "SymbolicFactorGraph.h"
 #include "SymbolicBayesNet.h"
@@ -20,8 +19,6 @@ using namespace std;
 
 namespace gtsam {
 
-	INSTANTIATE_LIE_CONFIG(Symbol, Point2)
-
 	// Explicitly instantiate so we don't have to include everywhere
 	template class FactorGraph<SymbolicFactor>;
 
@@ -52,39 +49,5 @@ namespace gtsam {
 		return eliminate(ordering);
 	}
 
-	/* ************************************************************************* */
-	void saveGraph(const SymbolicFactorGraph& fg, const SymbolicConfig& config, const std::string& s) {
-
-		Symbol key;
-		Point2 pt;
-		float scale = 100;
-
-		string dotfile = s + ".dot";
-		ofstream of(dotfile.c_str());
-		of << "graph G{" << endl;
-		of << "bgcolor=\"transparent\";" << endl;
-
-		BOOST_FOREACH(boost::tie(key, pt), config){
-			of << (string)key << "[label=\"" << (string)key << "\"][pos=\"" << pt.x()*scale << "," << pt.y()*scale << "\"];" << endl;
-		}
-
-		int index = 0;
-		BOOST_FOREACH(const SymbolicFactorGraph::sharedFactor& factor, fg) {
-			index++;
-			Point2 center;
-			BOOST_FOREACH(const Symbol& key, factor->keys())
-				center = center + config[key];
-			center = Point2(center.x() / factor->keys().size(), center.y() / factor->keys().size());
-			of << "f" << index << "[pos=\"" << center.x()*scale << "," << center.y()*scale << "\"][shape=\"point\"];" << endl;
-			BOOST_FOREACH(const Symbol& key, factor->keys())
-				of << "f" << index << "--" << (string)key << endl;
-		}
-		of<<"}";
-		of.close();
-
-		string cmd = boost::str(boost::format("neato -s -n -Tpdf %s -o %s.pdf") % dotfile % s);
-		system(cmd.c_str());
-	}
-
 	/* ************************************************************************* */
 }

cpp/SymbolicFactorGraph.h

@@ -5,8 +5,7 @@
  *      Author: Frank Dellaert
  */
 
-#ifndef SYMBOLICFACTORGRAPH_H_
+#pragma once
-#define SYMBOLICFACTORGRAPH_H_
 
 #include <string>
 #include <list>
@@ -18,10 +17,6 @@
 
 namespace gtsam {
 
-	class Point2;
-
-	typedef LieConfig<Symbol, Point2> SymbolicConfig;
-
 	class SymbolicConditional;
 
 	/** Symbolic Factor Graph */
@@ -87,8 +82,4 @@ namespace gtsam {
 		SymbolicBayesNet eliminateFrontals(const Ordering& ordering);
 	};
 
-	// save graph to the graphviz format
+} // namespace gtsam
-	void saveGraph(const SymbolicFactorGraph& fg, const SymbolicConfig& config, const std::string& s);
-}
-
-#endif /* SYMBOLICFACTORGRAPH_H_ */

cpp/Value.h

@@ -1,44 +0,0 @@
-/**
- * @file    Value.h
- * @brief   Abstract base class for values that can be updated using exmap
- * @author  Frank Dellaert
- */
-
-// \callgraph
-
-#pragma once
-
-#include "Vector.h"
-#include "Testable.h"
-
-namespace gtsam {
-
-  /**
-   * The value class should be templated with the derived class, e.g.
-   * class Rot3 : public Value<Rot3>. This allows us to define the
-   * return type of exmap as a Rot3 as well.
-   */
-  template <class Derived> class Value : public Testable<Derived> {
-
-  private:
-
-    const size_t dim_; // dimensionality of tangent space, e.g. 3 for Rot3
-
-  public:
-
-    Value(size_t dim) : dim_ (dim) {}
-
-    /**
-     * dimensionality of tangent space, e.g. 3 for Rot3
-     */
-    size_t dim() { return dim_;} 
-
-    /**
-     * Exponential map: add a delta vector, addition for most simple
-     * types, but fully exponential map for types such as Rot3, which
-     * takes a 3-dim delta vector to update a 9-dim representation.
-     * equality up to tolerance
-     */
-    virtual Derived exmap(const Vector& delta) const = 0;
-  };
-}

cpp/graph-inl.h

@@ -6,6 +6,7 @@
 
 #pragma once
 
+#include <stdexcept>
 #include <boost/foreach.hpp>
 #include <boost/graph/breadth_first_search.hpp>
 

cpp/gtsam.sln

@@ -1,20 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 10.00
-# Visual Studio 2008
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "gtsam", "gtsam.vcproj", "{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}"
-EndProject
-Global
-	GlobalSection(SolutionConfigurationPlatforms) = preSolution
-		Debug|Win32 = Debug|Win32
-		Release|Win32 = Release|Win32
-	EndGlobalSection
-	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}.Debug|Win32.Build.0 = Debug|Win32
-		{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}.Release|Win32.ActiveCfg = Release|Win32
-		{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}.Release|Win32.Build.0 = Release|Win32
-	EndGlobalSection
-	GlobalSection(SolutionProperties) = preSolution
-		HideSolutionNode = FALSE
-	EndGlobalSection
-EndGlobal

cpp/gtsam.vcproj

@@ -1,362 +0,0 @@
-<?xml version="1.0" encoding="gb2312"?>
-<VisualStudioProject
-	ProjectType="Visual C++"
-	Version="9.00"
-	Name="gtsam"
-	ProjectGUID="{8AC1F57D-77D6-4B79-B50C-2508F076EBA3}"
-	RootNamespace="gtsam"
-	Keyword="Win32Proj"
-	TargetFrameworkVersion="196613"
-	>
-	<Platforms>
-		<Platform
-			Name="Win32"
-		/>
-	</Platforms>
-	<ToolFiles>
-	</ToolFiles>
-	<Configurations>
-		<Configuration
-			Name="Debug|Win32"
-			OutputDirectory="$(SolutionDir)$(ConfigurationName)"
-			IntermediateDirectory="$(ConfigurationName)"
-			ConfigurationType="4"
-			CharacterSet="2"
-			>
-			<Tool
-				Name="VCPreBuildEventTool"
-			/>
-			<Tool
-				Name="VCCustomBuildTool"
-			/>
-			<Tool
-				Name="VCXMLDataGeneratorTool"
-			/>
-			<Tool
-				Name="VCWebServiceProxyGeneratorTool"
-			/>
-			<Tool
-				Name="VCMIDLTool"
-			/>
-			<Tool
-				Name="VCCLCompilerTool"
-				Optimization="0"
-				AdditionalIncludeDirectories="&quot;$(BOOST_DIR)&quot;"
-				PreprocessorDefinitions="WIN32;_DEBUG;_LIB;_CRT_SECURE_NO_WARNINGS;_SCL_SECURE_NO_WARNINGS"
-				MinimalRebuild="true"
-				BasicRuntimeChecks="3"
-				RuntimeLibrary="3"
-				UsePrecompiledHeader="0"
-				WarningLevel="3"
-				DebugInformationFormat="3"
-			/>
-			<Tool
-				Name="VCManagedResourceCompilerTool"
-			/>
-			<Tool
-				Name="VCResourceCompilerTool"
-			/>
-			<Tool
-				Name="VCPreLinkEventTool"
-			/>
-			<Tool
-				Name="VCLibrarianTool"
-				OutputFile="$(ProjectDir)\$(ConfigurationName)\lib$(ProjectName).lib"
-			/>
-			<Tool
-				Name="VCALinkTool"
-			/>
-			<Tool
-				Name="VCXDCMakeTool"
-			/>
-			<Tool
-				Name="VCBscMakeTool"
-			/>
-			<Tool
-				Name="VCFxCopTool"
-			/>
-			<Tool
-				Name="VCPostBuildEventTool"
-				CommandLine="mkdir  $(ProjectDir)\..\..\..\libs\;&#x0D;&#x0A;copy $(ProjectDir)\$(ConfigurationName)\lib$(ProjectName).lib  $(ProjectDir)\..\..\..\libs\;&#x0D;&#x0A;mkdir  $(ProjectDir)\..\..\..\include\;&#x0D;&#x0A;mkdir  $(ProjectDir)\..\..\..\include\gtsam\;&#x0D;&#x0A;copy  $(ProjectDir)\*.h $(ProjectDir)\..\..\..\include\gtsam\;&#x0D;&#x0A;"
-			/>
-		</Configuration>
-		<Configuration
-			Name="Release|Win32"
-			OutputDirectory="$(SolutionDir)$(ConfigurationName)"
-			IntermediateDirectory="$(ConfigurationName)"
-			ConfigurationType="2"
-			CharacterSet="1"
-			WholeProgramOptimization="1"
-			>
-			<Tool
-				Name="VCPreBuildEventTool"
-			/>
-			<Tool
-				Name="VCCustomBuildTool"
-			/>
-			<Tool
-				Name="VCXMLDataGeneratorTool"
-			/>
-			<Tool
-				Name="VCWebServiceProxyGeneratorTool"
-			/>
-			<Tool
-				Name="VCMIDLTool"
-			/>
-			<Tool
-				Name="VCCLCompilerTool"
-				Optimization="2"
-				EnableIntrinsicFunctions="true"
-				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;GTSAM_EXPORTS"
-				RuntimeLibrary="2"
-				EnableFunctionLevelLinking="true"
-				UsePrecompiledHeader="0"
-				WarningLevel="3"
-				DebugInformationFormat="3"
-			/>
-			<Tool
-				Name="VCManagedResourceCompilerTool"
-			/>
-			<Tool
-				Name="VCResourceCompilerTool"
-			/>
-			<Tool
-				Name="VCPreLinkEventTool"
-			/>
-			<Tool
-				Name="VCLinkerTool"
-				LinkIncremental="1"
-				GenerateDebugInformation="true"
-				SubSystem="2"
-				OptimizeReferences="2"
-				EnableCOMDATFolding="2"
-				TargetMachine="1"
-			/>
-			<Tool
-				Name="VCALinkTool"
-			/>
-			<Tool
-				Name="VCManifestTool"
-			/>
-			<Tool
-				Name="VCXDCMakeTool"
-			/>
-			<Tool
-				Name="VCBscMakeTool"
-			/>
-			<Tool
-				Name="VCFxCopTool"
-			/>
-			<Tool
-				Name="VCAppVerifierTool"
-			/>
-			<Tool
-				Name="VCPostBuildEventTool"
-			/>
-		</Configuration>
-	</Configurations>
-	<References>
-	</References>
-	<Files>
-		<Filter
-			Name="Source Files"
-			Filter="cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx"
-			UniqueIdentifier="{4FC737F1-C7A5-4376-A066-2A32D752A2FF}"
-			>
-			<File
-				RelativePath=".\cal3_S2.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\chordalBayesNet.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\conditionalGaussian.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\factorGraph.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\fgConfig.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\linearFactor.cpp"
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-				>
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-				>
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-			<File
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-				>
-			</File>
-			<File
-				RelativePath=".\Point3.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\Pose3.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\Rot3.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\simulated2D.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\smallExample.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\svdcmp.cpp"
-				>
-			</File>
-			<File
-				RelativePath=".\vector.cpp"
-				>
-			</File>
-		</Filter>
-		<Filter
-			Name="Header Files"
-			Filter="h;hpp;hxx;hm;inl;inc;xsd"
-			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
-			>
-			<File
-				RelativePath=".\cal3_S2.h"
-				>
-			</File>
-			<File
-				RelativePath=".\chordalBayesNet.h"
-				>
-			</File>
-			<File
-				RelativePath=".\conditionalGaussian.h"
-				>
-			</File>
-			<File
-				RelativePath=".\factor.h"
-				>
-			</File>
-			<File
-				RelativePath=".\factorGraph.h"
-				>
-			</File>
-			<File
-				RelativePath=".\fgConfig.h"
-				>
-			</File>
-			<File
-				RelativePath=".\gtsam.h"
-				>
-			</File>
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-				RelativePath=".\linearFactor.h"
-				>
-			</File>
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-				RelativePath=".\linearFactorGraph.h"
-				>
-			</File>
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-				RelativePath=".\LinearFactorSet.h"
-				>
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-				RelativePath=".\matrix.h"
-				>
-			</File>
-			<File
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-			</File>
-			<File
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-				>
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-			<File
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-				>
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-			<File
-				RelativePath=".\Pose3.h"
-				>
-			</File>
-			<File
-				RelativePath=".\Rot3.h"
-				>
-			</File>
-			<File
-				RelativePath=".\simulated2D.h"
-				>
-			</File>
-			<File
-				RelativePath=".\smallExample.h"
-				>
-			</File>
-			<File
-				RelativePath=".\svdcmp.h"
-				>
-			</File>
-			<File
-				RelativePath=".\Value.h"
-				>
-			</File>
-			<File
-				RelativePath=".\vector.h"
-				>
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-			UniqueIdentifier="{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}"
-			>
-		</Filter>
-		<File
-			RelativePath=".\Makefile"
-			>
-		</File>
-	</Files>
-	<Globals>
-	</Globals>
-</VisualStudioProject>

cpp/manual.mk

@@ -1,139 +0,0 @@
-# Makefile for gtsam/cpp
-# Author Frank Dellaert
-
-# on the Mac, libtool is called glibtool :-(
-# documentation see /opt/local/share/doc/libtool-1.5.26/manual.html
-ifeq ($(shell uname),Darwin)
-  LIBTOOL = glibtool
-else
-  LIBTOOL = libtool
-endif
-
-INSTALL = install
-
-# C++ flags
-CXXFLAGS += -isystem $(BOOST_DIR) -O5
-CXXFLAGS += -DBOOST_UBLAS_NDEBUG
-
-# specify the source files
-# basic
-sources = Vector.cpp svdcmp.cpp Matrix.cpp numericalDerivative.cpp Ordering.cpp
-# nodes
-sources += FGConfig.cpp GaussianFactor.cpp ConditionalGaussian.cpp NonlinearFactor.cpp 
-# graphs
-sources += FactorGraph.cpp GaussianFactorGraph.cpp NonlinearFactorGraph.cpp ChordalBayesNet.cpp
-# geometry
-sources += Point2.cpp Point3.cpp Rot3.cpp Pose3.cpp Cal3_S2.cpp
-
-# The header files will be installed in ~/include/gtsam
-headers = Value.h factor.h linearfactorset.h $(sources:.cpp=.h)
-
-# conventional object files
-object_files = $(sources:.cpp=.o)
-
-# For libtool to build a shared library, we need "shared" object files with extension .lo
-shared_object_files = $(sources:.cpp=.lo)
-
-# rule for shared compiling shared_object_files
-%.lo: %.o
-
-# rule for shared compiling shared_object_files
-%.lo: %.cpp
-	$(LIBTOOL) --tag=CXX --mode=compile $(COMPILE.cpp) $(OUTPUT_OPTION) $<
-
-# library version
-current = 0  # The most recent interface number that this library implements. 
-revision = 0 # The implementation number of the current interface 
-age = 0 # The difference between the newest and oldest interfaces that	\
-this library implements. In other words, the library implements all	\
-the interface numbers in the range from number current - age to		\
-current.
-# from libtool manual:
-# Here are a set of rules to help you update your library version information:
-#   Start with version information of ‘0:0:0’ for each libtool library.
-#   Update the version information only immediately before a public release of your software.
-#   If the library source code has changed at all since the last update, then increment revision
-#   If any interfaces have been added, removed, or changed since the last update, increment current, and set revision to 0.
-#   If any interfaces have been added since the last public release, then increment age.
-#   If any interfaces have been removed since the last public release, then set age to 0.
-version = $(current):$(revision):$(age)
-
-# this builds the shared library
-# note that libgtsam.la is the libtool target
-# the actual library is built in the hidden subdirectory .libs
-libgtsam.la : $(shared_object_files) 
-	$(LIBTOOL) --tag=CXX --mode=link g++ -version-info $(version) -o libgtsam.la -rpath $(HOME)/lib $(shared_object_files)
-
-# shortcut
-lib: libgtsam.la
-
-# this builds the static library (used for unit testing)
-# object files will be only ones remade if a file is touched because deps broken
-libgtsam.a : $(shared_object_files) $(object_files) 
-	$(LIBTOOL) --tag=CXX --mode=link g++ -o libgtsam.a -static $(HOME)/lib $(shared_object_files)
-
-# and this installs the shared library
-install: libgtsam.la
-	$(INSTALL) -d $(HOME)/include/gtsam
-	rm -f $(HOME)/include/gtsam/typedefs.h
-	cp -f $(headers) $(HOME)/include/gtsam
-	$(LIBTOOL) --mode=install cp libgtsam.la $(HOME)/lib/libgtsam.la
-
-# create the MATLAB toolbox
-interfacePath = .
-moduleName = gtsam
-toolboxpath = $(HOME)/toolbox/gtsam
-mexFlags = "-I$(BOOST_DIR) -I$(HOME)/include -I$(HOME)/include/gtsam -L$(HOME)/lib -lgtsam"
-matlab:
-	wrap $(interfacePath) $(moduleName) $(toolboxpath) $(mexFlags)
-
-# unit tests
-unit-tests = $(shell ls test*.cpp) 
-unit-tests: $(unit-tests:.cpp=.run)
-
-# timing tests
-timing-tests = $(shell ls time*.cpp) 
-timing-tests: $(timing-tests:.cpp=.run)
-
-# local executables are for testing and timing
-executables =  $(unit-tests:.cpp=) $(timing-tests:.cpp=)
-
-# link flags
-INCDIR ?= $(HOME)/include
-LIBDIR ?= $(HOME)/lib
-$(executables) : simulated2D.o smallExample.o libgtsam.a
-$(executables) : LDFLAGS += -I. -I$(INCDIR)
-$(executables) : LDLIBS += libgtsam.a -L$(LIBDIR) -lCppUnitLite
-
-tests: unit-tests timing-tests
-clean-tests:
-	-rm -rf $(executables)
-
-# make a version of timeGaussianFactor instrumented for Saturn profiler
-saturn: timeGaussianFactor
-saturn: CXXFLAGS += -finstrument-functions
-saturn: LDLIBS += -lSaturn
-
-# rule to run an executable
-%.run: %
-	./$^
-
-# clean will remove the hidden .libs directory by libtool as well
-clean: clean-tests
-	-rm -rf *.d *.o *.lo *.a *.la .libs *.dSYM
-
-.PHONY: clean clean-tests unit-tests timing-tests matlab deps
-
-# dependecy generation as described in
-# http://www.wlug.org.nz/MakefileHowto
-all-sources = $(sources) smallExample.cpp simulated2D.cpp
-
-# when building object files, -MMD specifies dependency generation into .d files
-(all-sources:.cpp=.o): CXXFLAGS += -MMD
-
-deps := $(all-sources:.cpp=.d)
-deps: $(all-sources)
-	$(CXX) -MMD -E $(CXXFLAGS) -I. -I$(INCDIR) $(all-sources) > /dev/null
-
--include $(deps)
-

cpp/testBayesNetPreconditioner.cpp

@@ -11,13 +11,11 @@
 #define GTSAM_MAGIC_KEY
 
 #include "Ordering.h"
-#include "smallExample.h"
 #include "BayesNetPreconditioner.h"
 #include "iterative-inl.h"
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 
 /* ************************************************************************* */
 TEST( BayesNetPreconditioner, operators )
@@ -62,68 +60,6 @@ TEST( BayesNetPreconditioner, operators )
 	CHECK(assert_equal(expected2,actual2));
 }
 
-/* ************************************************************************* */
-TEST( BayesNetPreconditioner, conjugateGradients )
-{
-	// Build a planar graph
-	GaussianFactorGraph Ab;
-	VectorConfig xtrue;
-	size_t N = 3;
-	boost::tie(Ab, xtrue) = planarGraph(N); // A*x-b
-
-	// Get the spanning tree and corresponding ordering
-	GaussianFactorGraph Ab1, Ab2; // A1*x-b1 and A2*x-b2
-	boost::tie(Ab1, Ab2) = splitOffPlanarTree(N, Ab);
-
-	// Eliminate the spanning tree to build a prior
-	Ordering ordering = planarOrdering(N);
-	GaussianBayesNet Rc1 = Ab1.eliminate(ordering); // R1*x-c1
-	VectorConfig xbar = optimize(Rc1); // xbar = inv(R1)*c1
-
-	// Create BayesNet-preconditioned system
-	BayesNetPreconditioner system(Ab,Rc1);
-
-	// Create zero config y0 and perturbed config y1
-	VectorConfig y0;
-	Vector z2 = zero(2);
-	BOOST_FOREACH(const Symbol& j, ordering) y0.insert(j,z2);
-
-	VectorConfig y1 = y0;
-	y1["x2003"] = Vector_(2, 1.0, -1.0);
-	VectorConfig x1 = system.x(y1);
-
-	// Check gradient for y0
-	VectorConfig expectedGradient0;
-	expectedGradient0.insert("x1001", Vector_(2,-1000.,-1000.));
-	expectedGradient0.insert("x1002", Vector_(2,    0., -300.));
-	expectedGradient0.insert("x1003", Vector_(2,    0., -300.));
-	expectedGradient0.insert("x2001", Vector_(2, -100.,  200.));
-	expectedGradient0.insert("x2002", Vector_(2, -100.,    0.));
-	expectedGradient0.insert("x2003", Vector_(2, -100., -200.));
-	expectedGradient0.insert("x3001", Vector_(2, -100.,  100.));
-	expectedGradient0.insert("x3002", Vector_(2, -100.,    0.));
-	expectedGradient0.insert("x3003", Vector_(2, -100., -100.));
-	VectorConfig actualGradient0 = system.gradient(y0);
-	CHECK(assert_equal(expectedGradient0,actualGradient0));
-#ifdef VECTORBTREE
-	CHECK(actualGradient0.cloned(y0));
-#endif
-
-	// Solve using PCG
-	bool verbose = false;
-	double epsilon = 1e-6; // had to crank this down !!!
-	size_t maxIterations = 100;
-	VectorConfig actual_y = gtsam::conjugateGradients<BayesNetPreconditioner,
-			VectorConfig, Errors>(system, y1, verbose, epsilon, epsilon, maxIterations);
-	VectorConfig actual_x = system.x(actual_y);
-	CHECK(assert_equal(xtrue,actual_x));
-
-	// Compare with non preconditioned version:
-	VectorConfig actual2 = conjugateGradientDescent(Ab, x1, verbose, epsilon,
-			maxIterations);
-	CHECK(assert_equal(xtrue,actual2));
-}
-
 /* ************************************************************************* */
 int main() {
 	TestResult tr;

cpp/testBayesTree.cpp

@@ -15,7 +15,6 @@ using namespace boost::assign;
 #include "SymbolicFactorGraph.h"
 #include "Ordering.h"
 #include "BayesTree-inl.h"
-#include "smallExample.h"
 #include "IndexTable.h"
 
 using namespace gtsam;

cpp/testBinaryBayesNet.cpp

@@ -24,7 +24,6 @@ using namespace boost::assign;
 
 #include "BinaryConditional.h"
 #include "BayesNet-inl.h"
-#include "smallExample.h"
 #include "Ordering.h"
 #include "SymbolMap.h"
 

cpp/testConstraintOptimizer.cpp

@@ -14,7 +14,6 @@
 
 #include <Ordering.h>
 #include <ConstraintOptimizer.h>
-#include <smallExample.h>
 
 #define GTSAM_MAGIC_KEY
 
@@ -23,7 +22,6 @@ using namespace boost::assign;
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 
 /* ************************************************************************* */
 // Example of a single Constrained QP problem from the matlab testCQP.m file.
@@ -382,83 +380,6 @@ TEST( matrix, line_search ) {
 	CHECK(final_error <= init_error);
 }
 
-/* ************************************************************************* */
-TEST( matrix, unconstrained_fg_ata ) {
-	// create a graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	Matrix A; Vector b;
-	Ordering ordering;
-	ordering += Symbol('l', 1), Symbol('x', 1), Symbol('x', 2);
-	boost::tie(A, b) = fg.matrix(ordering);
-	Matrix B_ata = prod(trans(A), A);
-
-	// solve subproblem
-	Vector actual = solve_ldl(B_ata, prod(trans(A), b));
-
-	// verify
-	Vector expected = createCorrectDelta().vector();
-	CHECK(assert_equal(expected,actual));
-}
-
-
-///* ************************************************************************* */
-//TEST( matrix, unconstrained_fg ) {
-//	// create a graph
-//	GaussianFactorGraph fg = createGaussianFactorGraph();
-//
-//	Matrix A; Vector b;
-//	Ordering ordering;
-//	ordering += Symbol('l', 1), Symbol('x', 1), Symbol('x', 2);
-//	boost::tie(A, b) = fg.matrix(ordering);
-//	Matrix B_ata = prod(trans(A), A);
-////	print(B_ata, "B_ata");
-////	print(b, "  b");
-//
-//	// parameters
-//	size_t maxIt = 50;
-//	double stepsize = 0.1;
-//
-//	// iterate to solve
-//	VectorConfig x = createZeroDelta();
-//	BFGSEstimator B(x.dim());
-//
-//	Vector step;
-//
-//	for (size_t i=0; i<maxIt; ++i) {
-////		cout << "Error at Iteration: " << i << " is " << fg.error(x) << endl;
-//
-//		// find the gradient
-//		Vector dfx = fg.gradient(x).vector();
-////		print(dfx, "   dfx");
-//		CHECK(assert_equal(-1.0 * prod(trans(A), b - A*x.vector()), dfx));
-//
-//		// update hessian
-//	    if (i>0) {
-//	    	B.update(dfx, step);
-//	    } else {
-//	    	B.update(dfx);
-//	    }
-//
-//	    // solve subproblem
-////	    print(B.getB(), " B_bfgs");
-//	    Vector delta = solve_ldl(B.getB(), -dfx);
-////	    Vector delta = solve_ldl(B_ata, -dfx);
-//
-////	    print(delta, "   delta");
-//
-//	    // update
-//		step = stepsize * delta;
-////	    step = linesearch(x, delta, penalty); // TODO: switch here
-//	    x = expmap(x, step);
-////	    print(step, "   step");
-//	}
-//
-//	// verify
-//	VectorConfig expected = createCorrectDelta();
-//	CHECK(assert_equal(expected,x, 1e-4));
-//}
-
 /* ************************************************************************* */
 int main() { TestResult tr; return TestRegistry::runAllTests(tr); }
 /* ************************************************************************* */

cpp/testGaussianFactor.cpp

@@ -21,11 +21,9 @@ using namespace boost::assign;
 #include "Ordering.h"
 #include "GaussianConditional.h"
 #include "inference-inl.h"
-#include "smallExample.h"
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 using namespace boost;
 
 static SharedDiagonal
@@ -33,22 +31,6 @@ static SharedDiagonal
 	constraintModel = noiseModel::Constrained::All(2);
 
 /* ************************************************************************* */
-TEST( GaussianFactor, linearFactor )
-{
-	Matrix I = eye(2);
-	Vector b = Vector_(2, 2.0, -1.0);
-	GaussianFactor expected("x1", -10*I,"x2", 10*I, b, noiseModel::Unit::Create(2));
-
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the factor "f2" from the factor graph
-	GaussianFactor::shared_ptr lf = fg[1];
-
-	// check if the two factors are the same
-	CHECK(assert_equal(expected,*lf));
-}
-
 TEST( GaussianFactor, constructor)
 {
 	Vector b = Vector_(3, 1., 2., 3.);
@@ -92,101 +74,6 @@ TEST( GaussianFactor, operators )
 	CHECK(assert_equal(expectedX2,x));
 }
 
-/* ************************************************************************* */
-TEST( GaussianFactor, keys )
-{
-	// get the factor "f2" from the small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-	GaussianFactor::shared_ptr lf = fg[1];
-	list<Symbol> expected;
-	expected.push_back("x1");
-	expected.push_back("x2");
-	CHECK(lf->keys() == expected);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, dimensions )
-{
-  // get the factor "f2" from the small linear factor graph
-  GaussianFactorGraph fg = createGaussianFactorGraph();
-
-  // Check a single factor
-  Dimensions expected;
-  insert(expected)("x1", 2)("x2", 2);
-  Dimensions actual = fg[1]->dimensions();
-  CHECK(expected==actual);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, getDim )
-{
-	// get a factor
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-	GaussianFactor::shared_ptr factor = fg[0];
-
-	// get the size of a variable
-	size_t actual = factor->getDim("x1");
-
-	// verify
-	size_t expected = 2;
-	CHECK(actual == expected);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, combine )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get two factors from it and insert the factors into a vector
-	vector<GaussianFactor::shared_ptr> lfg;
-	lfg.push_back(fg[4 - 1]);
-	lfg.push_back(fg[2 - 1]);
-
-	// combine in a factor
-	GaussianFactor combined(lfg);
-
-	// sigmas
-	double sigma2 = 0.1;
-	double sigma4 = 0.2;
-	Vector sigmas = Vector_(4, sigma4, sigma4, sigma2, sigma2);
-
-	// the expected combined linear factor
-	Matrix Ax2 = Matrix_(4, 2, // x2
-			-5., 0.,
-			+0., -5.,
-			10., 0.,
-			+0., 10.);
-
-	Matrix Al1 = Matrix_(4, 2,	// l1
-			5., 0.,
-			0., 5.,
-			0., 0.,
-			0., 0.);
-
-	Matrix Ax1 = Matrix_(4, 2,	// x1
-			0.00, 0., // f4
-			0.00, 0., // f4
-			-10., 0., // f2
-			0.00, -10. // f2
-	);
-
-	// the RHS
-	Vector b2(4);
-	b2(0) = -1.0;
-	b2(1) =  1.5;
-	b2(2) =  2.0;
-	b2(3) = -1.0;
-
-	// use general constructor for making arbitrary factors
-	vector<pair<Symbol, Matrix> > meas;
-	meas.push_back(make_pair("x2", Ax2));
-	meas.push_back(make_pair("l1", Al1));
-	meas.push_back(make_pair("x1", Ax1));
-	GaussianFactor expected(meas, b2, noiseModel::Diagonal::Sigmas(ones(4)));
-	CHECK(assert_equal(expected,combined));
-}
-
 /* ************************************************************************* */
 TEST( NonlinearFactorGraph, combine2){
 	double sigma1 = 0.0957;
@@ -304,65 +191,6 @@ TEST( GaussianFactor, linearFactorN){
   CHECK(assert_equal(expected,combinedFactor));
 }
 
-/* ************************************************************************* */
-TEST( GaussianFactor, error )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the first factor from the factor graph
-	GaussianFactor::shared_ptr lf = fg[0];
-
-	// check the error of the first factor with noisy config
-	VectorConfig cfg = createZeroDelta();
-
-	// calculate the error from the factor "f1"
-	// note the error is the same as in testNonlinearFactor
-	double actual = lf->error(cfg);
-	DOUBLES_EQUAL( 1.0, actual, 0.00000001 );
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, eliminate )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get two factors from it and insert the factors into a vector
-	vector<GaussianFactor::shared_ptr> lfg;
-	lfg.push_back(fg[4 - 1]);
-	lfg.push_back(fg[2 - 1]);
-
-	// combine in a factor
-	GaussianFactor combined(lfg);
-
-	// eliminate the combined factor
-	GaussianConditional::shared_ptr actualCG;
-	GaussianFactor::shared_ptr actualLF;
-	boost::tie(actualCG,actualLF) = combined.eliminate("x2");
-
-	// create expected Conditional Gaussian
-	Matrix I = eye(2)*sqrt(125.0);
-	Matrix R11 = I, S12 = -0.2*I, S13 = -0.8*I;
-	Vector d = I*Vector_(2,0.2,-0.14);
-
-	// Check the conditional Gaussian
-	GaussianConditional
-	expectedCG("x2", d, R11, "l1", S12, "x1", S13, repeat(2, 1.0));
-
-	// the expected linear factor
-	I = eye(2)/0.2236;
-	Matrix Bl1 = I, Bx1 = -I;
-	Vector b1 = I*Vector_(2,0.0,0.2);
-
-	GaussianFactor expectedLF("l1", Bl1, "x1", Bx1, b1, repeat(2,1.0));
-
-	// check if the result matches
-	CHECK(assert_equal(expectedCG,*actualCG,1e-3));
-	CHECK(assert_equal(expectedLF,*actualLF,1e-3));
-}
-
-
 /* ************************************************************************* */
 TEST( GaussianFactor, eliminate2 )
 {
@@ -470,96 +298,6 @@ TEST( GaussianFactor, empty )
 	CHECK(f.empty()==true);
 }
 
-/* ************************************************************************* */
-TEST( GaussianFactor, matrix )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the factor "f2" from the factor graph
-	//GaussianFactor::shared_ptr lf = fg[1]; // NOTE: using the older version
-	Vector b2 = Vector_(2, 0.2, -0.1);
-	Matrix I = eye(2);
-	GaussianFactor::shared_ptr lf(new GaussianFactor("x1", -I, "x2", I, b2, sigma0_1));
-
-	// render with a given ordering
-	Ordering ord;
-	ord += "x1","x2";
-
-	// Test whitened version
-	Matrix A_act1; Vector b_act1;
-	boost::tie(A_act1,b_act1) = lf->matrix(ord, true);
-
-	Matrix A1 = Matrix_(2,4,
-			-10.0,  0.0, 10.0,  0.0,
-			000.0,-10.0,  0.0, 10.0 );
-	Vector b1 = Vector_(2, 2.0, -1.0);
-
-	EQUALITY(A_act1,A1);
-	EQUALITY(b_act1,b1);
-
-	// Test unwhitened version
-	Matrix A_act2; Vector b_act2;
-	boost::tie(A_act2,b_act2) = lf->matrix(ord, false);
-
-
-	Matrix A2 = Matrix_(2,4,
-			-1.0,  0.0, 1.0,  0.0,
-			000.0,-1.0,  0.0, 1.0 );
-	//Vector b2 = Vector_(2, 2.0, -1.0);
-
-	EQUALITY(A_act2,A2);
-	EQUALITY(b_act2,b2);
-
-	// Ensure that whitening is consistent
-	shared_ptr<noiseModel::Gaussian> model = lf->get_model();
-	model->WhitenSystem(A_act2, b_act2);
-	EQUALITY(A_act1, A_act2);
-	EQUALITY(b_act1, b_act2);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, matrix_aug )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the factor "f2" from the factor graph
-	//GaussianFactor::shared_ptr lf = fg[1];
-	Vector b2 = Vector_(2, 0.2, -0.1);
-	Matrix I = eye(2);
-	GaussianFactor::shared_ptr lf(new GaussianFactor("x1", -I, "x2", I, b2, sigma0_1));
-
-	// render with a given ordering
-	Ordering ord;
-	ord += "x1","x2";
-
-	// Test unwhitened version
-	Matrix Ab_act1;
-	Ab_act1 = lf->matrix_augmented(ord, false);
-
-	Matrix Ab1 = Matrix_(2,5,
-			-1.0,  0.0, 1.0,  0.0,  0.2,
-			00.0,- 1.0, 0.0,  1.0, -0.1 );
-
-	EQUALITY(Ab_act1,Ab1);
-
-	// Test whitened version
-	Matrix Ab_act2;
-	Ab_act2 = lf->matrix_augmented(ord, true);
-
-	Matrix Ab2 = Matrix_(2,5,
-		   -10.0,  0.0, 10.0,  0.0,  2.0,
-			00.0, -10.0,  0.0, 10.0, -1.0 );
-
-	EQUALITY(Ab_act2,Ab2);
-
-	// Ensure that whitening is consistent
-	shared_ptr<noiseModel::Gaussian> model = lf->get_model();
-	model->WhitenInPlace(Ab_act1);
-	EQUALITY(Ab_act1, Ab_act2);
-}
-
 /* ************************************************************************* */
 // small aux. function to print out lists of anything
 template<class T>
@@ -568,80 +306,6 @@ void print(const list<T>& i) {
 	cout << endl;
 }
 
-/* ************************************************************************* */
-TEST( GaussianFactor, sparse )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the factor "f2" from the factor graph
-	GaussianFactor::shared_ptr lf = fg[1];
-
-	// render with a given ordering
-	Ordering ord;
-	ord += "x1","x2";
-
-	list<int> i,j;
-	list<double> s;
-	boost::tie(i,j,s) = lf->sparse(fg.columnIndices(ord));
-
-	list<int> i1,j1;
-	i1 += 1,2,1,2;
-	j1 += 1,2,3,4;
-
-	list<double> s1;
-	s1 += -10,-10,10,10;
-
-	CHECK(i==i1);
-	CHECK(j==j1);
-	CHECK(s==s1);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, sparse2 )
-{
-	// create a small linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get the factor "f2" from the factor graph
-	GaussianFactor::shared_ptr lf = fg[1];
-
-	// render with a given ordering
-	Ordering ord;
-	ord += "x2","l1","x1";
-
-	list<int> i,j;
-	list<double> s;
-	boost::tie(i,j,s) = lf->sparse(fg.columnIndices(ord));
-
-	list<int> i1,j1;
-	i1 += 1,2,1,2;
-	j1 += 5,6,1,2;
-
-	list<double> s1;
-	s1 += -10,-10,10,10;
-
-	CHECK(i==i1);
-	CHECK(j==j1);
-	CHECK(s==s1);
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactor, size )
-{
-	// create a linear factor graph
-	GaussianFactorGraph fg = createGaussianFactorGraph();
-
-	// get some factors from the graph
-	boost::shared_ptr<GaussianFactor> factor1 = fg[0];
-	boost::shared_ptr<GaussianFactor> factor2 = fg[1];
-	boost::shared_ptr<GaussianFactor> factor3 = fg[2];
-
-	CHECK(factor1->size() == 1);
-	CHECK(factor2->size() == 2);
-	CHECK(factor3->size() == 2);
-}
-
 /* ************************************************************************* */
 TEST( GaussianFactor, tally_separator )
 {

cpp/testISAM.cpp

@@ -17,7 +17,6 @@ using namespace boost::assign;
 #include "Ordering.h"
 #include "GaussianBayesNet.h"
 #include "ISAM-inl.h"
-#include "smallExample.h"
 
 using namespace std;
 using namespace gtsam;

cpp/testJunctionTree.cpp

@@ -16,12 +16,10 @@ using namespace boost::assign;
 
 #define GTSAM_MAGIC_KEY
 
-#include "smallExample.h"
 #include "JunctionTree-inl.h"
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 
 /* ************************************************************************* */
 /**
@@ -57,44 +55,6 @@ TEST( GaussianFactorGraph, constructor )
 	LONGS_EQUAL(2,               junctionTree.root()->children()[0]->size());
 }
 
-/* ************************************************************************* *
- Bayes tree for smoother with "nested dissection" ordering:
-	 C1		 x5 x6 x4
-	 C2		  x3 x2 : x4
-	 C3		    x1 : x2
-	 C4		  x7 : x6
-/* ************************************************************************* */
-TEST( GaussianFactorGraph, constructor2 )
-{
-	// create a graph
-	GaussianFactorGraph fg = createSmoother(7);
-
-	// create an ordering
-	Ordering ordering; ordering += "x1","x3","x5","x7","x2","x6","x4";
-
-	GaussianJunctionTree<GaussianFactorGraph> junctionTree(fg, ordering);
-	Ordering frontal1; frontal1 += "x5", "x6", "x4";
-	Ordering frontal2; frontal2 += "x3", "x2";
-	Ordering frontal3; frontal3 += "x1";
-	Ordering frontal4; frontal4 += "x7";
-	Unordered sep1;
-	Unordered sep2; sep2 += "x4";
-	Unordered sep3; sep3 += "x2";
-	Unordered sep4; sep4 += "x6";
-	CHECK(assert_equal(frontal1, junctionTree.root()->frontal()));
-	CHECK(assert_equal(sep1,     junctionTree.root()->separator()));
-	LONGS_EQUAL(5,               junctionTree.root()->size());
-	CHECK(assert_equal(frontal2, junctionTree.root()->children()[0]->frontal()));
-	CHECK(assert_equal(sep2,     junctionTree.root()->children()[0]->separator()));
-	LONGS_EQUAL(4,               junctionTree.root()->children()[0]->size());
-	CHECK(assert_equal(frontal3, junctionTree.root()->children()[0]->children()[0]->frontal()));
-	CHECK(assert_equal(sep3,     junctionTree.root()->children()[0]->children()[0]->separator()));
-	LONGS_EQUAL(2,               junctionTree.root()->children()[0]->children()[0]->size());
-	CHECK(assert_equal(frontal4, junctionTree.root()->children()[1]->frontal()));
-	CHECK(assert_equal(sep4,     junctionTree.root()->children()[1]->separator()));
-	LONGS_EQUAL(2,               junctionTree.root()->children()[1]->size());
-}
-
 /* ************************************************************************* */
 /**
  * x1 - x2 - x3 - x4
@@ -139,25 +99,6 @@ TEST( GaussianFactorGraph, eliminate )
 	CHECK(assert_equal(bayesTree_expected, bayesTree));
 }
 
-/* ************************************************************************* *
-TEST( GaussianFactorGraph, optimizeMultiFrontal )
-{
-	// create a graph
-	GaussianFactorGraph fg = createSmoother(7);
-
-	// create an ordering
-	Ordering ordering; ordering += "x1","x3","x5","x7","x2","x6","x4";
-
-	// optimize the graph
-	GaussianJunctionTree<GaussianFactorGraph> junctionTree(fg, ordering);
-	VectorConfig actual = junctionTree.optimize();
-
-	// verify
-//	VectorConfig expected = createCorrectDelta();
-//
-//  CHECK(assert_equal(expected,actual));
-}
-
 /* ************************************************************************* */
 int main() { TestResult tr; return TestRegistry::runAllTests(tr);}
 /* ************************************************************************* */

cpp/testLieConfig.cpp

@@ -13,7 +13,6 @@ using namespace boost::assign;
 
 #define GTSAM_MAGIC_KEY
 
-#include "Pose2.h"
 #include "LieConfig-inl.h"
 #include "Vector.h"
 

cpp/testOrdering.cpp

@@ -12,7 +12,6 @@ using namespace boost::assign;
 #define GTSAM_MAGIC_KEY
 
 #include "Ordering.h"
-#include "pose2SLAM.h"
 
 using namespace std;
 using namespace gtsam;

cpp/testSymbolicBayesNet.cpp

@@ -13,13 +13,11 @@ using namespace boost::assign;
 #define GTSAM_MAGIC_KEY
 
 #include "Ordering.h"
-#include "smallExample.h"
 #include "SymbolicBayesNet.h"
 #include "SymbolicFactorGraph.h"
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 
 Symbol _B_('B', 0), _L_('L', 0);
 SymbolicConditional::shared_ptr
@@ -39,31 +37,6 @@ TEST( SymbolicBayesNet, equals )
 	CHECK(!f1.equals(f2));
 }
 
-/* ************************************************************************* */
-TEST( SymbolicBayesNet, constructor )
-{
-	// Create manually
-	SymbolicConditional::shared_ptr
-		x2(new SymbolicConditional("x2","l1", "x1")),
-		l1(new SymbolicConditional("l1","x1")),
-		x1(new SymbolicConditional("x1"));
-	SymbolicBayesNet expected;
-	expected.push_back(x2);
-	expected.push_back(l1);
-	expected.push_back(x1);
-
-	// Create from a factor graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph fg(factorGraph);
-
-	// eliminate it
-	Ordering ordering;
-	ordering += "x2","l1","x1";
-  SymbolicBayesNet actual = fg.eliminate(ordering);
-
-  CHECK(assert_equal(expected, actual));
-}
-
 /* ************************************************************************* */
 TEST( SymbolicBayesNet, pop_front )
 {

cpp/testSymbolicFactorGraph.cpp

@@ -12,130 +12,15 @@ using namespace boost::assign;
 #define GTSAM_MAGIC_KEY
 
 #include "Ordering.h"
-#include "smallExample.h"
 #include "SymbolicFactorGraph.h"
 #include "SymbolicBayesNet.h"
 #include "FactorGraph-inl.h"
 
 using namespace std;
 using namespace gtsam;
-using namespace example;
 
 /* ************************************************************************* */
-TEST( SymbolicFactorGraph, symbolicFactorGraph )
+TEST( SymbolicFactorGraph, eliminate2 )
-{
-	// construct expected symbolic graph
-	SymbolicFactorGraph expected;
-	expected.push_factor("x1");
-	expected.push_factor("x1","x2");
-	expected.push_factor("l1","x1");
-	expected.push_factor("l1","x2");
-
-	// construct it from the factor graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph actual(factorGraph);
-
-	CHECK(assert_equal(expected, actual));
-}
-
-/* ************************************************************************* */
-TEST( SymbolicFactorGraph, findAndRemoveFactors )
-{
-	// construct it from the factor graph graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph actual(factorGraph);
-  SymbolicFactor::shared_ptr f1 = actual[0];
-  SymbolicFactor::shared_ptr f3 = actual[2];
-	actual.findAndRemoveFactors<SymbolicFactorGraph>("x2");
-
-	// construct expected graph after find_factors_and_remove
-	SymbolicFactorGraph expected;
-	SymbolicFactor::shared_ptr null;
-	expected.push_back(f1);
-	expected.push_back(null);
-	expected.push_back(f3);
-	expected.push_back(null);
-
-	CHECK(assert_equal(expected, actual));
-}
-/* ************************************************************************* */
-TEST( SymbolicFactorGraph, factors)
-{
-	// create a test graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph fg(factorGraph);
-
-	// ask for all factor indices connected to x1
-	list<size_t> x1_factors = fg.factors("x1");
-	int x1_indices[] = { 0, 1, 2 };
-	list<size_t> x1_expected(x1_indices, x1_indices + 3);
-	CHECK(x1_factors==x1_expected);
-
-	// ask for all factor indices connected to x2
-	list<size_t> x2_factors = fg.factors("x2");
-	int x2_indices[] = { 1, 3 };
-	list<size_t> x2_expected(x2_indices, x2_indices + 2);
-	CHECK(x2_factors==x2_expected);
-}
-
-/* ************************************************************************* */
-TEST( SymbolicFactorGraph, removeAndCombineFactors )
-{
-	// create a test graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph fg(factorGraph);
-
-  // combine all factors connected to x1
-  SymbolicFactor::shared_ptr actual = removeAndCombineFactors(fg,"x1");
-
-  // check result
-  SymbolicFactor expected("l1","x1","x2");
-  CHECK(assert_equal(expected,*actual));
-}
-
-/* ************************************************************************* */
-TEST( SymbolicFactorGraph, eliminateOne )
-{
-	// create a test graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph fg(factorGraph);
-
-	// eliminate
-	SymbolicConditional::shared_ptr actual = fg.eliminateOne("x1");
-
-  // create expected symbolic Conditional
-  SymbolicConditional expected("x1","l1","x2");
-
-  CHECK(assert_equal(expected,*actual));
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactorGraph, eliminate )
-{
-  // create expected Chordal bayes Net
-  SymbolicConditional::shared_ptr x2(new SymbolicConditional("x2", "l1", "x1"));
-  SymbolicConditional::shared_ptr l1(new SymbolicConditional("l1", "x1"));
-  SymbolicConditional::shared_ptr x1(new SymbolicConditional("x1"));
-
-  SymbolicBayesNet expected;
-  expected.push_back(x2);
-  expected.push_back(l1);
-  expected.push_back(x1);
-
-  // create a test graph
-	GaussianFactorGraph factorGraph = createGaussianFactorGraph();
-	SymbolicFactorGraph fg(factorGraph);
-
-	// eliminate it
-	Ordering ordering;
-	ordering += "x2","l1","x1";
-  SymbolicBayesNet actual = fg.eliminate(ordering);
-
-  CHECK(assert_equal(expected,actual));
-}
-
-/* ************************************************************************* */
-TEST( GaussianFactorGraph, eliminate2 )
 {
   // create a test graph
 	SymbolicFactorGraph fg;

geometry/Makefile.in

@@ -0,0 +1,823 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+#----------------------------------------------------------------------------------------------------
+# GTSAM geometry
+#----------------------------------------------------------------------------------------------------
+
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+check_PROGRAMS = testPoint2$(EXEEXT) testRot2$(EXEEXT) \
+	testPose2$(EXEEXT) testPoint3$(EXEEXT) testRot3$(EXEEXT) \
+	testPose3$(EXEEXT) testCal3_S2$(EXEEXT) \
+	testCalibratedCamera$(EXEEXT) testSimpleCamera$(EXEEXT) \
+	testTensors$(EXEEXT) testHomography2$(EXEEXT) \
+	testTrifocal$(EXEEXT)
+noinst_PROGRAMS = timeRot3$(EXEEXT)
+subdir = geometry
+DIST_COMMON = $(pkginclude_HEADERS) $(srcdir)/Makefile.am \
+	$(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
+	$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
+	$(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \
+	$(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+LTLIBRARIES = $(noinst_LTLIBRARIES)
+libgeometry_la_LIBADD =
+am__objects_1 = Point2.lo Rot2.lo Pose2.lo Point3.lo Rot3.lo Pose3.lo \
+	Cal3_S2.lo CalibratedCamera.lo SimpleCamera.lo \
+	projectiveGeometry.lo tensorInterface.lo
+am_libgeometry_la_OBJECTS = $(am__objects_1)
+libgeometry_la_OBJECTS = $(am_libgeometry_la_OBJECTS)
+PROGRAMS = $(noinst_PROGRAMS)
+testCal3_S2_SOURCES = testCal3_S2.cpp
+testCal3_S2_OBJECTS = testCal3_S2.$(OBJEXT)
+testCal3_S2_LDADD = $(LDADD)
+testCal3_S2_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testCalibratedCamera_SOURCES = testCalibratedCamera.cpp
+testCalibratedCamera_OBJECTS = testCalibratedCamera.$(OBJEXT)
+testCalibratedCamera_LDADD = $(LDADD)
+testCalibratedCamera_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testHomography2_SOURCES = testHomography2.cpp
+testHomography2_OBJECTS = testHomography2.$(OBJEXT)
+testHomography2_LDADD = $(LDADD)
+testHomography2_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testPoint2_SOURCES = testPoint2.cpp
+testPoint2_OBJECTS = testPoint2.$(OBJEXT)
+testPoint2_LDADD = $(LDADD)
+testPoint2_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testPoint3_SOURCES = testPoint3.cpp
+testPoint3_OBJECTS = testPoint3.$(OBJEXT)
+testPoint3_LDADD = $(LDADD)
+testPoint3_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testPose2_SOURCES = testPose2.cpp
+testPose2_OBJECTS = testPose2.$(OBJEXT)
+testPose2_LDADD = $(LDADD)
+testPose2_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testPose3_SOURCES = testPose3.cpp
+testPose3_OBJECTS = testPose3.$(OBJEXT)
+testPose3_LDADD = $(LDADD)
+testPose3_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testRot2_SOURCES = testRot2.cpp
+testRot2_OBJECTS = testRot2.$(OBJEXT)
+testRot2_LDADD = $(LDADD)
+testRot2_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testRot3_SOURCES = testRot3.cpp
+testRot3_OBJECTS = testRot3.$(OBJEXT)
+testRot3_LDADD = $(LDADD)
+testRot3_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testSimpleCamera_SOURCES = testSimpleCamera.cpp
+testSimpleCamera_OBJECTS = testSimpleCamera.$(OBJEXT)
+testSimpleCamera_LDADD = $(LDADD)
+testSimpleCamera_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testTensors_SOURCES = testTensors.cpp
+testTensors_OBJECTS = testTensors.$(OBJEXT)
+testTensors_LDADD = $(LDADD)
+testTensors_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+testTrifocal_SOURCES = testTrifocal.cpp
+testTrifocal_OBJECTS = testTrifocal.$(OBJEXT)
+testTrifocal_LDADD = $(LDADD)
+testTrifocal_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+timeRot3_SOURCES = timeRot3.cpp
+timeRot3_OBJECTS = timeRot3.$(OBJEXT)
+timeRot3_LDADD = $(LDADD)
+timeRot3_DEPENDENCIES = libgeometry.la ../base/libbase.la \
+	../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+	--mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+	--mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
+	$(LDFLAGS) -o $@
+SOURCES = $(libgeometry_la_SOURCES) testCal3_S2.cpp \
+	testCalibratedCamera.cpp testHomography2.cpp testPoint2.cpp \
+	testPoint3.cpp testPose2.cpp testPose3.cpp testRot2.cpp \
+	testRot3.cpp testSimpleCamera.cpp testTensors.cpp \
+	testTrifocal.cpp timeRot3.cpp
+DIST_SOURCES = $(libgeometry_la_SOURCES) testCal3_S2.cpp \
+	testCalibratedCamera.cpp testHomography2.cpp testPoint2.cpp \
+	testPoint3.cpp testPose2.cpp testPose3.cpp testRot2.cpp \
+	testRot3.cpp testSimpleCamera.cpp testTensors.cpp \
+	testTrifocal.cpp timeRot3.cpp
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__installdirs = "$(DESTDIR)$(pkgincludedir)"
+HEADERS = $(pkginclude_HEADERS)
+ETAGS = etags
+CTAGS = ctags
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+AR = @AR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+FGREP = @FGREP@
+GREP = @GREP@
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LD = @LD@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LIBTOOL = @LIBTOOL@
+LIPO = @LIPO@
+LN_S = @LN_S@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+MKDIR_P = @MKDIR_P@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
+OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+RANLIB = @RANLIB@
+SED = @SED@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+VERSION = @VERSION@
+abs_builddir = @abs_builddir@
+abs_srcdir = @abs_srcdir@
+abs_top_builddir = @abs_top_builddir@
+abs_top_srcdir = @abs_top_srcdir@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+boost = @boost@
+boost_serialization = @boost_serialization@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+builddir = @builddir@
+datadir = @datadir@
+datarootdir = @datarootdir@
+docdir = @docdir@
+dvidir = @dvidir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+htmldir = @htmldir@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localedir = @localedir@
+localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+pdfdir = @pdfdir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+psdir = @psdir@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+srcdir = @srcdir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+toolbox = @toolbox@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+# Tensors
+
+#----------------------------------------------------------------------------------------------------
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+# The headers are installed in $(includedir)/gtsam: 
+#----------------------------------------------------------------------------------------------------
+headers = tensors.h Tensor1.h Tensor2.h Tensor3.h Tensor4.h Tensor5.h \
+	Tensor1Expression.h Tensor2Expression.h Tensor3Expression.h \
+	Tensor5Expression.h $(sources:.cpp=.h)
+
+# Points and poses
+
+# Cameras
+sources = Point2.cpp Rot2.cpp Pose2.cpp Point3.cpp Rot3.cpp Pose3.cpp \
+	Cal3_S2.cpp CalibratedCamera.cpp SimpleCamera.cpp \
+	projectiveGeometry.cpp tensorInterface.cpp
+pkginclude_HEADERS = $(headers)
+noinst_LTLIBRARIES = libgeometry.la
+libgeometry_la_SOURCES = $(sources)
+AM_CPPFLAGS = -I$(boost) -I../base
+
+#----------------------------------------------------------------------------------------------------
+# rules to build local programs
+#----------------------------------------------------------------------------------------------------
+TESTS = $(check_PROGRAMS)
+AM_LDFLAGS = $(BOOST_LDFLAGS) $(boost_serialization) 
+LDADD = libgeometry.la ../base/libbase.la ../ldl/libldl.la ../CppUnitLite/libCppUnitLite.a
+AM_DEFAULT_SOURCE_EXT = .cpp
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .cpp .lo .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu geometry/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --gnu geometry/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+
+clean-noinstLTLIBRARIES:
+	-test -z "$(noinst_LTLIBRARIES)" || rm -f $(noinst_LTLIBRARIES)
+	@list='$(noinst_LTLIBRARIES)'; for p in $$list; do \
+	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
+	  test "$$dir" != "$$p" || dir=.; \
+	  echo "rm -f \"$${dir}/so_locations\""; \
+	  rm -f "$${dir}/so_locations"; \
+	done
+libgeometry.la: $(libgeometry_la_OBJECTS) $(libgeometry_la_DEPENDENCIES) 
+	$(CXXLINK)  $(libgeometry_la_OBJECTS) $(libgeometry_la_LIBADD) $(LIBS)
+
+clean-checkPROGRAMS:
+	@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
+	echo " rm -f" $$list; \
+	rm -f $$list || exit $$?; \
+	test -n "$(EXEEXT)" || exit 0; \
+	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+	echo " rm -f" $$list; \
+	rm -f $$list
+
+clean-noinstPROGRAMS:
+	@list='$(noinst_PROGRAMS)'; test -n "$$list" || exit 0; \
+	echo " rm -f" $$list; \
+	rm -f $$list || exit $$?; \
+	test -n "$(EXEEXT)" || exit 0; \
+	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+	echo " rm -f" $$list; \
+	rm -f $$list
+testCal3_S2$(EXEEXT): $(testCal3_S2_OBJECTS) $(testCal3_S2_DEPENDENCIES) 
+	@rm -f testCal3_S2$(EXEEXT)
+	$(CXXLINK) $(testCal3_S2_OBJECTS) $(testCal3_S2_LDADD) $(LIBS)
+testCalibratedCamera$(EXEEXT): $(testCalibratedCamera_OBJECTS) $(testCalibratedCamera_DEPENDENCIES) 
+	@rm -f testCalibratedCamera$(EXEEXT)
+	$(CXXLINK) $(testCalibratedCamera_OBJECTS) $(testCalibratedCamera_LDADD) $(LIBS)
+testHomography2$(EXEEXT): $(testHomography2_OBJECTS) $(testHomography2_DEPENDENCIES) 
+	@rm -f testHomography2$(EXEEXT)
+	$(CXXLINK) $(testHomography2_OBJECTS) $(testHomography2_LDADD) $(LIBS)
+testPoint2$(EXEEXT): $(testPoint2_OBJECTS) $(testPoint2_DEPENDENCIES) 
+	@rm -f testPoint2$(EXEEXT)
+	$(CXXLINK) $(testPoint2_OBJECTS) $(testPoint2_LDADD) $(LIBS)
+testPoint3$(EXEEXT): $(testPoint3_OBJECTS) $(testPoint3_DEPENDENCIES) 
+	@rm -f testPoint3$(EXEEXT)
+	$(CXXLINK) $(testPoint3_OBJECTS) $(testPoint3_LDADD) $(LIBS)
+testPose2$(EXEEXT): $(testPose2_OBJECTS) $(testPose2_DEPENDENCIES) 
+	@rm -f testPose2$(EXEEXT)
+	$(CXXLINK) $(testPose2_OBJECTS) $(testPose2_LDADD) $(LIBS)
+testPose3$(EXEEXT): $(testPose3_OBJECTS) $(testPose3_DEPENDENCIES) 
+	@rm -f testPose3$(EXEEXT)
+	$(CXXLINK) $(testPose3_OBJECTS) $(testPose3_LDADD) $(LIBS)
+testRot2$(EXEEXT): $(testRot2_OBJECTS) $(testRot2_DEPENDENCIES) 
+	@rm -f testRot2$(EXEEXT)
+	$(CXXLINK) $(testRot2_OBJECTS) $(testRot2_LDADD) $(LIBS)
+testRot3$(EXEEXT): $(testRot3_OBJECTS) $(testRot3_DEPENDENCIES) 
+	@rm -f testRot3$(EXEEXT)
+	$(CXXLINK) $(testRot3_OBJECTS) $(testRot3_LDADD) $(LIBS)
+testSimpleCamera$(EXEEXT): $(testSimpleCamera_OBJECTS) $(testSimpleCamera_DEPENDENCIES) 
+	@rm -f testSimpleCamera$(EXEEXT)
+	$(CXXLINK) $(testSimpleCamera_OBJECTS) $(testSimpleCamera_LDADD) $(LIBS)
+testTensors$(EXEEXT): $(testTensors_OBJECTS) $(testTensors_DEPENDENCIES) 
+	@rm -f testTensors$(EXEEXT)
+	$(CXXLINK) $(testTensors_OBJECTS) $(testTensors_LDADD) $(LIBS)
+testTrifocal$(EXEEXT): $(testTrifocal_OBJECTS) $(testTrifocal_DEPENDENCIES) 
+	@rm -f testTrifocal$(EXEEXT)
+	$(CXXLINK) $(testTrifocal_OBJECTS) $(testTrifocal_LDADD) $(LIBS)
+timeRot3$(EXEEXT): $(timeRot3_OBJECTS) $(timeRot3_DEPENDENCIES) 
+	@rm -f timeRot3$(EXEEXT)
+	$(CXXLINK) $(timeRot3_OBJECTS) $(timeRot3_LDADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Cal3_S2.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/CalibratedCamera.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Point2.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Point3.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Pose2.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Pose3.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Rot2.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/Rot3.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/SimpleCamera.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/projectiveGeometry.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tensorInterface.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testCal3_S2.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testCalibratedCamera.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testHomography2.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testPoint2.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testPoint3.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testPose2.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testPose3.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testRot2.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testRot3.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testSimpleCamera.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testTensors.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testTrifocal.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/timeRot3.Po@am__quote@
+
+.cpp.o:
+@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ $<
+
+.cpp.obj:
+@am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+
+.cpp.lo:
+@am__fastdepCXX_TRUE@	$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCXX_FALSE@	$(LTCXXCOMPILE) -c -o $@ $<
+
+mostlyclean-libtool:
+	-rm -f *.lo
+
+clean-libtool:
+	-rm -rf .libs _libs
+install-pkgincludeHEADERS: $(pkginclude_HEADERS)
+	@$(NORMAL_INSTALL)
+	test -z "$(pkgincludedir)" || $(MKDIR_P) "$(DESTDIR)$(pkgincludedir)"
+	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(pkgincludedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(pkgincludedir)" || exit $$?; \
+	done
+
+uninstall-pkgincludeHEADERS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(pkgincludedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(pkgincludedir)" && rm -f $$files
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	set x; \
+	here=`pwd`; \
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+	  test -n "$$unique" || unique=$$empty_fix; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
+	fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+		$(TAGS_FILES) $(LISP)
+	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+	unique=`for i in $$list; do \
+	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+	  done | \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
+	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+	     $$unique
+
+GTAGS:
+	here=`$(am__cd) $(top_builddir) && pwd` \
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
+
+distclean-tags:
+	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+check-TESTS: $(TESTS)
+	@failed=0; all=0; xfail=0; xpass=0; skip=0; \
+	srcdir=$(srcdir); export srcdir; \
+	list=' $(TESTS) '; \
+	$(am__tty_colors); \
+	if test -n "$$list"; then \
+	  for tst in $$list; do \
+	    if test -f ./$$tst; then dir=./; \
+	    elif test -f $$tst; then dir=; \
+	    else dir="$(srcdir)/"; fi; \
+	    if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
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+	      case " $(XFAIL_TESTS) " in \
+	      *[\ \	]$$tst[\ \	]*) \
+		xpass=`expr $$xpass + 1`; \
+		failed=`expr $$failed + 1`; \
+		col=$$red; res=XPASS; \
+	      ;; \
+	      *) \
+		col=$$grn; res=PASS; \
+	      ;; \
+	      esac; \
+	    elif test $$? -ne 77; then \
+	      all=`expr $$all + 1`; \
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+	      dashes="$$skipped"; \
+	  fi; \
+	  report=""; \
+	  if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
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+	      dashes="$$report"; \
+	  fi; \
+	  dashes=`echo "$$dashes" | sed s/./=/g`; \
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+	    echo "$$grn$$dashes"; \
+	  else \
+	    echo "$$red$$dashes"; \
+	  fi; \
+	  echo "$$banner"; \
+	  test -z "$$skipped" || echo "$$skipped"; \
+	  test -z "$$report" || echo "$$report"; \
+	  echo "$$dashes$$std"; \
+	  test "$$failed" -eq 0; \
+	else :; fi
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+distdir: $(DISTFILES)
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+	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+	list='$(DISTFILES)'; \
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+	esac; \
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+	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
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+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
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+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
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+	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
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+distclean-generic:
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+
+
+# rule to run an executable
+%.run: % $(LDADD)
+	./$^
+
+#----------------------------------------------------------------------------------------------------
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

geometry/Pose3.cpp

@@ -6,7 +6,6 @@
 #include <iostream>
 #include "Pose3.h"
 #include "Lie-inl.h"
-#include "LieConfig.h"
 
 using namespace std;
 using namespace boost::numeric::ublas;