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	diff --git a/app/CMakeLists.txt b/app/CMakeLists.txt
	index 3983c0a..c260ba6 100644
	--- a/app/CMakeLists.txt
	+++ b/app/CMakeLists.txt
	@@ -1,178 +1,192 @@
	# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	################################################################################
	# This file is part of NUISANCE.
	#
	# NUISANCE is free software: you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation, either version 3 of the License, or
	# (at your option) any later version.
	#
	# NUISANCE is distributed in the hope that it will be useful,
	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	# GNU General Public License for more details.
	#
	# You should have received a copy of the GNU General Public License
	# along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	################################################################################

	set(TARGETS_TO_BUILD)

	if(USE_MINIMIZER)
	add_executable(nuismin nuismin.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuismin)
	target_link_libraries(nuismin ${MODULETargets})
	target_link_libraries(nuismin ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuismin ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuismin PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	add_executable(nuissplines nuissplines.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuissplines)
	target_link_libraries(nuissplines ${MODULETargets})
	target_link_libraries(nuissplines ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuissplines ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuissplines PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	endif()

	include_directories(${RWENGINE_INCLUDE_DIRECTORIES})
	include_directories(${CMAKE_SOURCE_DIR}/src/Routines)
	include_directories(${CMAKE_SOURCE_DIR}/src/InputHandler)
	include_directories(${CMAKE_SOURCE_DIR}/src/Genie)
	include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	include_directories(${CMAKE_SOURCE_DIR}/src/Utils)
	include_directories(${CMAKE_SOURCE_DIR}/src/Splines)
	include_directories(${CMAKE_SOURCE_DIR}/src/Reweight)
	include_directories(${CMAKE_SOURCE_DIR}/src/FCN)
	include_directories(${CMAKE_SOURCE_DIR}/src/MCStudies)
	include_directories(${CMAKE_SOURCE_DIR}/src/Smearceptance)
	include_directories(${EXP_INCLUDE_DIRECTORIES})

	if (USE_NuWro AND NOT NUWRO_BUILT_FROM_FILE)
	add_executable(nuwro_nuisance nuwro_NUISANCE.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuwro_nuisance)
	target_link_libraries(nuwro_nuisance ${MODULETargets})
	target_link_libraries(nuwro_nuisance ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuwro_nuisance ${ROOT_LIBS})
	include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuwro_nuisance PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	if (USE_NEUT)
	add_executable(neut_nuisance neut_NUISANCE.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};neut_nuisance)
	target_link_libraries(neut_nuisance ${MODULETargets})
	target_link_libraries(neut_nuisance ${CMAKE_DEPENDLIB_FLAGS})
	target_link_libraries(neut_nuisance ${ROOT_LIBS})
	include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(neut_nuisance PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	if (BUILD_GEVGEN)
	add_executable(gevgen_nuisance gEvGen_NUISANCE.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};gevgen_nuisance)
	target_link_libraries(gevgen_nuisance ${MODULETargets})
	target_link_libraries(gevgen_nuisance ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(gevgen_nuisance ${ROOT_LIBS})
	include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	include_directories(${GENIE_INCLUDES}/Apps)
	include_directories(${GENIE_INCLUDES}/FluxDrivers)
	include_directories(${GENIE_INCLUDES}/EVGDrivers)
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(gevgen_nuisance PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	+
	+
	+ add_executable(gevgen_nuisance_mixed gEvGen_NUISANCE_MIXED.cxx)
	+ set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};gevgen_nuisance_mixed)
	+ target_link_libraries(gevgen_nuisance_mixed ${MODULETargets})
	+ target_link_libraries(gevgen_nuisance_mixed ${CMAKE_DEPENDLIB_FLAGS})
	+ # target_link_libraries(gevgen_nuisance_mixed ${ROOT_LIBS})
	+ include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	+ include_directories(${GENIE_INCLUDES}/Apps)
	+ include_directories(${GENIE_INCLUDES}/FluxDrivers)
	+ include_directories(${GENIE_INCLUDES}/EVGDrivers)
	+ if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	+ set_target_properties(gevgen_nuisance_mixed PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	+ endif()
	endif()

	if (USE_GiBUU)
	add_executable(DumpGiBUUEvents DumpGiBUUEvents.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};DumpGiBUUEvents)
	target_link_libraries(DumpGiBUUEvents ${MODULETargets})
	target_link_libraries(DumpGiBUUEvents ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(DumpGiBUUEvents ${ROOT_LIBS})
	include_directories(${CMAKE_SOURCE_DIR}/src/FitBase)
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(DumpGiBUUEvents PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	add_executable(nuiscomp nuiscomp.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuiscomp)
	target_link_libraries(nuiscomp ${MODULETargets})
	target_link_libraries(nuiscomp ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuiscomp ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuiscomp PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	add_executable(nuisflat nuisflat.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuisflat)
	target_link_libraries(nuisflat ${MODULETargets})
	target_link_libraries(nuisflat ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuisflat ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuisflat PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	add_executable(nuissmear nuissmear.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuissmear)
	target_link_libraries(nuissmear ${MODULETargets})
	target_link_libraries(nuissmear ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuissmear ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuissmear PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	add_executable(nuissyst nuissyst.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};nuissyst)
	target_link_libraries(nuissyst ${MODULETargets})
	target_link_libraries(nuissyst ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(nuissyst ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(nuissyst PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()

	if(USE_GENIE)
	add_executable(PrepareGENIE PrepareGENIE.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};PrepareGENIE)
	target_link_libraries(PrepareGENIE ${MODULETargets})
	target_link_libraries(PrepareGENIE ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(PrepareGENIE ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(PrepareGENIE PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	if(USE_NEUT)
	add_executable(PrepareNEUT PrepareNEUT.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};PrepareNEUT)
	target_link_libraries(PrepareNEUT ${MODULETargets})
	target_link_libraries(PrepareNEUT ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(PrepareNEUT ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(PrepareNEUT PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	# PREPARE NUWRO
	# Commented out for the time being until it is finished..
	if(USE_NuWro)
	add_executable(PrepareNuwro PrepareNuwroEvents.cxx)
	set(TARGETS_TO_BUILD ${TARGETS_TO_BUILD};PrepareNuwro)
	target_link_libraries(PrepareNuwro ${MODULETargets})
	target_link_libraries(PrepareNuwro ${CMAKE_DEPENDLIB_FLAGS})
	# target_link_libraries(PrepareNuwro ${ROOT_LIBS})
	if(NOT "${CMAKE_LINK_FLAGS}" STREQUAL "")
	set_target_properties(PrepareNuwro PROPERTIES LINK_FLAGS ${CMAKE_LINK_FLAGS})
	endif()
	endif()

	install(TARGETS ${TARGETS_TO_BUILD} DESTINATION bin)
	diff --git a/cmake/MINERvASetup.cmake b/cmake/MINERvASetup.cmake
	new file mode 100644
	index 0000000..0ccfcd9
	--- /dev/null
	+++ b/cmake/MINERvASetup.cmake
	@@ -0,0 +1,19 @@
	+# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
	+
	+################################################################################
	+# This file is part of NUISANCE.
	+#
	+# NUISANCE is free software: you can redistribute it and/or modify
	+# it under the terms of the GNU General Public License as published by
	+# the Free Software Foundation, either version 3 of the License, or
	+# (at your option) any later version.
	+#
	+# NUISANCE is distributed in the hope that it will be useful,
	+# but WITHOUT ANY WARRANTY; without even the implied warranty of
	+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	+# GNU General Public License for more details.
	+#
	+# You should have received a copy of the GNU General Public License
	+# along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	+################################################################################
	+LIST(APPEND EXTRA_CXX_FLAGS -D__MINERVA_RW_ENABLED__)
	diff --git a/cmake/ReweightEnginesSetup.cmake b/cmake/ReweightEnginesSetup.cmake
	index 44c80ff..87f47d4 100644
	--- a/cmake/ReweightEnginesSetup.cmake
	+++ b/cmake/ReweightEnginesSetup.cmake
	@@ -1,82 +1,87 @@
	# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	################################################################################
	# This file is part of NUISANCE.
	#
	# NUISANCE is free software: you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation, either version 3 of the License, or
	# (at your option) any later version.
	#
	# NUISANCE is distributed in the hope that it will be useful,
	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	# GNU General Public License for more details.
	#
	# You should have received a copy of the GNU General Public License
	# along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	################################################################################

	################################## NEUT ######################################
	if(USE_NEUT)
	include(${CMAKE_SOURCE_DIR}/cmake/NEUTSetup.cmake)
	cmessage(STATUS "Using NEUT Reweight engine.")
	set(USE_NEUT TRUE CACHE BOOL "Whether to enable NEUT (reweight) support. Requires external libraries. <FALSE>" FORCE)
	endif()
	################################# NuWro ######################################
	if(USE_NuWro)
	include(${CMAKE_SOURCE_DIR}/cmake/NuWroSetup.cmake)
	cmessage(STATUS "Using NuWro Reweight engine.")
	set(USE_NuWro TRUE CACHE BOOL "Whether to enable NuWro support. <FALSE>" FORCE)
	endif()
	################################## GENIE #####################################
	if(USE_GENIE)
	include(${CMAKE_SOURCE_DIR}/cmake/GENIESetup.cmake)
	cmessage(STATUS "Using GENIE Reweight engine.")
	set(USE_GENIE TRUE CACHE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>" FORCE)
	endif()

	################################## NIWG ######################################
	if(USE_NIWG)
	include(${CMAKE_SOURCE_DIR}/cmake/NIWGSetup.cmake)
	cmessage(STATUS "Using NIWG Reweight engine.")
	set(USE_NIWG TRUE CACHE BOOL "Whether to enable (T2K) NIWG ReWeight support. Requires external libraries. <FALSE>" FORCE)
	endif()
	################################## T2K ######################################
	if(USE_T2K)
	include(${CMAKE_SOURCE_DIR}/cmake/T2KSetup.cmake)
	cmessage(STATUS "Using T2K Reweight engine.")
	set(USE_T2K TRUE CACHE BOOL "Whether to enable T2KReWeight support. Requires external libraries. <FALSE>" FORCE)
	endif()
	-
	+################################## MINERvA ######################################
	+if(USE_MINERvA_RW)
	+ include(${CMAKE_SOURCE_DIR}/cmake/MINERvASetup.cmake)
	+ cmessage(STATUS "Using MINERvA Reweight engine.")
	+ set(USE_MINERvA_RW TRUE CACHE BOOL "Whether to enable MINERvA ReWeight support. <FALSE>" FORCE)
	+endif()
	################################################################################

	################################ Prob3++ ####################################
	include(${CMAKE_SOURCE_DIR}/cmake/Prob3++Setup.cmake)
	################################################################################


	cmessage(STATUS "Reweight engine include directories: ${RWENGINE_INCLUDE_DIRECTORIES}")

	if(NEED_ROOTEVEGEN)
	cmessage(STATUS "Require ROOT eve generation libraries")
	LIST(REVERSE ROOT_LIBS)
	LIST(APPEND ROOT_LIBS
	Gui
	Ged
	Geom
	TreePlayer
	EG
	Eve)
	LIST(REVERSE ROOT_LIBS)
	endif()

	if(NEED_ROOTPYTHIA6)
	cmessage(STATUS "Require ROOT Pythia6 libraries")
	LIST(APPEND ROOT_LIBS
	EGPythia6
	Pythia6)
	endif()


	LIST(APPEND EXTRA_LIBS ${ROOT_LIBS})
	diff --git a/cmake/cacheVariables.cmake b/cmake/cacheVariables.cmake
	index 5e88e9c..1c75a96 100644
	--- a/cmake/cacheVariables.cmake
	+++ b/cmake/cacheVariables.cmake
	@@ -1,206 +1,208 @@
	# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	################################################################################
	# This file is part of NUISANCE.
	#
	# NUISANCE is free software: you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation, either version 3 of the License, or
	# (at your option) any later version.
	#
	# NUISANCE is distributed in the hope that it will be useful,
	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	# GNU General Public License for more details.
	#
	# You should have received a copy of the GNU General Public License
	# along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	################################################################################

	function(CheckAndSetDefaultEnv VARNAME DEFAULT CACHETYPE DOCSTRING ENVNAME)
	#cmessage(DEBUG "Trying to assign variable ${VARNAME} into the cache.")
	if(NOT DEFINED ${VARNAME})
	if(DEFINED ENV{${ENVNAME}} AND NOT $ENV{${ENVNAME}} STREQUAL "")
	set(${VARNAME} $ENV{${ENVNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
	cmessage(DEBUG " Read ${VARNAME} from ENVVAR ${ENVNAME} as $ENV{${ENVNAME}}.")
	else()
	set(${VARNAME} ${DEFAULT} CACHE ${CACHETYPE} ${DOCSTRING})
	endif()
	else()
	set(${VARNAME} ${${VARNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
	unset(${VARNAME})
	endif()
	cmessage(CACHE "--Set cache variable: \"${VARNAME}\" to \"${${VARNAME}}\", in cache ${CACHETYPE}.")
	endfunction()

	function(CheckAndSetDefaultCache VARNAME DEFAULT CACHETYPE DOCSTRING)
	# cmessage(DEBUG "Trying to assign variable ${VARNAME} into the cache.")
	if(NOT DEFINED ${VARNAME})
	set(${VARNAME} ${DEFAULT} CACHE ${CACHETYPE} ${DOCSTRING})
	else()
	set(${VARNAME} ${${VARNAME}} CACHE ${CACHETYPE} ${DOCSTRING})
	unset(${VARNAME})
	endif()
	cmessage(CACHE "--Set cache variable: \"${VARNAME}\" to \"${${VARNAME}}\", in cache ${CACHETYPE}.")
	endfunction()

	function(CheckAndSetDefault VARNAME DEFAULT)
	# cmessage(DEBUG "Trying to assign variable ${VARNAME}.")
	if(NOT DEFINED ${VARNAME})
	set(${VARNAME} ${DEFAULT} PARENT_SCOPE)
	set(${VARNAME} ${DEFAULT})
	endif()
	cmessage(CACHE "--Set variable: \"${VARNAME}\" to \"${${VARNAME}}\".")
	endfunction()

	CheckAndSetDefaultCache(VERBOSE TRUE BOOL "Whether to configure loudly.")

	set (CMAKE_SKIP_BUILD_RPATH TRUE)

	#Changes default install path to be a subdirectory of the build dir.
	#Can set build dir at configure time with -DCMAKE_INSTALL_PREFIX=/install/path
	if(CMAKE_INSTALL_PREFIX STREQUAL "" OR CMAKE_INSTALL_PREFIX STREQUAL
	"/usr/local")
	set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/${CMAKE_SYSTEM_NAME}")
	elseif(NOT DEFINED CMAKE_INSTALL_PREFIX)
	set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/${CMAKE_SYSTEM_NAME}")
	endif()

	if(CMAKE_BUILD_TYPE STREQUAL "")
	set(CMAKE_BUILD_TYPE DEBUG)
	elseif(NOT DEFINED CMAKE_BUILD_TYPE)
	set(CMAKE_BUILD_TYPE DEBUG)
	endif()

	CheckAndSetDefaultCache(USE_MINIMIZER TRUE INTERNAL "Whether we are using the ROOT minimization libraries. <TRUE>")

	CheckAndSetDefaultCache(USE_HEPMC FALSE BOOL "Whether to enable HepMC input support. <FALSE>")
	CheckAndSetDefaultEnv(HEPMC "" PATH "Path to HepMC source tree root directory. Overrides environment variable \$HEPMC <>" HEPMC)
	CheckAndSetDefaultCache(HEPMC_MOMUNIT "GEV" STRING "HepMC momentum units [MEV\|GEV]. <GEV>")
	CheckAndSetDefaultCache(HEPMC_LENUNIT "CM" STRING "HepMC momentum units [MM\|CM]. <CM>")
	CheckAndSetDefaultCache(HEPMC_USED_EP FALSE INTERNAL "Whether we built HepMC or not. <FALSE>")

	CheckAndSetDefaultCache(USE_NEUT FALSE BOOL "Whether to enable NEUT (reweight) support. Requires external libraries. <FALSE>")
	CheckAndSetDefaultEnv(NEUT_ROOT "" PATH "Path to NEUT source tree root directory. Overrides environment variable \$NEUT_ROOT <>" NEUT_ROOT)
	CheckAndSetDefaultEnv(CERN "" PATH "Path to CERNLIB source tree root directory that NEUT was built against. Overrides environment variable \$CERN <>" CERN)
	CheckAndSetDefaultEnv(CERN_LEVEL "" STRING "CERNLIB Library version. Overrides environment variable \$CERN_LEVEL <>" CERN_LEVEL)

	CheckAndSetDefaultCache(USE_NuWro FALSE BOOL "Whether to enable NuWro support. <FALSE>")
	CheckAndSetDefaultEnv(NUWRO "" PATH "Path to NuWro source tree root directory. Overrides environment variable \$NUWRO <>" NUWRO)
	CheckAndSetDefaultEnv(NUWRO_INC "" PATH "Path to NuWro installed includes directory, needs to contain \"params_all.h\". Overrides environment variable \$NUWRO_INC <>" NUWRO_INC)
	CheckAndSetDefaultCache(NUWRO_INPUT_FILE "" FILEPATH "Path to an input NuWro event vector, which can be used to build NuWro i/o libraries. <>")
	CheckAndSetDefaultCache(NUWRO_BUILT_FROM_FILE FALSE INTERNAL "Whether the NuWro libraries were built by NUISANCE. <FALSE>")
	CheckAndSetDefaultCache(USE_NuWro_RW FALSE BOOL "Whether to try and build support for NuWro reweighting. <FALSE>")
	CheckAndSetDefaultCache(USE_NuWro_SRW_Event FALSE BOOL "Whether to use cut down NuWro reweight event format. Requires NuWro reweight. <FALSE>")

	CheckAndSetDefaultCache(USE_GENIE FALSE BOOL "Whether to enable GENIE (reweight) support. Requires external libraries. <FALSE>")
	CheckAndSetDefaultEnv(GENIE "" PATH "Path to GENIE source tree root directory. Overrides environment variable \$GENIE <>" GENIE)
	CheckAndSetDefaultEnv(LHAPDF_LIB "" PATH "Path to pre-built LHAPDF libraries. Overrides environment variable \$LHAPDF_LIB. <>" LHAPDF_LIB)
	CheckAndSetDefaultEnv(LHAPDF_INC "" PATH "Path to installed LHAPDF headers. Overrides environment variable \$LHAPDF_INC. <>" LHAPDF_INC)
	CheckAndSetDefaultEnv(LHAPATH "" PATH "Path to LHA PDF inputs. Overrides environment variable \$LHAPATH. <>" LHAPATH)
	CheckAndSetDefaultEnv(LIBXML2_LIB "" PATH "Path to pre-built LIBXML2 libraries. Overrides environment variable \$LIBXML2_LIB. <>" LIBXML2_LIB)
	CheckAndSetDefaultEnv(LIBXML2_INC "" PATH "Path to installed LIBXML2 headers. Overrides environment variable \$LIBXML2_INC. <>" LIBXML2_INC)
	CheckAndSetDefaultEnv(LOG4CPP_LIB "" PATH "Path to pre-built LOG4CPP libraries. Overrides environment variable \$LOG4CPP_LIB. <>" LOG4CPP_LIB)
	CheckAndSetDefaultEnv(LOG4CPP_INC "" PATH "Path to installed LOG4CPP headers. Overrides environment variable \$LOG4CPP_INC. <>" LOG4CPP_INC)

	CheckAndSetDefaultCache(BUILD_GEVGEN FALSE BOOL "Whether to build nuisance_gevgen app.")

	CheckAndSetDefaultCache(USE_T2K FALSE BOOL "Whether to enable T2KReWeight support. Requires external libraries. <FALSE>")
	CheckAndSetDefaultEnv(T2KREWEIGHT "" PATH "Path to installed T2KREWEIGHTReWeight. Overrides environment variable \$T2KREWEIGHT. <>" T2KREWEIGHT)

	CheckAndSetDefaultCache(USE_NIWG FALSE BOOL "Whether to enable (T2K) NIWG ReWeight support. Requires external libraries. <FALSE>")
	CheckAndSetDefaultEnv(NIWG_ROOT "" PATH "Path to installed NIWGReWeight. Overrides environment variable \$NIWG. <>" NIWG)

	+CheckAndSetDefaultCache(USE_MINERvA_RW FALSE BOOL "Whether to enable MINERvA ReWeight support. <FALSE>")
	+
	CheckAndSetDefaultEnv(PYTHIA6 "" PATH "Path to directory containing libPythia6.so. Overrides environment variable \$PYTHIA6 <>" PYTHIA6)

	CheckAndSetDefaultEnv(PYTHIA8 "" PATH "Path to directory containing libPythia8.so. Overrides environment variable \$PYTHIA8 <>" PYTHIA8)
	CheckAndSetDefaultCache(USE_PYTHIA8 FALSE BOOL "Whether to enable PYTHIA8 event support. <FALSE>")

	CheckAndSetDefaultCache(USE_GiBUU TRUE BOOL "Whether to enable GiBUU event support. <TRUE>")
	CheckAndSetDefaultCache(BUILD_GiBUU FALSE BOOL "Whether to build supporting GiBUU event tools along with a patched version of GiBUU. <FALSE>")

	CheckAndSetDefaultCache(USE_NUANCE TRUE BOOL "Whether to enable NUANCE event support. <TRUE>")

	CheckAndSetDefaultCache(USE_PROB3PP FALSE BOOL "Whether to download and compile in Prob3++ support. <FALSE>")

	CheckAndSetDefaultCache(NO_EXTERNAL_UPDATE TRUE BOOL "Whether to perform the update target for external dependencies. <TRUE>")

	CheckAndSetDefaultCache(USE_GPERFTOOLS FALSE BOOL "Whether to compile in google performance tools. <TRUE>")

	CheckAndSetDefault(NEED_PYTHIA6 FALSE)
	CheckAndSetDefault(NEED_PYTHIA8 FALSE)

	CheckAndSetDefault(NEED_ROOTEVEGEN FALSE)
	CheckAndSetDefault(NEED_ROOTPYTHIA6 FALSE)

	CheckAndSetDefaultCache(USE_OMP FALSE BOOL "Whether to enable multicore features (there currently are none...). <FALSE>")

	CheckAndSetDefault(NO_EXPERIMENTS FALSE)

	cmessage(STATUS "NO_EXPERIMENTS: ${NO_EXPERIMENTS}")

	CheckAndSetDefaultCache(NO_ANL ${NO_EXPERIMENTS} BOOL "Whether to NOT build ANL samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_ArgoNeuT ${NO_EXPERIMENTS} BOOL "Whether to NOT build ArgoNeuT samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_BEBC ${NO_EXPERIMENTS} BOOL "Whether to NOT build BEBC samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_BNL ${NO_EXPERIMENTS} BOOL "Whether to NOT build BNL samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_FNAL ${NO_EXPERIMENTS} BOOL "Whether to NOT build FNAL samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_GGM ${NO_EXPERIMENTS} BOOL "Whether to NOT build GGM samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_K2K ${NO_EXPERIMENTS} BOOL "Whether to NOT build K2K samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_MINERvA ${NO_EXPERIMENTS} BOOL "Whether to NOT build MINERvA samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_MiniBooNE ${NO_EXPERIMENTS} BOOL "Whether to NOT build MiniBooNE samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_T2K ${NO_EXPERIMENTS} BOOL "Whether to NOT build T2K samples. <-DNO_EXPERIMENTS=FALSE>")
	CheckAndSetDefaultCache(NO_SciBooNE ${NO_EXPERIMENTS} BOOL "Whether to NOT build SciBooNE samples. <-DNO_EXPERIMENTS=FALSE>")


	function(SAYVARS)

	LIST(APPEND VARS
	USE_HEPMC
	HEPMC
	HEPMC_MOMUNIT
	HEPMC_LENUNIT
	HEPMC_USED_EP
	USE_NEUT
	NEUT_ROOT
	CERN
	CERN_LEVEL
	USE_NuWro
	NUWRO
	NUWRO_INC
	NUWRO_INPUT_FILE
	NUWRO_BUILT_FROM_FILE
	USE_GENIE
	GENIE
	LHAPDF_LIB
	LHAPDF_INC
	LIBXML2_LIB
	LIBXML2_INC
	LOG4CPP_LIB
	GENIE_LOG4CPP_INC
	BUILD_GEVGEN
	USE_T2K
	USE_NIWG
	USE_GiBUU
	BUILD_GiBUU
	USE_NUANCE
	NO_EXTERNAL_UPDATE
	USE_GPERFTOOLS
	NO_ANL
	NO_ArgoNeuT
	NO_BEBC
	NO_BNL
	NO_FNAL
	NO_GGM
	NO_K2K
	NO_MINERvA
	NO_MiniBooNE
	NO_T2K
	NO_SciBooNE)

	foreach(v ${VARS})
	if(DEFINED ${v})
	cmessage(DEBUG "VARIABLE: \"${v}\" = \"${${v}}\"")
	endif()
	endforeach(v)

	endfunction()
	diff --git a/data/priors/philcallums-bctune/bctuneprior_WithNormRES.root b/data/priors/philcallums-bctune/bctuneprior_WithNormRES.root
	new file mode 100644
	index 0000000..5f1f4e8
	Binary files /dev/null and b/data/priors/philcallums-bctune/bctuneprior_WithNormRES.root differ
	diff --git a/data/priors/philcallums-bctune/makeprior_normres.py b/data/priors/philcallums-bctune/makeprior_normres.py
	new file mode 100644
	index 0000000..25cd2aa
	--- /dev/null
	+++ b/data/priors/philcallums-bctune/makeprior_normres.py
	@@ -0,0 +1,76 @@
	+from ROOT import *
	+
	+def ConvertToGENIEDial(name, val, err):
	+ if name == "MaRES":
	+ convval = ((val / 1.12) - 1.0) / 0.20
	+ converr = ((err / 1.12) / 0.20)
	+ return "MaCCRES", convval, converr
	+
	+ elif name == "DISNorm":
	+ convval = ((val - 100.0) / 100.0)/0.5
	+ converr = (err / 100.0)/0.5
	+ return "NonRESBGvnCC1pi,NonRESBGvpCC1pi,NonRESBGvbarnCC1pi,NonRESBGvbarpCC1pi", convval, converr
	+
	+# elif name == "DISNorm":
	+# convval = ((val - 100.0) / 100.0)/0.5
	+# converr = (err / 100.0)/0.5
	+# return "NonRESBGvnCC1pi,NonRESBGvpCC1pi", convval, converr
	+
	+ elif name == "RESNorm":
	+ convval = ((val - 100.0)/100.0)
	+ converr = err / 100.0
	+ return "MINERvARW_NormCCRES", convval, converr
	+
	+def MakePriorROOTFile(name, fit, cor):
	+
	+ out = TFile("bctuneprior_" + name + ".root","RECREATE")
	+ out.cd()
	+
	+ # Make Dial Plot
	+ dials = TH1D("dials", "dials;Dials;Dial Value",
	+ len(fit),0.0,float(len(fit)))
	+ i = 0
	+ for result in fit:
	+ name, val, err = ConvertToGENIEDial( result[0], result[1], result[2] )
	+ print name, val, err
	+ dials.GetXaxis().SetBinLabel(i+1, name)
	+ dials.SetBinContent(i+1, val)
	+ dials.SetBinError(i+1, err)
	+ i += 1
	+ dials.Write()
	+
	+ # Make Cover Plot
	+ covars = TH2D("covariance","covariance;Dials;Dials;Covar",
	+ len(fit),0.0,float(len(fit)),
	+ len(fit),0.0,float(len(fit)))
	+ for i in range(len(fit)):
	+ for j in range(len(fit)):
	+
	+ namei, vali, erri = ConvertToGENIEDial( fit[i][0], fit[i][1], fit[i][2] )
	+ namej, valj, errj = ConvertToGENIEDial( fit[j][0], fit[j][1], fit[j][2] )
	+
	+ covars.GetXaxis().SetBinLabel(i+1,namei)
	+ covars.GetYaxis().SetBinLabel(j+1,namej)
	+ covars.SetBinContent(i+1,j+1, errierrjcor[i][j])
	+ covars.Write()
	+
	+ # Close
	+ out.Close()
	+
	+
	+
	+
	+
	+# Fit results [val,err]
	+# Correlation should be in same order
	+name_res = "WithNormRES"
	+fit_res = [ ["MaRES", 0.94,0.05],
	+ ["DISNorm", 46, 4],
	+ ["RESNorm", 115,7] ]
	+cor_res = [ [1.0, -0.3, -0.9],
	+ [-0.3, 1.0, 0.2],
	+ [-0.9, 0.2, 1.0] ]
	+MakePriorROOTFile(name_res, fit_res, cor_res)
	+
	+
	+
	diff --git a/licence b/licence
	index 10926e8..94a9ed0 100644
	--- a/licence
	+++ b/licence
	@@ -1,675 +1,674 @@
	GNU GENERAL PUBLIC LICENSE
	Version 3, 29 June 2007

	Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
	Everyone is permitted to copy and distribute verbatim copies
	of this license document, but changing it is not allowed.

	Preamble

	The GNU General Public License is a free, copyleft license for
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	The licenses for most software and other practical works are designed
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	share and change all versions of a program--to make sure it remains free
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	GNU General Public License for most of our software; it applies also to
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	your programs, too.

	When we speak of free software, we are referring to freedom, not
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	Developers that use the GNU GPL protect your rights with two steps:
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	feature that (1) displays an appropriate copyright notice, and (2)
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	-
	diff --git a/src/FCN/JointFCN.cxx b/src/FCN/JointFCN.cxx
	index a4136e2..31023b2 100755
	--- a/src/FCN/JointFCN.cxx
	+++ b/src/FCN/JointFCN.cxx
	@@ -1,1087 +1,1010 @@
	#include "JointFCN.h"
	#include <stdio.h>
	#include "FitUtils.h"

	-// //***************************************************
	-// JointFCN::JointFCN(std::string cardfile, TFile* outfile) {
	-// //***************************************************
	-
	-// fOutputDir = gDirectory;
	-// FitPar::Config().out = outfile;
	-
	-// fCardFile = cardfile;
	-
	-// LoadSamples(fCardFile);
	-
	-// fCurIter = 0;
	-// fMCFilled = false;
	-
	-// fOutputDir->cd();
	-
	-// fIterationTree = NULL;
	-// fDialVals = NULL;
	-// fNDials = 0;
	-
	-// fUsingEventManager = FitPar::Config().GetParB("EventManager");
	-// fOutputDir->cd();
	-// };

	+//***************************************************
	JointFCN::JointFCN(TFile* outfile) {
	+//***************************************************
	+
	fOutputDir = gDirectory;
	if (outfile) FitPar::Config().out = outfile;

	std::vector<nuiskey> samplekeys = Config::QueryKeys("sample");
	LoadSamples(samplekeys);

	std::vector<nuiskey> covarkeys = Config::QueryKeys("covar");
	LoadPulls(covarkeys);

	fCurIter = 0;
	fMCFilled = false;

	- fIterationTree = NULL;
	+ fIterationTree = false;
	fDialVals = NULL;
	fNDials = 0;

	fUsingEventManager = FitPar::Config().GetParB("EventManager");
	fOutputDir->cd();
	}

	+//***************************************************
	JointFCN::JointFCN(std::vector<nuiskey> samplekeys, TFile* outfile) {
	+//***************************************************
	+
	fOutputDir = gDirectory;
	if (outfile) FitPar::Config().out = outfile;

	LoadSamples(samplekeys);

	fCurIter = 0;
	fMCFilled = false;

	fOutputDir->cd();

	- fIterationTree = NULL;
	+ fIterationTree = false;
	fDialVals = NULL;
	fNDials = 0;

	fUsingEventManager = FitPar::Config().GetParB("EventManager");
	fOutputDir->cd();
	}

	//***************************************************
	JointFCN::~JointFCN() {
	//***************************************************

	// Delete Samples
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	delete exp;
	}

	for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	ParamPull* pull = *iter;
	delete pull;
	}

	// Sort Tree
	if (fIterationTree) DestroyIterationTree();
	if (fDialVals) delete fDialVals;
	if (fSampleLikes) delete fSampleLikes;
	};

	//***************************************************
	void JointFCN::CreateIterationTree(std::string name, FitWeight* rw) {
	- //***************************************************
	-
	- LOG(FIT) << " Creating new iteration tree! " << std::endl;
	- if (fIterationTree && !name.compare(fIterationTree->GetName())) {
	- fIterationTree->Reset();
	- return;
	- }
	-
	- fIterationTree = new TTree(name.c_str(), name.c_str());
	-
	- // Setup Main Branches
	- fIterationTree->Branch("total_likelihood", &fLikelihood,
	- "total_likelihood/D");
	- fIterationTree->Branch("total_ndof", &fNDOF, "total_ndof/I");
	+//***************************************************

	- // Setup Sample Arrays
	- int ninputs = fSamples.size() + fPulls.size();
	- fSampleLikes = new double[ninputs];
	- fSampleNDOF = new int[ninputs];
	- fNDOF = GetNDOF();
	+ LOG(FIT) << " Creating new iteration container! " << std::endl;
	+ DestroyIterationTree();
	+ fIterationTreeName = name;

	- // Setup Sample Branches
	- int count = 0;
	- for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	+ // Add sample likelihoods and ndof
	+ for (MeasListConstIter iter = fSamples.begin();
	+ iter != fSamples.end();
	iter++) {
	- MeasurementBase* exp = *iter;

	+ MeasurementBase* exp = *iter;
	std::string name = exp->GetName();
	- std::string liketag = name + "_likelihood";
	- std::string ndoftag = name + "_ndof";

	- fIterationTree->Branch(liketag.c_str(), &fSampleLikes[count],
	- (liketag + "/D").c_str());
	- fIterationTree->Branch(ndoftag.c_str(), &fSampleNDOF[count],
	- (ndoftag + "/D").c_str());
	+ std::string liketag = name + "_likelihood";
	+ fNameValues.push_back(liketag);
	+ fCurrentValues.push_back(0.0);

	- count++;
	+ std::string ndoftag = name + "_ndof";
	+ fNameValues.push_back(ndoftag);
	+ fCurrentValues.push_back(0.0);
	}

	- for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	- ParamPull* pull = *iter;
	+ // Add Pull terms
	+ for (PullListConstIter iter = fPulls.begin();
	+ iter != fPulls.end(); iter++) {

	+ ParamPull* pull = *iter;
	std::string name = pull->GetName();
	+
	std::string liketag = name + "_likelihood";
	+ fNameValues.push_back(liketag);
	+ fCurrentValues.push_back(0.0);
	+
	std::string ndoftag = name + "_ndof";
	+ fNameValues.push_back(ndoftag);
	+ fCurrentValues.push_back(0.0);
	+ }

	- fIterationTree->Branch(liketag.c_str(), &fSampleLikes[count],
	- (liketag + "/D").c_str());
	- fIterationTree->Branch(ndoftag.c_str(), &fSampleNDOF[count],
	- (ndoftag + "/D").c_str());
	+ // Add Likelihoods
	+ fNameValues.push_back("total_likelihood");
	+ fCurrentValues.push_back(0.0);

	- count++;
	- }
	+ fNameValues.push_back("total_ndof");
	+ fCurrentValues.push_back(0.0);

	- // Add Dial Branches
	- std::vector<std::string> dials = rw->GetDialNames();
	- fNDials = dials.size();
	- fDialVals = new double[fNDials];
	+ // Setup Containers
	+ fSampleN = fSamples.size() + fPulls.size();
	+ fSampleLikes = new double[fSampleN];
	+ fSampleNDOF = new int[fSampleN];

	- for (int i = 0; i < fNDials; i++) {
	- fIterationTree->Branch(dials[i].c_str(), &fDialVals[i],
	- (dials[i] + "/D").c_str());
	+ // Add Dials
	+ std::vector<std::string> dials = rw->GetDialNames();
	+ for (size_t i = 0; i < dials.size(); i++){
	+ fNameValues.push_back( dials[i] );
	+ fCurrentValues.push_back( 0.0 );
	}
	+ fNDials = dials.size();
	+ fDialVals = new double[fNDials];
	+
	+ // Set IterationTree Flag
	+ fIterationTree = true;
	+
	}

	//***************************************************
	void JointFCN::DestroyIterationTree() {
	- //***************************************************
	+//***************************************************
	+
	+ fIterationCount.clear();
	+ fCurrentValues.clear();
	+ fNameValues.clear();
	+ fIterationValues.clear();

	- if (!fIterationTree) {
	- delete fIterationTree;
	- }
	}

	//***************************************************
	void JointFCN::WriteIterationTree() {
	- //***************************************************
	+//***************************************************
	+ LOG(FIT) << "Writing iteration tree" << std::endl;
	+
	+ // Make a new TTree
	+ TTree* itree = new TTree(fIterationTreeName.c_str(),
	+ fIterationTreeName.c_str());
	+
	+ double* vals = new double[fNameValues.size()];
	+ int count = 0;
	+
	+ itree->Branch("iteration",&count,"Iteration/I");
	+ for (int i = 0; i < fNameValues.size(); i++) {
	+ itree->Branch( fNameValues[i].c_str(),
	+ &vals[i],
	+ (fNameValues[i] + "/D").c_str() );
	+ }
	+
	+ // Fill Iterations
	+ for (size_t i = 0; i < fIterationValues.size(); i++){
	+ std::vector<double> itervals = fIterationValues[i];
	+
	+ // Fill iteration state
	+ count = fIterationCount[i];
	+ for (size_t j = 0; j < itervals.size(); j++){
	+ vals[j] = itervals[j];
	+ }

	- if (!fIterationTree) {
	- ERR(FTL) << "Can't save empty iteration tree!" << std::endl;
	- throw;
	+ // Save to TTree
	+ itree->Fill();
	}
	- fIterationTree->Write();
	+
	+ // Write to file
	+ itree->Write();
	}

	//***************************************************
	void JointFCN::FillIterationTree(FitWeight* rw) {
	- //***************************************************
	+//***************************************************

	- if (!fIterationTree) {
	- ERR(FTL) << "Trying to fill iteration_tree when it is NULL!" << std::endl;
	- throw;
	+ // Loop over samples count
	+ int count = 0;
	+ for (int i = 0; i < fSampleN; i++){
	+ fCurrentValues[count++] = fSampleLikes[i];
	+ fCurrentValues[count++] = double(fSampleNDOF[i]);
	}

	+ // Fill Totals
	+ fCurrentValues[count++] = fLikelihood;
	+ fCurrentValues[count++] = double(fNDOF);
	+
	+ // Loop Over Parameter Counts
	rw->GetAllDials(fDialVals, fNDials);
	- fIterationTree->Fill();
	+ for (int i = 0; i < fNDials; i++){
	+ fCurrentValues[count++] = double(fDialVals[i]);
	+ }
	+
	+ // Push Back Into Container
	+ fIterationCount.push_back( fCurIter );
	+ fIterationValues.push_back(fCurrentValues);
	}

	//***************************************************
	double JointFCN::DoEval(const double* x) {
	//***************************************************

	// WEIGHT ENGINE
	fDialChanged = FitBase::GetRW()->HasRWDialChanged(x);
	FitBase::GetRW()->UpdateWeightEngine(x);
	if (fDialChanged) {
	FitBase::GetRW()->Reconfigure();
	FitBase::EvtManager().ResetWeightFlags();
	}
	if (LOG_LEVEL(REC)) {
	FitBase::GetRW()->Print();
	}

	// SORT SAMPLES
	ReconfigureSamples();

	// GET TEST STAT
	fLikelihood = GetLikelihood();
	-
	+ fNDOF = GetNDOF();
	+
	// PRINT PROGRESS
	LOG(FIT) << "Current Stat (iter. " << this->fCurIter << ") = " << fLikelihood
	<< std::endl;

	// UPDATE TREE
	if (fIterationTree) FillIterationTree(FitBase::GetRW());

	return fLikelihood;
	}

	//***************************************************
	int JointFCN::GetNDOF() {
	//***************************************************

	int totaldof = 0;
	int count = 0;

	// Total number of Free bins in each MC prediction
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	int dof = exp->GetNDOF();

	// Save Seperate DOF
	if (fIterationTree) {
	fSampleNDOF[count] = dof;
	}

	// Add to total
	totaldof += dof;
	count++;
	}

	// Loop over pulls
	for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	ParamPull* pull = *iter;
	double dof = pull->GetLikelihood();

	// Save seperate DOF
	if (fIterationTree) {
	fSampleNDOF[count] = dof;
	}

	// Add to total
	totaldof += dof;
	count++;
	}

	// Set Data Variable
	- fNDOF = totaldof;
	+ fSampleNDOF[count] = totaldof;

	return totaldof;
	}

	//***************************************************
	double JointFCN::GetLikelihood() {
	//***************************************************

	LOG(MIN) << std::left << std::setw(43) << "Getting likelihoods..."
	<< " : "
	<< "-2logL" << std::endl;

	// Loop and add up likelihoods in an uncorrelated way
	double like = 0.0;
	int count = 0;
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	double newlike = exp->GetLikelihood();
	int ndof = exp->GetNDOF();
	// Save seperate likelihoods
	if (fIterationTree) {
	fSampleLikes[count] = newlike;
	}

	LOG(MIN) << "-> " << std::left << std::setw(40) << exp->GetName() << " : "
	<< newlike << "/" << ndof << std::endl;

	// Add Weight Scaling
	// like *= FitBase::GetRW()->GetSampleLikelihoodWeight(exp->GetName());

	// Add to total
	like += newlike;
	count++;
	}

	// Loop over pulls
	for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	ParamPull* pull = *iter;
	double newlike = pull->GetLikelihood();

	// Save seperate likelihoods
	if (fIterationTree) {
	fSampleLikes[count] = newlike;
	}

	// Add to total
	like += newlike;
	count++;
	}

	// Set Data Variable
	fLikelihood = like;

	return like;
	};

	void JointFCN::LoadSamples(std::vector<nuiskey> samplekeys) {
	LOG(MIN) << "Loading Samples : " << samplekeys.size() << std::endl;
	for (size_t i = 0; i < samplekeys.size(); i++) {
	nuiskey key = samplekeys[i];

	// Get Sample Options
	std::string samplename = key.GetS("name");
	std::string samplefile = key.GetS("input");
	std::string sampletype = key.GetS("type");
	std::string fakeData = "";

	LOG(MIN) << "Loading Sample : " << samplename << std::endl;

	fOutputDir->cd();
	MeasurementBase* NewLoadedSample = SampleUtils::CreateSample(key);

	if (!NewLoadedSample) {
	ERR(FTL) << "Could not load sample provided: " << samplename << std::endl;
	ERR(FTL) << "Check spelling with that in src/FCN/SampleList.cxx"
	<< std::endl;
	throw;
	} else {
	fSamples.push_back(NewLoadedSample);
	}
	}
	}

	+//***************************************************
	void JointFCN::LoadPulls(std::vector<nuiskey> pullkeys) {
	+//***************************************************
	for (size_t i = 0; i < pullkeys.size(); i++) {
	nuiskey key = pullkeys[i];

	std::string pullname = key.GetS("name");
	std::string pullfile = key.GetS("input");
	std::string pulltype = key.GetS("type");

	fOutputDir->cd();
	- std::cout << "Creating Pull Term : " << std::endl;
	- sleep(1);
	fPulls.push_back(new ParamPull(pullname, pullfile, pulltype));
	}
	-
	- // // Sample Inputs
	- // if (!samplevect[0].compare("covar") \|\| !samplevect[0].compare("pulls")
	- // \|\|
	- // !samplevect[0].compare("throws")) {
	- // // Get all inputs
	- // std::string name = samplevect[1];
	- // std::string files = samplevect[2];
	- // std::string type = "DEFAULT";
	-
	- // if (samplevect.size() > 3) {
	- // type = samplevect[3];
	- // } else if (!samplevect[0].compare("pull")) {
	- // type = "GAUSPULL";
	- // } else if (!samplevect[0].compare("throws")) {
	- // type = "GAUSTHROWS";
	- // }
	-
	- // // Create Pull Class
	- // LOG(MIN) << "Loading up pull term: " << name << " << " << files << "
	- // ("
	- // << type << ")" << std::endl;
	- // std::string fakeData = "";
	- // fOutputDir->cd();
	- // fPulls.push_back(new ParamPull(name, files, type));
	- // }
	}

	-// //***************************************************
	-// void JointFCN::LoadSamples(std::string cardinput)
	-// //***************************************************
	-// {
	-// LOG(MIN) << "Initializing Samples" << std::endl;
	-
	-// // Read the card file here and load objects
	-// std::string line;
	-// std::ifstream card(cardinput.c_str(), ifstream::in);
	-
	-// // Make sure they are created in correct working DIR
	-// fOutputDir->cd();
	-
	-// while (std::getline(card >> std::ws, line, '\n')) {
	-// // Skip Empties
	-// if (line.c_str()[0] == '#') continue;
	-// if (line.empty()) continue;
	-
	-// // Parse line
	-// std::vector<std::string> samplevect = GeneralUtils::ParseToStr(line, "
	-// ");
	-
	-// // Sample Inputs
	-// if (!samplevect[0].compare("sample")) {
	-// // Get all inputs
	-// std::string name = samplevect[1];
	-// std::string files = samplevect[2];
	-// std::string type = "DEFAULT";
	-// if (samplevect.size() > 3) type = samplevect[3];
	-
	-// // Create Sample Class
	-// LOG(MIN) << "Loading up sample: " << name << " << " << files << " ("
	-// << type << ")" << std::endl;
	-// std::string fakeData = "";
	-// fOutputDir->cd();
	-// MeasurementBase* NewLoadedSample = SampleUtils::CreateSample(name,
	-// files, type,
	-// fakeData, FitBase::GetRW());
	-
	-// if (!NewLoadedSample) {
	-// ERR(FTL) << "Could not load sample provided: " << name << std::endl;
	-// ERR(FTL) << "Check spelling with that in src/FCN/SampleList.cxx"
	-// << std::endl;
	-// throw;
	-// } else {
	-// fSamples.push_back(NewLoadedSample);
	-// }
	-// }
	-
	-// // Sample Inputs
	-// if (!samplevect[0].compare("covar") \|\| !samplevect[0].compare("pulls") \|\|
	-// !samplevect[0].compare("throws")) {
	-// // Get all inputs
	-// std::string name = samplevect[1];
	-// std::string files = samplevect[2];
	-// std::string type = "DEFAULT";
	-
	-// if (samplevect.size() > 3) {
	-// type = samplevect[3];
	-// } else if (!samplevect[0].compare("pull")) {
	-// type = "GAUSPULL";
	-// } else if (!samplevect[0].compare("throws")) {
	-// type = "GAUSTHROWS";
	-// }
	-
	-// // Create Pull Class
	-// LOG(MIN) << "Loading up pull term: " << name << " << " << files << " ("
	-// << type << ")" << std::endl;
	-// std::string fakeData = "";
	-// fOutputDir->cd();
	-// fPulls.push_back(new ParamPull(name, files, type));
	-// }
	-// }
	-// card.close();
	-// };
	-
	//***************************************************
	void JointFCN::ReconfigureSamples(bool fullconfig) {
	- //***************************************************
	+//***************************************************

	int starttime = time(NULL);
	LOG(REC) << "Starting Reconfigure iter. " << this->fCurIter << std::endl;
	// std::cout << fUsingEventManager << " " << fullconfig << " " << fMCFilled <<
	// std::endl;
	// Event Manager Reconf
	if (fUsingEventManager) {
	if (!fullconfig and fMCFilled)
	ReconfigureFastUsingManager();
	else
	ReconfigureUsingManager();

	} else {
	// Loop over all Measurement Classes
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;

	// If RW Either do signal or full reconfigure.
	if (fDialChanged or !fMCFilled or fullconfig) {
	if (!fullconfig and fMCFilled)
	exp->ReconfigureFast();
	else
	exp->Reconfigure();

	// If RW Not needed just do normalisation
	} else {
	exp->Renormalise();
	}
	}
	}

	// Loop over pulls and update
	for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	ParamPull* pull = *iter;
	pull->Reconfigure();
	}

	fMCFilled = true;
	LOG(MIN) << "Finished Reconfigure iter. " << fCurIter << " in "
	<< time(NULL) - starttime << "s" << std::endl;

	fCurIter++;
	}

	//***************************************************
	void JointFCN::ReconfigureSignal() {
	- //***************************************************
	- this->ReconfigureSamples(false);
	+//***************************************************
	+ ReconfigureSamples(false);
	}

	//***************************************************
	void JointFCN::ReconfigureAllEvents() {
	//***************************************************
	FitBase::GetRW()->Reconfigure();
	FitBase::EvtManager().ResetWeightFlags();
	ReconfigureSamples(true);
	}

	std::vector<InputHandlerBase*> JointFCN::GetInputList() {
	std::vector<InputHandlerBase*> InputList;
	fIsAllSplines = true;

	MeasListConstIter iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);

	std::vector<MeasurementBase*> subsamples = exp->GetSubSamples();
	for (size_t i = 0; i < subsamples.size(); i++) {
	InputHandlerBase* inp = subsamples[i]->GetInput();
	if (std::find(InputList.begin(), InputList.end(), inp) ==
	InputList.end()) {
	if (subsamples[i]->GetInput()->GetType() != kSPLINEPARAMETER)
	fIsAllSplines = false;

	InputList.push_back(subsamples[i]->GetInput());
	}
	}
	}

	return InputList;
	}

	std::vector<MeasurementBase*> JointFCN::GetSubSampleList() {
	std::vector<MeasurementBase*> SampleList;

	MeasListConstIter iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);

	std::vector<MeasurementBase*> subsamples = exp->GetSubSamples();
	for (size_t i = 0; i < subsamples.size(); i++) {
	SampleList.push_back(subsamples[i]);
	}
	}

	return SampleList;
	}

	//***************************************************
	void JointFCN::ReconfigureUsingManager() {
	- //***************************************************
	+//***************************************************

	// 'Slow' Event Manager Reconfigure
	LOG(REC) << "Event Manager Reconfigure" << std::endl;
	int timestart = time(NULL);

	// Reset all samples
	MeasListConstIter iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);
	exp->ResetAll();
	}

	// If we are siving signal, reset all containers.
	bool savesignal = (FitPar::Config().GetParB("SignalReconfigures"));

	if (savesignal) {
	// Reset all of our event signal vectors
	fSignalEventBoxes.clear();
	fSignalEventFlags.clear();
	fSampleSignalFlags.clear();
	fSignalEventSplines.clear();
	}

	// Make sure we have a list of inputs
	if (fInputList.empty()) {
	fInputList = GetInputList();
	fSubSampleList = GetSubSampleList();
	}

	// If all inputs are splines make sure the readers are told
	// they need to be reconfigured.
	std::vector<InputHandlerBase*>::iterator inp_iter = fInputList.begin();

	if (fIsAllSplines) {
	for (; inp_iter != fInputList.end(); inp_iter++) {
	InputHandlerBase* curinput = (*inp_iter);

	// Tell reader in each BaseEvent it needs a Reconfigure next weight calc.
	BaseFitEvt* curevent = curinput->FirstBaseEvent();
	if (curevent->fSplineRead) {
	curevent->fSplineRead->SetNeedsReconfigure(true);
	}
	}
	}

	// MAIN INPUT LOOP ====================

	int fillcount = 0;
	int inputcount = 0;
	inp_iter = fInputList.begin();

	// Loop over each input in manager
	for (; inp_iter != fInputList.end(); inp_iter++) {
	InputHandlerBase* curinput = (*inp_iter);

	// Get event information
	FitEvent* curevent = curinput->FirstNuisanceEvent();
	curinput->CreateCache();

	int i = 0;
	int nevents = curinput->GetNEvents();
	int countwidth = nevents / 5;

	// Start event loop iterating until we get a NULL pointer.
	while (curevent) {
	// Get Event Weight
	curevent->RWWeight = FitBase::GetRW()->CalcWeight(curevent);
	curevent->Weight = curevent->RWWeight * curevent->InputWeight;
	double rwweight = curevent->Weight;
	// std::cout << "RWWeight = " << curevent->RWWeight << " " <<
	// curevent->InputWeight << std::endl;

	// Logging
	// std::cout << CHECKLOG(1) << std::endl;
	if (LOGGING(REC)) {
	if (i % countwidth == 0) {
	QLOG(REC, curinput->GetName()
	- << " : Processed " << i << " events. [M, W] = ["
	- << curevent->Mode << ", " << rwweight << "]");
	+ << " : Processed " << i << " events. [M, W] = ["
	+ << curevent->Mode << ", " << rwweight << "]");
	}
	}

	// Setup flag for if signal found in at least one sample
	bool foundsignal = false;

	// Create a new signal bitset for this event
	std::vector<bool> signalbitset(fSubSampleList.size());

	// Create a new signal box vector for this event
	std::vector<MeasurementVariableBox*> signalboxes;

	// Start measurement iterator
	size_t measitercount = 0;
	std::vector<MeasurementBase*>::iterator meas_iter =
	- fSubSampleList.begin();
	+ fSubSampleList.begin();

	// Loop over all subsamples (sub in JointMeas)
	for (; meas_iter != fSubSampleList.end(); meas_iter++) {
	MeasurementBase* curmeas = (*meas_iter);

	// Compare input pointers, to current input, skip if not.
	// Pointer tells us if it matches without doing ID checks.
	if (curinput != curmeas->GetInput()) {
	if (savesignal) {
	// Set bit to 0 as definitely not signal
	signalbitset[measitercount] = 0;
	}

	// Count up what measurement we are on.
	measitercount++;

	// Skip sample as input not signal.
	continue;
	}

	// Fill events for matching inputs.
	MeasurementVariableBox* box = curmeas->FillVariableBox(curevent);

	bool signal = curmeas->isSignal(curevent);
	curmeas->SetSignal(signal);
	curmeas->FillHistograms(curevent->Weight);

	// If its Signal tally up fills
	if (signal) {
	fillcount++;
	}

	// If we are saving signal/splines fill the bitset
	if (savesignal) {
	signalbitset[measitercount] = signal;
	}

	// If signal save a clone of the event box for use later.
	if (savesignal and signal) {
	foundsignal = true;
	signalboxes.push_back(box->CloneSignalBox());
	}

	// Keep track of Measurement we are on.
	measitercount++;
	}

	// Once we've filled the measurements, if saving signal
	// push back if any sample flagged this event as signal
	if (savesignal) {
	fSignalEventFlags.push_back(foundsignal);
	}

	// Save the vector of signal boxes for this event
	if (savesignal and foundsignal) {
	fSignalEventBoxes.push_back(signalboxes);
	fSampleSignalFlags.push_back(signalbitset);
	}

	// If all inputs are splines we can save the spline coefficients
	// for fast in memory reconfigures later.
	if (fIsAllSplines and savesignal and foundsignal) {
	// Make temp vector to push back with
	std::vector<float> coeff;
	for (size_t l = 0; l < (UInt_t)curevent->fSplineRead->GetNPar(); l++) {
	coeff.push_back(curevent->fSplineCoeff[l]);
	}

	// Push back to signal event splines. Kept in sync with
	// fSignalEventBoxes size.
	// int splinecount = fSignalEventSplines.size();
	fSignalEventSplines.push_back(coeff);

	// if (splinecount % 1000 == 0) {
	// std::cout << "Pushed Back Coeff " << splinecount << " : ";
	// for (size_t l = 0; l < fSignalEventSplines[splinecount].size(); l++)
	// {
	// std::cout << " " << fSignalEventSplines[splinecount][l];
	// }
	// std::cout << std::endl;
	// }
	}

	// Clean up vectors once done with this event
	signalboxes.clear();
	signalbitset.clear();

	// Iterate to the next event.
	curevent = curinput->NextNuisanceEvent();
	i++;
	}

	curinput->RemoveCache();

	// Keep track of what input we are on.
	inputcount++;
	}

	// End of Event Loop ===============================

	// Now event loop is finished loop over all Measurements
	// Converting Binned events to XSec Distributions
	iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);
	exp->ConvertEventRates();
	}

	// Print out statements on approximate memory usage for profiling.
	LOG(REC) << "Filled " << fillcount << " signal events." << std::endl;
	if (savesignal) {
	int mem =
	- ( // sizeof(fSignalEventBoxes) +
	- // fSignalEventBoxes.size() * sizeof(fSignalEventBoxes.at(0)) +
	- sizeof(MeasurementVariableBox1D) * fillcount) *
	- 1E-6;
	+ ( // sizeof(fSignalEventBoxes) +
	+ // fSignalEventBoxes.size() * sizeof(fSignalEventBoxes.at(0)) +
	+ sizeof(MeasurementVariableBox1D) * fillcount) *
	+ 1E-6;
	LOG(REC) << " -> Saved " << fillcount
	<< " signal boxes for faster access. (~" << mem << " MB)"
	<< std::endl;
	if (fIsAllSplines and !fSignalEventSplines.empty()) {
	int splmem = sizeof(float) * fSignalEventSplines.size() *
	fSignalEventSplines[0].size() * 1E-6;
	LOG(REC) << " -> Saved " << fillcount << " " << fSignalEventSplines.size()
	<< " spline sets into memory. (~" << splmem << " MB)"
	<< std::endl;
	}
	}

	LOG(REC) << "Time taken ReconfigureUsingManager() : "
	<< time(NULL) - timestart << std::endl;

	// Check SignalReconfigures works for all samples
	- if (savesignal){
	+ if (savesignal) {
	double likefull = GetLikelihood();
	ReconfigureFastUsingManager();
	double likefast = GetLikelihood();
	-
	+
	if (fabs(likefull - likefast) > 0.0001)
	- {
	- ERROR(FTL,"Fast and Full Likelihoods DIFFER! : " << likefull << " : " << likefast);
	- ERROR(FTL,"This means some samples you are using are not setup to use SignalReconfigures=1");
	- ERROR(FTL,"Please turn OFF signal reconfigures.");
	- throw;
	- } else {
	+ {
	+ ERROR(FTL, "Fast and Full Likelihoods DIFFER! : " << likefull << " : " << likefast);
	+ ERROR(FTL, "This means some samples you are using are not setup to use SignalReconfigures=1");
	+ ERROR(FTL, "Please turn OFF signal reconfigures.");
	+ throw;
	+ } else {
	LOG(FIT) << "Likelihoods for FULL and FAST match. Will use FAST next time." << std::endl;
	}
	}

	// End of reconfigure
	return;
	};

	//***************************************************
	void JointFCN::ReconfigureFastUsingManager() {
	- //***************************************************
	+//***************************************************

	LOG(FIT) << " -> Doing FAST using manager" << std::endl;
	// Get Start time for profilling
	int timestart = time(NULL);

	// Reset all samples
	MeasListConstIter iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);
	exp->ResetAll();
	}

	// Check for saved variables if not do a full reconfigure.
	if (fSignalEventFlags.empty()) {
	ERR(WRN) << "Signal Flags Empty! Using normal manager." << std::endl;
	ReconfigureUsingManager();
	return;
	}

	bool fFillNuisanceEvent =
	- FitPar::Config().GetParB("FullEventOnSignalReconfigure");
	+ FitPar::Config().GetParB("FullEventOnSignalReconfigure");

	// Setup fast vector iterators.
	std::vector<bool>::iterator inpsig_iter = fSignalEventFlags.begin();
	std::vector<std::vector<MeasurementVariableBox*> >::iterator box_iter =
	- fSignalEventBoxes.begin();
	+ fSignalEventBoxes.begin();
	std::vector<std::vector<float> >::iterator spline_iter =
	- fSignalEventSplines.begin();
	+ fSignalEventSplines.begin();
	std::vector<std::vector<bool> >::iterator samsig_iter =
	- fSampleSignalFlags.begin();
	+ fSampleSignalFlags.begin();
	int splinecount = 0;

	// Setup stuff for logging
	int fillcount = 0;
	int nevents = fSignalEventFlags.size();
	int countwidth = nevents / 20;

	// If All Splines tell splines they need a reconfigure.
	std::vector<InputHandlerBase*>::iterator inp_iter = fInputList.begin();
	if (fIsAllSplines) {
	LOG(REC) << "All Spline Inputs so using fast spline loop." << std::endl;
	for (; inp_iter != fInputList.end(); inp_iter++) {
	InputHandlerBase* curinput = (*inp_iter);

	// Tell each fSplineRead in BaseFitEvent to reconf next weight calc
	BaseFitEvt* curevent = curinput->FirstBaseEvent();
	if (curevent->fSplineRead)
	curevent->fSplineRead->SetNeedsReconfigure(true);
	}
	}

	// Loop over all possible spline inputs
	double* coreeventweights = new double[fSignalEventBoxes.size()];
	splinecount = 0;

	inp_iter = fInputList.begin();
	inpsig_iter = fSignalEventFlags.begin();
	spline_iter = fSignalEventSplines.begin();

	// Loop over all signal flags
	// For each valid signal flag add one to splinecount
	// Get Splines from that count and add to weight
	// Add splinecount
	int sigcount = 0;
	splinecount = 0;

	// #pragma omp parallel for shared(splinecount,sigcount)
	for (uint iinput = 0; iinput < fInputList.size(); iinput++) {
	InputHandlerBase* curinput = fInputList[iinput];
	BaseFitEvt* curevent = curinput->FirstBaseEvent();

	for (int i = 0; i < curinput->GetNEvents(); i++) {
	double rwweight = 0.0;
	if (fSignalEventFlags[sigcount]) {
	// Get Event Info
	if (!fIsAllSplines) {
	if (fFillNuisanceEvent)
	curinput->GetNuisanceEvent(i);
	else
	curevent = curinput->GetBaseEvent(i);
	} else {
	curevent->fSplineCoeff = &fSignalEventSplines[splinecount][0];
	}

	curevent->RWWeight = FitBase::GetRW()->CalcWeight(curevent);
	curevent->Weight = curevent->RWWeight * curevent->InputWeight;
	rwweight = curevent->Weight;

	coreeventweights[splinecount] = rwweight;
	if (splinecount % countwidth == 0) {
	LOG(REC) << "Processed " << splinecount
	<< " event weights. W = " << rwweight << std::endl;
	}

	// #pragma omp atomic
	splinecount++;
	}

	// #pragma omp atomic
	sigcount++;
	}
	}
	LOG(SAM) << "Processed event weights." << std::endl;

	// #pragma omp barrier

	// Reset Iterators
	inpsig_iter = fSignalEventFlags.begin();
	spline_iter = fSignalEventSplines.begin();
	box_iter = fSignalEventBoxes.begin();
	samsig_iter = fSampleSignalFlags.begin();
	int nsplineweights = splinecount;
	splinecount = 0;

	// Start of Fast Event Loop ============================

	// Start input iterators
	// Loop over number of inputs
	for (int ispline = 0; ispline < nsplineweights; ispline++) {
	double rwweight = coreeventweights[ispline];

	// Get iterators for this event
	std::vector<bool>::iterator subsamsig_iter = (*samsig_iter).begin();
	std::vector<MeasurementVariableBox*>::iterator subbox_iter =
	- (*box_iter).begin();
	+ (*box_iter).begin();

	// Loop over all sub measurements.
	std::vector<MeasurementBase*>::iterator meas_iter = fSubSampleList.begin();
	for (; meas_iter != fSubSampleList.end(); meas_iter++, subsamsig_iter++) {
	MeasurementBase* curmeas = (*meas_iter);

	// If event flagged as signal for this sample fill from the box.
	if (*subsamsig_iter) {
	curmeas->SetSignal(true);
	curmeas->FillHistogramsFromBox((*subbox_iter), rwweight);

	// Move onto next box if there is one.
	subbox_iter++;
	fillcount++;
	}
	}

	if (ispline % countwidth == 0) {
	LOG(REC) << "Filled " << ispline << " sample weights." << std::endl;
	}

	// Iterate over the main signal event containers.
	samsig_iter++;
	box_iter++;
	spline_iter++;
	splinecount++;
	}
	// End of Fast Event Loop ===================

	LOG(SAM) << "Filled sample distributions." << std::endl;

	// Now loop over all Measurements
	// Convert Binned events
	iterSam = fSamples.begin();
	for (; iterSam != fSamples.end(); iterSam++) {
	MeasurementBase* exp = (*iterSam);
	exp->ConvertEventRates();
	}

	// Cleanup coreeventweights
	if (fIsAllSplines) {
	delete coreeventweights;
	}

	// Print some reconfigure profiling.
	LOG(REC) << "Filled " << fillcount << " signal events." << std::endl;
	LOG(REC) << "Time taken ReconfigureFastUsingManager() : "
	<< time(NULL) - timestart << std::endl;
	}

	//***************************************************
	void JointFCN::Write() {
	- //***************************************************
	+//***************************************************

	// Save a likelihood/ndof plot
	LOG(MIN) << "Writing likelihood plot.." << std::endl;
	std::vector<double> likes;
	std::vector<double> ndofs;
	std::vector<std::string> names;
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	- iter++){
	+ iter++) {
	MeasurementBase* exp = *iter;
	double like = exp->GetLikelihood();
	double ndof = exp->GetNDOF();
	std::string name = exp->GetName();
	likes.push_back(like);
	ndofs.push_back(ndof);
	names.push_back(name);
	}
	- TH1D likehist = TH1D("likelihood_hist","likelihood_hist",
	- likes.size(), 0.0, double(likes.size()));
	- TH1D ndofhist = TH1D("ndof_hist","ndof_hist",
	- ndofs.size(), 0.0, double(ndofs.size()));
	- TH1D divhist = TH1D("likedivndof_hist","likedivndof_hist",
	- likes.size(), 0.0, double(likes.size()));
	- for (size_t i = 0; i < likehist.GetNbinsX(); i++){
	- likehist.SetBinContent(i+1, likes[i]);
	- ndofhist.SetBinContent(i+1, ndofs[i]);
	- if (ndofs[i] != 0.0){
	- divhist.SetBinContent(i+1, likes[i]/ndofs[i]);
	+ TH1D likehist = TH1D("likelihood_hist", "likelihood_hist",
	+ likes.size(), 0.0, double(likes.size()));
	+ TH1D ndofhist = TH1D("ndof_hist", "ndof_hist",
	+ ndofs.size(), 0.0, double(ndofs.size()));
	+ TH1D divhist = TH1D("likedivndof_hist", "likedivndof_hist",
	+ likes.size(), 0.0, double(likes.size()));
	+ for (size_t i = 0; i < likehist.GetNbinsX(); i++) {
	+ likehist.SetBinContent(i + 1, likes[i]);
	+ ndofhist.SetBinContent(i + 1, ndofs[i]);
	+ if (ndofs[i] != 0.0) {
	+ divhist.SetBinContent(i + 1, likes[i] / ndofs[i]);
	}
	- likehist.GetXaxis()->SetBinLabel(i+1, names[i].c_str());
	- ndofhist.GetXaxis()->SetBinLabel(i+1, names[i].c_str());
	- divhist.GetXaxis()->SetBinLabel(i+1, names[i].c_str());
	+ likehist.GetXaxis()->SetBinLabel(i + 1, names[i].c_str());
	+ ndofhist.GetXaxis()->SetBinLabel(i + 1, names[i].c_str());
	+ divhist.GetXaxis()->SetBinLabel(i + 1, names[i].c_str());
	}
	likehist.Write();
	ndofhist.Write();
	divhist.Write();

	// Loop over individual experiments and call Write
	LOG(MIN) << "Writing each of the data classes..." << std::endl;
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	exp->Write();
	}

	// Save Pull Terms
	for (PullListConstIter iter = fPulls.begin(); iter != fPulls.end(); iter++) {
	ParamPull* pull = *iter;
	pull->Write();
	}

	if (FitPar::Config().GetParB("EventManager")) {
	// Get list of inputs
	std::map<int, InputHandlerBase*> fInputs =
	- FitBase::EvtManager().GetInputs();
	+ FitBase::EvtManager().GetInputs();
	std::map<int, InputHandlerBase*>::const_iterator iterInp;

	for (iterInp = fInputs.begin(); iterInp != fInputs.end(); iterInp++) {
	InputHandlerBase* input = (iterInp->second);

	input->GetFluxHistogram()->Write();
	input->GetXSecHistogram()->Write();
	input->GetEventHistogram()->Write();
	}
	}
	};

	//***************************************************
	void JointFCN::SetFakeData(std::string fakeinput) {
	- //***************************************************
	+//***************************************************

	LOG(MIN) << "Setting fake data from " << fakeinput << std::endl;
	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	exp->SetFakeDataValues(fakeinput);
	}

	return;
	}

	//***************************************************
	void JointFCN::ThrowDataToy() {
	- //***************************************************
	+//***************************************************

	for (MeasListConstIter iter = fSamples.begin(); iter != fSamples.end();
	iter++) {
	MeasurementBase* exp = *iter;
	exp->ThrowDataToy();
	}

	return;
	}
	diff --git a/src/FCN/JointFCN.h b/src/FCN/JointFCN.h
	index 361a75a..bf87424 100755
	--- a/src/FCN/JointFCN.h
	+++ b/src/FCN/JointFCN.h
	@@ -1,165 +1,176 @@
	#ifndef _JOINT_FCN_H_
	#define _JOINT_FCN_H_
	/*!
	* \addtogroup FCN
	* @{
	*/

	#include <iostream>
	#include <vector>
	#include <fstream>
	#include <list>

	// ROOT headers
	#include "TTree.h"
	#include "TH1D.h"
	#include "TH2D.h"
	#include <TMatrixDSym.h>
	#include "TGraphErrors.h"
	#include <TVectorD.h>
	#include <TMath.h>

	#include "FitUtils.h"

	// External fitter headers
	#include "MeasurementBase.h"
	#include "SampleList.h"

	#define GetCurrentDir getcwd
	#include "EventManager.h"
	#include "Math/Functor.h"
	#include "ParamPull.h"

	#include "NuisConfig.h"
	#include "NuisKey.h"
	#include "MeasurementVariableBox.h"
	#include "MeasurementVariableBox1D.h"

	using namespace FitUtils;
	using namespace FitBase;
	//! Main FCN Class which ROOT's joint function needs to evaulate the chi2 at each stage of the fit.
	class JointFCN
	{
	public:

	//! Constructor
	//! cardfile = Path to input card file listing samples
	JointFCN(std::vector<nuiskey> samplekeys, TFile* outfile=NULL);
	JointFCN(TFile* outfile=NULL); // Loads from global config
	//! Destructor
	~JointFCN();

	//! Create sample list from cardfile
	void LoadSamples(std::vector<nuiskey> samplekeys);
	void LoadPulls(std::vector<nuiskey> pullkeys);

	//! Main Likelihood evaluation FCN
	double DoEval(const double *x);

	//! Func Wrapper for ROOT
	inline double operator() (const std::vector<double> & x) {
	double* x_array = new double[x.size()];
	return this->DoEval(x_array);
	};

	//! Func Wrapper for ROOT
	inline double operator() (const double *x) {
	return this->DoEval(x);
	};

	//! Create a TTree to save all dial value iterations for this FCN
	void CreateIterationTree(std::string name, FitWeight* rw);

	//! Fills dial values and sample likelihoods into tree
	void FillIterationTree(FitWeight* rw);

	//! Writes TTree to fOutput directory
	void WriteIterationTree();

	//! Deletes TTree
	void DestroyIterationTree();

	//! Get Degrees of Freedom for samples (NBins)
	int GetNDOF();

	//! Return NDOF wrapper
	inline unsigned int NDim() {return this->GetNDOF();};

	//! Reconfigure samples where we force all events to be looped over.
	void ReconfigureAllEvents() ;

	//! Call Reconfigure on samples.
	//! Choice of reconfigure type depends on whether dials have changed
	//! and the MC has been filled.
	void ReconfigureSamples(bool fullconfig = false);

	//! Call reconfigure on only signal events (defaults to all events if CurIter=0)
	void ReconfigureSignal();

	//! Gets likelihood for all samples in FCN (assuming uncorrelated)
	double GetLikelihood();

	//! Returns list of pointers to the samples
	inline std::list<MeasurementBase*> GetSampleList(){ return fSamples; }

	//! Return list of pointers to all the pulls
	inline std::list<ParamPull*> GetPullList(){ return fPulls; };

	//! Write all samples to output DIR
	void Write();

	//! Set Fake data from file/MC
	void SetFakeData(std::string fakeinput);

	//! Reconfigure looping over duplicate inputs
	void ReconfigureUsingManager();

	//! Reconfigure Fast looping over duplicate inputs
	void ReconfigureFastUsingManager();


	/// Throws data according to current stats
	void ThrowDataToy();

	std::vector<MeasurementBase*> GetSubSampleList();
	std::vector<InputHandlerBase*> GetInputList();

	private:

	//! Append the experiments to include in the fit to this list
	std::list<MeasurementBase*> fSamples;

	//! Append parameter pull terms to include penalties in the fit to this list
	std::list<ParamPull*> fPulls;

	TDirectory *fOutputDir; //!< Directory to save contents

	std::string fCardFile; //!< Input Card text file

	bool fDialChanged; //!< Flag for if RW dials changed
	UInt_t fCurIter; //!< Counter for how many times reconfigure called
	bool fMCFilled; //!< Check MC has at least been filled once

	- TTree* fIterationTree; //!< Tree to save RW values on each function call
	+ bool fIterationTree; //!< Tree to save RW values on each function call
	int fNDials; //!< Number of RW Dials in FitWeight
	double* fDialVals; //!< Current Values of RW Dials
	double fLikelihood; //!< Current likelihood for joint sample likelihood
	double fNDOF; //!< Total NDOF
	double* fSampleLikes; //!< Likelihoods for each individual measurement in list
	int * fSampleNDOF; //!< NDOF for each individual measurement in list

	bool fUsingEventManager; //!< Flag for doing joint comparisons

	std::vector< std::vector<float> > fSignalEventSplines;
	std::vector< std::vector<MeasurementVariableBox*> > fSignalEventBoxes;
	std::vector< bool > fSignalEventFlags;
	std::vector< std::vector<bool> > fSampleSignalFlags;

	std::vector<InputHandlerBase*> fInputList;
	std::vector<MeasurementBase*> fSubSampleList;
	bool fIsAllSplines;

	+
	+ std::vector< int > fIterationCount;
	+ std::vector< double > fCurrentValues;
	+ std::vector< std::string > fNameValues;
	+ std::vector< std::vector<double> > fIterationValues;
	+ int fSampleN;
	+ std::string fIterationTreeName;
	+
	+
	+
	+
	};

	/! @} /
	#endif // _JOINT_FCN_H_
	diff --git a/src/FitBase/ParamPull.cxx b/src/FitBase/ParamPull.cxx
	index 4a0c6bc..cd101bc 100644
	--- a/src/FitBase/ParamPull.cxx
	+++ b/src/FitBase/ParamPull.cxx
	@@ -1,810 +1,849 @@
	// Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	/*******************************************************************************
	* This file is part of NUISANCE.
	*
	* NUISANCE is free software: you can redistribute it and/or modify
	* it under the terms of the GNU General Public License as published by
	* the Free Software Foundation, either version 3 of the License, or
	* (at your option) any later version.
	*
	* NUISANCE is distributed in the hope that it will be useful,
	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	* GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License
	* along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	*******************************************************************************/
	#include "ParamPull.h"

	//*******************************************************************************
	ParamPull::ParamPull(std::string name, std::string inputfile, std::string type, std::string dials) {
	//*******************************************************************************

	fMinHist = NULL;
	fMaxHist = NULL;
	fTypeHist = NULL;
	fDialSelection = dials;
	+ fLimitHist = NULL;

	fName = name;
	fInput = inputfile;
	fType = type;

	// Set the pull type
	SetType(fType);
	std::cout << fType << std::endl;

	// Setup Histograms from input file
	SetupHistograms(fInput);
	};

	//*******************************************************************************
	void ParamPull::SetType(std::string type) {
	//*******************************************************************************

	fType = type;
	// Assume Default if empty
	if (type.empty() \|\| type == "DEFAULT") {
	ERR(WRN) << "No type specified for ParmPull class " << fName << std::endl;
	ERR(WRN) << "Assuming GAUSTHROW/GAUSPULL" << std::endl;

	type = "GAUSTHROW/GAUSPULL";
	}

	// Set Dial options
	if (type.find("FRAC") != std::string::npos) {

	fDialOptions = "FRAC";
	fPlotTitles = ";; Fractional RW Value";

	} else if (type.find("ABS") != std::string::npos) {

	fDialOptions = "ABS";
	fPlotTitles = ";; ABS RW Value";

	} else {

	fDialOptions = "";
	fPlotTitles = ";; RW Value";

	}

	// Parse throw types
	if (type.find("GAUSPULL") != std::string::npos) fCalcType = kGausPull;
	else fCalcType = kNoPull;

	if (type.find("GAUSTHROW") != std::string::npos) fThrowType = kGausThrow;
	+ else if (type.find("FLATTHROW") != std::string::npos) fThrowType = kFlatThrow;
	else fThrowType = kNoThrow;

	// Extra check to see if throws or pulls are turned off
	if (type.find("NOPULL") != std::string::npos) fCalcType = kNoPull;
	if (type.find("NOTHROW") != std::string::npos) fThrowType = kNoThrow;

	}

	//*******************************************************************************
	void ParamPull::SetupHistograms(std::string input) {
	//*******************************************************************************

	// Extract Types from Input
	fFileType = "";
	const int nfiletypes = 4;
	const std::string filetypes[nfiletypes] = {"FIT", "ROOT", "TXT", "DIAL"};

	for (int i = 0; i < nfiletypes; i++) {
	std::string tempTypes = filetypes[i] + ":";
	if (input.find(tempTypes) != std::string::npos) {
	fFileType = filetypes[i];
	input.replace(input.find(tempTypes), tempTypes.size(), "");
	break;
	}
	}

	// Read Files
	if (!fFileType.compare("FIT")) ReadFitFile(input);
	else if (!fFileType.compare("ROOT")) ReadRootFile(input);
	else if (!fFileType.compare("VECT")) ReadVectFile(input);
	else if (!fFileType.compare("DIAL")) ReadDialInput(input);
	else {
	ERR(FTL) << "Unknown ParamPull Type: " << input << std::endl;
	throw;
	}

	// Check Dials are all good
	CheckDialsValid();

	// Setup MC Histogram
	fMCHist = (TH1D*) fDataHist->Clone();
	fMCHist->Reset();
	fMCHist->SetNameTitle( (fName + "_MC").c_str(),
	(fName + " MC" + fPlotTitles).c_str() );

	// If no Covar input make an uncorrelated one
	if (!fCovar) {
	fCovar = StatUtils::MakeDiagonalCovarMatrix(fDataHist, 1.0);
	}

	// If no types or limits are provided give them a default option
	if (!fMinHist) {
	fMinHist = (TH1D*) fDataHist->Clone();
	fMinHist->SetNameTitle( (fName + "_min").c_str(),
	(fName + " min" + fPlotTitles).c_str() );
	for (int i = 0; i < fMinHist->GetNbinsX(); i++) {
	// TODO (P.Stowell) Change this to a NULL system where limits are actually free!
	fMinHist->SetBinContent(i + 1, fDataHist->GetBinContent(i + 1) - 1E6);
	}
	}

	if (!fMaxHist) {
	fMaxHist = (TH1D*) fDataHist->Clone();
	fMaxHist->SetNameTitle( (fName + "_min").c_str(),
	(fName + " min" + fPlotTitles).c_str() );
	for (int i = 0; i < fMaxHist->GetNbinsX(); i++) {
	fMaxHist->SetBinContent(i + 1, fDataHist->GetBinContent(i + 1) - 1E6);
	}
	}

	// Set types from state, or to unknown
	if (!fTypeHist) {

	int deftype = -1;
	if (fType.find("T2K") != std::string::npos) { deftype = kT2K; }
	else if (fType.find("NEUT") != std::string::npos) { deftype = kNEUT; }
	else if (fType.find("NIWG") != std::string::npos) { deftype = kNIWG; }
	else if (fType.find("GENIE") != std::string::npos) { deftype = kGENIE; }
	else if (fType.find("NORM") != std::string::npos) { deftype = kNORM; }
	else if (fType.find("NUWRO") != std::string::npos) { deftype = kNUWRO; }

	fTypeHist = new TH1I( (fName + "_type").c_str(),
	(fName + " type" + fPlotTitles).c_str(),
	fDataHist->GetNbinsX(), 0, fDataHist->GetNbinsX() );

	for (int i = 0; i < fTypeHist->GetNbinsX(); i++) {
	fTypeHist->SetBinContent(i + 1, deftype );
	}
	}


	// Sort Covariances
	fInvCovar = StatUtils::GetInvert(fCovar);
	fDecomp = StatUtils::GetDecomp(fCovar);

	// Create DataTrue for Throws
	fDataTrue = (TH1D*) fDataHist->Clone();
	fDataTrue->SetNameTitle( (fName + "_truedata").c_str(),
	(fName + " truedata" + fPlotTitles).c_str() );

	fDataOrig = (TH1D*) fDataHist->Clone();
	fDataOrig->SetNameTitle( (fName + "_origdata").c_str(),
	(fName + " origdata" + fPlotTitles).c_str() );

	// Select only dials we want
	if (!fDialSelection.empty()) {
	(fDataHist) = RemoveBinsNotInString(fDataHist, fDialSelection);



	}

	}

	//*******************************************************************************
	TH1D ParamPull::RemoveBinsNotInString(TH1D hist, std::string mystr) {
	//*******************************************************************************

	// Make list of allowed bins
	std::vector<std::string> allowedbins;
	for (int i = 0; i < hist.GetNbinsX(); i++) {
	std::string syst = std::string(hist.GetXaxis()->GetBinLabel(i + 1));

	if (mystr.find(syst) != std::string::npos) {
	allowedbins.push_back(syst);
	}
	}

	// Make new histogram
	UInt_t nbins = allowedbins.size();
	TH1D newhist = TH1D( hist.GetName(), hist.GetTitle(),
	(Int_t)nbins, 0.0, (Double_t)nbins);

	// Setup bins
	for (UInt_t i = 0; i < nbins; i++) {
	// Set Labels
	newhist.GetXaxis()->SetBinLabel(i + 1, allowedbins[i].c_str());

	// Copy Values
	for (Int_t j = 0; j < hist.GetNbinsX(); j++) {
	if (!allowedbins[i].compare(hist.GetXaxis()->GetBinLabel(j + 1))) {
	newhist.SetBinContent(i + 1, hist.GetBinContent(j + 1) );
	newhist.SetBinError(i + 1, hist.GetBinError(j + 1) );
	}
	}
	}

	return newhist;
	}

	//*******************************************************************************
	TH1I ParamPull::RemoveBinsNotInString(TH1I hist, std::string mystr) {
	//*******************************************************************************

	// Make list of allowed bins
	std::vector<std::string> allowedbins;
	for (int i = 0; i < hist.GetNbinsX(); i++) {
	std::string syst = std::string(hist.GetXaxis()->GetBinLabel(i + 1));

	if (mystr.find(syst) != std::string::npos) {
	allowedbins.push_back(syst);
	}
	}

	// Make new histogram
	UInt_t nbins = allowedbins.size();
	TH1I newhist = TH1I( hist.GetName(), hist.GetTitle(),
	(Int_t)nbins, 0.0, (Int_t)nbins);

	// Setup bins
	for (UInt_t i = 0; i < nbins; i++) {
	// Set Labels
	newhist.GetXaxis()->SetBinLabel(i + 1, allowedbins[i].c_str());

	// Copy Values
	for (Int_t j = 0; j < hist.GetNbinsX(); j++) {
	if (!allowedbins[i].compare(hist.GetXaxis()->GetBinLabel(j + 1))) {
	newhist.SetBinContent(i + 1, hist.GetBinContent(j + 1) );
	newhist.SetBinError(i + 1, hist.GetBinError(j + 1) );
	}
	}
	}

	return newhist;
	}

	//*******************************************************************************
	void ParamPull::ReadFitFile(std::string input) {
	//*******************************************************************************

	TFile* tempfile = new TFile(input.c_str(), "READ");

	// Read Data
	fDataHist = (TH1D*) tempfile->Get("fit_dials_free");
	if (!fDataHist) {
	ERR(FTL) << "Can't find TH1D hist fit_dials in " << fName << std::endl;
	ERR(FTL) << "File Entries:" << std::endl;
	tempfile->ls();

	throw;
	}

	fDataHist->SetDirectory(0);
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " data" + fPlotTitles).c_str() );

	// Read Covar
	TH2D* tempcov = (TH2D*) tempfile->Get("covariance_free");
	if (!tempcov) {
	ERR(FTL) << "Can't find TH2D covariance_free in " << fName << std::endl;
	ERR(FTL) << "File Entries:" << std::endl;
	tempfile->ls();

	throw;
	}

	// Setup Covar
	int nbins = fDataHist->GetNbinsX();
	fCovar = new TMatrixDSym( nbins );

	for (int i = 0; i < nbins; i++) {
	for (int j = 0; j < nbins; j++) {
	(*fCovar)(i, j) = tempcov->GetBinContent(i + 1, j + 1);
	}
	}

	return;
	}

	//*******************************************************************************
	void ParamPull::ReadRootFile(std::string input) {
	//*******************************************************************************

	std::vector<std::string> inputlist = GeneralUtils::ParseToStr(input, ";");

	// Check all given
	if (inputlist.size() < 2) {
	ERR(FTL) << "Covar supplied in 'ROOT' format should have 3 semi-colon seperated entries!" << std::endl
	<< "ROOT:filename;histname[;covarname]" << std::endl;
	ERR(FTL) << "histname = TH1D, covarname = TH2D" << std::endl;
	throw;
	}

	// Get Entries
	std::string filename = inputlist[0];
	LOG(DEB) << filename << std::endl;
	std::string histname = inputlist[1];
	LOG(DEB) << histname << std::endl;
	LOG(DEB) << input << std::endl;

	// Read File
	TFile* tempfile = new TFile(filename.c_str(), "READ");
	+ if (tempfile->IsZombie()){
	+ LOG(FIT) << "Looking for ParamPull input inside database" << std::endl;
	+ filename = FitPar::GetDataBase() + "/" + filename;
	+ tempfile = new TFile(filename.c_str(), "READ");
	+ }
	if (tempfile->IsZombie()) {
	ERR(FTL) << "Can't find file in " << fName << std::endl;
	ERR(FTL) << "location = " << filename << std::endl;
	throw;
	}

	// Read Hist
	fDataHist = (TH1D*) tempfile->Get(histname.c_str());
	if (!fDataHist) {
	ERR(FTL) << "Can't find TH1D hist " << histname << " in " << fName << std::endl;
	ERR(FTL) << "File Entries:" << std::endl;
	tempfile->ls();

	throw;
	}
	fDataHist->SetDirectory(0);
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " data" + fPlotTitles).c_str() );

	LOG(DEB) << "READING COVAR" << std::endl;
	// Read Covar
	if (inputlist.size() > 2) {
	std::string covarname = inputlist[2];
	LOG(DEB) << "COVARNAME = " << covarname << std::endl;

	TH2D* tempcov = (TH2D*) tempfile->Get(covarname.c_str());
	if (!tempcov) {
	ERR(FTL) << "Can't find TH2D covar " << covarname << " in " << fName << std::endl;
	ERR(FTL) << "File Entries:" << std::endl;
	tempfile->ls();

	throw;
	}

	// Setup Covar
	int nbins = fDataHist->GetNbinsX();
	fCovar = new TMatrixDSym( nbins );

	for (int i = 0; i < nbins; i++) {
	for (int j = 0; j < nbins; j++) {
	(*fCovar)(i, j) = tempcov->GetBinContent(i + 1, j + 1);
	}
	}

	// Uncorrelated
	} else {
	LOG(SAM) << "No Covar provided so using diagonal errors for "
	<< fName << std::endl;
	fCovar = NULL;
	}
	}

	//*******************************************************************************
	void ParamPull::ReadVectFile(std::string input) {
	//*******************************************************************************

	std::vector<std::string> inputlist = GeneralUtils::ParseToStr(input, ";");
	if (inputlist.size() < 4) {
	ERR(FTL) << "Need 3 inputs for vector input in " << fName << std::endl;
	ERR(FTL) << "Inputs: " << input << std::endl;
	throw;
	}

	// Open File
	std::string rootname = inputlist[0];
	TFile* tempfile = new TFile(rootname.c_str(), "READ");
	if (tempfile->IsZombie()) {
	ERR(FTL) << "Can't find file in " << fName << std::endl;
	ERR(FTL) << "location = " << rootname << std::endl;
	throw;
	}

	// Get Name
	std::string tagname = inputlist[1];
	// TVector<std::string> dialtags = tempfile->Get(tagname.c_str());
	// if (!dialtags){
	// ERR(FTL) << "Can't find list of dial names!" << std::endl;
	// }

	// Get Values
	std::string valuename = inputlist[2];
	TVectorD* dialvals = (TVectorD*)tempfile->Get(valuename.c_str());
	if (!dialvals) {
	ERR(FTL) << "Can't find dial values" << std::endl;
	}

	// Get Matrix
	std::string matrixname = inputlist[3];
	TMatrixD* matrixvals = (TMatrixD*)tempfile->Get(matrixname.c_str());
	if (!matrixvals) {
	ERR(FTL) << "Can't find matirx values" << std::endl;
	}

	// Get Types
	if (inputlist.size() > 4) {
	std::string typesname = inputlist[3];
	}

	// Get Minimum
	if (inputlist.size() > 5) {
	std::string minname = inputlist[4];
	}

	// Get Maximum
	if (inputlist.size() > 6) {
	std::string maxname = inputlist[5];
	}

	}

	//*******************************************************************************
	void ParamPull::ReadDialInput(std::string input) {
	//*******************************************************************************

	std::vector<std::string> inputlist = GeneralUtils::ParseToStr(input, ";");
	if (inputlist.size() < 3) {
	ERR(FTL) << "Need 3 inputs for dial input in " << fName << std::endl;
	ERR(FTL) << "Inputs: " << input << std::endl;
	throw;
	}

	std::vector<double> inputvals = GeneralUtils::ParseToDbl(input, ";");
	std::string dialname = inputlist[0];
	double val = inputvals[1];
	double err = inputvals[2];

	fDataHist = new TH1D( (fName + "_data").c_str(),
	(fName + "_data" + fPlotTitles).c_str(), 1, 0, 1);
	fDataHist->SetBinContent(1, val);
	fDataHist->SetBinError(1, err);
	fDataHist->GetXaxis()->SetBinLabel(1, dialname.c_str());

	+
	+ fLimitHist = new TH1D( (fName + "_limits").c_str(),
	+ (fName + "_limits" + fPlotTitles).c_str(), 1, 0, 1);
	+ fLimitHist->Reset();
	+ if (inputvals.size() > 4) {
	+ fLimitHist->SetBinContent(1, (inputvals[3] + inputvals[4]) / 2.0);
	+ fLimitHist->SetBinError(1, (inputvals[4] - inputvals[3]) / 2.0);
	+ }
	+
	fCovar = NULL;
	}

	//*******************************************************************************
	std::map<std::string, int> ParamPull::GetAllDials() {
	//*******************************************************************************

	std::map<std::string, int> dialtypemap;

	for (int i = 0; i < fDataHist->GetNbinsX(); i++) {

	std::string name = fDataHist->GetXaxis()->GetBinLabel(i + 1);
	int type = fTypeHist->GetBinContent(i + 1);

	dialtypemap[name] = type;

	}

	return dialtypemap;
	}


	//*******************************************************************************
	bool ParamPull::CheckDialsValid() {
	//*******************************************************************************

	return true;
	std::string helpstring = "";

	for (int i = 0; i < fDataHist->GetNbinsX(); i++) {
	std::string name = std::string(fDataHist->GetXaxis()->GetBinLabel(i + 1));

	// If dial exists its all good
	if (FitBase::GetRW()->DialIncluded(name)) continue;

	// If it doesn't but its a sample norm also continue
	if (name.find("_norm") != std::string::npos) {
	ERR(WRN) << "Norm dial included in covar but not set in FitWeight." << std::endl;
	ERR(WRN) << "Assuming its a sample norm and skipping..." << std::endl;
	}

	// Dial unknown so print a help statement
	std::ostringstream tempstr;
	tempstr << "unknown_parameter " << name << " "
	<< fDataHist->GetBinContent(i + 1) << " "
	<< fDataHist->GetBinContent(i + 1) - fDataHist->GetBinError(i + 1) << " "
	<< fDataHist->GetBinContent(i + 1) + fDataHist->GetBinError(i + 1) << " "
	<< fDataHist->GetBinError(i + 1) << " ";

	if (!fType.empty()) tempstr << fType << std::endl;
	else tempstr << "FREE" << std::endl;
	helpstring += tempstr.str();
	}

	// Show statement before failing
	if (!helpstring.empty()) {

	ERR(WRN) << "Dial(s) included in covar but not set in FitWeight." << std::endl
	<< "ParamPulls needs to know how you want it to be treated." << std::endl
	<< "Include the following lines into your card:" << std::endl;

	ERR(WRN) << helpstring << std::endl;
	throw;
	return false;
	} else {
	return true;
	}

	}



	//*******************************************************************************
	void ParamPull::Reconfigure() {
	//*******************************************************************************

	FitWeight* rw = FitBase::GetRW();

	// Get Dial Names that are valid
	std::vector<std::string> namevec = rw->GetDialNames();
	std::vector<double> valuevec = rw->GetDialValues();

	// Set Bin Values from RW
	for (UInt_t i = 0; i < namevec.size(); i++) {

	// Loop over bins and check name matches
	std::string syst = namevec.at(i);
	double systval = valuevec.at(i);
	std::vector<std::string> allsyst = GeneralUtils::ParseToStr(syst, ",");

	// Proper Reconf using RW
	for (int j = 0; j < fMCHist->GetNbinsX(); j++) {

	// Search for the name of this bin in the corrent dial
	std::string binname = std::string(fMCHist->GetXaxis()->GetBinLabel(j + 1) );

	// Check Full Name
	if (!syst.compare(binname.c_str())) {
	fMCHist->SetBinContent(j + 1, systval);
	break;
	}


	std::vector<std::string> splitbinname = GeneralUtils::ParseToStr(binname, ",");
	for (size_t l = 0; l < splitbinname.size(); l++) {
	std::string singlebinname = splitbinname[l];
	for (size_t k = 0; k < allsyst.size(); k++) {
	if (!allsyst[k].compare(singlebinname.c_str())) {
	fMCHist->SetBinContent(j + 1, systval);
	}
	}
	}
	}



	}

	return;
	};

	//*******************************************************************************
	void ParamPull::ResetToy(void) {
	//*******************************************************************************

	if (fDataHist) delete fDataHist;

	LOG(DEB) << "Resetting toy" << std::endl;
	LOG(DEB) << fDataTrue << std::endl;
	fDataHist = (TH1D*)fDataTrue->Clone();
	LOG(DEB) << "Setting name" << std::endl;
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " data" + fPlotTitles).c_str() );

	}



	//*******************************************************************************
	void ParamPull::SetFakeData(std::string fakeinput) {
	//*******************************************************************************

	// Set from MC Setting
	if (!fakeinput.compare("MC")) {

	// Copy MC into data
	if (fDataHist) delete fDataHist;
	fDataHist = (TH1D*)fMCHist->Clone();
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " fakedata" + fPlotTitles).c_str() );

	// Copy original data errors
	for (int i = 0; i < fDataOrig->GetNbinsX(); i++) {
	fDataHist->SetBinError(i + 1, fDataOrig->GetBinError(i + 1) );
	}

	// Make True Toy Central Value Hist
	fDataTrue = (TH1D*) fDataHist->Clone();
	fDataTrue->SetNameTitle( (fName + "_truedata").c_str(),
	(fName + " truedata" + fPlotTitles).c_str() );

	} else {

	ERR(FTL) << "Trying to set fake data for ParamPulls not from MC!" << std::endl;
	ERR(FTL) << "Not currently implemented.." << std::endl;
	throw;

	}
	}

	//*******************************************************************************
	void ParamPull::RemoveFakeData() {
	//*******************************************************************************

	delete fDataHist;
	fDataHist = (TH1D*)fDataOrig->Clone();
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " data" + fPlotTitles).c_str() );

	fDataTrue = (TH1D*) fDataHist->Clone();
	fDataTrue->SetNameTitle( (fName + "_truedata").c_str(),
	(fName + " truedata" + fPlotTitles).c_str() );

	}

	//*******************************************************************************
	double ParamPull::GetLikelihood() {
	//*******************************************************************************

	double like = 0.0;

	switch (fCalcType) {

	// Gaussian Calculation with correlations
	case kGausPull:
	like = StatUtils::GetChi2FromCov(fDataHist, fMCHist, fInvCovar, NULL);
	like *= 1E-76;
	break;

	// Default says this has no pull
	case kNoThrow:
	default:
	like = 0.0;
	break;
	}


	LOG(DEB) << "Likelihood = " << like << " " << fCalcType << std::endl;
	return like;

	};

	//*******************************************************************************
	int ParamPull::GetNDOF() {
	//*******************************************************************************

	int ndof = 0;

	if (fCalcType != kNoThrow) {
	- ndof += fDataHist->GetNbinsX();
	+ ndof = fDataHist->GetNbinsX();
	}

	return ndof;
	};


	//*******************************************************************************
	void ParamPull::ThrowCovariance() {
	//*******************************************************************************

	// Reset toy for throw
	ResetToy();
	- LOG(DEB) << "Toy Reset " << std::endl;
	+ LOG(FIT) << "Creating new toy dataset" << std::endl;

	// Generate random Gaussian throws
	std::vector<double> randthrows;
	for (int i = 0; i < fDataHist->GetNbinsX(); i++) {
	double randtemp = 0.0;

	switch (fThrowType) {

	// Gaussian Throws
	case kGausThrow:
	randtemp = gRandom->Gaus(0.0, 1.0);
	break;

	+ // Uniform Throws
	+ case kFlatThrow:
	+ randtemp = gRandom->Uniform(0.0, 1.0);
	+ if (fLimitHist) {
	+ randtemp = fLimitHist->GetBinContent(i + 1) + fLimitHist->GetBinError(i + 1) * ( randtemp * 2 - 1 );
	+ }
	+ break;
	+
	// No Throws (DEFAULT)
	default:
	break;
	}

	randthrows.push_back(randtemp);
	}

	// Create Bin Modifications
	double totalres = 0.0;
	for (int i = 0; i < fDataHist->GetNbinsX(); i++) {

	// Calc Bin Mod
	double binmod = 0.0;
	- for (int j = 0; j < fDataHist->GetNbinsX(); j++) {
	- // std::cout << "DECOMP " << j << " " << i << " " << randthrows.at(j) << std::endl;
	- binmod += (fDecomp)(j, i) randthrows.at(j);
	+
	+ if (fThrowType == kGausThrow) {
	+ for (int j = 0; j < fDataHist->GetNbinsX(); j++) {
	+ binmod += (fDecomp)(j, i) randthrows.at(j);
	+ }
	+ } else if (fThrowType == kFlatThrow) {
	+ binmod = randthrows.at(i) - fDataHist->GetBinContent(i + 1);
	}

	+
	// Add up fraction dif
	totalres += binmod;

	// Add to current data
	fDataHist->SetBinContent(i + 1, fDataHist->GetBinContent(i + 1) + binmod);
	}

	// Rename
	fDataHist->SetNameTitle( (fName + "_data").c_str(),
	(fName + " toydata" + fPlotTitles).c_str() );

	- // Print Status
	- LOG(REC) << "Created new toy histogram. Total Dif = "
	- << totalres << std::endl;
	+ // Check Limits
	+ if (fLimitHist) {
	+ for (int i = 0; i < fLimitHist->GetNbinsX(); i++) {
	+ if (fLimitHist->GetBinError(i + 1) == 0.0) continue;
	+ if (fDataHist->GetBinContent(i + 1) > fLimitHist->GetBinContent(i + 1) + fLimitHist->GetBinError(i + 1) \|\|
	+ fDataHist->GetBinContent(i + 1) < fLimitHist->GetBinContent(i + 1) - fLimitHist->GetBinError(i + 1)) {
	+ this->ThrowCovariance();
	+ }
	+ }
	+ }
	+
	return;
	};


	//*******************************************************************************
	TH2D ParamPull::GetCovar() {
	//*******************************************************************************

	TH2D tempCov = TH2D(*fInvCovar);

	for (int i = 0; i < tempCov.GetNbinsX(); i++) {
	tempCov.GetXaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	tempCov.GetYaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	}

	tempCov.SetNameTitle((fName + "_INVCOV").c_str(),
	(fName + " InvertedCovariance;Dials;Dials").c_str());

	return tempCov;
	}

	//*******************************************************************************
	TH2D ParamPull::GetFullCovar() {
	//*******************************************************************************

	TH2D tempCov = TH2D(*fCovar);

	for (int i = 0; i < tempCov.GetNbinsX(); i++) {
	tempCov.GetXaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	tempCov.GetYaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	}

	tempCov.SetNameTitle((fName + "_COV").c_str(),
	(fName + " Covariance;Dials;Dials").c_str());

	return tempCov;
	}

	//*******************************************************************************
	TH2D ParamPull::GetDecompCovar() {
	//*******************************************************************************

	TH2D tempCov = TH2D(*fCovar);

	for (int i = 0; i < tempCov.GetNbinsX(); i++) {
	tempCov.GetXaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	tempCov.GetYaxis()->SetBinLabel(i + 1, fDataHist->GetXaxis()->GetBinLabel(i + 1));
	}

	tempCov.SetNameTitle((fName + "_DEC").c_str(),
	(fName + " Decomposition;Dials;Dials").c_str());

	return tempCov;
	}


	//*******************************************************************************
	void ParamPull::Write(std::string writeoptt) {
	//*******************************************************************************

	fDataHist->Write();
	fMCHist->Write();
	-
	+ if (fLimitHist) {
	+ fLimitHist->Write();
	+ }
	GetCovar().Write();
	GetFullCovar().Write();
	GetDecompCovar().Write();

	return;
	};

	diff --git a/src/FitBase/ParamPull.h b/src/FitBase/ParamPull.h
	index 22e707d..7da9eac 100644
	--- a/src/FitBase/ParamPull.h
	+++ b/src/FitBase/ParamPull.h
	@@ -1,188 +1,193 @@
	// Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	/*******************************************************************************
	* This file is part of NUISANCE.
	*
	* NUISANCE is free software: you can redistribute it and/or modify
	* it under the terms of the GNU General Public License as published by
	* the Free Software Foundation, either version 3 of the License, or
	* (at your option) any later version.
	*
	* NUISANCE is distributed in the hope that it will be useful,
	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	* GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License
	* along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	*******************************************************************************/

	#ifndef PARAM_PULL_H_SEEN
	#define PARAM_PULL_H_SEEN

	/*!
	* \addtogroup FitBase
	* @{
	*/

	#include <stdlib.h>
	#include <numeric>
	#include <math.h>
	#include <iostream>
	#include <sstream>
	#include <fstream>
	#include <list>
	#include <vector>

	// ROOT includes
	#include <TROOT.h>
	#include <TH1D.h>
	#include <TTree.h>
	#include <TFile.h>
	#include <TMatrixDSym.h>
	#include <TDecompSVD.h>
	#include <TVectorD.h>

	// Fit Includes
	#include "PlotUtils.h"
	#include "StatUtils.h"
	#include "FitWeight.h"
	#include "FitLogger.h"
	#include "EventManager.h"
	#include "TVector.h"

	using namespace std;

	//! Enums to allow Non Guassian Pulls in Future
	enum FitPullTypes {
	kUnknownPull = -1,
	kNoPull = 0,
	kGausPull = 1
	};

	enum FitThrowTypes {
	kUnknownThrow = -1,
	kNoThrow = 0,
	- kGausThrow = 1
	+ kGausThrow = 1,
	+ kFlatThrow = 2
	};

	//! Used to produce gaussian penalty terms in the fit.
	class ParamPull {
	public:

	//! Default Constructor
	ParamPull(std::string name, std::string inputfile, std::string type, std::string dials="");

	//! Default destructor
	virtual ~ParamPull(void) {};

	// Set dial types (DEFAULT,ABS,FRAC)
	void SetType(std::string type);

	// Setup Histogram inputs (from previous fit file, or ROOT file)
	void SetupHistograms(std::string input);

	// Read a previous NUISANCE file
	void ReadFitFile(std::string input);

	// Read a ROOT file with any histograms in
	void ReadRootFile(std::string input);

	// Read Text file
	void ReadVectFile(std::string input);

	// Read a single dial central value and error
	void ReadDialInput(std::string input);

	//! Reconfigure function reads in current RW engine dials and sets their value to MC
	void Reconfigure(void);

	//! Get likelihood given the current values
	double GetLikelihood(void);

	//! Get NDOF if used in likelihoods
	int GetNDOF(void);

	// Get Covariance Matrices as plots
	TH2D GetCovar(void);
	TH2D GetFullCovar(void);
	TH2D GetDecompCovar(void);

	// Get Covariance Matrices
	inline TMatrixDSym GetCovarMatrix (void) const { return *fInvCovar; };
	inline TMatrixDSym GetFullCovarMatrix (void) const { return *fCovar; };
	inline TMatrixDSym GetDecompCovarMatrix (void) const { return *fDecomp; };

	//! Save the histograms
	void Write(std::string writeopt="");

	//! Throw the dial values using the current covariance. Useful for parameter throws.
	void ThrowCovariance(void);

	//! Compare dials to RW
	bool CheckDialsValid(void);

	//! Reset toy data back to original data
	void ResetToy(void);

	//! Read fake data from MC
	void SetFakeData(std::string fakeinput);

	//! Reset fake data back to original data (before fake data or throws)
	void RemoveFakeData();

	// Get Functions
	inline std::string GetName (void) const { return fName; };
	inline std::string GetInput (void) const { return fInput; };
	inline std::string GetType (void) const { return fType; };
	inline std::string GetFileType (void) const { return fFileType; };
	inline std::string GetDialOptions (void) const { return fDialOptions; };

	std::map<std::string, int> GetAllDials();

	inline TH1D GetDataHist (void) const { return *fDataHist; };
	inline TH1D GetDataTrue (void) const { return *fDataTrue; };
	inline TH1D GetDataOrig (void) const { return *fDataOrig; };
	inline TH1D GetMCHist (void) const { return *fMCHist; };
	inline TH1D GetMaxHist (void) const { return *fMaxHist; };
	inline TH1D GetMinHist (void) const { return *fMinHist; };
	inline TH1I GetDialTypes (void) const { return *fTypeHist; };
	+ inline TH1D GetLimitHist (void) const { return *fLimitHist; };
	+

	private:

	TH1D RemoveBinsNotInString(TH1D hist, std::string mystr);
	TH1I RemoveBinsNotInString(TH1I hist, std::string mystr);

	std::string fName; //!< Pull Name
	std::string fInput; //!< Pull input string
	std::string fType; //!< Pull options type
	std::string fFileType; //!< Pull input file types
	std::string fPlotTitles; //! Axis format
	std::string fDialOptions; //!< Dial handling options
	std::string fDialSelection; //!< Dial Selection

	TH1D* fMCHist; //!< Current MC Histogram
	TH1D* fDataHist; //!< Current data Histogram
	TH1D* fDataTrue; //!< True Data (before histogram throws)
	TH1D* fDataOrig; //!< Orig Data (without toys or fake data)
	TH1D* fMaxHist; //!< Maximum limit on MC/Data
	TH1D* fMinHist; //!< Maximum limit on MC/Data
	TH1I* fTypeHist; //!< Dial Types

	int fCalcType; //!< Method to calculate likelihood
	int fThrowType; //!< Method to calculate throws

	TMatrixDSym* fCovar; //!< Covariance
	TMatrixDSym* fInvCovar; //!< Inverted Covariance
	TMatrixDSym* fDecomp; //!< Decomposition
	+
	+ TH1D* fLimitHist;

	};

	// Class TypeDefs
	typedef std::list<ParamPull*>::const_iterator PullListConstIter;
	typedef std::list<ParamPull*>::iterator PullListIter;
	typedef std::vector<ParamPull*>::const_iterator PullVectConstIter;
	typedef std::vector<ParamPull*>::iterator PullVectIter;

	/! @} /
	#endif
	diff --git a/src/FitBase/SampleSettings.cxx b/src/FitBase/SampleSettings.cxx
	index 5388c0d..f574209 100644
	--- a/src/FitBase/SampleSettings.cxx
	+++ b/src/FitBase/SampleSettings.cxx
	@@ -1,226 +1,231 @@
	#include "SampleSettings.h"

	SampleSettings::SampleSettings() {
	};

	SampleSettings::SampleSettings(nuiskey key) {
	fKeyValues = key;
	if (!key.Has("type")) key.AddS("type", "DEFAULT");
	}

	std::string SampleSettings::GetName() {
	return GetS("name");
	}

	void SampleSettings::SetS(std::string name, std::string val) {
	fKeyValues.SetS(name, val);
	};

	bool SampleSettings::Found(std::string name, std::string substr) {
	std::string compstring = fKeyValues.GetS(name);
	return compstring.find(substr) != std::string::npos;
	}


	void SampleSettings::SetXTitle(std::string name) {
	SetDefault("xtitle", name);
	};

	void SampleSettings::SetYTitle(std::string name) {
	SetDefault("ytitle", name);
	};


	void SampleSettings::SetZTitle(std::string name) {
	SetDefault("ztitle", name);
	};

	void SampleSettings::SetNormError(double norm) {
	SetDefault("norm_error", GeneralUtils::DblToStr(norm));
	};

	double SampleSettings::GetNormError() {
	return GetD("norm_error");
	};

	std::string SampleSettings::GetCovarInput() {
	return GetS("covar");
	}

	void SampleSettings::SetAllowedTypes(std::string allowed, std::string defaulttype) {
	SetDefault("default_types", allowed);
	SetDefault("allowed_types", defaulttype);
	};

	void SampleSettings::SetEnuRangeFromFlux(TH1D* fluxhist) {
	double enu_min = fluxhist->GetXaxis()->GetXmin();
	double enu_max = fluxhist->GetXaxis()->GetXmax();
	SetEnuRange(enu_min, enu_max);
	};

	void SampleSettings::SetEnuRange(double min, double max) {
	SetDefault("enu_min", min);
	SetDefault("enu_max", max);
	};

	void SampleSettings::Set(std::string name, double d) {
	SetDefault(name, d);
	}

	void SampleSettings::Set(std::string name, int i) {
	SetDefault(name, i);
	}

	void SampleSettings::Set(std::string name, std::string s) {
	SetDefault(name, s);
	}



	void SampleSettings::DefineAllowedTargets(std::string targ) {
	// fAllowedTargets = TargetUtils::ParseTargetsToIntVect(targ);
	};


	void SampleSettings::FoundFill(std::string name, std::string substr, bool& cont, bool def) {
	std::string compstring = fKeyValues.GetS(name);
	if (compstring.find(substr) != std::string::npos) {
	cont = def;
	} else {
	cont = !def;
	}
	};


	void SampleSettings::SetTitle(std::string val) {
	SetDefault("title", val);
	};

	void SampleSettings::SetDataInput(std::string val) {
	SetDefault("data", val);
	};

	std::string SampleSettings::GetMapInput() {
	return GetS("map");
	}
	void SampleSettings::SetMapInput(std::string val) {
	SetDefault("map", val);
	}

	void SampleSettings::SetErrorInput(std::string val) {
	SetDefault("error", val);
	};



	void SampleSettings::SetCovarInput(std::string val) {
	SetDefault("covar", val);
	};

	+void SampleSettings::SetShapeCovarInput(std::string val) {
	+ SetDefault("shapecovar", val);
	+};
	+
	+
	void SampleSettings::SetDefault(std::string name, std::string val) {
	if (!fKeyValues.Has(name)) fKeyValues.AddS(name, val);
	};

	void SampleSettings::SetDefault(std::string name, double val ) {
	if (!fKeyValues.Has(name)) fKeyValues.AddD(name, val);
	};

	void SampleSettings::SetHasExtraHistograms(bool opt) {
	fHasExtraHistograms = opt;
	};

	void SampleSettings::DefineAllowedSpecies(std::string species) {
	fAllowedTargets = BeamUtils::ParseSpeciesToIntVect(species);
	};

	std::string SampleSettings::Title() {
	return GetS("title");
	}

	std::string SampleSettings::GetDataInput() {
	return GetS("data");
	};


	std::string SampleSettings::GetErrorInput() {
	return GetS("error");
	};

	std::string SampleSettings::PlotTitles() {
	return ";" + GetS("xtitle") + ";" + GetS("ytitle");
	};

	std::string SampleSettings::GetFullTitles() {
	return Title() + PlotTitles();
	}

	int SampleSettings::GetI(std::string name) {
	return fKeyValues.GetI(name);
	}

	bool SampleSettings::GetB(std::string name){
	return fKeyValues.GetB(name);
	}


	double SampleSettings::GetD(std::string name) {
	return fKeyValues.GetD(name);
	}

	std::string SampleSettings::GetS(std::string name) {
	return fKeyValues.GetS(name);
	}

	void SampleSettings::SetSuggestedFlux(std::string str) {
	SetS("suggested_flux", str);
	}

	void SampleSettings::SetDescription(std::string str) {
	SetS("description", str);
	}

	void SampleSettings::Write(std::string name) {

	if (name.empty()) name = this->GetS("name") + "_settings";

	// Make a new canvas
	TCanvas* c1 = new TCanvas( name.c_str(), name.c_str(), 800, 600 );
	c1->cd();

	// Make new TPaveText
	TPaveText pttitle = TPaveText(0.05, 0.85, 0.95, 0.95);
	pttitle.AddText( name.c_str() );
	pttitle.SetTextAlign(11);
	pttitle.SetTextSize(15);
	pttitle.Draw();


	TPaveText pt = TPaveText(0.05, 0.05, 0.95, 0.80);
	std::vector<std::string> keys = fKeyValues.GetAllKeys();
	for (int i = 0; i < keys.size(); i++) {

	std::string keyval = fKeyValues.GetS(keys[i]);
	std::vector<std::string> lines = GeneralUtils::ParseToStr(keyval, "\n");

	if (lines.size() == 1) {
	pt.AddText( ("#bullet #bf{" + keys[i] + "} : " + fKeyValues.GetS(keys[i])).c_str() );
	} else {
	pt.AddText( ("#bullet #bf{" + keys[i] + "} : ").c_str() );
	for (int j = 0; j < lines.size(); j++) {
	pt.AddText((" \|--> " + lines[j]).c_str() );
	}
	}
	}

	pt.SetTextAlign(11);
	pt.SetTextSize(14);
	pt.Draw("SAME");


	c1->Write();
	delete c1;
	}

	void SampleSettings::SetOnlyMC(bool state) {
	SetDefault("onlymc", state);
	}
	diff --git a/src/FitBase/SampleSettings.h b/src/FitBase/SampleSettings.h
	index e689eeb..358a584 100644
	--- a/src/FitBase/SampleSettings.h
	+++ b/src/FitBase/SampleSettings.h
	@@ -1,74 +1,77 @@
	#ifndef SAMPLESETTINGS_H
	#define SAMPLESETTINGS_H
	#include "NuisConfig.h"
	#include "NuisKey.h"
	#include "TH1D.h"
	#include "BeamUtils.h"
	#include "TPaveText.h"
	#include "TCanvas.h"

	class SampleSettings {
	public:
	SampleSettings();
	SampleSettings(nuiskey key);

	inline std::string Name(){return GetName();};
	std::string GetName();
	void SetS(std::string name, std::string val);
	void SetXTitle(std::string name);
	void SetYTitle(std::string name);
	void SetZTitle(std::string name);
	void SetNormError(double norm);
	double GetNormError();

	void SetAllowedTypes(std::string allowed, std::string defaulttype="FIX");
	void SetEnuRangeFromFlux(TH1D* fluxhist);
	void SetEnuRange(double min, double max);
	std::string Title();
	void DefineAllowedTargets(std::string targ);

	void FoundFill(std::string name, std::string substr, bool& cont, bool def);
	// void FoundFill(std::string name, std::string substr, double& val, double )
	bool Found(std::string name, std::string substr);
	void SetTitle(std::string val);
	void SetDataInput(std::string val);
	void SetErrorInput(std::string val);
	std::string GetErrorInput();

	std::string GetMapInput();
	void SetMapInput(std::string val);
	void SetCovarInput(std::string val);
	+ void SetShapeCovarInput(std::string val);

	void SetDefault(std::string name, std::string val);
	void SetDefault(std::string name, double val);
	void SetHasExtraHistograms(bool opt = true);
	void DefineAllowedSpecies(std::string species);
	void SetSuggestedFlux(std::string str);
	void SetDescription(std::string str);

	void Write(std::string name="");

	std::string GetFullTitles();

	bool Has(std::string name){return fKeyValues.Has(name);};

	std::string GetDataInput();
	std::string PlotTitles();
	std::string GetS(std::string name);
	int GetI(std::string name);
	double GetD(std::string name);
	std::string GetCovarInput();
	void SetOnlyMC(bool state=true);
	bool GetB(std::string name);

	void Set(std::string name, int i);
	void Set(std::string name, std::string s);
	void Set(std::string name, double d);

	+
	+
	std::vector<int> fAllowedTargets;
	std::vector<int> fAllowedSpecies;
	nuiskey fKeyValues;
	bool fHasExtraHistograms;
	};

	#endif
	diff --git a/src/Reweight/CMakeLists.txt b/src/Reweight/CMakeLists.txt
	index 1f9270c..685133c 100644
	--- a/src/Reweight/CMakeLists.txt
	+++ b/src/Reweight/CMakeLists.txt
	@@ -1,79 +1,81 @@
	# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	################################################################################
	# This file is part of NUISANCE.
	#
	# NUISANCE is free software: you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation, either version 3 of the License, or
	# (at your option) any later version.
	#
	# NUISANCE is distributed in the hope that it will be useful,
	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	# GNU General Public License for more details.
	#
	# You should have received a copy of the GNU General Public License
	# along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	################################################################################
	set(IMPLFILES
	GlobalDialList.cxx
	FitWeight.cxx
	WeightEngineBase.cxx
	NEUTWeightEngine.cxx
	NuWroWeightEngine.cxx
	GENIEWeightEngine.cxx
	WeightUtils.cxx
	SampleNormEngine.cxx
	LikelihoodWeightEngine.cxx
	SplineWeightEngine.cxx
	NUISANCESyst.cxx
	T2KWeightEngine.cxx
	NUISANCEWeightEngine.cxx
	NUISANCEWeightCalcs.cxx
	NIWGWeightEngine.cxx
	OscWeightEngine.cxx
	+MINERvAWeightCalcs.cxx
	)

	set(HEADERFILES
	GlobalDialList.h
	FitWeight.h
	WeightEngineBase.h
	NEUTWeightEngine.h
	NuWroWeightEngine.h
	GENIEWeightEngine.h
	WeightUtils.h
	SampleNormEngine.h
	LikelihoodWeightEngine.h
	SplineWeightEngine.h
	NUISANCESyst.h
	T2KWeightEngine.h
	NUISANCEWeightEngine.h
	NUISANCEWeightCalcs.h
	NIWGWeightEngine.h
	OscWeightEngine.h
	+MINERvAWeightCalcs.h
	)

	set(LIBNAME Reweight)

	if(CMAKE_BUILD_TYPE MATCHES DEBUG)
	add_library(${LIBNAME} STATIC ${IMPLFILES})
	else(CMAKE_BUILD_TYPE MATCHES RELEASE)
	add_library(${LIBNAME} SHARED ${IMPLFILES})
	endif()

	include_directories(${MINIMUM_INCLUDE_DIRECTORIES})

	set_target_properties(${LIBNAME} PROPERTIES VERSION
	"${ExtFit_VERSION_MAJOR}.${ExtFit_VERSION_MINOR}.${ExtFit_VERSION_REVISION}")
	#set_target_properties(${LIBNAME} PROPERTIES LINK_FLAGS ${ROOT_LD_FLAGS})

	if(DEFINED PROJECTWIDE_EXTRA_DEPENDENCIES)
	add_dependencies(${LIBNAME} ${PROJECTWIDE_EXTRA_DEPENDENCIES})
	endif()

	install(TARGETS ${LIBNAME} DESTINATION lib)
	#Can uncomment this to install the headers... but is it really neccessary?
	install(FILES ${HEADERFILES} DESTINATION include)

	set(MODULETargets ${MODULETargets} ${LIBNAME} PARENT_SCOPE)
	diff --git a/src/Reweight/MINERvAWeightCalcs.cxx b/src/Reweight/MINERvAWeightCalcs.cxx
	index 5fefde9..ebd453a 100644
	--- a/src/Reweight/MINERvAWeightCalcs.cxx
	+++ b/src/Reweight/MINERvAWeightCalcs.cxx
	@@ -1,345 +1,469 @@
	#ifdef __MINERVA_RW_ENABLED__
	#ifdef __GENIE_ENABLED__

	#include "MINERvAWeightCalcs.h"
	#include "BaseFitEvt.h"

	namespace nuisance {
	namespace reweight {

	+
	+//*******************************************************
	+MINERvAReWeight_QE::MINERvAReWeight_QE() {
	+ //*******************************************************
	+ fTwk_NormCCQE = 0.0;
	+ fDef_NormCCQE = 1.0;
	+ fCur_NormCCQE = fDef_NormCCQE;
	+}
	+
	+MINERvAReWeight_QE::~MINERvAReWeight_QE(){};
	+
	+double MINERvAReWeight_QE::CalcWeight(BaseFitEvt* evt) {
	+ // Check GENIE
	+ if (evt->fType != kGENIE) return 1.0;
	+
	+ // Extract the GENIE Record
	+ GHepRecord* ghep = static_cast<GHepRecord*>(evt->genie_event->event);
	+ const Interaction* interaction = ghep->Summary();
	+ const InitialState& init_state = interaction->InitState();
	+ const ProcessInfo& proc_info = interaction->ProcInfo();
	+ const Target& tgt = init_state.Tgt();
	+
	+ // If the event is not QE this Calc doesn't handle it
	+ if (!proc_info.IsQuasiElastic()) return 1.0;
	+
	+ // WEIGHT CALCULATIONS -------------
	+ double w = 1.0;
	+
	+ // CCQE Dial
	+ if (!proc_info.IsWeakCC()) w *= fCur_NormCCQE;
	+
	+ // Return Combined Weight
	+ return w;
	+}
	+
	+void MINERvAReWeight_QE::SetDialValue(std::string name, double val) {
	+ SetDialValue(Reweight::ConvDial(name, kCUSTOM), val);
	+}
	+
	+void MINERvAReWeight_QE::SetDialValue(int rwenum, double val) {
	+ // Check Handled
	+ int curenum = rwenum % 1000;
	+ if (!IsHandled(curenum)) return;
	+
	+ // Set Values
	+ if (curenum == kMINERvARW_NormCCQE) {
	+ fTwk_NormCCQE = val;
	+ fCur_NormCCQE = fDef_NormCCQE + fTwk_NormCCQE;
	+ }
	+
	+ // Define Tweaked
	+ fTweaked = ((fTwk_NormCCQE != 0.0));
	+}
	+
	+bool MINERvAReWeight_QE::IsHandled(int rwenum) {
	+ int curenum = rwenum % 1000;
	+
	+ switch (curenum) {
	+ case kMINERvARW_NormCCQE:
	+ return true;
	+ default:
	+ return false;
	+ }
	+}
	+
	+
	+//*******************************************************
	MINERvAReWeight_MEC::MINERvAReWeight_MEC() {
	+ //*******************************************************
	fTwk_NormCCMEC = 0.0;
	fDef_NormCCMEC = 1.0;
	fCur_NormCCMEC = fDef_NormCCMEC;
	}

	-virtual ~MINERvAReWeight_MEC::MINERvAReWeight_MEC(){};
	+MINERvAReWeight_MEC::~MINERvAReWeight_MEC(){};

	double MINERvAReWeight_MEC::CalcWeight(BaseFitEvt* evt) {
	// Check GENIE
	if (evt->fType != kGENIE) return 1.0;

	// Extract the GENIE Record
	GHepRecord* ghep = static_cast<GHepRecord*>(evt->genie_event->event);
	const Interaction* interaction = ghep->Summary();
	const InitialState& init_state = interaction->InitState();
	const ProcessInfo& proc_info = interaction->ProcInfo();
	const Target& tgt = init_state.Tgt();

	// If the event is not MEC this Calc doesn't handle it
	if (!proc_info.IsMEC()) return 1.0;

	// WEIGHT CALCULATIONS -------------
	double w = 1.0;

	// CCMEC Dial
	- if (!proc_info.IsCC()) w *= fCur_NormCCMEC;
	+ if (!proc_info.IsWeakCC()) w *= fCur_NormCCMEC;

	// Return Combined Weight
	return w;
	}

	void MINERvAReWeight_MEC::SetDialValue(std::string name, double val) {
	SetDialValue(Reweight::ConvDial(name, kCUSTOM), val);
	}

	void MINERvAReWeight_MEC::SetDialValue(int rwenum, double val) {
	// Check Handled
	int curenum = rwenum % 1000;
	if (!IsHandled(curenum)) return;

	// Set Values
	- if (curenum == kMINERvARW_NormCCMEC) fTwk_NormCCMEC = val;
	+ if (curenum == kMINERvARW_NormCCMEC) {
	+ fTwk_NormCCMEC = val;
	+ fCur_NormCCMEC = fDef_NormCCMEC + fTwk_NormCCMEC;
	+ }

	// Define Tweaked
	fTweaked = ((fTwk_NormCCMEC != 0.0));
	}

	bool MINERvAReWeight_MEC::IsHandled(int rwenum) {
	int curenum = rwenum % 1000;

	switch (curenum) {
	case kMINERvARW_NormCCMEC:
	return true;
	default:
	return false;
	}
	}
	+
	+//*******************************************************
	+MINERvAReWeight_RES::MINERvAReWeight_RES() {
	+ //*******************************************************
	+ fTwk_NormCCRES = 0.0;
	+ fDef_NormCCRES = 1.0;
	+ fCur_NormCCRES = fDef_NormCCRES;
	+}
	+
	+MINERvAReWeight_RES::~MINERvAReWeight_RES(){};
	+
	+double MINERvAReWeight_RES::CalcWeight(BaseFitEvt* evt) {
	+
	+ // std::cout << "Caculating RES" << std::endl;
	+ // Check GENIE
	+ if (evt->fType != kGENIE) return 1.0;
	+
	+ // Extract the GENIE Record
	+ GHepRecord* ghep = static_cast<GHepRecord*>(evt->genie_event->event);
	+ const Interaction* interaction = ghep->Summary();
	+ const InitialState& init_state = interaction->InitState();
	+ const ProcessInfo& proc_info = interaction->ProcInfo();
	+ const Target& tgt = init_state.Tgt();
	+
	+ // If the event is not RES this Calc doesn't handle it
	+ if (!proc_info.IsResonant()) return 1.0;
	+
	+ // WEIGHT CALCULATIONS -------------
	+ double w = 1.0;
	+
	+ // CCRES Dial
	+ if (proc_info.IsWeakCC()) w *= fCur_NormCCRES;
	+
	+ // Return Combined Weight
	+ return w;
	+}
	+
	+void MINERvAReWeight_RES::SetDialValue(std::string name, double val) {
	+ SetDialValue(Reweight::ConvDial(name, kCUSTOM), val);
	+}
	+
	+void MINERvAReWeight_RES::SetDialValue(int rwenum, double val) {
	+ // Check Handled
	+ int curenum = rwenum % 1000;
	+ if (!IsHandled(curenum)) return;
	+
	+ // Set Values
	+ if (curenum == kMINERvARW_NormCCRES) {
	+ fTwk_NormCCRES = val;
	+ fCur_NormCCRES = fDef_NormCCRES + fTwk_NormCCRES;
	+ }
	+
	+ // Define Tweaked
	+ fTweaked = ((fTwk_NormCCRES != 0.0));
	+}
	+
	+bool MINERvAReWeight_RES::IsHandled(int rwenum) {
	+ int curenum = rwenum % 1000;
	+
	+ switch (curenum) {
	+ case kMINERvARW_NormCCRES:
	+ return true;
	+ default:
	+ return false;
	+ }
	+}
	+
	+//*******************************************************
	+RikRPA::RikRPA() {
	+ //*******************************************************
	+
	+ // - Syst : kMINERvA_RikRPA_ApplyRPA
	+ // - Type : Binary
	+ // - Limits : 0.0 (false) -> 1.0 (true)
	+ // - Default : 0.0
	+ fApplyDial_RPACorrection = false;
	+
	+ // - Syst : kMINERvA_RikRPA_LowQ2
	+ // - Type : Absolute
	+ // - Limits : 1.0 -> 1.0
	+ // - Default : 0.0
	+ // - Frac Error : 100%
	+ fDefDial_RPALowQ2 = 0.0;
	+ fCurDial_RPALowQ2 = fDefDial_RPALowQ2;
	+ fErrDial_RPALowQ2 = 0.0;
	+
	+ // - Syst : kMINERvA_RikRPA_HighQ2
	+ // - Type : Absolute
	+ // - Limits : 1.0 -> 1.0
	+ // - Default : 0.0
	+ // - Frac Error : 100%
	+ fDefDial_RPAHighQ2 = 0.0;
	+ fCurDial_RPAHighQ2 = fDefDial_RPAHighQ2;
	+ fErrDial_RPAHighQ2 = 1.0;
	+
	+ fEventWeights = new double[5];
	+
	+ for (size_t i = 0; i < kMaxCalculators; i++) {
	+ // fRPACalculators[i] = NULL;
	+ }
	+
	+ fTweaked = false;
	+}
	+
	+RikRPA::~RikRPA() {
	+ delete fEventWeights;
	+
	+ for (size_t i = 0; i < kMaxCalculators; i++) {
	+ // if (fRPACalculators[i]) delete fRPACalculators[i];
	+ // fRPACalculators[i] = NULL;
	+ }
	+}
	+
	+double RikRPA::CalcWeight(BaseFitEvt* evt) {
	+ // LOG(FIT) << "Calculating RikRPA" << std::endl;
	+ // Return 1.0 if not tweaked
	+ if (!fTweaked) return 1.0;
	+
	+ double w = 1.0;
	+
	+ // Extract the GENIE Record
	+ GHepRecord* ghep = static_cast<GHepRecord*>(evt->genie_event->event);
	+ const Interaction* interaction = ghep->Summary();
	+ const InitialState& init_state = interaction->InitState();
	+ const ProcessInfo& proc_info = interaction->ProcInfo();
	+ // const Kinematics & kine = interaction->Kine();
	+ // const XclsTag & xcls = interaction->ExclTag();
	+ const Target& tgt = init_state.Tgt();
	+
	+ // If not QE return 1.0
	+ // LOG(FIT) << "RikRPA : Event QE = " << proc_info.IsQuasiElastic() <<
	+ // std::endl;
	+ if (!tgt.IsNucleus()) return 1.0;
	+ if (!proc_info.IsQuasiElastic()) return 1.0;
	+
	+ // Extract Beam and Target PDG
	+ GHepParticle* neutrino = ghep->Probe();
	+ int bpdg = neutrino->Pdg();
	+
	+ GHepParticle* target = ghep->Particle(1);
	+ assert(target);
	+ int tpdg = target->Pdg();
	+
	+ // Find the enum we need
	+ int calcenum = GetRPACalcEnum(bpdg, tpdg);
	+ if (calcenum == -1) return 1.0;
	+
	+ // Check we have the RPA Calc setup for this enum
	+ // if not, set it up at that point
	+ // if (!fRPACalculators[calcenum]) SetupRPACalculator(calcenum);
	+ // weightRPA* rpacalc = fRPACalculators[calcenum];
	+ // if (!rpacalc) {
	+ // THROW("Failed to grab the RPA Calculator : " << calcenum);
	+ // }
	+
	+ // Extract Q0-Q3
	+ GHepParticle* fsl = ghep->FinalStatePrimaryLepton();
	+ const TLorentzVector& k1 = *(neutrino->P4());
	+ const TLorentzVector& k2 = *(fsl->P4());
	+ double q0 = fabs((k1 - k2).E());
	+ double q3 = fabs((k1 - k2).Vect().Mag());
	+
	+ // Now use q0-q3 and RPA Calculator to fill fWeights
	+ // LOG(FIT) << "Getting Weights = " << q0 << " " << q3 << std::endl;
	+ // rpacalc->getWeight(q0, q3, fEventWeights);
	+
	+ // Apply Interpolation (for the time being simple linear)
	+
	+ // Syst Application : kMINERvA_RikRPA_ApplyRPA
	+ if (fApplyDial_RPACorrection) {
	+ w *= fEventWeights[0]; // CV
	+ }
	+
	+ LOG(FIT) << " fCurDial_RPALowQ2 = " << fCurDial_RPALowQ2
	+ << " fCurDial_RPAHighQ2 = " << fCurDial_RPAHighQ2 << " Weights "
	+ << fEventWeights[0] << " " << fEventWeights[1] << " "
	+ << fEventWeights[2] << " " << fEventWeights[3] << " "
	+ << fEventWeights[4] << std::endl;
	+
	+ // Syst Application : kMINERvA_RikRPA_LowQ2
	+ if (fabs(fCurDial_RPALowQ2) > 0.0) {
	+ double interpw = fEventWeights[0];
	+
	+ if (fCurDial_RPALowQ2 > 0.0) {
	+ interpw = fEventWeights[0] - (fEventWeights[0] - fEventWeights[1]) *
	+ fCurDial_RPALowQ2; // WLow+ } else if
	+ } else if (fCurDial_RPALowQ2 < 0.0) {
	+ interpw = fEventWeights[0] - (fEventWeights[2] - fEventWeights[0]) *
	+ fCurDial_RPALowQ2; // WLow-
	+ }
	+ w *= interpw / fEventWeights[0]; // Div by CV again
	+ }
	+
	+ // Syst Application : kMINERvA_RikRPA_HighQ2
	+ if (fabs(fCurDial_RPAHighQ2) > 0.0) {
	+ double interpw = fEventWeights[0];
	+ if (fCurDial_RPAHighQ2 > 0.0) {
	+ interpw = fEventWeights[0] - (fEventWeights[0] - fEventWeights[3]) *
	+ fCurDial_RPAHighQ2; // WHigh+ } else
	+ if (fCurDial_RPAHighQ2 < 0.0) {
	+ interpw = fEventWeights[0] - (fEventWeights[4] - fEventWeights[0]) *
	+ fCurDial_RPAHighQ2; // WHigh-
	+ }
	+ w *= interpw / fEventWeights[0]; // Div by CV again
	+ }
	+ }
	+
	+ // LOG(FIT) << "RPA Weight = " << w << std::endl;
	+ return w;
	} // namespace reweight
	-} // namespace nuisance
	-#endif
	-#endif

	+void RikRPA::SetDialValue(std::string name, double val) {
	+ SetDialValue(Reweight::ConvDial(name, kCUSTOM), val);
	+}

	+void RikRPA::SetDialValue(int rwenum, double val) {
	+ int curenum = rwenum % 1000;
	+
	+ // Check Handled
	+ if (!IsHandled(curenum)) return;
	+ if (curenum == kMINERvARW_RikRPA_ApplyRPA)
	+ fApplyDial_RPACorrection = (val > 0.5);
	+ if (curenum == kMINERvARW_RikRPA_LowQ2) fCurDial_RPALowQ2 = val;
	+ if (curenum == kMINERvARW_RikRPA_HighQ2) fCurDial_RPAHighQ2 = val;
	+
	+ // Assign flag to say stuff has changed
	+ fTweaked = (fApplyDial_RPACorrection \|\|
	+ fabs(fCurDial_RPAHighQ2 - fDefDial_RPAHighQ2) > 0.0 \|\|
	+ fabs(fCurDial_RPALowQ2 - fDefDial_RPALowQ2) > 0.0);
	+}

	+bool RikRPA::IsHandled(int rwenum) {
	+ int curenum = rwenum % 1000;
	+ switch (curenum) {
	+ case kMINERvARW_RikRPA_ApplyRPA:
	+ return true;
	+ case kMINERvARW_RikRPA_LowQ2:
	+ return true;
	+ case kMINERvARW_RikRPA_HighQ2:
	+ return true;
	+ default:
	+ return false;
	+ }
	+}

	+void RikRPA::SetupRPACalculator(int calcenum) {
	+ std::string rwdir = FitPar::GetDataBase() + "/reweight/MINERvA/RikRPA/";
	+ std::string fidir = "";
	+ switch (calcenum) {
	+ case kNuMuC12:
	+ fidir = "outNievesRPAratio-nu12C-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuO16:
	+ fidir = "outNievesRPAratio-nu16O-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuAr40:
	+ fidir = "outNievesRPAratio-nu40Ar-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuCa40:
	+ fidir = "outNievesRPAratio-nu40Ca-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuFe56:
	+ fidir = "outNievesRPAratio-nu56Fe-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuBarC12:
	+ fidir = "outNievesRPAratio-anu12C-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuBarO16:
	+ fidir = "outNievesRPAratio-anu16O-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuBarAr40:
	+ fidir = "outNievesRPAratio-anu40Ar-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuBarCa40:
	+ fidir = "outNievesRPAratio-anu40Ca-20GeV-20170202.root";
	+ break;
	+
	+ case kNuMuBarFe56:
	+ fidir = "outNievesRPAratio-anu56Fe-20GeV-20170202.root";
	+ break;
	+ }

	+ LOG(FIT) << "Loading RPA CALC : " << fidir << std::endl;
	+ TDirectory* olddir = gDirectory;

	-// RikRPA::RikRPA() {
	+ // fRPACalculators[calcenum] = new weightRPA(rwdir + "/" + fidir);
	+ olddir->cd();
	+ return;
	+}

	-// // - Syst : kMINERvA_RikRPA_ApplyRPA
	-// // - Type : Binary
	-// // - Limits : 0.0 (false) -> 1.0 (true)
	-// // - Default : 0.0
	-// fApplyDial_RPACorrection = false;
	+int RikRPA::GetRPACalcEnum(int bpdg, int tpdg) {
	+ if (bpdg == 14 && tpdg == 1000060120)
	+ return kNuMuC12;
	+ else if (bpdg == 14 && tpdg == 1000080160)
	+ return kNuMuO16;
	+ else if (bpdg == 14 && tpdg == 1000180400)
	+ return kNuMuAr40;
	+ else if (bpdg == 14 && tpdg == 1000200400)
	+ return kNuMuCa40;
	+ else if (bpdg == 14 && tpdg == 1000280560)
	+ return kNuMuFe56;
	+ else if (bpdg == -14 && tpdg == 1000060120)
	+ return kNuMuBarC12;
	+ else if (bpdg == -14 && tpdg == 1000080160)
	+ return kNuMuBarO16;
	+ else if (bpdg == -14 && tpdg == 1000180400)
	+ return kNuMuBarAr40;
	+ else if (bpdg == -14 && tpdg == 1000200400)
	+ return kNuMuBarCa40;
	+ else if (bpdg == -14 && tpdg == 1000280560)
	+ return kNuMuBarFe56;
	+ else {
	+ ERROR(WRN, "Unknown beam and target combination for RPA Calcs! "
	+ << bpdg << " " << tpdg);
	+ }

	-// // - Syst : kMINERvA_RikRPA_LowQ2
	-// // - Type : Absolute
	-// // - Limits : 1.0 -> 1.0
	-// // - Default : 0.0
	-// // - Frac Error : 100%
	-// fDefDial_RPALowQ2 = 0.0;
	-// fCurDial_RPALowQ2 = fDefDial_RPALowQ2;
	-// fErrDial_RPALowQ2 = 0.0;
	+ return -1;
	+}

	-// // - Syst : kMINERvA_RikRPA_HighQ2
	-// // - Type : Absolute
	-// // - Limits : 1.0 -> 1.0
	-// // - Default : 0.0
	-// // - Frac Error : 100%
	-// fDefDial_RPAHighQ2 = 0.0;
	-// fCurDial_RPAHighQ2 = fDefDial_RPAHighQ2;
	-// fErrDial_RPAHighQ2 = 1.0;
	-
	-// fEventWeights = new double[5];
	-
	-// for (size_t i = 0; i < kMaxCalculators; i++) {
	-// fRPACalculators[i] = NULL;
	-// }
	-
	-// fTweaked = false;
	-// }
	-
	-// RikRPA::~RikRPA() {
	-
	-// delete fEventWeights;
	-
	-// for (size_t i = 0; i < kMaxCalculators; i++) {
	-// if (fRPACalculators[i]) delete fRPACalculators[i];
	-// fRPACalculators[i] = NULL;
	-// }
	-
	-// }
	-
	-// double RikRPA::CalcWeight(BaseFitEvt* evt) {
	-// // LOG(FIT) << "Calculating RikRPA" << std::endl;
	-// // Return 1.0 if not tweaked
	-// if (!fTweaked) return 1.0;
	-
	-// double w = 1.0;
	-
	-// // Extract the GENIE Record
	-// GHepRecord* ghep = static_cast<GHepRecord*>(evt->genie_event->event);
	-// const Interaction* interaction = ghep->Summary();
	-// const InitialState& init_state = interaction->InitState();
	-// const ProcessInfo& proc_info = interaction->ProcInfo();
	-// // const Kinematics & kine = interaction->Kine();
	-// // const XclsTag & xcls = interaction->ExclTag();
	-// const Target& tgt = init_state.Tgt();
	-
	-// // If not QE return 1.0
	-// // LOG(FIT) << "RikRPA : Event QE = " << proc_info.IsQuasiElastic() <<
	-// std::endl;
	-// if (!tgt.IsNucleus()) return 1.0;
	-// if (!proc_info.IsQuasiElastic()) return 1.0;
	-
	-// // Extract Beam and Target PDG
	-// GHepParticle* neutrino = ghep->Probe();
	-// int bpdg = neutrino->Pdg();
	-
	-// GHepParticle* target = ghep->Particle(1);
	-// assert(target);
	-// int tpdg = target->Pdg();
	-
	-// // Find the enum we need
	-// int calcenum = GetRPACalcEnum(bpdg, tpdg);
	-// if (calcenum == -1) return 1.0;
	-
	-// // Check we have the RPA Calc setup for this enum
	-// // if not, set it up at that point
	-// if (!fRPACalculators[calcenum]) SetupRPACalculator(calcenum);
	-// weightRPA* rpacalc = fRPACalculators[calcenum];
	-// if (!rpacalc) {
	-// THROW("Failed to grab the RPA Calculator : " << calcenum);
	-// }
	-
	-// // Extract Q0-Q3
	-// GHepParticle* fsl = ghep->FinalStatePrimaryLepton();
	-// const TLorentzVector& k1 = *(neutrino->P4());
	-// const TLorentzVector& k2 = *(fsl->P4());
	-// double q0 = fabs((k1 - k2).E());
	-// double q3 = fabs((k1 - k2).Vect().Mag());
	-
	-// // Now use q0-q3 and RPA Calculator to fill fWeights
	-// // LOG(FIT) << "Getting Weights = " << q0 << " " << q3 << std::endl;
	-// rpacalc->getWeight(q0, q3, fEventWeights);
	-
	-// // Apply Interpolation (for the time being simple linear)
	-
	-// // Syst Application : kMINERvA_RikRPA_ApplyRPA
	-// if (fApplyDial_RPACorrection) {
	-// w *= fEventWeights[0]; // CV
	-// }
	-
	-// LOG(FIT) << " fCurDial_RPALowQ2 = " << fCurDial_RPALowQ2
	-// << " fCurDial_RPAHighQ2 = " << fCurDial_RPAHighQ2 << " Weights "
	-// << fEventWeights[0] << " " << fEventWeights[1] << " "
	-// << fEventWeights[2] << " " << fEventWeights[3] << " "
	-// << fEventWeights[4] << std::endl;
	-
	-// // Syst Application : kMINERvA_RikRPA_LowQ2
	-// if (fabs(fCurDial_RPALowQ2) > 0.0) {
	-// double interpw = fEventWeights[0];
	-
	-// if (fCurDial_RPALowQ2 > 0.0) {
	-// interpw = fEventWeights[0] -
	-// (fEventWeights[0] - fEventWeights[1]) *
	-// fCurDial_RPALowQ2; // WLow+ } else if
	-// (fCurDial_RPALowQ2 < 0.0) {
	-// interpw = fEventWeights[0] - (fEventWeights[2] - fEventWeights[0]) *
	-// fCurDial_RPALowQ2; // WLow-
	-// }
	-// w *= interpw / fEventWeights[0]; // Div by CV again
	-// }
	-
	-// // Syst Application : kMINERvA_RikRPA_HighQ2
	-// if (fabs(fCurDial_RPAHighQ2) > 0.0) {
	-// double interpw = fEventWeights[0];
	-// if (fCurDial_RPAHighQ2 > 0.0) {
	-// interpw = fEventWeights[0] -
	-// (fEventWeights[0] - fEventWeights[3]) *
	-// fCurDial_RPAHighQ2; // WHigh+ } else
	-// if
	-// (fCurDial_RPAHighQ2 < 0.0) {
	-// interpw = fEventWeights[0] - (fEventWeights[4] - fEventWeights[0])
	-// *
	-// fCurDial_RPAHighQ2; // WHigh-
	-// }
	-// w *= interpw / fEventWeights[0]; // Div by CV again
	-// }
	-
	-// // LOG(FIT) << "RPA Weight = " << w << std::endl;
	-
	-// return w;
	-// }
	-
	-// void RikRPA::SetDialValue(std::string name, double val) {
	-// SetDialValue(Reweight::ConvDial(name, kCUSTOM), val);
	-// }
	-
	-// void RikRPA::SetDialValue(int rwenum, double val) {
	-// int curenum = rwenum % 1000;
	-
	-// // Check Handled
	-// if (!IsHandled(curenum)) return;
	-// if (curenum == kMINERvA_RikRPA_ApplyRPA)
	-// fApplyDial_RPACorrection = (val > 0.5);
	-// if (curenum == kMINERvA_RikRPA_LowQ2) fCurDial_RPALowQ2 = val;
	-// if (curenum == kMINERvA_RikRPA_HighQ2) fCurDial_RPAHighQ2 = val;
	-
	-// // Assign flag to say stuff has changed
	-// fTweaked = (fApplyDial_RPACorrection \|\|
	-// fabs(fCurDial_RPAHighQ2 - fDefDial_RPAHighQ2) > 0.0 \|\|
	-// fabs(fCurDial_RPALowQ2 - fDefDial_RPALowQ2) > 0.0);
	-// }
	-
	-// bool RikRPA::IsHandled(int rwenum) {
	-// int curenum = rwenum % 1000;
	-// switch (curenum) {
	-// case kMINERvA_RikRPA_ApplyRPA:
	-// return true;
	-// case kMINERvA_RikRPA_LowQ2:
	-// return true;
	-// case kMINERvA_RikRPA_HighQ2:
	-// return true;
	-// default:
	-// return false;
	-// }
	-// }
	-
	-// void RikRPA::SetupRPACalculator(int calcenum) {
	-// std::string rwdir = FitPar::GetDataBase() +
	-// "/reweight/MINERvA/RikRPA/"; std::string fidir = ""; switch (calcenum)
	-// {
	-// case kNuMuC12:
	-// fidir = "outNievesRPAratio-nu12C-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuO16:
	-// fidir = "outNievesRPAratio-nu16O-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuAr40:
	-// fidir = "outNievesRPAratio-nu40Ar-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuCa40:
	-// fidir = "outNievesRPAratio-nu40Ca-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuFe56:
	-// fidir = "outNievesRPAratio-nu56Fe-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuBarC12:
	-// fidir = "outNievesRPAratio-anu12C-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuBarO16:
	-// fidir = "outNievesRPAratio-anu16O-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuBarAr40:
	-// fidir = "outNievesRPAratio-anu40Ar-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuBarCa40:
	-// fidir = "outNievesRPAratio-anu40Ca-20GeV-20170202.root";
	-// break;
	-
	-// case kNuMuBarFe56:
	-// fidir = "outNievesRPAratio-anu56Fe-20GeV-20170202.root";
	-// break;
	-// }
	-
	-// LOG(FIT) << "Loading RPA CALC : " << fidir << std::endl;
	-// TDirectory* olddir = gDirectory;
	-
	-// fRPACalculators[calcenum] = new weightRPA(rwdir + "/" + fidir);
	-// olddir->cd();
	-// return;
	-// }
	-
	-// int RikRPA::GetRPACalcEnum(int bpdg, int tpdg) {
	-// if (bpdg == 14 && tpdg == 1000060120)
	-// return kNuMuC12;
	-// else if (bpdg == 14 && tpdg == 1000080160)
	-// return kNuMuO16;
	-// else if (bpdg == 14 && tpdg == 1000180400)
	-// return kNuMuAr40;
	-// else if (bpdg == 14 && tpdg == 1000200400)
	-// return kNuMuCa40;
	-// else if (bpdg == 14 && tpdg == 1000280560)
	-// return kNuMuFe56;
	-// else if (bpdg == -14 && tpdg == 1000060120)
	-// return kNuMuBarC12;
	-// else if (bpdg == -14 && tpdg == 1000080160)
	-// return kNuMuBarO16;
	-// else if (bpdg == -14 && tpdg == 1000180400)
	-// return kNuMuBarAr40;
	-// else if (bpdg == -14 && tpdg == 1000200400)
	-// return kNuMuBarCa40;
	-// else if (bpdg == -14 && tpdg == 1000280560)
	-// return kNuMuBarFe56;
	-// else {
	-// ERROR(WRN, "Unknown beam and target combination for RPA Calcs! "
	-// << bpdg << " " << tpdg);
	-// }
	-
	-// return -1;
	-// }
	-// } // namespace reweight
	-// } // namespace nuisance
	-
	-// #endif // __GENIE_ENABLED__
	-// #endif //__MINERVA_RW_ENABLED__
	+} // namespace reweight
	+} // namespace nuisance
	+#endif
	+#endif
	diff --git a/src/Reweight/MINERvAWeightCalcs.h b/src/Reweight/MINERvAWeightCalcs.h
	index ec059dc..d3ec9a1 100644
	--- a/src/Reweight/MINERvAWeightCalcs.h
	+++ b/src/Reweight/MINERvAWeightCalcs.h
	@@ -1,96 +1,136 @@
	#ifndef MINERVA_WEIGHT_CALCS
	#define MINERVA_WEIGHT_CALCS

	#include <string>

	-// #ifdef __MINERVA_RW_ENABLED__
	-// #ifdef __GENIE_ENABLED__
	+#ifdef __MINERVA_RW_ENABLED__
	+#ifdef __GENIE_ENABLED__
	#include "Conventions/Units.h"
	#include "EVGCore/EventRecord.h"
	#include "FitEvent.h"
	#include "FitParameters.h"
	#include "GHEP/GHepParticle.h"
	#include "GHEP/GHepRecord.h"
	#include "GHEP/GHepUtils.h"
	#include "GeneralUtils.h"
	#include "NUISANCESyst.h"
	#include "NUISANCEWeightCalcs.h"
	#include "Ntuple/NtpMCEventRecord.h"
	#include "PDG/PDGUtils.h"
	#include "WeightUtils.h"
	// #include "weightRPA.h"
	using namespace genie;
	class BaseFitEvt;


	namespace nuisance {
	namespace reweight {

	// MEC Dials
	+class MINERvAReWeight_QE : public NUISANCEWeightCalc {
	+ public:
	+ MINERvAReWeight_QE();
	+ virtual ~MINERvAReWeight_QE();
	+
	+ double CalcWeight(BaseFitEvt* evt);
	+ void SetDialValue(std::string name, double val);
	+ void SetDialValue(int rwenum, double val);
	+ bool IsHandled(int rwenum);
	+
	+ double fTwk_NormCCQE;
	+ double fCur_NormCCQE;
	+ double fDef_NormCCQE;
	+ bool fTweaked;
	+
	+};
	+
	+
	+// MEC Dials
	class MINERvAReWeight_MEC : public NUISANCEWeightCalc {
	public:
	MINERvAReWeight_MEC();
	virtual ~MINERvAReWeight_MEC();

	double CalcWeight(BaseFitEvt* evt);
	void SetDialValue(std::string name, double val);
	void SetDialValue(int rwenum, double val);
	bool IsHandled(int rwenum);

	double fTwk_NormCCMEC;
	double fCur_NormCCMEC;
	double fDef_NormCCMEC;
	-}
	-
	-// /// RPA Weight Calculator that applies RPA systematics
	-// /// to GENIE events. GENIE EVENTS ONLY!
	-// class RikRPA : public NUISANCEWeightCalc {
	-// public:
	-// RikRPA();
	-// ~RikRPA();
	-
	-// double CalcWeight(BaseFitEvt* evt);
	-// void SetDialValue(std::string name, double val);
	-// void SetDialValue(int rwenum, double val);
	-// bool IsHandled(int rwenum);
	-
	-// void SetupRPACalculator(int calcenum);
	-// int GetRPACalcEnum(int bpdg, int tpdg);
	-
	-// bool fApplyDial_RPACorrection;
	-
	-// double fTwkDial_RPALowQ2;
	-// double fDefDial_RPALowQ2;
	-// double fCurDial_RPALowQ2;
	-// double fErrDial_RPALowQ2;
	-
	-// double fTwkDial_RPAHighQ2;
	-// double fDefDial_RPAHighQ2;
	-// double fCurDial_RPAHighQ2;
	-// double fErrDial_RPAHighQ2;
	-
	-// double* fEventWeights;
	-// bool fTweaked;
	-
	-// const static int kMaxCalculators = 10;
	-// enum rpacalcenums {
	-// kNuMuC12,
	-// kNuMuO16,
	-// kNuMuAr40,
	-// kNuMuCa40,
	-// kNuMuFe56,
	-// kNuMuBarC12,
	-// kNuMuBarO16,
	-// kNuMuBarAr40,
	-// kNuMuBarCa40,
	-// kNuMuBarFe56
	-// };
	-// weightRPA* fRPACalculators[kMaxCalculators];
	-// };
	+ bool fTweaked;
	+
	+};
	+
	+// RES Dials
	+class MINERvAReWeight_RES : public NUISANCEWeightCalc {
	+ public:
	+ MINERvAReWeight_RES();
	+ virtual ~MINERvAReWeight_RES();
	+
	+ double CalcWeight(BaseFitEvt* evt);
	+ void SetDialValue(std::string name, double val);
	+ void SetDialValue(int rwenum, double val);
	+ bool IsHandled(int rwenum);
	+
	+ double fTwk_NormCCRES;
	+ double fCur_NormCCRES;
	+ double fDef_NormCCRES;
	+ bool fTweaked;
	+
	+ };
	+
	+/// RPA Weight Calculator that applies RPA systematics
	+/// to GENIE events. GENIE EVENTS ONLY!
	+class RikRPA : public NUISANCEWeightCalc {
	+public:
	+ RikRPA();
	+ ~RikRPA();
	+
	+ double CalcWeight(BaseFitEvt* evt);
	+ void SetDialValue(std::string name, double val);
	+ void SetDialValue(int rwenum, double val);
	+ bool IsHandled(int rwenum);
	+
	+ void SetupRPACalculator(int calcenum);
	+ int GetRPACalcEnum(int bpdg, int tpdg);
	+
	+ bool fApplyDial_RPACorrection;
	+
	+ double fTwkDial_RPALowQ2;
	+ double fDefDial_RPALowQ2;
	+ double fCurDial_RPALowQ2;
	+ double fErrDial_RPALowQ2;
	+
	+ double fTwkDial_RPAHighQ2;
	+ double fDefDial_RPAHighQ2;
	+ double fCurDial_RPAHighQ2;
	+ double fErrDial_RPAHighQ2;
	+
	+ double* fEventWeights;
	+ bool fTweaked;
	+
	+ const static int kMaxCalculators = 10;
	+ enum rpacalcenums {
	+ kNuMuC12,
	+ kNuMuO16,
	+ kNuMuAr40,
	+ kNuMuCa40,
	+ kNuMuFe56,
	+ kNuMuBarC12,
	+ kNuMuBarO16,
	+ kNuMuBarAr40,
	+ kNuMuBarCa40,
	+ kNuMuBarFe56
	+ };
	+ // weightRPA* fRPACalculators[kMaxCalculators];
	+};
	+
	}; // namespace reweight
	}; // namespace nuisance

	-// #endif // __GENIE_ENABLED__
	-// #endif //__MINERVA_RW_ENABLED__
	+#endif // __GENIE_ENABLED__
	+#endif //__MINERVA_RW_ENABLED__

	#endif
	diff --git a/src/Reweight/NUISANCESyst.cxx b/src/Reweight/NUISANCESyst.cxx
	index 44366e1..6063aa3 100644
	--- a/src/Reweight/NUISANCESyst.cxx
	+++ b/src/Reweight/NUISANCESyst.cxx
	@@ -1,52 +1,61 @@
	#include "NUISANCESyst.h"

	int Reweight::ConvertNUISANCEDial(std::string type) {

	for (int i = kUnkownNUISANCEDial + 1; i < kNUISANCEDial_LAST; i++) {
	if (!type.compare(ConvNUISANCEDial(i).c_str())) {
	return i;
	}
	}
	return kUnkownNUISANCEDial;
	};

	std::string Reweight::ConvNUISANCEDial(int type) {

	switch (type) {
	case kGaussianCorr_CCQE_norm: { return "GaussianCorr_CCQE_norm"; }
	case kGaussianCorr_CCQE_tilt: { return "GaussianCorr_CCQE_tilt"; }
	case kGaussianCorr_CCQE_Pq0: { return "GaussianCorr_CCQE_Pq0"; }
	case kGaussianCorr_CCQE_Wq0: { return "GaussianCorr_CCQE_Wq0"; }
	case kGaussianCorr_CCQE_Pq3: { return "GaussianCorr_CCQE_Pq3"; }
	case kGaussianCorr_CCQE_Wq3: { return "GaussianCorr_CCQE_Wq3"; }
	case kGaussianCorr_2p2h_norm: { return "GaussianCorr_2p2h_norm"; }
	case kGaussianCorr_2p2h_tilt: { return "GaussianCorr_2p2h_tilt"; }
	case kGaussianCorr_2p2h_Pq0: { return "GaussianCorr_2p2h_Pq0"; }
	case kGaussianCorr_2p2h_Wq0: { return "GaussianCorr_2p2h_Wq0"; }
	case kGaussianCorr_2p2h_Pq3: { return "GaussianCorr_2p2h_Pq3"; }
	case kGaussianCorr_2p2h_Wq3: { return "GaussianCorr_2p2h_Wq3"; }
	case kGaussianCorr_2p2h_PPandNN_norm: { return "GaussianCorr_2p2h_PPandNN_norm"; }
	case kGaussianCorr_2p2h_PPandNN_tilt: { return "GaussianCorr_2p2h_PPandNN_tilt"; }
	case kGaussianCorr_2p2h_PPandNN_Pq0: { return "GaussianCorr_2p2h_PPandNN_Pq0"; }
	case kGaussianCorr_2p2h_PPandNN_Wq0: { return "GaussianCorr_2p2h_PPandNN_Wq0"; }
	case kGaussianCorr_2p2h_PPandNN_Pq3: { return "GaussianCorr_2p2h_PPandNN_Pq3"; }
	case kGaussianCorr_2p2h_PPandNN_Wq3: { return "GaussianCorr_2p2h_PPandNN_Wq3"; }
	case kGaussianCorr_2p2h_NP_norm: { return "GaussianCorr_2p2h_NP_norm"; }
	case kGaussianCorr_2p2h_NP_tilt: { return "GaussianCorr_2p2h_NP_tilt"; }
	case kGaussianCorr_2p2h_NP_Pq0: { return "GaussianCorr_2p2h_NP_Pq0"; }
	case kGaussianCorr_2p2h_NP_Wq0: { return "GaussianCorr_2p2h_NP_Wq0"; }
	case kGaussianCorr_2p2h_NP_Pq3: { return "GaussianCorr_2p2h_NP_Pq3"; }
	case kGaussianCorr_2p2h_NP_Wq3: { return "GaussianCorr_2p2h_NP_Wq3"; }
	case kGaussianCorr_CC1pi_norm: { return "GaussianCorr_CC1pi_norm"; }
	case kGaussianCorr_CC1pi_tilt: { return "GaussianCorr_CC1pi_tilt"; }
	case kGaussianCorr_CC1pi_Pq0: { return "GaussianCorr_CC1pi_Pq0"; }
	case kGaussianCorr_CC1pi_Wq0: { return "GaussianCorr_CC1pi_Wq0"; }
	case kGaussianCorr_CC1pi_Pq3: { return "GaussianCorr_CC1pi_Pq3"; }
	case kGaussianCorr_CC1pi_Wq3: { return "GaussianCorr_CC1pi_Wq3"; }
	case kGaussianCorr_AllowSuppression: { return "GaussianCorr_AllowSuppression"; }
	+
	case kModeNorm_NormRES: { return "NormRES"; }

	+ case kMINERvARW_NormCCQE: { return "MINERvARW_NormCCQE"; }
	+ case kMINERvARW_NormCCMEC: { return "MINERvARW_NormCCMEC"; }
	+ case kMINERvARW_NormCCRES: { return "MINERvARW_NormCCRES"; }
	+
	+ case kMINERvARW_RikRPA_ApplyRPA: { return "MINERvARW_RikRPA_ApplyRPA"; }
	+ case kMINERvARW_RikRPA_LowQ2: { return "MINERvARW_RikRPA_LowQ2"; }
	+ case kMINERvARW_RikRPA_HighQ2: { return "MINERvARW_RikRPA_HighQ2"; }
	+
	default: return "unknown_nuisance_dial";
	}

	};
	diff --git a/src/Reweight/NUISANCESyst.h b/src/Reweight/NUISANCESyst.h
	index 296c956..3fec5a7 100644
	--- a/src/Reweight/NUISANCESyst.h
	+++ b/src/Reweight/NUISANCESyst.h
	@@ -1,50 +1,58 @@
	#ifndef NUISANCESyst_H
	#define NUISANCESyst_H
	#include "GeneralUtils.h"

	namespace Reweight {

	enum NUISANCESyst {
	kUnkownNUISANCEDial = 0,
	kGaussianCorr_CCQE_norm,
	kGaussianCorr_CCQE_tilt,
	kGaussianCorr_CCQE_Pq0,
	kGaussianCorr_CCQE_Wq0,
	kGaussianCorr_CCQE_Pq3,
	kGaussianCorr_CCQE_Wq3,
	kGaussianCorr_2p2h_norm,
	kGaussianCorr_2p2h_tilt,
	kGaussianCorr_2p2h_Pq0,
	kGaussianCorr_2p2h_Wq0,
	kGaussianCorr_2p2h_Pq3,
	kGaussianCorr_2p2h_Wq3,
	kGaussianCorr_2p2h_PPandNN_norm,
	kGaussianCorr_2p2h_PPandNN_tilt,
	kGaussianCorr_2p2h_PPandNN_Pq0,
	kGaussianCorr_2p2h_PPandNN_Wq0,
	kGaussianCorr_2p2h_PPandNN_Pq3,
	kGaussianCorr_2p2h_PPandNN_Wq3,
	kGaussianCorr_2p2h_NP_norm,
	kGaussianCorr_2p2h_NP_tilt,
	kGaussianCorr_2p2h_NP_Pq0,
	kGaussianCorr_2p2h_NP_Wq0,
	kGaussianCorr_2p2h_NP_Pq3,
	kGaussianCorr_2p2h_NP_Wq3,
	kGaussianCorr_CC1pi_norm,
	kGaussianCorr_CC1pi_tilt,
	kGaussianCorr_CC1pi_Pq0,
	kGaussianCorr_CC1pi_Wq0,
	kGaussianCorr_CC1pi_Pq3,
	kGaussianCorr_CC1pi_Wq3,
	kGaussianCorr_AllowSuppression,

	kModeNorm_NormRES,

	+ kMINERvARW_NormCCQE,
	+ kMINERvARW_NormCCMEC,
	+ kMINERvARW_NormCCRES,
	+
	+ kMINERvARW_RikRPA_ApplyRPA,
	+ kMINERvARW_RikRPA_LowQ2,
	+ kMINERvARW_RikRPA_HighQ2,
	+
	kNUISANCEDial_LAST
	};

	int ConvertNUISANCEDial(std::string type);
	std::string ConvNUISANCEDial(int type);

	};
	#endif
	diff --git a/src/Reweight/NUISANCEWeightEngine.cxx b/src/Reweight/NUISANCEWeightEngine.cxx
	index e7344ca..116385c 100644
	--- a/src/Reweight/NUISANCEWeightEngine.cxx
	+++ b/src/Reweight/NUISANCEWeightEngine.cxx
	@@ -1,129 +1,110 @@
	#include "NUISANCEWeightEngine.h"
	#include "NUISANCEWeightCalcs.h"

	-NUISANCEWeightEngine::NUISANCEWeightEngine(std::string name) {
	+#ifdef __MINERVA_RW_ENABLED__
	+#ifdef __GENIE_ENABLED__
	+#include "MINERvAWeightCalcs.h"
	+#endif
	+#endif
	+

	+NUISANCEWeightEngine::NUISANCEWeightEngine(std::string name) {
	// Setup the NUISANCE Reweight engine
	fCalcName = name;
	LOG(FIT) << "Setting up NUISANCE Custom RW : " << fCalcName << std::endl;

	// Load in all Weight Calculations
	- fWeightCalculators.push_back( new GaussianModeCorr() );
	- fWeightCalculators.push_back( new ModeNormCalc() );
	+ fWeightCalculators.push_back(new GaussianModeCorr());
	+ fWeightCalculators.push_back(new ModeNormCalc());
	+
	+#ifdef __MINERVA_RW_ENABLED__
	+#ifdef __GENIE_ENABLED__
	+ fWeightCalculators.push_back(new nuisance::reweight::MINERvAReWeight_MEC());
	+ fWeightCalculators.push_back(new nuisance::reweight::MINERvAReWeight_RES());
	+ fWeightCalculators.push_back(new nuisance::reweight::RikRPA());
	+#endif
	+#endif
	+
	// Set Abs Twk Config
	fIsAbsTwk = true;
	-
	};

	-
	void NUISANCEWeightEngine::IncludeDial(std::string name, double startval) {
	-
	// Get First enum
	int nuisenum = Reweight::ConvDial(name, kCUSTOM);

	// Setup Maps
	- fEnumIndex[nuisenum];// = std::vector<size_t>(0);
	- fNameIndex[name]; // = std::vector<size_t>(0);
	+ fEnumIndex[nuisenum]; // = std::vector<size_t>(0);
	+ fNameIndex[name]; // = std::vector<size_t>(0);

	// Split by commas
	std::vector<std::string> allnames = GeneralUtils::ParseToStr(name, ",");
	for (uint i = 0; i < allnames.size(); i++) {
	std::string singlename = allnames[i];

	// Get RW
	- int singleenum = Reweight::ConvDial(singlename, kCUSTOM);
	+ int singleenum = Reweight::ConvDial(singlename, kCUSTOM);

	// Fill Maps
	int index = fValues.size();
	fValues.push_back(0.0);
	fNUISANCEEnums.push_back(singleenum);

	// Initialize dial
	std::cout << "Registering " << singlename << " from " << name << std::endl;

	// Setup index
	fEnumIndex[nuisenum].push_back(index);
	fNameIndex[name].push_back(index);
	}

	// Set Value if given
	if (startval != -999.9) {
	SetDialValue(nuisenum, startval);
	}
	};

	-
	void NUISANCEWeightEngine::SetDialValue(int nuisenum, double val) {
	std::vector<size_t> indices = fEnumIndex[nuisenum];
	for (uint i = 0; i < indices.size(); i++) {
	fValues[indices[i]] = val;
	}
	}

	void NUISANCEWeightEngine::SetDialValue(std::string name, double val) {
	std::vector<size_t> indices = fNameIndex[name];
	for (uint i = 0; i < indices.size(); i++) {
	fValues[indices[i]] = val;
	}
	}

	void NUISANCEWeightEngine::Reconfigure(bool silent) {
	-
	for (size_t i = 0; i < fNUISANCEEnums.size(); i++) {
	-
	- for (std::vector<NUISANCEWeightCalc*>::iterator calciter = fWeightCalculators.begin();
	+ for (std::vector<NUISANCEWeightCalc*>::iterator calciter =
	+ fWeightCalculators.begin();
	calciter != fWeightCalculators.end(); calciter++) {
	-
	- NUISANCEWeightCalc* nuiscalc = static_cast<NUISANCEWeightCalc>(calciter);
	+ NUISANCEWeightCalc* nuiscalc =
	+ static_cast<NUISANCEWeightCalc>(calciter);

	if (nuiscalc->IsHandled(fNUISANCEEnums[i])) {
	nuiscalc->SetDialValue(fNUISANCEEnums[i], fValues[i]);
	}
	}
	}
	}

	-
	-
	-double NUISANCEWeightEngine::CalcWeight(BaseFitEvt * evt) {
	+double NUISANCEWeightEngine::CalcWeight(BaseFitEvt* evt) {
	double rw_weight = 1.0;

	// Cast as usable class
	- for (std::vector<NUISANCEWeightCalc*>::iterator iter = fWeightCalculators.begin();
	+ for (std::vector<NUISANCEWeightCalc*>::iterator iter =
	+ fWeightCalculators.begin();
	iter != fWeightCalculators.end(); iter++) {
	NUISANCEWeightCalc* nuiscalc = static_cast<NUISANCEWeightCalc>(iter);

	rw_weight *= nuiscalc->CalcWeight(evt);
	}

	// Return rw_weight
	return rw_weight;
	}
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	-
	diff --git a/src/Routines/SystematicRoutines.cxx b/src/Routines/SystematicRoutines.cxx
	index 4c846a5..d33b35e 100755
	--- a/src/Routines/SystematicRoutines.cxx
	+++ b/src/Routines/SystematicRoutines.cxx
	@@ -1,1516 +1,1517 @@
	// Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	/*******************************************************************************
	* This file is part of NUISANCE.
	*
	* NUISANCE is free software: you can redistribute it and/or modify
	* it under the terms of the GNU General Public License as published by
	* the Free Software Foundation, either version 3 of the License, or
	* (at your option) any later version.
	*
	* NUISANCE is distributed in the hope that it will be useful,
	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	* GNU General Public License for more details.
	*
	* You should have received a copy of the GNU General Public License
	* along with NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	*******************************************************************************/
	#include "SystematicRoutines.h"

	void SystematicRoutines::Init(){

	fInputFile = "";
	fInputRootFile = NULL;

	fOutputFile = "";
	fOutputRootFile = NULL;

	fCovar = fCovarFree = NULL;
	fCorrel = fCorrelFree = NULL;
	fDecomp = fDecompFree = NULL;

	fStrategy = "ErrorBands";
	fRoutines.clear();
	fRoutines.push_back("ErrorBands");

	fCardFile = "";

	fFakeDataInput = "";

	fSampleFCN = NULL;

	fAllowedRoutines = ("ErrorBands,PlotLimits");

	};

	SystematicRoutines::~SystematicRoutines(){
	};

	SystematicRoutines::SystematicRoutines(int argc, char* argv[]){

	// Initialise Defaults
	Init();
	nuisconfig configuration = Config::Get();

	// Default containers
	std::string cardfile = "";
	std::string maxevents = "-1";
	int errorcount = 0;
	int verbocount = 0;
	std::vector<std::string> xmlcmds;
	std::vector<std::string> configargs;
	fNThrows = 250;
	fStartThrows = 0;
	fThrowString = "";
	// Make easier to handle arguments.
	std::vector<std::string> args = GeneralUtils::LoadCharToVectStr(argc, argv);
	ParserUtils::ParseArgument(args, "-c", fCardFile, true);
	ParserUtils::ParseArgument(args, "-o", fOutputFile, false, false);
	ParserUtils::ParseArgument(args, "-n", maxevents, false, false);
	ParserUtils::ParseArgument(args, "-f", fStrategy, false, false);
	ParserUtils::ParseArgument(args, "-d", fFakeDataInput, false, false);
	ParserUtils::ParseArgument(args, "-s", fStartThrows, false, false);
	ParserUtils::ParseArgument(args, "-t", fNThrows, false, false);
	ParserUtils::ParseArgument(args, "-p", fThrowString, false, false);
	ParserUtils::ParseArgument(args, "-i", xmlcmds);
	ParserUtils::ParseArgument(args, "-q", configargs);
	ParserUtils::ParseCounter(args, "e", errorcount);
	ParserUtils::ParseCounter(args, "v", verbocount);
	ParserUtils::CheckBadArguments(args);

	// Add extra defaults if none given
	if (fCardFile.empty() and xmlcmds.empty()) {
	ERR(FTL) << "No input supplied!" << std::endl;
	throw;
	}

	if (fOutputFile.empty() and !fCardFile.empty()) {
	fOutputFile = fCardFile + ".root";
	ERR(WRN) << "No output supplied so saving it to: " << fOutputFile << std::endl;

	} else if (fOutputFile.empty()) {
	ERR(FTL) << "No output file or cardfile supplied!" << std::endl;
	throw;
	}

	// Configuration Setup =============================

	// Check no comp key is available
	if (Config::Get().GetNodes("nuiscomp").empty()) {
	fCompKey = Config::Get().CreateNode("nuiscomp");
	} else {
	fCompKey = Config::Get().GetNodes("nuiscomp")[0];
	}

	if (!fCardFile.empty()) fCompKey.AddS("cardfile", fCardFile);
	if (!fOutputFile.empty()) fCompKey.AddS("outputfile", fOutputFile);
	if (!fStrategy.empty()) fCompKey.AddS("strategy", fStrategy);

	// Load XML Cardfile
	configuration.LoadConfig( fCompKey.GetS("cardfile"), "");

	// Add CMD XML Structs
	for (size_t i = 0; i < xmlcmds.size(); i++) {
	configuration.AddXMLLine(xmlcmds[i]);
	}

	// Add Config Args
	for (size_t i = 0; i < configargs.size(); i++) {
	configuration.OverrideConfig(configargs[i]);
	}
	if (maxevents.compare("-1")){
	configuration.OverrideConfig("MAXEVENTS=" + maxevents);
	}

	// Finish configuration XML
	configuration.FinaliseConfig(fCompKey.GetS("outputfile") + ".xml");

	// Add Error Verbo Lines
	verbocount += Config::Get().GetParI("VERBOSITY");
	errorcount += Config::Get().GetParI("ERROR");
	std::cout << "[ NUISANCE ]: Setting VERBOSITY=" << verbocount << std::endl;
	std::cout << "[ NUISANCE ]: Setting ERROR=" << errorcount << std::endl;
	SETVERBOSITY(verbocount);

	// Proper Setup
	if (fStrategy.find("ErrorBands") != std::string::npos \|\|
	fStrategy.find("MergeErrors") != std::string::npos){
	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");
	}

	// fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");
	SetupSystematicsFromXML();

	SetupCovariance();
	SetupRWEngine();
	SetupFCN();
	GetCovarFromFCN();

	// Run();

	return;
	};

	void SystematicRoutines::SetupSystematicsFromXML(){

	LOG(FIT) << "Setting up nuismin" << std::endl;

	// Setup Parameters ------------------------------------------
	std::vector<nuiskey> parkeys = Config::QueryKeys("parameter");
	if (!parkeys.empty()) {
	LOG(FIT) << "Number of parameters : " << parkeys.size() << std::endl;
	}

	for (size_t i = 0; i < parkeys.size(); i++) {
	nuiskey key = parkeys.at(i);

	// Check for type,name,nom
	if (!key.Has("type")) {
	ERR(FTL) << "No type given for parameter " << i << std::endl;
	throw;
	} else if (!key.Has("name")) {
	ERR(FTL) << "No name given for parameter " << i << std::endl;
	throw;
	} else if (!key.Has("nominal")) {
	ERR(FTL) << "No nominal given for parameter " << i << std::endl;
	throw;
	}

	// Get Inputs
	std::string partype = key.GetS("type");
	std::string parname = key.GetS("name");
	double parnom = key.GetD("nominal");
	double parlow = parnom - 1;
	double parhigh = parnom + 1;
	double parstep = 1;


	// Override if state not given
	if (!key.Has("state")){
	key.SetS("state","FIX");
	}

	std::string parstate = key.GetS("state");

	// Extra limits
	if (key.Has("low")) {
	parlow = key.GetD("low");
	parhigh = key.GetD("high");
	parstep = key.GetD("step");

	LOG(FIT) << "Read " << partype << " : "
	<< parname << " = "
	<< parnom << " : "
	<< parlow << " < p < " << parhigh
	<< " : " << parstate << std::endl;
	} else {
	LOG(FIT) << "Read " << partype << " : "
	<< parname << " = "
	<< parnom << " : "
	<< parstate << std::endl;
	}

	// Run Parameter Conversion if needed
	if (parstate.find("ABS") != std::string::npos) {
	parnom = FitBase::RWAbsToSigma( partype, parname, parnom );
	parlow = FitBase::RWAbsToSigma( partype, parname, parlow );
	parhigh = FitBase::RWAbsToSigma( partype, parname, parhigh );
	parstep = FitBase::RWAbsToSigma( partype, parname, parstep );
	} else if (parstate.find("FRAC") != std::string::npos) {
	parnom = FitBase::RWFracToSigma( partype, parname, parnom );
	parlow = FitBase::RWFracToSigma( partype, parname, parlow );
	parhigh = FitBase::RWFracToSigma( partype, parname, parhigh );
	parstep = FitBase::RWFracToSigma( partype, parname, parstep );
	}

	// Push into vectors
	fParams.push_back(parname);

	fTypeVals[parname] = FitBase::ConvDialType(partype);;
	fStartVals[parname] = parnom;
	fCurVals[parname] = parnom;

	fErrorVals[parname] = 0.0;

	fStateVals[parname] = parstate;
	bool fixstate = parstate.find("FIX") != std::string::npos;
	fFixVals[parname] = fixstate;
	fStartFixVals[parname] = fFixVals[parname];

	fMinVals[parname] = parlow;
	fMaxVals[parname] = parhigh;
	fStepVals[parname] = parstep;

	}

	// Setup Samples ----------------------------------------------
	std::vector<nuiskey> samplekeys = Config::QueryKeys("sample");
	if (!samplekeys.empty()) {
	LOG(FIT) << "Number of samples : " << samplekeys.size() << std::endl;
	}

	for (size_t i = 0; i < samplekeys.size(); i++) {
	nuiskey key = samplekeys.at(i);

	// Get Sample Options
	std::string samplename = key.GetS("name");
	std::string samplefile = key.GetS("input");

	std::string sampletype =
	key.Has("type") ? key.GetS("type") : "DEFAULT";

	double samplenorm =
	key.Has("norm") ? key.GetD("norm") : 1.0;

	// Print out
	LOG(FIT) << "Read sample info " << i << " : "
	<< samplename << std::endl
	<< "\t\t input -> " << samplefile << std::endl
	<< "\t\t state -> " << sampletype << std::endl
	<< "\t\t norm -> " << samplenorm << std::endl;

	// If FREE add to parameters otherwise continue
	if (sampletype.find("FREE") == std::string::npos) {
	continue;
	}

	// Form norm dial from samplename + sampletype + "_norm";
	std::string normname = samplename + "_norm";

	// Check normname not already present
	if (fTypeVals.find(normname) != fTypeVals.end()) {
	continue;
	}

	// Add new norm dial to list if its passed above checks
	fParams.push_back(normname);

	fTypeVals[normname] = kNORM;
	fStateVals[normname] = sampletype;
	fCurVals[normname] = samplenorm;

	fErrorVals[normname] = 0.0;

	fMinVals[normname] = 0.1;
	fMaxVals[normname] = 10.0;
	fStepVals[normname] = 0.5;

	bool state = sampletype.find("FREE") == std::string::npos;
	fFixVals[normname] = state;
	fStartFixVals[normname] = state;
	}

	// Setup Fake Parameters -----------------------------
	std::vector<nuiskey> fakekeys = Config::QueryKeys("fakeparameter");
	if (!fakekeys.empty()) {
	LOG(FIT) << "Number of fake parameters : " << fakekeys.size() << std::endl;
	}

	for (size_t i = 0; i < fakekeys.size(); i++) {
	nuiskey key = fakekeys.at(i);

	// Check for type,name,nom
	if (!key.Has("name")) {
	ERR(FTL) << "No name given for fakeparameter " << i << std::endl;
	throw;
	} else if (!key.Has("nom")) {
	ERR(FTL) << "No nominal given for fakeparameter " << i << std::endl;
	throw;
	}

	// Get Inputs
	std::string parname = key.GetS("name");
	double parnom = key.GetD("nom");

	// Push into vectors
	fFakeVals[parname] = parnom;
	}
	}


	void SystematicRoutines::ReadCard(std::string cardfile){

	// Read cardlines into vector
	std::vector<std::string> cardlines = GeneralUtils::ParseFileToStr(cardfile,"\n");
	FitPar::Config().cardLines = cardlines;

	// Read Samples first (norm params can be overridden)
	int linecount = 0;
	for (std::vector<std::string>::iterator iter = cardlines.begin();
	iter != cardlines.end(); iter++){
	std::string line = (*iter);
	linecount++;

	// Skip Empties
	if (line.empty()) continue;
	if (line.c_str()[0] == '#') continue;

	// Read Valid Samples
	int samstatus = ReadSamples(line);

	// Show line if bad to help user
	if (samstatus == kErrorStatus) {
	ERR(FTL) << "Bad Input in cardfile " << fCardFile
	<< " at line " << linecount << "!" << std::endl;
	LOG(FIT) << line << std::endl;
	throw;
	}
	}

	// Read Parameters second
	linecount = 0;
	for (std::vector<std::string>::iterator iter = cardlines.begin();
	iter != cardlines.end(); iter++){
	std::string line = (*iter);
	linecount++;

	// Skip Empties
	if (line.empty()) continue;
	if (line.c_str()[0] == '#') continue;

	// Try Parameter Reads
	int parstatus = ReadParameters(line);
	int fakstatus = ReadFakeDataPars(line);

	// Show line if bad to help user
	if (parstatus == kErrorStatus \|\|
	fakstatus == kErrorStatus ){
	ERR(FTL) << "Bad Parameter Input in cardfile " << fCardFile
	<< " at line " << linecount << "!" << std::endl;
	LOG(FIT) << line << std::endl;
	throw;
	}
	}

	return;
	};

	int SystematicRoutines::ReadParameters(std::string parstring){

	std::string inputspec = "RW Dial Inputs Syntax \n"
	"free input w/ limits: TYPE NAME START MIN MAX STEP [STATE] \n"
	"fix input: TYPE NAME VALUE [STATE] \n"
	"free input w/o limits: TYPE NAME START FREE,[STATE] \n"
	"Allowed Types: \n"
	"neut_parameter,niwg_parameter,t2k_parameter,"
	"nuwro_parameter,gibuu_parameter";

	// Check sample input
	if (parstring.find("parameter") == std::string::npos) return kGoodStatus;

	// Parse inputs
	std::vector<std::string> strvct = GeneralUtils::ParseToStr(parstring, " ");

	// Skip if comment or parameter somewhere later in line
	if (strvct[0].c_str()[0] == '#' \|\|
	strvct[0].find("parameter") == std::string::npos){
	return kGoodStatus;
	}

	// Check length
	if (strvct.size() < 3){
	ERR(FTL) << "Input rw dials need to provide at least 3 inputs." << std::endl;
	std::cout << inputspec << std::endl;
	return kErrorStatus;
	}

	// Setup default inputs
	std::string partype = strvct[0];
	std::string parname = strvct[1];
	double parval = GeneralUtils::StrToDbl(strvct[2]);
	double minval = parval - 1.0;
	double maxval = parval + 1.0;
	double stepval = 1.0;
	std::string state = "FIX"; //[DEFAULT]

	// Check Type
	if (FitBase::ConvDialType(partype) == kUNKNOWN){
	ERR(FTL) << "Unknown parameter type! " << partype << std::endl;
	std::cout << inputspec << std::endl;
	return kErrorStatus;
	}

	// Check Parameter Name
	if (FitBase::GetDialEnum(partype, parname) == -1){
	ERR(FTL) << "Bad RW parameter name! " << partype << " " << parname << std::endl;
	std::cout << inputspec << std::endl;
	return kErrorStatus;
	}

	// Option Extra (No Limits)
	if (strvct.size() == 4){
	state = strvct[3];
	}

	// Check for weirder inputs
	if (strvct.size() > 4 && strvct.size() < 6){
	ERR(FTL) << "Provided incomplete limits for " << parname << std::endl;
	std::cout << inputspec << std::endl;
	return kErrorStatus;
	}

	// Option Extra (With limits and steps)
	if (strvct.size() >= 6){
	minval = GeneralUtils::StrToDbl(strvct[3]);
	maxval = GeneralUtils::StrToDbl(strvct[4]);
	stepval = GeneralUtils::StrToDbl(strvct[5]);
	}

	// Option Extra (dial state after limits)
	if (strvct.size() == 7){
	state = strvct[6];
	}

	// Run Parameter Conversion if needed
	if (state.find("ABS") != std::string::npos){
	parval = FitBase::RWAbsToSigma( partype, parname, parval );
	minval = FitBase::RWAbsToSigma( partype, parname, minval );
	maxval = FitBase::RWAbsToSigma( partype, parname, maxval );
	stepval = FitBase::RWAbsToSigma( partype, parname, stepval );
	} else if (state.find("FRAC") != std::string::npos){
	parval = FitBase::RWFracToSigma( partype, parname, parval );
	minval = FitBase::RWFracToSigma( partype, parname, minval );
	maxval = FitBase::RWFracToSigma( partype, parname, maxval );
	stepval = FitBase::RWFracToSigma( partype, parname, stepval );
	}

	// Check no repeat params
	if (std::find(fParams.begin(), fParams.end(), parname) != fParams.end()){
	ERR(FTL) << "Duplicate parameter names given for " << parname << std::endl;
	throw;
	}

	// Setup Containers
	fParams.push_back(parname);

	fTypeVals[parname] = FitBase::ConvDialType(partype);

	fStartVals[parname] = parval;
	fCurVals[parname] = fStartVals[parname];

	fErrorVals[parname] = 0.0;

	fStateVals[parname] = state;

	bool fixstate = state.find("FIX") != std::string::npos;
	fFixVals[parname] = fixstate;
	fStartFixVals[parname] = fFixVals[parname];

	fMinVals[parname] = minval;
	fMaxVals[parname] = maxval;
	fStepVals[parname] = stepval;

	// Print the parameter
	LOG(MIN) << "Read Parameter " << parname << " " << parval << " "
	<< minval << " " << maxval << " "
	<< stepval << " " << state << std::endl;

	// Tell reader its all good
	return kGoodStatus;
	}

	//*******************************************
	int SystematicRoutines::ReadFakeDataPars(std::string parstring){
	//******************************************

	std::string inputspec = "Fake Data Dial Inputs Syntax \n"
	"fake value: fake_parameter NAME VALUE \n"
	"Name should match dialnames given in actual dial specification.";

	// Check sample input
	if (parstring.find("fake_parameter") == std::string::npos)
	return kGoodStatus;

	// Parse inputs
	std::vector<std::string> strvct = GeneralUtils::ParseToStr(parstring, " ");

	// Skip if comment or parameter somewhere later in line
	if (strvct[0].c_str()[0] == '#' \|\|
	strvct[0] == "fake_parameter"){
	return kGoodStatus;
	}

	// Check length
	if (strvct.size() < 3){
	ERR(FTL) << "Fake dials need to provide at least 3 inputs." << std::endl;
	std::cout << inputspec << std::endl;
	return kErrorStatus;
	}

	// Read Inputs
	std::string parname = strvct[1];
	double parval = GeneralUtils::StrToDbl(strvct[2]);

	// Setup Container
	fFakeVals[parname] = parval;

	// Print the fake parameter
	LOG(MIN) << "Read Fake Parameter " << parname << " " << parval << std::endl;

	// Tell reader its all good
	return kGoodStatus;
	}

	//******************************************
	int SystematicRoutines::ReadSamples(std::string samstring){
	//******************************************
	const static std::string inputspec =
	"\tsample <sample_name> <input_type>:inputfile.root [OPTS] "
	"[norm]\nsample_name: Name "
	"of sample to include. e.g. MiniBooNE_CCQE_XSec_1DQ2_nu\ninput_type: The "
	"input event format. e.g. NEUT, GENIE, EVSPLN, ...\nOPTS: Additional, "
	"optional sample options.\nnorm: Additional, optional sample "
	"normalisation factor.";

	// Check sample input
	if (samstring.find("sample") == std::string::npos)
	return kGoodStatus;

	// Parse inputs
	std::vector<std::string> strvct = GeneralUtils::ParseToStr(samstring, " ");

	// Skip if comment or parameter somewhere later in line
	if (strvct[0].c_str()[0] == '#' \|\|
	strvct[0] != "sample"){
	return kGoodStatus;
	}

	// Check length
	if (strvct.size() < 3){
	ERR(FTL) << "Sample need to provide at least 3 inputs." << std::endl;
	return kErrorStatus;
	}

	// Setup default inputs
	std::string samname = strvct[1];
	std::string samfile = strvct[2];

	if (samfile == "FIX") {
	ERR(FTL) << "Input filename was \"FIX\", this line is probably malformed "
	"in the input card file. Line:\'"
	<< samstring << "\'" << std::endl;
	ERR(FTL) << "Expect sample lines to look like:\n\t" << inputspec
	<< std::endl;

	throw;
	}

	std::string samtype = "DEFAULT";
	double samnorm = 1.0;

	// Optional Type
	if (strvct.size() > 3) {
	samtype = strvct[3];
	// samname += "_"+samtype;
	// Also get rid of the / and replace it with underscore because it might not be supported character
	// while (samname.find("/") != std::string::npos) {
	// samname.replace(samname.find("/"), 1, std::string("_"));
	// }
	}

	// Optional Norm
	if (strvct.size() > 4) samnorm = GeneralUtils::StrToDbl(strvct[4]);

	// Add Sample Names as Norm Dials
	std::string normname = samname + "_norm";

	// Check no repeat params
	if (std::find(fParams.begin(), fParams.end(), normname) != fParams.end()){
	ERR(FTL) << "Duplicate samples given for " << samname << std::endl;
	throw;
	}

	fParams.push_back(normname);

	fTypeVals[normname] = kNORM;
	fStartVals[normname] = samnorm;
	fCurVals[normname] = fStartVals[normname];
	fErrorVals[normname] = 0.0;

	fMinVals[normname] = 0.1;
	fMaxVals[normname] = 10.0;
	fStepVals[normname] = 0.5;

	bool state = samtype.find("FREE") == std::string::npos;
	fFixVals[normname] = state;
	fStartFixVals[normname] = state;

	// Print read in
	LOG(MIN) << "Read sample " << samname << " "
	<< samfile << " " << samtype << " "
	<< samnorm << std::endl;

	// Tell reader its all good
	return kGoodStatus;
	}

	/*
	Setup Functions
	*/
	//*************************************
	void SystematicRoutines::SetupRWEngine(){
	//*************************************

	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string name = fParams[i];
	FitBase::GetRW() -> IncludeDial(name, fTypeVals.at(name) );
	}
	UpdateRWEngine(fStartVals);

	return;
	}

	//*************************************
	void SystematicRoutines::SetupFCN(){
	//*************************************

	LOG(FIT)<<"Making the jointFCN"<<std::endl;
	if (fSampleFCN) delete fSampleFCN;
	fSampleFCN = new JointFCN(fOutputRootFile);
	SetFakeData();

	return;
	}


	//*************************************
	void SystematicRoutines::SetFakeData(){
	//*************************************

	if (fFakeDataInput.empty()) return;

	if (fFakeDataInput.compare("MC") == 0){

	LOG(FIT)<<"Setting fake data from MC starting prediction." <<std::endl;
	UpdateRWEngine(fFakeVals);

	FitBase::GetRW()->Reconfigure();
	fSampleFCN->ReconfigureAllEvents();
	fSampleFCN->SetFakeData("MC");

	UpdateRWEngine(fCurVals);

	LOG(FIT)<<"Set all data to fake MC predictions."<<std::endl;
	} else {
	fSampleFCN->SetFakeData(fFakeDataInput);
	}

	return;
	}

	//*****************************************
	void SystematicRoutines::GetCovarFromFCN(){
	//*****************************************
	LOG(FIT) << "Loading ParamPull objects from FCN to build covar" << std::endl;

	// Make helperstring
	std::ostringstream helperstr;

	// Keep track of what is being thrown
	std::map<std::string, std::string> dialthrowhandle;

	// Get Covariance Objects from FCN
	std::list<ParamPull*> inputpulls = fSampleFCN->GetPullList();
	for (PullListConstIter iter = inputpulls.begin();
	iter != inputpulls.end(); iter++){

	ParamPull* pull = (*iter);

	if (pull->GetType().find("THROW")){
	fInputThrows.push_back(pull);
	fInputCovar.push_back(pull->GetFullCovarMatrix());
	fInputDials.push_back(pull->GetDataHist());

	LOG(FIT) << "Read ParamPull: " << pull->GetName() << " " << pull->GetType() << std::endl;
	}

	TH1D dialhist = pull->GetDataHist();
	TH1D minhist = pull->GetMinHist();
	TH1D maxhist = pull->GetMaxHist();
	TH1I typehist = pull->GetDialTypes();

	for (int i = 0; i < dialhist.GetNbinsX(); i++){
	std::string name = std::string(dialhist.GetXaxis()->GetBinLabel(i+1));
	dialthrowhandle[name] = pull->GetName();

	if (fCurVals.find(name) == fCurVals.end()){

	// Add to Containers
	fParams.push_back(name);
	fCurVals[name] = dialhist.GetBinContent(i+1);
	fStartVals[name] = dialhist.GetBinContent(i+1);
	fMinVals[name] = minhist.GetBinContent(i+1);
	fMaxVals[name] = maxhist.GetBinContent(i+1);
	fStepVals[name] = 1.0;
	fFixVals[name] = false;
	fStartFixVals[name] = false;
	fTypeVals[name] = typehist.GetBinContent(i+1);
	fStateVals[name] = "FREE" + pull->GetType();

	// Maker Helper
	helperstr << std::string(16, ' ' ) << FitBase::ConvDialType(fTypeVals[name]) << " "
	<< name << " " << fMinVals[name] << " "
	<< fMaxVals[name] << " " << fStepVals[name] << " " << fStateVals[name]
	<< std::endl;
	}
	}
	}

	// Check if no throws given
	if (fInputThrows.empty()){

	ERR(WRN) << "No covariances given to nuissyst" << std::endl;
	ERR(WRN) << "Pushing back an uncorrelated gaussian throw error for each free parameter using step size" << std::endl;

	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string syst = fParams[i];
	if (fFixVals[syst]) continue;

	// Make Terms
	std::string name = syst + "_pull";

	std::ostringstream pullterm;
	pullterm << "DIAL:" << syst << ";"
	<< fStartVals[syst] << ";"
	<< fStepVals[syst];

	std::string type = "GAUSTHROW/NEUT";

	// Push Back Pulls
	ParamPull* pull = new ParamPull( name, pullterm.str(), type );
	fInputThrows.push_back(pull);
	fInputCovar.push_back(pull->GetFullCovarMatrix());
	fInputDials.push_back(pull->GetDataHist());

	// Print Whats added
	ERR(WRN) << "Added ParamPull : " << name << " " << pullterm.str() << " " << type << std::endl;

	// Add helper string for future fits
	helperstr << std::string(16, ' ' ) << "covar " << name << " " << pullterm.str() << " " << type << std::endl;

	// Keep Track of Throws
	dialthrowhandle[syst] = pull->GetName();
	}
	}

	// Print Helper String
	if (!helperstr.str().empty()){
	LOG(FIT) << "To remove these statements in future studies, add the lines below to your card:" << std::endl;
	// Can't use the logger properly because this can be multi-line. Use cout and added spaces to look better!
	std::cout << helperstr.str();
	sleep(2);
	}



	// Print Throw State
	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string syst = fParams[i];
	if (dialthrowhandle.find(syst) != dialthrowhandle.end()){
	LOG(FIT) << "Dial " << i << ". " << setw(40) << syst << " = THROWING with " << dialthrowhandle[syst] << std::endl;
	} else {
	LOG(FIT) << "Dial " << i << ". " << setw(40) << syst << " = FIXED" << std::endl;
	}
	}

	// Pause anyway
	sleep(1);
	return;
	}




	/*
	Fitting Functions
	*/
	//*************************************
	void SystematicRoutines::UpdateRWEngine(std::map<std::string,double>& updateVals){
	//*************************************

	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string name = fParams[i];

	if (updateVals.find(name) == updateVals.end()) continue;
	FitBase::GetRW()->SetDialValue(name,updateVals.at(name));
	}

	FitBase::GetRW()->Reconfigure();
	return;
	}

	//*************************************
	void SystematicRoutines::PrintState(){
	//*************************************
	LOG(FIT)<<"------------"<<std::endl;

	// Count max size
	int maxcount = 0;
	for (UInt_t i = 0; i < fParams.size(); i++){
	maxcount = max(int(fParams[i].size()), maxcount);
	}

	// Header
	LOG(FIT) << " # " << left << setw(maxcount) << "Parameter "
	<< " = "
	<< setw(10) << "Value" << " +- "
	<< setw(10) << "Error" << " "
	<< setw(8) << "(Units)" << " "
	<< setw(10) << "Conv. Val" << " +- "
	<< setw(10) << "Conv. Err" << " "
	<< setw(8) << "(Units)" << std::endl;

	// Parameters
	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string syst = fParams.at(i);

	std::string typestr = FitBase::ConvDialType(fTypeVals[syst]);
	std::string curunits = "(sig.)";
	double curval = fCurVals[syst];
	double curerr = fErrorVals[syst];

	if (fStateVals[syst].find("ABS") != std::string::npos){
	curval = FitBase::RWSigmaToAbs(typestr, syst, curval);
	curerr = (FitBase::RWSigmaToAbs(typestr, syst, curerr) -
	FitBase::RWSigmaToAbs(typestr, syst, 0.0));
	curunits = "(Abs.)";
	} else if (fStateVals[syst].find("FRAC") != std::string::npos){
	curval = FitBase::RWSigmaToFrac(typestr, syst, curval);
	curerr = (FitBase::RWSigmaToFrac(typestr, syst, curerr) -
	FitBase::RWSigmaToFrac(typestr, syst, 0.0));
	curunits = "(Frac)";
	}

	std::string convunits = "(" + FitBase::GetRWUnits(typestr, syst) + ")";
	double convval = FitBase::RWSigmaToAbs(typestr, syst, curval);
	double converr = (FitBase::RWSigmaToAbs(typestr, syst, curerr) -
	FitBase::RWSigmaToAbs(typestr, syst, 0.0));

	std::ostringstream curparstring;

	curparstring << " " << setw(3) << left
	<< i << ". "
	<< setw(maxcount) << syst << " = "
	<< setw(10) << curval << " +- "
	<< setw(10) << curerr << " "
	<< setw(8) << curunits << " "
	<< setw(10) << convval << " +- "
	<< setw(10) << converr << " "
	<< setw(8) << convunits;


	LOG(FIT) << curparstring.str() << std::endl;
	}

	LOG(FIT)<<"------------"<<std::endl;
	double like = fSampleFCN->GetLikelihood();
	LOG(FIT) << std::left << std::setw(46) << "Likelihood for JointFCN: " << like << std::endl;
	LOG(FIT)<<"------------"<<std::endl;
	}



	/*
	Write Functions
	*/
	//*************************************
	void SystematicRoutines::SaveResults(){
	//*************************************
	if (!fOutputRootFile)
	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");

	fOutputRootFile->cd();

	SaveCurrentState();

	}

	//*************************************
	void SystematicRoutines::SaveCurrentState(std::string subdir){
	//*************************************

	LOG(FIT)<<"Saving current full FCN predictions" <<std::endl;

	// Setup DIRS
	TDirectory* curdir = gDirectory;
	if (!subdir.empty()){
	TDirectory* newdir =(TDirectory*) gDirectory->mkdir(subdir.c_str());
	newdir->cd();
	}

	FitBase::GetRW()->Reconfigure();
	fSampleFCN->ReconfigureAllEvents();
	fSampleFCN->Write();

	// Change back to current DIR
	curdir->cd();

	return;
	}

	//*************************************
	void SystematicRoutines::SaveNominal(){
	//*************************************
	if (!fOutputRootFile)
	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");

	fOutputRootFile->cd();

	LOG(FIT)<<"Saving Nominal Predictions (be cautious with this)" <<std::endl;
	FitBase::GetRW()->Reconfigure();
	SaveCurrentState("nominal");

	};

	//*************************************
	void SystematicRoutines::SavePrefit(){
	//*************************************
	if (!fOutputRootFile)
	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");

	fOutputRootFile->cd();

	LOG(FIT)<<"Saving Prefit Predictions"<<std::endl;
	UpdateRWEngine(fStartVals);
	SaveCurrentState("prefit");
	UpdateRWEngine(fCurVals);

	};


	/*
	MISC Functions
	*/
	//*************************************
	int SystematicRoutines::GetStatus(){
	//*************************************

	return 0;
	}

	//*************************************
	void SystematicRoutines::SetupCovariance(){
	//*************************************

	// Remove covares if they exist
	if (fCovar) delete fCovar;
	if (fCovarFree) delete fCovarFree;
	if (fCorrel) delete fCorrel;
	if (fCorrelFree) delete fCorrelFree;
	if (fDecomp) delete fDecomp;
	if (fDecompFree) delete fDecompFree;

	int NFREE = 0;
	int NDIM = 0;

	// Get NFREE from min or from vals (for cases when doing throws)
	NDIM = fParams.size();
	for (UInt_t i = 0; i < fParams.size(); i++){
	if (!fFixVals[fParams[i]]) NFREE++;
	}

	if (NDIM == 0) return;

	fCovar = new TH2D("covariance","covariance",NDIM,0,NDIM,NDIM,0,NDIM);
	if (NFREE > 0){
	fCovarFree = new TH2D("covariance_free",
	"covariance_free",
	NFREE,0,NFREE,
	NFREE,0,NFREE);
	}

	// Set Bin Labels
	int countall = 0;
	int countfree = 0;
	for (UInt_t i = 0; i < fParams.size(); i++){

	fCovar->GetXaxis()->SetBinLabel(countall+1,fParams[i].c_str());
	fCovar->GetYaxis()->SetBinLabel(countall+1,fParams[i].c_str());
	countall++;

	if (!fFixVals[fParams[i]] and NFREE > 0){
	fCovarFree->GetXaxis()->SetBinLabel(countfree+1,fParams[i].c_str());
	fCovarFree->GetYaxis()->SetBinLabel(countfree+1,fParams[i].c_str());
	countfree++;
	}
	}

	fCorrel = PlotUtils::GetCorrelationPlot(fCovar,"correlation");
	fDecomp = PlotUtils::GetDecompPlot(fCovar,"decomposition");

	if (NFREE > 0)fCorrelFree = PlotUtils::GetCorrelationPlot(fCovarFree, "correlation_free");
	if (NFREE > 0)fDecompFree = PlotUtils::GetDecompPlot(fCovarFree,"decomposition_free");

	return;
	};

	//*************************************
	void SystematicRoutines::ThrowCovariance(bool uniformly){
	//*************************************

	// Set fThrownVals to all values in currentVals
	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string name = fParams.at(i);
	fThrownVals[name] = fCurVals[name];
	}

	for (PullListConstIter iter = fInputThrows.begin();
	iter != fInputThrows.end(); iter++){
	ParamPull* pull = *iter;

	pull->ThrowCovariance();
	TH1D dialhist = pull->GetDataHist();

	for (int i = 0; i < dialhist.GetNbinsX(); i++){
	std::string name = std::string(dialhist.GetXaxis()->GetBinLabel(i+1));
	if (fCurVals.find(name) != fCurVals.end()){
	fThrownVals[name] = dialhist.GetBinContent(i+1);
	}
	}

	// Reset throw incase pulls are calculated.
	pull->ResetToy();

	}

	return;
	};

	//*************************************
	void SystematicRoutines::PlotLimits(){
	//*************************************
	std::cout << "Plotting Limits" << std::endl;
	if (!fOutputRootFile)
	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");

	TDirectory* limfolder = (TDirectory*) fOutputRootFile->mkdir("Limits");
	limfolder->cd();

	// Set all parameters at their starting values
	for (UInt_t i = 0; i < fParams.size(); i++){
	fCurVals[fParams[i]] = fStartVals[fParams[i]];
	}

	TDirectory* nomfolder = (TDirectory*) limfolder->mkdir("nominal");
	nomfolder->cd();

	UpdateRWEngine(fCurVals);
	fSampleFCN->ReconfigureAllEvents();
	fSampleFCN->Write();

	limfolder->cd();
	std::vector<std::string> allfolders;


	// Loop through each parameter
	for (UInt_t i = 0; i < fParams.size(); i++){
	std::string syst = fParams[i];
	std::cout << "Starting Param " << syst << std::endl;
	if (fFixVals[syst]) continue;

	// Loop Downwards
	while (fCurVals[syst] > fMinVals[syst]){
	fCurVals[syst] = fCurVals[syst] - fStepVals[syst];

	// Check Limit
	if (fCurVals[syst] < fMinVals[syst])
	fCurVals[syst] = fMinVals[syst];

	// Check folder exists
	std::string curvalstring = std::string( Form( (syst + "_%f").c_str(), fCurVals[syst] ) );
	if (std::find(allfolders.begin(), allfolders.end(), curvalstring) != allfolders.end())
	break;

	// Make new folder for variation
	TDirectory* minfolder = (TDirectory*) limfolder->mkdir(Form( (syst + "_%f").c_str(), fCurVals[syst] ) );
	minfolder->cd();

	allfolders.push_back(curvalstring);

	// Update Iterations
	double *vals = FitUtils::GetArrayFromMap( fParams, fCurVals );
	fSampleFCN->DoEval( vals );
	delete vals;

	// Save to folder
	fSampleFCN->Write();
	}

	// Reset before next loop
	fCurVals[syst] = fStartVals[syst];

	// Loop Upwards now
	while (fCurVals[syst] < fMaxVals[syst]){
	fCurVals[syst] = fCurVals[syst] + fStepVals[syst];

	// Check Limit
	if (fCurVals[syst] > fMaxVals[syst])
	fCurVals[syst] = fMaxVals[syst];

	// Check folder exists
	std::string curvalstring = std::string( Form( (syst + "_%f").c_str(), fCurVals[syst] ) );
	if (std::find(allfolders.begin(), allfolders.end(), curvalstring) != allfolders.end())
	break;

	// Make new folder
	TDirectory* maxfolder = (TDirectory*) limfolder->mkdir(Form( (syst + "_%f").c_str(), fCurVals[syst] ) );
	maxfolder->cd();

	allfolders.push_back(curvalstring);

	// Update Iterations
	double *vals = FitUtils::GetArrayFromMap( fParams, fCurVals );
	fSampleFCN->DoEval( vals );
	delete vals;

	// Save to file
	fSampleFCN->Write();
	}

	// Reset before leaving
	fCurVals[syst] = fStartVals[syst];
	UpdateRWEngine(fCurVals);
	}

	return;
	}

	//*************************************
	void SystematicRoutines::Run(){
	//*************************************

	std::cout << "Running routines "<< std::endl;
	fRoutines = GeneralUtils::ParseToStr(fStrategy,",");

	for (UInt_t i = 0; i < fRoutines.size(); i++){

	std::string routine = fRoutines.at(i);
	int fitstate = kFitUnfinished;
	LOG(FIT)<<"Running Routine: "<<routine<<std::endl;

	if (routine.compare("PlotLimits") == 0) PlotLimits();
	else if (routine.compare("ErrorBands") == 0) GenerateErrorBands();
	else if (routine.compare("ThrowErrors") == 0) GenerateThrows();
	else if (routine.compare("MergeErrors") == 0) MergeThrows();
	else {
	std::cout << "Unknown ROUTINE : " << routine << std::endl;
	}

	// If ending early break here
	if (fitstate == kFitFinished \|\| fitstate == kNoChange){
	LOG(FIT) << "Ending fit routines loop." << std::endl;
	break;
	}
	}

	return;
	}

	void SystematicRoutines::GenerateErrorBands(){
	GenerateThrows();
	MergeThrows();
	}

	//*************************************
	void SystematicRoutines::GenerateThrows(){
	//*************************************


	TFile* tempfile = new TFile((fOutputFile + ".throws.root").c_str(),"RECREATE");
	tempfile->cd();

	int nthrows = fNThrows;
	int startthrows = fStartThrows;
	int endthrows = startthrows + nthrows;

	if (nthrows < 0) nthrows = endthrows;
	if (startthrows < 0) startthrows = 0;
	if (endthrows < 0) endthrows = startthrows + nthrows;

	int seed = (gRandom->Uniform(0.0,1.0)100000 + 100000000(startthrows + endthrows) + time(NULL))/35;
	gRandom->SetSeed(seed);
	LOG(FIT) << "Using Seed : " << seed << std::endl;
	LOG(FIT) << "nthrows = " << nthrows << std::endl;
	LOG(FIT) << "startthrows = " << startthrows << std::endl;
	LOG(FIT) << "endthrows = " << endthrows << std::endl;



	UpdateRWEngine(fCurVals);
	fSampleFCN->ReconfigureAllEvents();

	if (startthrows == 0){
	LOG(FIT) << "Making nominal " << std::endl;
	TDirectory* nominal = (TDirectory*) tempfile->mkdir("nominal");
	nominal->cd();
	fSampleFCN->Write();
	}

	LOG(SAM) << "nthrows = " << nthrows << std::endl;
	LOG(SAM) << "startthrows = " << startthrows << std::endl;
	LOG(SAM) << "endthrows = " << endthrows << std::endl;

	TTree* parameterTree = new TTree("throws","throws");
	double chi2;
	for (UInt_t i = 0; i < fParams.size(); i++)
	parameterTree->Branch(fParams[i].c_str(), &fThrownVals[fParams[i]], (fParams[i] + "/D").c_str());
	parameterTree->Branch("chi2",&chi2,"chi2/D");
	fSampleFCN->CreateIterationTree("error_iterations", FitBase::GetRW());

	// Would anybody actually want to do uniform throws of any parameter??
	bool uniformly = FitPar::Config().GetParB("error_uniform");

	// Run Throws and save
	for (Int_t i = 0; i < endthrows+1; i++){

	LOG(FIT) << "Loop " << i << std::endl;
	ThrowCovariance(uniformly);
	if (i < startthrows) continue;
	if (i == 0) continue;
	LOG(FIT) << "Throw " << i << " ================================" << std::endl;
	// Generate Random Parameter Throw
	// ThrowCovariance(uniformly);

	TDirectory* throwfolder = (TDirectory*)tempfile->mkdir(Form("throw_%i",i));
	throwfolder->cd();

	// Run Eval
	double *vals = FitUtils::GetArrayFromMap( fParams, fThrownVals );
	chi2 = fSampleFCN->DoEval( vals );
	delete vals;

	// Save the FCN
	fSampleFCN->Write();

	parameterTree->Fill();
	}

	+ tempfile->cd();
	fSampleFCN->WriteIterationTree();

	tempfile->Close();
	}

	void SystematicRoutines::MergeThrows(){


	fOutputRootFile = new TFile(fCompKey.GetS("outputfile").c_str(), "RECREATE");
	fOutputRootFile->cd();


	// Make a container folder
	TDirectory* errorDIR = (TDirectory*) fOutputRootFile->mkdir("error_bands");
	errorDIR->cd();

	TDirectory* outnominal = (TDirectory*) fOutputRootFile->mkdir("nominal_throw");
	outnominal->cd();

	// Split Input Files
	if (!fThrowString.empty()) fThrowList = GeneralUtils::ParseToStr(fThrowString,",");

	// Add default if no throwlist given
	if (fThrowList.size() < 1) fThrowList.push_back( fOutputFile + ".throws.root" );

	/// Save location of file containing nominal
	std::string nominalfile;
	bool nominalfound;

	// Loop over files and check they exist.
	for (uint i = 0; i < fThrowList.size(); i++){
	std::string file = fThrowList[i];
	bool found = false;

	// normal
	std::string newfile = file;
	TFile* throwfile = new TFile(file.c_str(),"READ");
	if (throwfile and !throwfile->IsZombie()){
	found = true;
	}

	// normal.throws.root
	if (!found){
	newfile = file + ".throws.root";
	throwfile = new TFile((file + ".throws.root").c_str(),"READ");
	if (throwfile and !throwfile->IsZombie()) {
	found = true;
	}
	}

	// If its found save to throwlist, else save empty.
	// Also search for nominal
	if (found){
	fThrowList[i] = newfile;

	LOG(FIT) << "Throws File :" << newfile << std::endl;

	// Find input which contains nominal
	if (throwfile->Get("nominal")){
	nominalfound = true;
	nominalfile = newfile;
	}

	throwfile->Close();

	} else {
	fThrowList[i] = "";
	}

	delete throwfile;
	}

	// Make sure we have a nominal file
	if (!nominalfound or nominalfile.empty()){
	ERR(FTL) << "No nominal found when mergining! Exiting!" << std::endl;
	throw;
	}



	// Get the nominal throws file
	TFile* tempfile = new TFile((nominalfile).c_str(),"READ");
	tempfile->cd();
	TDirectory* nominal = (TDirectory*)tempfile->Get("nominal");
	// int nthrows = FitPar::Config().GetParI("error_throws");
	bool uniformly = FitPar::Config().GetParB("error_uniform");

	// Check percentage of bad files is okay.
	int badfilecount = 0;
	for (uint i = 0; i < fThrowList.size(); i++){
	if (!fThrowList[i].empty()){
	LOG(FIT) << "Loading Throws From File " << i << " : "
	<< fThrowList[i] << std::endl;
	} else {
	badfilecount++;
	}
	}

	// Check we have at least one good file
	if ((uint)badfilecount == fThrowList.size()){
	ERR(FTL) << "Found no good throw files for MergeThrows" << std::endl;
	throw;
	} else if (badfilecount > fThrowList.size()*0.25){
	ERR(WRN) << "Over 25% of your throw files are dodgy. Please check this is okay!" << std::endl;
	ERR(WRN) << "Will continue for the time being..." << std::endl;
	sleep(5);
	}

	// Now go through the keys in the temporary file and look for TH1D, and TH2D plots
	TIter next(nominal->GetListOfKeys());
	TKey *key;
	while ((key = (TKey*)next())) {
	TClass *cl = gROOT->GetClass(key->GetClassName());
	if (!cl->InheritsFrom("TH1D") and !cl->InheritsFrom("TH2D")) continue;
	TH1* baseplot = (TH1D*)key->ReadObj();
	std::string plotname = std::string(baseplot->GetName());
	LOG(FIT) << "Creating error bands for " << plotname;
	if (LOG_LEVEL(FIT)){
	if (!uniformly) std::cout << " : Using COVARIANCE Throws! " << std::endl;
	else std::cout << " : Using UNIFORM THROWS!!! " << std::endl;
	}

	int nbins = 0;
	if (cl->InheritsFrom("TH1D")) nbins = ((TH1D*)baseplot)->GetNbinsX();
	else nbins = ((TH1D)baseplot)->GetNbinsX() ((TH1D*)baseplot)->GetNbinsY();

	// Setup TProfile with RMS option
	TProfile* tprof = new TProfile((plotname + "_prof").c_str(),(plotname + "_prof").c_str(),nbins, 0, nbins, "S");

	// Setup The TTREE
	double* bincontents;
	bincontents = new double[nbins];

	double* binlowest;
	binlowest = new double[nbins];

	double* binhighest;
	binhighest = new double[nbins];

	errorDIR->cd();
	TTree* bintree = new TTree((plotname + "_tree").c_str(), (plotname + "_tree").c_str());
	for (Int_t i = 0; i < nbins; i++){
	bincontents[i] = 0.0;
	binhighest[i] = 0.0;
	binlowest[i] = 0.0;
	bintree->Branch(Form("content_%i",i),&bincontents[i],Form("content_%i/D",i));
	}

	// Make new throw plot
	TH1* newplot;

	// Run Throw Merging.
	for (UInt_t i = 0; i < fThrowList.size(); i++){

	TFile* throwfile = new TFile(fThrowList[i].c_str(), "READ");

	// Loop over all throws in a folder
	TIter nextthrow(throwfile->GetListOfKeys());
	TKey *throwkey;
	while ((throwkey = (TKey*)nextthrow())) {

	// Skip non throw folders
	if (std::string(throwkey->GetName()).find("throw_") == std::string::npos) continue;

	// Get Throw DIR
	TDirectory* throwdir = (TDirectory*)throwkey->ReadObj();

	// Get Plot From Throw
	newplot = (TH1*)throwdir->Get(plotname.c_str());
	if (!newplot) continue;

	// Loop Over Plot
	for (Int_t j = 0; j < nbins; j++){
	tprof->Fill(j+0.5, newplot->GetBinContent(j+1));
	bincontents[j] = newplot->GetBinContent(j+1);

	if (bincontents[j] < binlowest[j] or i == 0) binlowest[j] = bincontents[j];
	if (bincontents[j] > binhighest[j] or i == 0) binhighest[j] = bincontents[j];
	}

	errorDIR->cd();
	bintree->Fill();
	}
	}

	errorDIR->cd();

	if (uniformly){
	LOG(FIT) << "Uniformly Calculating Plot Errors!" << std::endl;
	}

	TH1* statplot = (TH1*) baseplot->Clone();

	for (Int_t j = 0; j < nbins; j++){

	if (!uniformly){
	// if ((baseplot->GetBinError(j+1)/baseplot->GetBinContent(j+1)) < 1.0) {
	// baseplot->SetBinError(j+1,sqrt(pow(tprof->GetBinError(j+1),2) + pow(baseplot->GetBinError(j+1),2)));
	// } else {
	baseplot->SetBinContent(j+1,tprof->GetBinContent(j+1));
	baseplot->SetBinError(j+1,tprof->GetBinError(j+1));
	// }
	} else {
	baseplot->SetBinContent(j+1, 0.0);//(binlowest[j] + binhighest[j]) / 2.0);
	baseplot->SetBinError(j+1, 0.0); //(binhighest[j] - binlowest[j])/2.0);
	}
	}

	errorDIR->cd();
	baseplot->Write();
	tprof->Write();
	bintree->Write();

	outnominal->cd();
	for (int i = 0; i < nbins; i++){
	baseplot->SetBinError(i+1, sqrt(pow(statplot->GetBinError(i+1),2) + pow(baseplot->GetBinError(i+1),2)));
	}
	baseplot->Write();

	delete statplot;
	delete baseplot;
	delete tprof;
	delete bintree;
	delete [] bincontents;
	}

	return;
	};

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