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	diff --git a/CMakeLists.txt b/CMakeLists.txt
	index 342761b..eb7a6d1 100644
	--- a/CMakeLists.txt
	+++ b/CMakeLists.txt
	@@ -1,82 +1,78 @@
	# Copyright 2018 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/>.
	################################################################################
	cmake_minimum_required (VERSION 2.8 FATAL_ERROR)

	#Use the compilers found in the path
	find_program(CMAKE_C_COMPILER NAMES $ENV{CC} gcc PATHS ENV PATH NO_DEFAULT_PATH)
	find_program(CMAKE_CXX_COMPILER NAMES $ENV{CXX} g++ PATHS ENV PATH NO_DEFAULT_PATH)

	project(NUISANCE)

	include(ExternalProject)

	set (NUISANCE_VERSION_MAJOR 3)
	set (NUISANCE_VERSION_MINOR 0)
	set (NUISANCE_VERSION_REVISION 0)

	set (NUISANCE_VERSION_STRING "v${NUISANCE_VERSION_MAJOR}r${NUISANCE_VERSION_MINOR}")
	if(${NUISANCE_VERSION_REVISION} STRGREATER "0")
	set (NUISANCE_VERSION_STRING "${NUISANCE_VERSION_STRING}p${NUISANCE_VERSION_REVISION}")
	endif()

	#Set this to TRUE to enable build debugging messages
	set(BUILD_DEBUG_MSGS TRUE)

	include(${CMAKE_SOURCE_DIR}/cmake/cmessage.cmake)
	include(${CMAKE_SOURCE_DIR}/cmake/cacheVariables.cmake)
	include(${CMAKE_SOURCE_DIR}/cmake/parseConfigApp.cmake)
	include(${CMAKE_SOURCE_DIR}/cmake/StringAndListUtils.cmake)

	cmessage(STATUS "CMAKE_INSTALL_PREFIX: \"${CMAKE_INSTALL_PREFIX}\"")
	cmessage(STATUS "CMAKE_BUILD_TYPE: \"${CMAKE_BUILD_TYPE}\"")

	################################################################################
	# Check Dependencies
	################################################################################

	################################## ROOT ######################################
	include(${CMAKE_SOURCE_DIR}/cmake/ROOTSetup.cmake)

	################################# InputHandler #################################
	include(${CMAKE_SOURCE_DIR}/cmake/InputHandlerSetup.cmake)

	################################# Pythia6/8 ###################################
	include(${CMAKE_SOURCE_DIR}/cmake/pythia6Setup.cmake)

	################################## FHICLCPP ####################################
	include(${CMAKE_SOURCE_DIR}/cmake/fhiclcppSetup.cmake)

	#Want this after fhiclcpp which will add the install directory
	include_directories(${CMAKE_SOURCE_DIR}/src)

	################################## COMPILER ####################################
	include(${CMAKE_SOURCE_DIR}/cmake/c++CompilerSetup.cmake)

	################################################################################

	add_subdirectory(src)

	-configure_file(cmake/setup.sh.in
	- "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" @ONLY)
	-install(FILES
	- "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" DESTINATION
	- ${CMAKE_INSTALL_PREFIX})
	+add_subdirectory(scripts)

	add_subdirectory(config)
	add_subdirectory(data)
	diff --git a/cmake/c++CompilerSetup.cmake b/cmake/c++CompilerSetup.cmake
	index 17399d9..5083311 100644
	--- a/cmake/c++CompilerSetup.cmake
	+++ b/cmake/c++CompilerSetup.cmake
	@@ -1,57 +1,57 @@
	# Copyright 2018 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(CXX_WARNINGS -Wall -Wextra)

	LIST(APPEND EXTRA_CXX_FLAGS ${CXX_WARNINGS} -Werror -Wno-delete-non-virtual-dtor -Wno-unused "-D__FILENAME__=\"$(subst ${CMAKE_SOURCE_DIR}/,,$(abspath $<))\"")

	BuildFlagString(NUISANCE_LINK_DIRS "-L" ${EXTRA_LINK_DIRS})

	LIST(APPEND EXTRA_LIBS dl)
	BuildLibraryFlagString(STR_EXTRA_LIBS ${EXTRA_LIBS})
	BuildFlagString(STR_EXTRA_SHAREDOBJS " " ${EXTRA_SHAREDOBJS})

	#This ends up holding all of the libraries and search paths for extenal dependencies
	CatStringsIfNotEmpty(NUISANCE_DEPEND_LIBS
	${STR_EXTRA_SHAREDOBJS}
	${STR_EXTRA_LIBS})

	BuildFlagString(STR_EXTRA_LINK_FLAGS " " ${EXTRA_LINK_FLAGS})

	CatStringsIfNotEmpty(CMAKE_LINK_FLAGS
	${CMAKE_LINK_FLAGS}
	${STR_EXTRA_LINK_FLAGS})

	get_directory_property(NUISANCE_INCLUDE_DIRS INCLUDE_DIRECTORIES)

	BuildFlagString(NUISANCE_CXX_FLAGS " " ${EXTRA_CXX_FLAGS})
	CatStringsIfNotEmpty(NUISANCE_CXX_FLAGS ${CMAKE_CXX_FLAGS} ${NUISANCE_CXX_FLAGS} )

	if (VERBOSE)
	cmessage (STATUS "C++ Compiler : ${CXX_COMPILER_NAME}")
	cmessage (STATUS " Flags : ${NUISANCE_CXX_FLAGS}")
	cmessage (STATUS " Release Flags : ${CMAKE_CXX_FLAGS_RELEASE}")
	cmessage (STATUS " Debug Flags : ${CMAKE_CXX_FLAGS_DEBUG}")
	- cmessage (STATUS " Include Dris : ${NUISANCE_INCLUDE_DIRS}")
	+ cmessage (STATUS " Include Dirs : ${NUISANCE_INCLUDE_DIRS}")
	cmessage (STATUS " Linker Flags : ${CMAKE_LINK_FLAGS}")
	cmessage (STATUS " Link Dirs : ${NUISANCE_LINK_DIRS}")
	cmessage (STATUS " Lib Flags : ${NUISANCE_DEPEND_LIBS}")
	endif()

	add_compile_options(${EXTRA_CXX_FLAGS})
	diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
	new file mode 100644
	index 0000000..d6ea15b
	--- /dev/null
	+++ b/scripts/CMakeLists.txt
	@@ -0,0 +1 @@
	+add_subdirectory(to_configure)
	diff --git a/scripts/to_configure/CMakeLists.txt b/scripts/to_configure/CMakeLists.txt
	new file mode 100644
	index 0000000..ab6657a
	--- /dev/null
	+++ b/scripts/to_configure/CMakeLists.txt
	@@ -0,0 +1,28 @@
	+configure_file(setup.sh.in
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh @ONLY)
	+configure_file(nuisbuild.in
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuisbuild @ONLY)
	+configure_file(nuiseventprocgen.in
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuiseventprocgen @ONLY)
	+
	+install(
	+ FILES
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh
	+ DESTINATION
	+ ${CMAKE_INSTALL_PREFIX}
	+ )
	+
	+install(
	+ FILES
	+ SimpleDataComparison.cxx.in SimpleMCStudy.cxx.in
	+ DESTINATION
	+ file_stubs
	+ )
	+
	+install(
	+ PROGRAMS
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuisbuild
	+ ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/nuiseventprocgen
	+ DESTINATION
	+ bin
	+ )
	diff --git a/scripts/to_configure/SimpleDataComparison.cxx.in b/scripts/to_configure/SimpleDataComparison.cxx.in
	new file mode 100644
	index 0000000..a82f398
	--- /dev/null
	+++ b/scripts/to_configure/SimpleDataComparison.cxx.in
	@@ -0,0 +1,180 @@
	+// Copyright 2018 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 "samples/SimpleDataComparison.hxx"
	+
	+#include "utility/EventTopologyUtility.hxx"
	+#include "utility/FullEventUtility.hxx"
	+#include "utility/KinematicUtility.hxx"
	+#include "utility/PDGCodeUtility.hxx"
	+
	+using namespace nuis::event;
	+using namespace nuis::utility;
	+
	+class __SAMPLE_NAME__ : public __SDC_TYPE__ {
	+
	+ //! Add any extra plots that you want to fill as data members of the
	+ //! comparisons class.
	+ // std::unique_ptr<TH1> Extra_plot;
	+
	+public:
	+ __SAMPLE_NAME__() { ReadGlobalConfigDefaults(); }
	+
	+ std::string GetDocumentation() { return ""; }
	+ fhicl::ParameterSet GetExampleConfiguration() {
	+ fhicl::ParameterSet exps = __SDC_TYPE__::GetExampleConfiguration();
	+
	+ return exps;
	+ }
	+
	+ void Initialize(fhicl::ParameterSet const &instance_sample_configuration) {
	+
	+ //! Set the verbosity of the sample logging macros.
	+ if (instance_sample_configuration.has_key("verbosity")) {
	+ SetSampleVerbosity(
	+ instance_sample_configuration.get<std::string>("verbosity"));
	+
	+ //! Use these macros within member functions to log to the terminal
	+ //! See src/samples/IEventProcessor.hxx for more details.
	+ IEventProcessor_INFO(
	+ "Verbosity set: "
	+ << instance_sample_configuration.get<std::string>("verbosity"));
	+ }
	+
	+ // Get the global configuration for this sample, if it exists.
	+ fhicl::ParameterSet const &global_sample_configuration =
	+ nuis::config::GetDocument().get<fhicl::ParameterSet>(
	+ std::string("global.sample_configuration.") + Name(),
	+ fhicl::ParameterSet());
	+
	+ //! This will automatically set the data histogram to be loaded.
	+ // SetData(
	+ // GetDataDir() +
	+ // "path/to/data;histname");
	+
	+ //! Instantiate any extra plots that you want to fill
	+ // Extra_plot = std::unique_ptr<TH1D>(
	+ // new TH1D("Extra_plot",
	+ // "title;xlabel;ylabel",
	+ // nbinsx,xlow,xhigh));
	+
	+ // Perform any per-sample configuration in the base class
	+ __SDC_TYPE__::Initialize(instance_sample_configuration);
	+
	+ //! Define your event signal here.
	+ IsSigFunc = [](FullEvent const &fev) -> bool {
	+ //! See src/utility/EventTopologyUtility.hxx for more pre-defined
	+ //! topological signals.
	+ // if (!IsCC0Pi(fev)) {
	+ // return false;
	+ // }
	+
	+ //! See src/event/FullEvent.hxx for the full event class definition.
	+ //! See src/utility/FullEventUtility.hxx for more helper methods for
	+ //! interacting with the event class.
	+
	+ //! Get the initial state anti-muon neutrino
	+ // Particle ISNumuBar = GetHMISParticle(fev, {pdgcodes::kNuMuBar});
	+ //! An nuis::event::Particle that return true for !part is invalid and
	+ //! does not exist on the particle stack. i.e. here, the selection fails
	+ //! if the event didn't have an initial state numubar.
	+ // if (!ISNumuBar) {
	+ // return false;
	+ // }
	+
	+ //! Get the final state anti-muon
	+ // Particle FSMuPlus = GetHMFSParticle(fev, {pdgcodes::kMuPlus});
	+ // if (!FSMuPlus) {
	+ // return false;
	+ // }
	+
	+ //! Cut on kinematic properties of the true final state.
	+ // if (FSMuPlus.CosTheta() < 0.84) {
	+ // return false;
	+ // }
	+
	+ //! Select the event!
	+ return true;
	+ };
	+
	+ //! 1D Projection function
	+ //! This function takes selected events and returns an array of size, the
	+ //! dimensionality of the comparisons (__SDC_TYPE__::NDim)
	+ CompProjFunc =
	+ [](FullEvent const &fev) -> std::array<double, __SDC_TYPE__::NDim> {
	+ // Particle FSMuPlus = GetHMFSParticle(fev, {pdgcodes::kMuPlus});
	+ // return {FSMuPlus.P()};
	+ return {
	+ 1,
	+ };
	+ };
	+
	+ //! Here you fill any custom histograms or TTrees that your sample handles.
	+ //! Note the [&] means that the generated closure object will take a
	+ //! reference to any in scope variables that are used within the lambda
	+ //! body. As this method is then called outside of the scope of this
	+ //! Initialize method, you should not use any method-locals within the
	+ //! ProcessExtraFunc body. Class members are fine as this will only be
	+ //! called when the same instance of this class is alive.
	+ ProcessExtraFunc = [&](FullEvent const &fev, bool isSel,
	+ double weight) -> void {
	+ //! Whether this event passed the selection function. (Saves you manually
	+ //! reselecting events with the IsSigFunc)
	+ if (isSel) {
	+ // Particle FSMuPlus = GetHMFSParticle(fev, {pdgcodes::kMuPlus});
	+ //! The TH_Helper class provides some templated helper methods for
	+ //! filling histogram types that are decided at compile time, these are
	+ //! used by the SimpleDataComparison base class to provide a dimension
	+ //! and precision agnostic interface, but they can also be used by user
	+ //! classes if you see fit. See src/utility/HistogramUtility.hxx for
	+ //! more details.
	+ // TH_Helper<TH1>::Fill(Extra_plot, {FSMuPlus.CosTheta()}, weight);
	+ }
	+ };
	+ }
	+
	+ std::string Name() { return "__SAMPLE_NAME__"; }
	+
	+ //! Here you can write any custom histograms to TTrees that your sample has
	+ //! been handling.
	+ void Write() {
	+ //! The base class writes the default MC and data histograms to the output
	+ //! directory automatically, so you only have to include logic to write any
	+ //! custom histograms or TTrees out here.
	+ __SDC_TYPE__::Write();
	+
	+ //! The nuis::persistency helper methods will help write your objects to the
	+ //! correct place and in a TFile that will be closed before the program
	+ //! exits.
	+ //! They will write a copy of the TObject that is passed, so you do not need
	+ //! to release/worry about double freeing any histograms passed.
	+ //! write_directory is set up by the baseclass and is configurable in the
	+ //! instance configuration.
	+ // nuis::persistency::WriteToOutputFile<TH1>(Extra_plot,
	+ // Extra_plot->GetName(),
	+ // write_directory);
	+ //! It probably isn't a good idea to write a TTree with the above method, instead, try using nuis::persistency::GetOutputFile() to get the TFile and then manually writing/giving ownership of your TTree to the output file.
	+ }
	+};
	+
	+//! These declarations allow your class to be loaded dynamically by NUISANCE
	+DECLARE_PLUGIN(IDataComparison, __SAMPLE_NAME__);
	+DECLARE_PLUGIN(IEventProcessor, __SAMPLE_NAME__);
	diff --git a/scripts/to_configure/SimpleMCStudy.cxx.in b/scripts/to_configure/SimpleMCStudy.cxx.in
	new file mode 100644
	index 0000000..e52906a
	--- /dev/null
	+++ b/scripts/to_configure/SimpleMCStudy.cxx.in
	@@ -0,0 +1,117 @@
	+// Copyright 2018 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 "samples/SimpleMCStudy.hxx"
	+
	+#include "utility/EventTopologyUtility.hxx"
	+#include "utility/FullEventUtility.hxx"
	+#include "utility/KinematicUtility.hxx"
	+#include "utility/PDGCodeUtility.hxx"
	+
	+using namespace nuis::event;
	+using namespace nuis::utility;
	+
	+class __SAMPLE_NAME__ : public SimpleMCStudy {
	+
	+ //! Add any plots that you want to fill as data members of the
	+ //! comparisons class.
	+ // std::unique_ptr<TH1> myPlot;
	+
	+public:
	+ __SAMPLE_NAME__() { ReadGlobalConfigDefaults(); }
	+
	+ void Initialize(fhicl::ParameterSet const &instance_sample_configuration) {
	+
	+ //! Set the verbosity of the sample logging macros.
	+ if (instance_sample_configuration.has_key("verbosity")) {
	+ SetSampleVerbosity(
	+ instance_sample_configuration.get<std::string>("verbosity"));
	+
	+ //! Use these macros within member functions to log to the terminal
	+ //! See src/samples/IEventProcessor.hxx for more details.
	+ IEventProcessor_INFO(
	+ "Verbosity set: "
	+ << instance_sample_configuration.get<std::string>("verbosity"));
	+ }
	+
	+ // Get the global configuration for this sample, if it exists.
	+ fhicl::ParameterSet const &global_sample_configuration =
	+ nuis::config::GetDocument().get<fhicl::ParameterSet>(
	+ std::string("global.sample_configuration.") + Name(),
	+ fhicl::ParameterSet());
	+
	+ //! Instantiate any plots that you want to fill
	+ // myPlot = std::unique_ptr<TH1D>(
	+ // new TH1D("myPlot",
	+ // "title;xlabel;ylabel",
	+ // nbinsx,xlow,xhigh));
	+
	+ // Perform any per-sample configuration in the base class
	+ SimpleMCStudy::Initialize(instance_sample_configuration);
	+
	+ //! Here you do whatever you want to do on a per-event basis.
	+ //! This method will be run for every event given by the input handler, the
	+ //! weight allows differential xsecs to be plotted easily and also contains
	+ //! any requested reweightable parameter variations.
	+ ProcessEventFunction = [&](nuis::event::FullEvent const &ev,
	+ double weight) -> void {
	+ //! Select events
	+ //! See src/utility/EventTopologyUtility.hxx for more pre-defined
	+ //! topological signals.
	+ // if (!IsCC0Pi(fev)) {
	+ // return false;
	+ // }
	+
	+ //! Build composite variables
	+ //! See src/event/FullEvent.hxx for the full event class definition.
	+ //! See src/utility/FullEventUtility.hxx for more helper methods for
	+ //! interacting with the event class.
	+ // Particle FSMuPlus = GetHMFSParticle(fev, {pdgcodes::kMuPlus});
	+
	+ //! Fill your histograms!
	+ // myPlot->Fill(FSMuPlus.CosTheta(), weight);
	+ };
	+ }
	+
	+ std::string Name() { return "__SAMPLE_NAME__"; }
	+
	+ //! Here you can write any custom histograms to TTrees that your sample has
	+ //! been handling.
	+ void Write() {
	+ //! The nuis::persistency helper methods will help write your objects to the
	+ //! correct place and in a TFile that will be closed before the program
	+ //! exits.
	+ //! They will write a copy of the TObject that is passed, so you do not need
	+ //! to release/worry about double freeing any histograms passed.
	+ //! write_directory is set up by the baseclass and is configurable in the
	+ //! instance configuration.
	+ // nuis::persistency::WriteToOutputFile<TH1>(Extra_plot,
	+ // Extra_plot->GetName(),
	+ // write_directory);
	+ //! It probably isn't a good idea to write a TTree with the above method,
	+ //! instead, try using nuis::persistency::GetOutputFile() to get the TFile
	+ //! and then manually writing/giving ownership of your TTree to the output
	+ //! file.
	+ }
	+};
	+
	+//! These declarations allow your class to be loaded dynamically by NUISANCE
	+DECLARE_PLUGIN(IEventProcessor, __SAMPLE_NAME__);
	diff --git a/scripts/to_configure/nuisbuild.in b/scripts/to_configure/nuisbuild.in
	new file mode 100644
	index 0000000..316b790
	--- /dev/null
	+++ b/scripts/to_configure/nuisbuild.in
	@@ -0,0 +1,101 @@
	+# 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/>.
	+################################################################################
	+
	+#!/bin/bash
	+
	+EXTRA_COMPILE_FLAGS=""
	+EXTRA_LINK_FLAGS=""
	+INPUT_FILE_NAME=""
	+OUTPUT_LIB_NAME=""
	+
	+SCRIPTNAME=${0}
	+
	+while [[ ${#} -gt 0 ]]; do
	+
	+ key="$1"
	+ case $key in
	+
	+ -i\|--implementation-file)
	+
	+ if [[ ${#} -lt 2 ]]; then
	+ echo "[ERROR]: ${1} expected a value."
	+ exit 1
	+ fi
	+
	+ INPUT_FILE_NAME="$2"
	+ echo "[OPT]: Reading event processor implementation from: ${INPUT_FILE_NAME}"
	+ shift # past argument
	+ ;;
	+
	+ --compile-flags)
	+
	+ if [[ ${#} -lt 2 ]]; then
	+ echo "[ERROR]: ${1} expected a value."
	+ exit 1
	+ fi
	+
	+ EXTRA_COMPILE_FLAGS="$2"
	+ echo "[OPT]: Including extra compile flags: ${EXTRA_COMPILE_FLAGS}"
	+ shift # past argument
	+ ;;
	+
	+ --link-flags)
	+
	+ if [[ ${#} -lt 2 ]]; then
	+ echo "[ERROR]: ${1} expected a value."
	+ exit 1
	+ fi
	+
	+ EXTRA_LINK_FLAGS="$2"
	+ echo "[OPT]: Including extra linker flags: ${EXTRA_LINK_FLAGS}"
	+ shift # past argument
	+ ;;
	+
	+ -?\|--help)
	+
	+ echo "[RUNLIKE] ${SCRIPTNAME}"
	+ echo -e "\t-i\|--implementation-file : Path to IEventProcessor subclass to build into dynamically loadable shared object."
	+ echo -e "\t--compile-flags : Extra compile flags to pass to the compiler."
	+ echo -e "\t--link-flags : Extra linker flags to pass to the linker."
	+ echo -e "\t-?\|--help : Print this message."
	+ exit 0
	+ ;;
	+
	+ *)
	+ # unknown option
	+ echo "Unknown option $1"
	+ exit 1
	+ ;;
	+
	+ esac
	+ shift
	+done
	+
	+OUTPUT_LIB_NAME=${INPUT_FILE_NAME%.*}.so
	+
	+#Removes the NUISANCE filename descriptor that uses a gmake trick to insert the file name into the compiler options
	+NUISANCE_CXX_FLAGS_GMAKE_SCRUB=$(echo '@NUISANCE_CXX_FLAGS@' \| sed s/-D__FILENAME__=\".*\"//g)
	+
	+echo "@CMAKE_CXX_COMPILER@ ${INPUT_FILE_NAME} -shared -fPIC -o ${OUTPUT_LIB_NAME} ${NUISANCE_CXX_FLAGS_GMAKE_SCRUB} ${EXTRA_COMPILE_FLAGS} -D__FILENAME__=\"${INPUT_FILE_NAME##*/}\" -I. -I@CMAKE_INSTALL_PREFIX@/include @CMAKE_LINK_FLAGS@ ${EXTRA_LINK_FLAGS} -L@CMAKE_INSTALL_PREFIX@/lib @NUISANCE_LINK_DIRS@ @NUISANCE_DEPEND_LIBS@"
	+
	+if ! @CMAKE_CXX_COMPILER@ ${INPUT_FILE_NAME} -shared -fPIC -o ${OUTPUT_LIB_NAME} ${NUISANCE_CXX_FLAGS_GMAKE_SCRUB} ${EXTRA_COMPILE_FLAGS} -D__FILENAME__=\"${INPUT_FILE_NAME##*/}\" -I. -I@CMAKE_INSTALL_PREFIX@/include @CMAKE_LINK_FLAGS@ ${EXTRA_LINK_FLAGS} -L@CMAKE_INSTALL_PREFIX@/lib @NUISANCE_LINK_DIRS@ @NUISANCE_DEPEND_LIBS@; then
	+ echo "[ERROR]: Failed to compile ${INPUT_FILE_NAME} -> ${OUTPUT_LIB_NAME}"
	+else
	+ echo "[INFO]: Successfully build: ${OUTPUT_LIB_NAME}."
	+fi
	diff --git a/scripts/to_configure/nuiseventprocgen.in b/scripts/to_configure/nuiseventprocgen.in
	new file mode 100644
	index 0000000..fb60275
	--- /dev/null
	+++ b/scripts/to_configure/nuiseventprocgen.in
	@@ -0,0 +1,131 @@
	+# 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/>.
	+################################################################################
	+
	+#!/bin/bash
	+
	+CLASS_NAME=""
	+NDIMS="0"
	+INPUT_FILE_NAME=""
	+USE_POLY="0"
	+SDC_TYPE=""
	+
	+while [[ ${#} -gt 0 ]]; do
	+
	+ key="$1"
	+ case $key in
	+
	+ -c\|--class-name)
	+
	+ if [[ ${#} -lt 2 ]]; then
	+ echo "[ERROR]: ${1} expected a value."
	+ exit 1
	+ fi
	+
	+ CLASS_NAME="$2"
	+ echo "[OPT]: Generating class named: ${CLASS_NAME} in implementation file: ${CLASS_NAME}.cxx"
	+ shift # past argument
	+ ;;
	+
	+ --MC)
	+
	+ INPUT_FILE_NAME="SimpleMCStudy.cxx.in"
	+ echo "[OPT]: Generating simple MC study stub class."
	+ ;;
	+
	+ --data)
	+
	+ INPUT_FILE_NAME="SimpleDataComparison.cxx.in"
	+ echo "[OPT]: Generating data comparison stub class."
	+ NDIMS="1"
	+ ;;
	+
	+ -n\|--n-dimensions)
	+
	+ if [[ ${#} -lt 2 ]]; then
	+ echo "[ERROR]: ${1} expected a value."
	+ exit 1
	+ fi
	+
	+ NDIMS="${2}"
	+ echo "[OPT]: Using a ${NDIMS} dimensional comparison"
	+ shift # past argument
	+ ;;
	+
	+ --poly)
	+
	+ USE_POLY="1"
	+ echo "[OPT]: Using a TH2Poly comparion."
	+ ;;
	+
	+ -?\|--help)
	+
	+ echo "[RUNLIKE] ${SCRIPTNAME}"
	+ echo -e "\t-c\|--class-name : Name of generated event processor"
	+ echo -e "\t class."
	+ echo -e "\t--MC : Generate a simple MC study shell."
	+ echo -e "\t--data : Generate a 'sample' shell."
	+ echo -e "\t-n\|--n-dimensions : Dimension of the data comparison"
	+ echo -e "\t <default = 1>. Only valid for"
	+ echo -e "\t --data (Currently can only be 1"
	+ echo -e "\t or 2)."
	+ echo -e "\t--poly : Build data comparison using"
	+ echo -e "\t TH2Poly. Only valid for --data "
	+ echo -e "\t -n 2"
	+ echo -e "\t-?\|--help : Print this message."
	+ exit 0
	+ ;;
	+
	+ *)
	+ # unknown option
	+ echo "Unknown option $1"
	+ exit 1
	+ ;;
	+
	+ esac
	+ shift
	+done
	+
	+if [ ${INPUT_FILE_NAME} == "SimpleDataComparison.cxx.in" ]; then
	+ if [ ${NDIMS} == "1" ]; then
	+ SDC_TYPE=SimpleDataComparison_1D
	+ elif [ ${NDIMS} == "2" ]; then
	+ if [ ${USE_POLY} == "1" ]; then
	+ SDC_TYPE=SimpleDataComparison_2DPoly
	+ else
	+ SDC_TYPE=SimpleDataComparison_2D
	+ fi
	+ else
	+ echo "[ERROR]: Can only currently set dimensionality to 1 or 2 dimensions."
	+ exit 1
	+ fi
	+fi
	+
	+if [ -e ${CLASS_NAME}.cxx ]; then
	+ echo "[ERROR]: ${CLASS_NAME}.cxx already exists, not overwriting. Please use a different class name."
	+ exit 2
	+fi
	+
	+cp @CMAKE_INSTALL_PREFIX@/file_stubs/${INPUT_FILE_NAME} ${CLASS_NAME}.cxx
	+
	+sed -i "s/__SAMPLE_NAME__/${CLASS_NAME}/g" ${CLASS_NAME}.cxx
	+if [ ! -z ${SDC_TYPE} ]; then
	+ sed -i "s/__SDC_TYPE__/${SDC_TYPE}/g" ${CLASS_NAME}.cxx
	+fi
	+
	+echo "[INFO]: Generated ${CLASS_NAME}.cxx"
	diff --git a/cmake/setup.sh.in b/scripts/to_configure/setup.sh.in
	similarity index 100%
	rename from cmake/setup.sh.in
	rename to scripts/to_configure/setup.sh.in
	diff --git a/scripts/dumpgenieconfig.py b/scripts_old/dumpgenieconfig.py
	similarity index 100%
	rename from scripts/dumpgenieconfig.py
	rename to scripts_old/dumpgenieconfig.py
	diff --git a/scripts/maketarball.sh b/scripts_old/maketarball.sh
	similarity index 100%
	rename from scripts/maketarball.sh
	rename to scripts_old/maketarball.sh
	diff --git a/scripts/nuiscardgen b/scripts_old/nuiscardgen
	similarity index 100%
	rename from scripts/nuiscardgen
	rename to scripts_old/nuiscardgen
	diff --git a/scripts/nuissamples b/scripts_old/nuissamples
	similarity index 100%
	rename from scripts/nuissamples
	rename to scripts_old/nuissamples
	diff --git a/scripts/plotlimitdist.py b/scripts_old/plotlimitdist.py
	similarity index 100%
	rename from scripts/plotlimitdist.py
	rename to scripts_old/plotlimitdist.py
	diff --git a/scripts/plotnuiscomp.py b/scripts_old/plotnuiscomp.py
	similarity index 100%
	rename from scripts/plotnuiscomp.py
	rename to scripts_old/plotnuiscomp.py
	diff --git a/scripts/plotnuismin.py b/scripts_old/plotnuismin.py
	similarity index 100%
	rename from scripts/plotnuismin.py
	rename to scripts_old/plotnuismin.py
	diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
	index b615e75..d5b8f1d 100644
	--- a/src/CMakeLists.txt
	+++ b/src/CMakeLists.txt
	@@ -1,15 +1,16 @@
	add_subdirectory(config)
	add_subdirectory(event)
	+add_subdirectory(exception)
	+add_subdirectory(generator)
	add_subdirectory(input)
	+add_subdirectory(parameters)
	+add_subdirectory(persistency)
	add_subdirectory(plugins)
	+add_subdirectory(samples)
	add_subdirectory(utility)
	-add_subdirectory(generator)
	-add_subdirectory(persistency)
	-add_subdirectory(parameters)
	add_subdirectory(variation)

	-add_subdirectory(samples)
	SET(INuADataComparisons_List ${INuADataComparisons_List} PARENT_SCOPE)
	SET(INuADataComparisons_FHiCL ${INuADataComparisons_FHiCL} PARENT_SCOPE)

	add_subdirectory(app)
	diff --git a/src/samples/CMakeLists.txt b/src/samples/CMakeLists.txt
	index a31710c..6313da0 100644
	--- a/src/samples/CMakeLists.txt
	+++ b/src/samples/CMakeLists.txt
	@@ -1,23 +1,24 @@
	set(samples_header_files
	IEventProcessor.hxx
	IDataComparison.hxx
	- SimpleDataComparison.hxx)
	+ SimpleDataComparison.hxx
	+ SimpleMCStudy.hxx)

	install(FILES ${samples_header_files} DESTINATION include/samples)

	add_subdirectory(MCTools)

	add_subdirectory(nuA)

	cmessage(DEBUG "INuADataComparisons: ${INuADataComparisons}")

	SET(INuADataComparisons_List)
	if(NOT IDataComparisons STREQUAL "")
	string(REPLACE ";" ", " INuADataComparisons_List "${INuADataComparisons}")
	endif()

	cmessage(DEBUG "INuADataComparisons_List: ${INuADataComparisons_List}")


	SET(INuADataComparisons_List ${INuADataComparisons_List} PARENT_SCOPE)
	SET(INuADataComparisons_FHiCL ${INuADataComparisons_FHiCL} PARENT_SCOPE)
	diff --git a/src/samples/SimpleDataComparison.hxx b/src/samples/SimpleDataComparison.hxx
	index 36f8e7a..a63e4df 100644
	--- a/src/samples/SimpleDataComparison.hxx
	+++ b/src/samples/SimpleDataComparison.hxx
	@@ -1,424 +1,426 @@
	// Copyright 2018 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 SAMPLES_SIMPLEDATACOMPARISON_HXX_SEEN
	-#define SAMPLES_SIMPLEDATACOMPARISON_HXX_SEEN
	+#pragma once

	#include "samples/IDataComparison.hxx"

	#include "event/FullEvent.hxx"

	#include "input/InputManager.hxx"

	#include "persistency/ROOTOutput.hxx"

	#include "utility/FileSystemUtility.hxx"
	#include "utility/HistogramUtility.hxx"
	#include "utility/KinematicUtility.hxx"
	#include "utility/ROOTUtility.hxx"
	#include "utility/StatsUtility.hxx"

	#include <array>
	#include <functional>
	#include <limits>
	#include <memory>
	#include <vector>

	-template <size_t NDim, typename NumericT = double,
	- typename HT = typename nuis::utility::HType_Helper<NDim, void>::type>
	+template <size_t nd, typename NumericT = double,
	+ typename HT = typename nuis::utility::HType_Helper<nd, void>::type>
	class SimpleDataComparison : public IDataComparison {

	NEW_NUIS_EXCEPT(invalid_SimpleDataComparison_initialization);
	NEW_NUIS_EXCEPT(SimpleDataComparison_already_finalized);

	protected:
	using HistType = HT;
	using TH_Help = typename nuis::utility::TH_Helper<HistType>;

	+ static size_t const NDim = nd;
	+
	nuis::input::InputManager::Input_id_t fIH_id;
	std::string write_directory;
	size_t NMaxSample_override;
	int fIsShapeOnly;
	int fIsFluxUnfolded;

	std::vector<bool> fSignalCache;
	std::vector<std::array<NumericT, NDim>> fProjectionCache;

	std::string fDataInputDescriptor;
	std::unique_ptr<HistType> fData;
	std::string fMaskInputDescriptor;
	std::unique_ptr<HistType> fMask;
	std::string fCovarianceInputDescriptor;
	std::unique_ptr<TH2> fCovariance;
	std::unique_ptr<HistType> fPrediction;
	std::unique_ptr<HistType> fPrediction_xsec;
	std::unique_ptr<HistType> fPrediction_shape;
	std::unique_ptr<HistType> fPrediction_comparison;
	bool fComparisonFinalized;

	std::string fJournalReference;
	std::string fTargetMaterial;
	std::string fFluxDescription;
	std::string fSignalDescription;

	nuis::utility::ENuRange energy_cut;

	std::function<bool(nuis::event::FullEvent const &)> IsSigFunc;
	std::function<std::array<NumericT, NDim>(nuis::event::FullEvent const &)>
	CompProjFunc;

	// If assigned by subclass will be called on for all events, bool signifies
	// whether the event was selected.
	std::function<void(nuis::event::FullEvent const &, bool, double)>
	ProcessExtraFunc;

	public:
	SimpleDataComparison() {
	fIH_id = std::numeric_limits<nuis::input::InputManager::Input_id_t>::max();
	write_directory = "";
	NMaxSample_override = std::numeric_limits<size_t>::max();
	fDataInputDescriptor = "";
	fData = nullptr;
	fMaskInputDescriptor = "";
	fMask = nullptr;
	fCovarianceInputDescriptor = "";
	fCovariance = nullptr;
	fPrediction = nullptr;
	fPrediction_xsec = nullptr;
	fPrediction_shape = nullptr;
	fPrediction_comparison = nullptr;
	fComparisonFinalized = false;
	IsSigFunc = [](nuis::event::FullEvent const &) -> bool { return true; };
	CompProjFunc =
	[](nuis::event::FullEvent const &) -> std::array<NumericT, NDim> {
	std::array<NumericT, NDim> arr;
	for (NumericT &el : arr) {
	el = 0;
	}
	return arr;
	};

	ProcessExtraFunc =
	std::function<void(nuis::event::FullEvent const &, bool, double)>();

	fJournalReference = "";
	fTargetMaterial = "";
	fFluxDescription = "";
	fSignalDescription = "";
	fIsShapeOnly = -1;
	fIsFluxUnfolded = -1;

	energy_cut = nuis::utility::ENuRange{std::numeric_limits<double>::max(),
	std::numeric_limits<double>::max()};
	}

	fhicl::ParameterSet fGlobalConfig;
	fhicl::ParameterSet fInstanceConfig;

	void ReadGlobalConfigDefaults() {
	fGlobalConfig = nuis::config::GetDocument().get<fhicl::ParameterSet>(
	std::string("global.sample_configuration.") + Name(),
	fhicl::ParameterSet());

	if (!fJournalReference.length()) {
	fJournalReference = fGlobalConfig.get<std::string>("journal_reference",
	fJournalReference);
	}
	if (!fTargetMaterial.length()) {
	fTargetMaterial =
	fGlobalConfig.get<std::string>("target_material", fTargetMaterial);
	}
	if (!fFluxDescription.length()) {
	fFluxDescription =
	fGlobalConfig.get<std::string>("flux_description", fFluxDescription);
	}
	if (!fSignalDescription.length()) {
	fSignalDescription = fGlobalConfig.get<std::string>("signal_description",
	fSignalDescription);
	}

	if (fIsShapeOnly == -1) {
	fIsShapeOnly = fGlobalConfig.get<bool>("shape_only", false);
	}
	if (fIsFluxUnfolded == -1) {
	fIsFluxUnfolded = fGlobalConfig.get<bool>("flux_unfolded", false);
	}

	if ((energy_cut.first == std::numeric_limits<double>::max()) &&
	(fGlobalConfig.has_key("enu_range"))) {
	energy_cut = fGlobalConfig.get<std::pair<double, double>>("enu_range");
	}
	}

	virtual std::string GetJournalReference() { return fJournalReference; }
	virtual std::string GetTargetMaterial() { return fTargetMaterial; }
	virtual std::string GetFluxDescription() { return fFluxDescription; }
	virtual std::string GetSignalDescription() { return fSignalDescription; }

	void SetShapeOnly(bool iso) { fIsShapeOnly = iso; }
	void SetFluxUnfolded(bool ifo) { fIsFluxUnfolded = ifo; }

	void SetData(std::string const &data_descriptor) {
	fDataInputDescriptor = data_descriptor;
	}

	void SetMask(std::string const &mask_descriptor) {
	fMaskInputDescriptor = mask_descriptor;
	}

	void SetCovariance(std::string const &cov_descriptor) {
	fCovarianceInputDescriptor = cov_descriptor;
	}

	virtual void FillProjection(std::array<NumericT, NDim> const &proj,
	NumericT event_weight) {
	TH_Help::Fill(fPrediction, proj, event_weight);
	}

	virtual void FinalizeComparison() {
	if (fComparisonFinalized) {
	throw SimpleDataComparison_already_finalized()
	<< "[ERROR]: Attempted to re-finalize a comparison for "
	"SimpleDataComparison: "
	<< std::quoted(Name());
	}
	fPrediction_xsec =
	nuis::utility::Clone(fPrediction, false, "Prediction_xsec");

	IInputHandler const &IH =
	nuis::input::InputManager::Get().GetInputHandler(fIH_id);

	TH_Help::Scale(fPrediction_xsec, 1.0, "width");

	// If we have a flux cut
	if (energy_cut.first != std::numeric_limits<double>::max()) {
	TH_Help::Scale(fPrediction_xsec, IH.GetXSecScaleFactor(energy_cut));
	}

	fPrediction_shape =
	nuis::utility::Clone(fPrediction_xsec, false, "Prediction_shape");
	if (fData) {
	TH_Help::Scale(fPrediction_shape,
	TH_Help::Integral(fData, "width") /
	TH_Help::Integral(fPrediction_shape, "width"));

	} else {
	IEventProcessor_WARN(
	"When Finalizing comparison, no Data histogram available.");
	}

	if (fIsFluxUnfolded) {
	// fPrediction_comparison
	} else if (fIsShapeOnly) {
	fPrediction_comparison = nuis::utility::Clone(fPrediction_shape, false,
	"Prediction_comparison");
	} else {
	fPrediction_comparison = nuis::utility::Clone(fPrediction_xsec, false,
	"Prediction_comparison");
	}
	fComparisonFinalized = true;
	}

	void Initialize(fhicl::ParameterSet const &instance_sample_configuration) {

	fInstanceConfig = instance_sample_configuration;

	if (fInstanceConfig.has_key("verbosity")) {
	SetSampleVerbosity(fInstanceConfig.get<std::string>("verbosity"));
	} else {
	SetSampleVerbosity("Reticent");
	}

	ReadGlobalConfigDefaults();

	if (fInstanceConfig.has_key("fake_data")) {
	fData = nuis::utility::GetHistogram<HistType>(
	fInstanceConfig.get<std::string>("fake_data_histogram"));
	} else if (!fGlobalConfig.get<bool>("has_data", true) \|\|
	!fInstanceConfig.get<bool>("has_data", true)) {
	// Explicitly not expecting data
	} else {
	if (!fDataInputDescriptor.length()) {
	if (!fGlobalConfig.has_key("data_descriptor")) {
	throw invalid_SimpleDataComparison_initialization()
	<< "[ERROR]: SimpleDataComparison::Initialize for "
	"IDataComparison: "
	<< std::quoted(Name())
	<< " failed as no input data was set by a call to "
	"SimpleDataComparison::SetData and no data_descriptor for "
	"this SimpleDataComparison could be found in the global "
	"configuration.";
	}
	fDataInputDescriptor =
	fGlobalConfig.get<std::string>("data_descriptor");
	}
	fData = nuis::utility::GetHistogram<HistType>(fDataInputDescriptor);
	}

	if (!fPrediction) {
	if (!fData) {
	throw invalid_SimpleDataComparison_initialization()
	<< "[ERROR]: SimpleDataComparison::Initialize for "
	"IDataComparison: "
	<< std::quoted(Name())
	<< " failed. As `has_data: false` was set in the configuration "
	"(global: "
	<< (!fGlobalConfig.get<bool>("has_data", true))
	<< ", instance: " << !fInstanceConfig.get<bool>("has_data", true)
	<< "), the instance constructor must supply the fPrediction "
	"binning, and it wasn't.";
	}
	fPrediction = nuis::utility::Clone(fData, true, "Prediction");
	}

	if (fCovarianceInputDescriptor.length()) {
	fCovariance =
	nuis::utility::GetHistogram<TH2D>(fCovarianceInputDescriptor);
	} else if (fGlobalConfig.has_key("covariance_descriptor")) {
	fCovariance = nuis::utility::GetHistogram<TH2D>(
	fGlobalConfig.get<std::string>("covariance_descriptor"));
	}

	if (fMaskInputDescriptor.length()) {
	fMask = nuis::utility::GetHistogram<HistType>(fMaskInputDescriptor);
	} else if (fGlobalConfig.has_key("mask_descriptor")) {
	fMask = nuis::utility::GetHistogram<HistType>(
	fGlobalConfig.get<std::string>("mask_descriptor"));
	}

	if (fInstanceConfig.has_key("verbosity")) {
	SetSampleVerbosity(fInstanceConfig.get<std::string>("verbosity"));
	}

	NMaxSample_override =
	fInstanceConfig.get<size_t>("nmax", std::numeric_limits<size_t>::max());

	write_directory =
	fInstanceConfig.get<std::string>("write_directory", Name());

	fIH_id =
	nuis::input::InputManager::Get().EnsureInputLoaded(fInstanceConfig);
	}

	void ProcessSample(size_t nmax = std::numeric_limits<size_t>::max()) {
	if (fIH_id ==
	std::numeric_limits<nuis::input::InputManager::Input_id_t>::max()) {
	throw uninitialized_IEventProcessor();
	}
	IInputHandler const &IH =
	nuis::input::InputManager::Get().GetInputHandler(fIH_id);

	nmax = std::min(NMaxSample_override, nmax);

	size_t NEvsToProcess = std::min(nmax, IH.GetNEvents());

	double nmax_scaling = double(IH.GetNEvents()) / double(NEvsToProcess);

	size_t NToShout = NEvsToProcess / 10;
	IEventProcessor_INFO("Sample " << std::quoted(Name()) << " processing "
	<< NEvsToProcess << " events.");

	IInputHandler::ev_index_t ev_idx = 0;

	bool DetermineSignalEvents = !fSignalCache.size();

	nuis::utility::Clear<HistType>(*fPrediction);
	fComparisonFinalized = false;

	size_t cache_ctr = 0;

	while (ev_idx < NEvsToProcess) {
	if (DetermineSignalEvents) {
	nuis::event::FullEvent const &fev = IH.GetFullEvent(ev_idx);
	bool is_sig = IsSigFunc(fev);
	fSignalCache.push_back(is_sig);
	if (is_sig) {
	fProjectionCache.push_back(CompProjFunc(fev));
	}
	if (ProcessExtraFunc) {
	ProcessExtraFunc(fev, is_sig,
	IH.GetEventWeight(ev_idx) * nmax_scaling);
	}
	}

	if (NToShout && !(ev_idx % NToShout)) {
	IEventProcessor_INFO("\tProcessed " << ev_idx << "/" << NEvsToProcess
	<< " events.");
	}

	if (fSignalCache[ev_idx]) {
	FillProjection(fProjectionCache[cache_ctr++],
	IH.GetEventWeight(ev_idx) * nmax_scaling);
	}

	ev_idx++;
	}
	IEventProcessor_INFO("\t" << fProjectionCache.size() << "/" << NEvsToProcess
	<< " events passed selection.");
	}
	void Write() {
	if (!fComparisonFinalized) {
	FinalizeComparison();
	}

	nuis::persistency::WriteToOutputFile<HistType>(
	fPrediction_comparison, "Prediction", write_directory);
	nuis::persistency::WriteToOutputFile<HistType>(
	fPrediction_xsec, "Prediction_xsec", write_directory);

	if (fData) {
	nuis::persistency::WriteToOutputFile<HistType>(fData, "Data",
	write_directory);
	nuis::persistency::WriteToOutputFile<HistType>(
	fPrediction_shape, "Prediction_shape", write_directory);
	}
	}

	double GetGOF() {
	if (!fComparisonFinalized) {
	FinalizeComparison();
	}
	if (fData && fPrediction_comparison) {
	return nuis::utility::GetChi2(fData, fPrediction_comparison);
	} else
	return std::numeric_limits<double>::max();
	}
	double GetNDOGuess() {
	if (fData) {
	return TH_Help::Nbins(fData);
	}
	return 0;
	}

	fhicl::ParameterSet GetExampleConfiguration() {
	fhicl::ParameterSet exps;
	exps.put<std::string>("name", Name());
	exps.put<std::string>("input_type", "Generator");
	exps.put<std::string>("file", "Events.root");
	exps.put<std::string>("write_directory", Name());
	exps.put<std::string>("fake_data_histogram", "/path/to/file.root;h_name");

	return exps;
	}
	};

	-typedef SimpleDataComparison<1> SimpleDataComparison_1D;
	-typedef SimpleDataComparison<2> SimpleDataComparison_2D;
	-
	-#endif
	+typedef SimpleDataComparison<1, double, TH1D> SimpleDataComparison_1D;
	+typedef SimpleDataComparison<2, double, TH2D> SimpleDataComparison_2D;
	+typedef SimpleDataComparison<1, float, TH1F> SimpleDataComparison_1F;
	+typedef SimpleDataComparison<2, float, TH2F> SimpleDataComparison_2F;
	+typedef SimpleDataComparison<2, double, TH2Poly> SimpleDataComparison_2DPoly;
	diff --git a/src/samples/SimpleMCStudy.hxx b/src/samples/SimpleMCStudy.hxx
	new file mode 100644
	index 0000000..c8a55d5
	--- /dev/null
	+++ b/src/samples/SimpleMCStudy.hxx
	@@ -0,0 +1,108 @@
	+// Copyright 2018 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/>.
	+ *******************************************************************************/
	+
	+#pragma once
	+
	+#include "samples/IEventProcessor.hxx"
	+
	+#include "event/FullEvent.hxx"
	+
	+#include "input/InputManager.hxx"
	+
	+#include <functional>
	+
	+class SimpleMCStudy : public IEventProcessor {
	+protected:
	+ nuis::input::InputManager::Input_id_t fIH_id;
	+ std::string write_directory;
	+ size_t NMaxSample_override;
	+
	+ std::function<void(nuis::event::FullEvent const &, double)>
	+ ProcessEventFunction;
	+
	+public:
	+ SimpleMCStudy() {
	+ fIH_id = std::numeric_limits<nuis::input::InputManager::Input_id_t>::max();
	+ write_directory = "";
	+ NMaxSample_override = std::numeric_limits<size_t>::max();
	+
	+ ProcessEventFunction = std::function<void(nuis::event::FullEvent const &, double)>();
	+ }
	+
	+ fhicl::ParameterSet fGlobalConfig;
	+ fhicl::ParameterSet fInstanceConfig;
	+
	+ void ReadGlobalConfigDefaults() {
	+ fGlobalConfig = nuis::config::GetDocument().get<fhicl::ParameterSet>(
	+ std::string("global.sample_configuration.") + Name(),
	+ fhicl::ParameterSet());
	+ }
	+
	+ void Initialize(fhicl::ParameterSet const &instance_sample_configuration) {
	+
	+ fInstanceConfig = instance_sample_configuration;
	+
	+ if (fInstanceConfig.has_key("verbosity")) {
	+ SetSampleVerbosity(fInstanceConfig.get<std::string>("verbosity"));
	+ } else {
	+ SetSampleVerbosity("Reticent");
	+ }
	+
	+ ReadGlobalConfigDefaults();
	+
	+ NMaxSample_override =
	+ fInstanceConfig.get<size_t>("nmax", std::numeric_limits<size_t>::max());
	+
	+ write_directory =
	+ fInstanceConfig.get<std::string>("write_directory", Name());
	+
	+ fIH_id =
	+ nuis::input::InputManager::Get().EnsureInputLoaded(fInstanceConfig);
	+ }
	+
	+ void ProcessSample(size_t nmax = std::numeric_limits<size_t>::max()) {
	+ if (fIH_id ==
	+ std::numeric_limits<nuis::input::InputManager::Input_id_t>::max()) {
	+ throw uninitialized_IEventProcessor();
	+ }
	+ IInputHandler const &IH =
	+ nuis::input::InputManager::Get().GetInputHandler(fIH_id);
	+
	+ nmax = std::min(NMaxSample_override, nmax);
	+
	+ size_t NEvsToProcess = std::min(nmax, IH.GetNEvents());
	+
	+ double nmax_scaling = double(IH.GetNEvents()) / double(NEvsToProcess);
	+
	+ size_t NToShout = NEvsToProcess / 10;
	+ IEventProcessor_INFO("Sample " << std::quoted(Name()) << " processing "
	+ << NEvsToProcess << " events.");
	+
	+ IInputHandler::ev_index_t ev_idx = 0;
	+
	+ while (ev_idx < NEvsToProcess) {
	+ nuis::event::FullEvent const &fev = IH.GetFullEvent(ev_idx);
	+ ProcessEventFunction(fev, IH.GetEventWeight(ev_idx) * nmax_scaling);
	+ ev_idx++;
	+ }
	+
	+ IEventProcessor_INFO("Sample " << std::quoted(Name()) << " processed "
	+ << NEvsToProcess << " events.");
	+ }
	+};

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