From 3180f2aded1000754e87ea3e77484302032c3fa8 Mon Sep 17 00:00:00 2001
From: Daniel Barrow <danbarrow257@gmail.com>
Date: Tue, 12 Nov 2024 05:56:54 -0600
Subject: [PATCH 1/9] Pull core which has access to OscProb engine in
 NuOscillator

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9b8b8d6..faec621 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -116,7 +116,7 @@ find_package(MaCh3)
 if(NOT MaCh3_FOUND)
   CPMFindPackage(
       NAME MaCh3
-      GIT_TAG "v1.2.0_alpha"
+      GIT_TAG "feature/dbarrow257/OscProb"
       GITHUB_REPOSITORY mach3-software/MaCh3
   )
 else()

From d86d000fa8cf12db9c7aab4e07d6ef7d42cdc5bb Mon Sep 17 00:00:00 2001
From: Daniel Barrow <danbarrow257@gmail.com>
Date: Tue, 12 Nov 2024 05:57:59 -0600
Subject: [PATCH 2/9] Update setup script to pull more recent ROOT install

---
 setup_dune_env.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup_dune_env.sh b/setup_dune_env.sh
index 0f423d8..b52ed0e 100755
--- a/setup_dune_env.sh
+++ b/setup_dune_env.sh
@@ -1,6 +1,6 @@
 source /cvmfs/larsoft.opensciencegrid.org/spack-packages/setup-env.sh
-spack load root@6.28.06
-spack load cmake
+spack load root@6.28.12
 spack load gcc@12.2.0
+
 export CXX=`which g++` # this might be specific for Fermilab?
 export CC=`which gcc` # this might be specific for Fermilab?

From c676ddd7714adf528cea30ce6fa9eadc3d608f80 Mon Sep 17 00:00:00 2001
From: Daniel Barrow <danbarrow257@gmail.com>
Date: Wed, 20 Nov 2024 09:57:30 -0600
Subject: [PATCH 3/9] Use an older branch of MaCh3 core whilst I debug the
 interface between DUNE MaCh3 and the new core code

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index faec621..cdacee3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -116,7 +116,7 @@ find_package(MaCh3)
 if(NOT MaCh3_FOUND)
   CPMFindPackage(
       NAME MaCh3
-      GIT_TAG "feature/dbarrow257/OscProb"
+      GIT_TAG "48a9500"
       GITHUB_REPOSITORY mach3-software/MaCh3
   )
 else()

From 7dca871d388269540fcc7691333880f62c4c1b14 Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Fri, 7 Feb 2025 06:54:02 -0600
Subject: [PATCH 4/9] Add apps to automatize and make 2d parameter variations

---
 configs/Variations_Atmospherics.yaml | 120 ++++++++++++++++++++++++++
 src/CMakeLists.txt                   |   3 +
 src/SigmaVariation2D.cpp             | 111 ++++++++++++++++++++++++
 src/Variations.cpp                   | 124 +++++++++++++++++++++++++++
 src/Variations2D.cpp                 | 124 +++++++++++++++++++++++++++
 5 files changed, 482 insertions(+)
 create mode 100644 configs/Variations_Atmospherics.yaml
 create mode 100644 src/SigmaVariation2D.cpp
 create mode 100644 src/Variations.cpp
 create mode 100644 src/Variations2D.cpp

diff --git a/configs/Variations_Atmospherics.yaml b/configs/Variations_Atmospherics.yaml
new file mode 100644
index 0000000..cc729de
--- /dev/null
+++ b/configs/Variations_Atmospherics.yaml
@@ -0,0 +1,120 @@
+General:
+  OutputFile: "parameter_study_sterile/test_2d_var/test_var_sterile_all param_thetav1_AllMC_trueE_trueCos.root"
+
+  DUNESamples: ["configs/Samples/AtmSample_AllMC.yaml"]
+
+  #Nu-FIT
+  #OscillationParameters: [0.310, 0.582, 0.224, 7.39E-5, 2.5254E-3, -2.498, 25]
+
+  #Nu-FIT 5.2 w. SK atm
+  #OscillationParameters: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233]
+  OscillationParameters: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
+  #OscillationParameters: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, -0.5, 0.2, 0.4, 0.3, 0.5, 0.25, 0., 0., 0., 0.2, 0.4, 0.4]
+
+  #T2K-like best-fit
+  #OscillationParameters: [0.307, 0.528, 0.0218, 7.53e-5, 2.509e-3, -1.601, 25]
+
+  Variations:
+    - Parameter: 
+        Name: sin2th_14
+        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
+        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
+
+    - Parameter: 
+        Name: sin2th_24
+        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
+        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
+
+    - Parameter: 
+        Name: sin2th_34
+        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
+        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
+
+    - Parameter:
+        Name: delm2_14
+        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
+        VarValues: [0., 0.00001, 0.0001, 0.001, 0.01, 0.1, 1.]
+
+    - Parameter:
+        Name: delta_14
+        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
+        VarValues: [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265]
+
+    - Parameter:
+        Name: delta_24
+        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
+        VarValues: [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265]
+  
+  Systematics:
+    XsecCovFile: ["configs/CovObjs/xsec_covariance_DUNE_systs_2022a_FD_v3.yaml"]
+    XsecCovName: "xsec_cov"
+    XsecStepScale: 0.1
+    XsecAtGen: false 
+    OscCovFile: ["configs/CovObjs/OscProb_test.yaml"]
+    OscCovName: "osc_cov"
+
+  Fitter:
+    FitTestLikelihood: false
+
+  MCMC:
+    NSteps: 2000
+    AutoSave: 10000
+
+  Output:
+    FileName: "TestEventRates.root"
+    OUTPUTNAME: "TestLLH.root"
+
+  ProcessMCMC: No
+  Seed: 0
+  Debug: No
+
+"Projections": [
+  {
+    "Name": "RecoNuEnergy", 
+    "VarString": "RecoNeutrinoEnergy",
+    "VarBins": [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.2,1.4],
+    "KinematicCuts": [
+      {
+        "Range": [0.1,0.8],
+        "Name": "TrueNuEnergy", 
+        "VarString": "TrueNeutrinoEnergy"
+      }, 
+      {
+        "Range": [0.4,1.0],
+        "Name": "TrueCosZ", 
+        "VarString": "TrueCosineZ"
+      }
+    ], 
+    "CategoryCuts": [
+      {
+        "Name": "OscillationChannel_Single", 
+        "VarString": "OscChannel",
+        "Breakdown": [[0.0],  [1.0],  [2.0],  [3.0],  [4.0],  [5.0],  [6.0],  [7.0],  [8.0],  [9.0], [10.0], [11.0]],
+	"Names":     ["nue_x_nue","nue_x_numu","nue_x_nutau","numu_x_nue","numu_x_numu","numu_x_nutau","nuebar_x_nuebar","nuebar_x_numubar","nuebar_x_nutaubar","numubar_x_nuebar","numubar_x_numubar","numubar_x_nutaubar"],
+      },
+      {
+        "Name": "OscillationChannel_Group", 
+        "VarString": "OscChannel",
+        "Breakdown": [[0.0, 1.0, 2.0, 3.0, 4.0, 5.0],  [6.0, 7.0, 8.0, 9.0, 10.0, 11.0]],
+	"Names":     ["Nu","Nubar"],
+      },
+      {
+        "Name": "Mode_Single", 
+        "VarString": "Mode",
+        "Breakdown": [[0.0] , [1.0], [2.0], [3.0], [4.0], [5.0], [6.0], [7.0], [8.0], [9.0], [10.0], [11.0], [12.0], [13.0], [14.0], [15.0], [16.0], [17.0], [18.0], [19.0], [20.0], [21.0], [22.0], [23.0], [24.0], [25.0], [26.0]],
+      },
+      {
+        "Name": "Mode_Group", 
+        "VarString": "Mode",
+        "Breakdown": [ [0.0],   [2.0],   [3.0],   [9.0],  [15.0],  [16.0], [1.0, 4.0, 5.0, 6.0, 7.0, 8.0, 10.0, 11.0, 12.0, 13.0], [14.0, 17.0, 18.0, 19.0, 20.0, 21.0, 22.0, 23.0, 24.0, 25.0, 26.0]],
+	"Names":     ["CCQE", "CCDIS", "CCRES", "CCMEC", "NCDIS", "NCRES",                                                "CCOth",                                                            "NCOth"],
+      }
+    ],
+  },
+
+  {
+    "Name": "TrueNuEnergy",
+    "VarString": "TrueNeutrinoEnergy",
+    "VarBins": [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.2,1.4,1.6,1.8,2.0,2.2,2.4,2.6,2.8,3.0,3.5,4.0,4.5,5.0,6.0,7.0,8.0,9.0,10.0],
+  }
+]
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6590947..7cdfb47 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,6 +6,9 @@ foreach(app
 	Projections
 	SigmaVariation
 	LikelihoodScan
+  SigmaVariation2D
+  Variations
+  Variations2D
       )
       
     add_executable(${app} ${app}.cpp)
diff --git a/src/SigmaVariation2D.cpp b/src/SigmaVariation2D.cpp
new file mode 100644
index 0000000..4b659f6
--- /dev/null
+++ b/src/SigmaVariation2D.cpp
@@ -0,0 +1,111 @@
+#include <iostream>
+#include <chrono>
+#include <iomanip>
+#include <vector>
+
+#include <TH2D.h>
+#include <THStack.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TRint.h>
+#include <TLegend.h>
+#include <TColor.h>
+#include <TMath.h>
+
+#include "mcmc/mcmc.h"
+#include "samplePDFDUNE/MaCh3DUNEFactory.h"
+#include "samplePDFDUNE/StructsDUNE.h"
+
+int main(int argc, char * argv[]) {
+  if(argc == 1){
+    MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
+    return 1;
+  }
+  manager* FitManager = new manager(argv[1]);
+
+  //###############################################################################################################################
+
+  //DB Sigma variations in units of each parameters Sigma
+  std::vector<double> sigmaVariations = {-3, -1, 0, 1, 3};
+
+  //###############################################################################################################################
+  //Create samplePDFFD objects
+  
+  covarianceXsec* xsec = nullptr;
+  covarianceOsc* osc = nullptr;
+
+  std::vector<samplePDFFDBase*> DUNEPdfs;
+  MakeMaCh3DuneInstance(FitManager, DUNEPdfs, xsec, osc);
+
+  //###############################################################################################################################
+  //Perform reweight and print total integral
+
+  MACH3LOG_INFO("=======================================================");
+  for(samplePDFFDBase* Sample: DUNEPdfs){
+    Sample->reweight();
+    MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get2DHist()->Integral());
+  }
+  
+  //###############################################################################################################################
+  //DB Can't use the core sigma variations as it's entirely set up around the concept of multiple selections per samplePDF object
+  //   Thats not the case in the FD code, which has one selection per samplePDF object
+  //   Consequently have to write out own code
+  
+  std::vector<covarianceBase*> CovObjs;
+  CovObjs.emplace_back(xsec);
+  CovObjs.emplace_back(osc);
+
+  MACH3LOG_INFO("=======================================================");
+
+  std::string OutputFileName = FitManager->raw()["General"]["OutputFile"].as<std::string>();
+  TFile* File = TFile::Open(OutputFileName.c_str(),"RECREATE");
+  
+  for (covarianceBase* CovObj: CovObjs) {
+    MACH3LOG_INFO("Starting Variations for covarianceBase Object: {}",CovObj->getName());
+    
+    int nPars = CovObj->getNpars();
+    for (int iPar=0;iPar<nPars;iPar++) {
+      std::string ParName = CovObj->GetParName(iPar);
+      double VarInit = CovObj->getParInit(iPar);
+      double VarSigma = CovObj->getDiagonalError(iPar);
+      
+      MACH3LOG_INFO("\tParameter : {:<30} - Variations around value : {:<10.7f} , in units of 1 Sigma : {:<10.7f}",ParName,VarInit,VarSigma);
+
+      File->cd();
+      File->mkdir(ParName.c_str());
+      File->cd(ParName.c_str());
+      
+      for (size_t iSigVar=0;iSigVar<sigmaVariations.size();iSigVar++) {
+	double VarVal = VarInit + sigmaVariations[iSigVar]*VarSigma;
+	if (VarVal < CovObj->GetLowerBound(iPar)) VarVal = CovObj->GetLowerBound(iPar);
+	if (VarVal > CovObj->GetUpperBound(iPar)) VarVal = CovObj->GetUpperBound(iPar);
+	
+	MACH3LOG_INFO("\t\tVariation {:<5.3f} - Parameter Value : {:<10.7f}",sigmaVariations[iSigVar],VarVal);
+	CovObj->setParProp(iPar,VarVal);
+
+	for (size_t iSample=0;iSample<DUNEPdfs.size();iSample++) {
+	  std::string SampleName = DUNEPdfs[iSample]->GetName();
+	  
+	  File->cd(ParName.c_str());
+	  if (iSigVar == 0) {
+	    File->mkdir((ParName+"/"+SampleName).c_str());
+	  }
+	  File->cd((ParName+"/"+SampleName).c_str());
+	  
+	  DUNEPdfs[iSample]->reweight();
+	  TH2* Hist = DUNEPdfs[iSample]->get2DHist();
+	  MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
+	  
+	  Hist->Write(Form("Variation_%i",(int)iSigVar));
+	}
+      }
+
+      CovObj->setParProp(iPar,VarInit);
+    }
+
+    MACH3LOG_INFO("=======================================================");
+  }
+
+  File->Close();
+  
+}
diff --git a/src/Variations.cpp b/src/Variations.cpp
new file mode 100644
index 0000000..043eb19
--- /dev/null
+++ b/src/Variations.cpp
@@ -0,0 +1,124 @@
+#include <iostream>
+#include <chrono>
+#include <iomanip>
+#include <vector>
+
+#include <TH1D.h>
+#include <THStack.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TRint.h>
+#include <TLegend.h>
+#include <TColor.h>
+#include <TMath.h>
+
+#include "mcmc/mcmc.h"
+#include "samplePDFDUNE/MaCh3DUNEFactory.h"
+#include "samplePDFDUNE/StructsDUNE.h"
+
+int main(int argc, char * argv[]) {
+  if(argc == 1){
+    MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
+    return 1;
+  }
+  manager* FitManager = new manager(argv[1]);
+
+  
+  //###############################################################################################################################
+  //Create samplePDFFD objects
+  
+  covarianceXsec* xsec = nullptr;
+  covarianceOsc* osc = nullptr;
+
+  std::vector<samplePDFFDBase*> DUNEPdfs;
+  MakeMaCh3DuneInstance(FitManager, DUNEPdfs, xsec, osc);
+
+  std::vector<double> oscpars = FitManager->raw()["General"]["OscillationParameters"].as<std::vector<double>>();
+
+  //###############################################################################################################################
+  //Perform reweight and print total integral
+
+  MACH3LOG_INFO("=======================================================");
+  for(samplePDFFDBase* Sample: DUNEPdfs){
+    Sample->reweight();
+    MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get1DHist()->Integral());
+  }
+  
+  //###############################################################################################################################
+  //DB Can't use the core sigma variations as it's entirely set up around the concept of multiple selections per samplePDF object
+  //   Thats not the case in the FD code, which has one selection per samplePDF object
+  //   Consequently have to write out own code
+  
+  std::vector<covarianceBase*> CovObjs;
+  CovObjs.emplace_back(xsec);
+  CovObjs.emplace_back(osc);
+
+  MACH3LOG_INFO("=======================================================");
+
+  std::string OutputFileName = FitManager->raw()["General"]["OutputFile"].as<std::string>();
+  TFile* File = TFile::Open(OutputFileName.c_str(),"RECREATE");
+
+  
+  for (covarianceBase* CovObj: CovObjs) {
+    MACH3LOG_INFO("Starting Variations for covarianceBase Object: {}",CovObj->getName());
+    
+    int nPars = CovObj->getNpars();
+
+    for (int iPar=0;iPar<nPars;iPar++) {
+      std::string ParName = CovObj->GetParName(iPar);
+
+      for (auto const &param : FitManager->raw()["General"]["Variations"]) {
+
+        std::string VarName = (param["Parameter"]["Name"].as<std::string>());
+
+        if(ParName == VarName) {
+
+          MACH3LOG_INFO("\tParameter : {:<30}",ParName);
+
+          if(!param["Parameter"]["OscParDefault"]){ //if specific default values not specified for the parameter then use global default ones
+            CovObj->setParameters(oscpars);
+          }
+          else {
+            CovObj->setParameters((param["Parameter"]["OscParDefault"].as<std::vector<double>>()));
+          }
+
+          std::vector<double> valVariations = (param["Parameter"]["VarValues"].as<std::vector<double>>());
+
+          File->cd();
+          File->mkdir(ParName.c_str());
+          File->cd(ParName.c_str());
+      
+          for (size_t iSigVar=0;iSigVar<valVariations.size();iSigVar++) {
+	          double VarVal = valVariations[iSigVar];
+	
+	          MACH3LOG_INFO("\t\tParameter Value : {:<10.7f}",VarVal);
+            CovObj->setParProp(iPar,VarVal);
+
+	          for (size_t iSample=0;iSample<DUNEPdfs.size();iSample++) {
+	            std::string SampleName = DUNEPdfs[iSample]->GetName();
+	  
+	            File->cd(ParName.c_str());
+	            if (iSigVar == 0) {
+	              File->mkdir((ParName+"/"+SampleName).c_str());
+	            }
+	            File->cd((ParName+"/"+SampleName).c_str());
+	  
+	            DUNEPdfs[iSample]->reweight();
+	            TH1* Hist = DUNEPdfs[iSample]->get1DHist();
+	            MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
+	  
+	            Hist->Write(Form("Variation_%.2e",VarVal));
+	          }
+          }
+
+        }
+      }
+    }
+
+    MACH3LOG_INFO("=======================================================");
+  }
+  
+
+  File->Close();
+  
+}
diff --git a/src/Variations2D.cpp b/src/Variations2D.cpp
new file mode 100644
index 0000000..2d10cba
--- /dev/null
+++ b/src/Variations2D.cpp
@@ -0,0 +1,124 @@
+#include <iostream>
+#include <chrono>
+#include <iomanip>
+#include <vector>
+
+#include <TH2D.h>
+#include <THStack.h>
+#include <TStyle.h>
+#include <TCanvas.h>
+#include <TRint.h>
+#include <TLegend.h>
+#include <TColor.h>
+#include <TMath.h>
+
+#include "mcmc/mcmc.h"
+#include "samplePDFDUNE/MaCh3DUNEFactory.h"
+#include "samplePDFDUNE/StructsDUNE.h"
+
+int main(int argc, char * argv[]) {
+  if(argc == 1){
+    MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
+    return 1;
+  }
+  manager* FitManager = new manager(argv[1]);
+
+  
+  //###############################################################################################################################
+  //Create samplePDFFD objects
+  
+  covarianceXsec* xsec = nullptr;
+  covarianceOsc* osc = nullptr;
+
+  std::vector<samplePDFFDBase*> DUNEPdfs;
+  MakeMaCh3DuneInstance(FitManager, DUNEPdfs, xsec, osc);
+
+  std::vector<double> oscpars = FitManager->raw()["General"]["OscillationParameters"].as<std::vector<double>>();
+
+  //###############################################################################################################################
+  //Perform reweight and print total integral
+
+  MACH3LOG_INFO("=======================================================");
+  for(samplePDFFDBase* Sample: DUNEPdfs){
+    Sample->reweight();
+    MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get2DHist()->Integral());
+  }
+  
+  //###############################################################################################################################
+  //DB Can't use the core sigma variations as it's entirely set up around the concept of multiple selections per samplePDF object
+  //   Thats not the case in the FD code, which has one selection per samplePDF object
+  //   Consequently have to write out own code
+  
+  std::vector<covarianceBase*> CovObjs;
+  CovObjs.emplace_back(xsec);
+  CovObjs.emplace_back(osc);
+
+  MACH3LOG_INFO("=======================================================");
+
+  std::string OutputFileName = FitManager->raw()["General"]["OutputFile"].as<std::string>();
+  TFile* File = TFile::Open(OutputFileName.c_str(),"RECREATE");
+
+  
+  for (covarianceBase* CovObj: CovObjs) {
+    MACH3LOG_INFO("Starting Variations for covarianceBase Object: {}",CovObj->getName());
+    
+    int nPars = CovObj->getNpars();
+
+    for (int iPar=0;iPar<nPars;iPar++) {
+      std::string ParName = CovObj->GetParName(iPar);
+
+      for (auto const &param : FitManager->raw()["General"]["Variations"]) {
+
+        std::string VarName = (param["Parameter"]["Name"].as<std::string>());
+
+        if(ParName == VarName) {
+
+          MACH3LOG_INFO("\tParameter : {:<30}",ParName);
+
+          if(!param["Parameter"]["OscParDefault"]){ //if specific default values not specified for the parameter then use global default ones
+            CovObj->setParameters(oscpars);
+          }
+          else {
+            CovObj->setParameters((param["Parameter"]["OscParDefault"].as<std::vector<double>>()));
+          }
+
+          std::vector<double> valVariations = (param["Parameter"]["VarValues"].as<std::vector<double>>());
+
+          File->cd();
+          File->mkdir(ParName.c_str());
+          File->cd(ParName.c_str());
+      
+          for (size_t iSigVar=0;iSigVar<valVariations.size();iSigVar++) {
+	          double VarVal = valVariations[iSigVar];
+	
+	          MACH3LOG_INFO("\t\tParameter Value : {:<10.7f}",VarVal);
+            CovObj->setParProp(iPar,VarVal);
+
+	          for (size_t iSample=0;iSample<DUNEPdfs.size();iSample++) {
+	            std::string SampleName = DUNEPdfs[iSample]->GetName();
+	  
+	            File->cd(ParName.c_str());
+	            if (iSigVar == 0) {
+	              File->mkdir((ParName+"/"+SampleName).c_str());
+	            }
+	            File->cd((ParName+"/"+SampleName).c_str());
+	  
+	            DUNEPdfs[iSample]->reweight();
+	            TH2* Hist = DUNEPdfs[iSample]->get2DHist();
+	            MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
+	  
+	            Hist->Write(Form("Variation_%.2e",VarVal));
+	          }
+          }
+
+        }
+      }
+    }
+
+    MACH3LOG_INFO("=======================================================");
+  }
+  
+
+  File->Close();
+  
+}

From aa479ac1be89de7b1b82d99ef691de52dd93a1d9 Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Mon, 10 Feb 2025 10:28:37 -0600
Subject: [PATCH 5/9] Remove non efficient doubling apps and fuse 1D et 2D
 variations in same app

---
 .../ExampleAtmosphericBinning.root            | Bin 12719 -> 0 bytes
 src/CMakeLists.txt                            |   2 -
 src/SigmaVariation2D.cpp                      | 111 ----------------
 src/Variations.cpp                            |   6 +-
 src/Variations2D.cpp                          | 124 ------------------
 5 files changed, 5 insertions(+), 238 deletions(-)
 delete mode 100644 inputs/Atmospherics/ExampleAtmosphericBinning.root
 delete mode 100644 src/SigmaVariation2D.cpp
 delete mode 100644 src/Variations2D.cpp

diff --git a/inputs/Atmospherics/ExampleAtmosphericBinning.root b/inputs/Atmospherics/ExampleAtmosphericBinning.root
deleted file mode 100644
index f15c313db1f578d6ceb1651dc46b4ca264785be6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 12719
zcmbt*V~{3Yux7ibjcMEVv^j0twr$(CZQHgvt+#F4#?JTcjlKJ4_ukm8h^)%UbIx;~
z`cV;;Pv&v3wRHjlx*r1q0x|*uVyyjZ#(#Z@zXtr*^uYe!{su@=fPi3s0s+5tU+^NH
zBVBb7anU>l^j!ZP{cl}aK>q+~*;n-;0sa0L`R{H(K;TLu=2pgd!fyK3c2>sxPS&=L
zc4o#7=7s|1Ha6xqrgRSf(EG2(fx!R4{TCYusOvAR-e3C{9|(w{{J$cNT>TF>3jKfA
z^Zvu_pBD!*0#g!W6hacVF?KL@=XW!A{0~a7|1&~BA!@8bsUh{l1Q|%50>};cGR>Vm
z*}HYr_MZF7IwsCNM=-NFOoB2=R45D@6^@EB9JZK=rHnhFoH?}s7?moS$!G=<fypEX
z%CwQ^+I{=E3*bESJ-P-sY+Qb;-hQ**?!NZaeHIYV=j!(h@?-6f0Lzz}lh;);B>17i
z>zJz@%Kaf7<NliA@%rNS>Sj03lmKn%x=N`qsSf4wW__<&#`}w3c5_+yaituO1(F|Z
z>BN<YADVcj+<l&pg*+|hGVh7B%p5Zyp5Vj;9W7a<c)1SymYq^T1g78^d+L1=mDGZm
z&7u{2Fq|h6ulv0~@ONLf>_sq@xSf8yD#*Ut`1mM+KBLSP=XjRlHbg7hy{mZaY8Mat
zZvWof&v1V`JYV@SwJJ{yGopi5Q^cHNCQ38u8G)nn**9+_oVY_2b9-4ej2!G0tMz0$
z7<w@9Cy7(@{>c1max7k;E}Cxp-Hd9|E|0qXkrWlkv6wjTAxAUvgCN^+Sri_acEWyT
zDsY4y=ehlvEFR;VBcuK6#}DG0CopnZ>llUu`JvYwV-f)!my#8z67o3PI{xLwe4sns
zrm{w!svr;^-%neoOSv1J*O{gqwywrkLZVJnuq~EhA+=3z;OlN_@=xm1-Ot4`RV+&|
zFZRr@?x8SrXz*5bDV#3oVDqfi`Bu`M!Xr)6$qvn%+sl48K0M=>gA<h+;oBhD{T8ck
zoz|UuQpZFtds?}on&ay)9}X1n_}MrNrvQ4qfox}Fz%Dgt=Rq>u(hZCK+SXbw*l<X%
z0lST+puO|{=s<)S1=N~JujU6;5|xT8qx(kCd<5;6Ip(RH$;CJciz29T>H#aBRC#Da
zObhj^W#$ex=^^BGt;!2pr{D}r3usR>{j+-k0Q4{<diMD2J&#-F=1la+i~_%j6Ro%$
z7&XNd_si}B0`>GYWO4w3pY$`y%n|~MD!aMlddXDau(BI2H0|4u%3;kCG@7w&Z97ej
zT_?DLKENM;kW#MNA?B)V5wa{M3o6;Y8>-?Rfk|}*@H^UBQ|Km)dXc;NcrolMKx00&
zjO<WQ&J*l~2&Oc@<?YlsLX*M^koxl?=P=+Ja7>GLcH#z}Fe#Zg^NaflkDO;QdB%>1
z1rYd_+=I00@0rJ2pIN>mOvKF434somBpB%WC>4zSi&@F~q1KfxNMxe(&oUUknba@t
z6~$zDz89I;gPe>Ye1F{!qGZ;-Sly!X%Vf5^@&3~y4Lv?))RO6G%8cKQV`@F308_J;
zuf(1yw;vg^e(7JvjAlNYSSgFf5Yxn_ybYM1gSr)ttj;2tJM^)IaL<%yH>wJ`qJ304
zFO@ccIgvnqGeVY}q&fP~lxW|&hgvTP+Ff1xqf_mW6z*TQYMaD!OzDoJ(xdPi&FHWi
z&(|CsuDS3{Te3dM9+C(eTo%57@3~M`OdS#!Oo7bvHAG2E=q6Gyv=9*tLCs6YmJN`g
z+ykA-cyq-UbK;+c6^0Oe#JJQh?uz@hWCqCwhI2E7tqV;jculp(ZgIQUu$QKgBBZD<
z`JaZ(@=DHxP7KFE(?PhQ@b^Ut-kcV5NLX}gfO!zy>!%L2p%H%aZs#}24Y2G=>I?&9
zK0(tJ6~bA}UnewGjZF4lFxpk?vtdTq0;$6HnS{GEC!E*3DhH*&+PYke3Kds^Y|lBH
z<W2{9>lJMFlfy<QF+6hB+!Roo#vGfhTT^p`liZ$7_vjC5)<?1{>hL`BYzKFlx&pHH
zrTU?YL?3(eEqhgP!MZ8_R~jvzJAl_&AI-_CT>$#sYhsGW+~k$Rufs&dhc$6FoO3nE
z?(s_^m8q|}bx(kd$`jrL=0zvFwF-i_{#o(1i-UmfDuby<7}5j1r;R<+FytH0XSr)a
z=3K70d+CZ61ZWc%0W1X{=9bq96Rg$dpPVN}U<iSi-dNk|V1Lo;2-=7${k$tX9gt!;
zh;-xJM;=~?z>K9+viU5Awoj>#;z@A^jC}mnnF7$jbnX7PuWS9fX`!B9eefY-0ErrK
zmw~v`zIf;UQT>xS&iZgU84QUYbvtryq>zb`?h9gOy|lVLV;)_g!L!!f-l&FP{o~ck
z9L7rq9OF?6uhSo}$D%48ubF)}W1&q}=yVwIxf}!fPq-pD&ePdRHvM8rt$l)9feZ<`
zPmU&2KSV^Za%?U10_DLSUZy{&Fr1s3u*GCU{*=kNCyLQye9GMmvy4EAm?k|(YBdBf
zW-F4Euq$G$Ykqm%bkIc=Pgq+@$@$fDey`554eMpqvXfE=V~@}lEt6~)1m5NiZpNPy
zGkonSCVh9qW8m{rH5681ku9ngsYiMHh4XALHm4X53|;nF$uB6SnaMMjK6m{{+}oDy
zEDX?}-<@i?n*wEU7d|$1$%c_iX~q#FW$i~XeRy!^08MMCqI6z0f>4Z~RBVpb=vS%_
z#h2V;O*``F>glmVm$Jo4b=z<SDk+Q#6#$p*a}syU@3v?EIHC(zUB!jztp@WBD+7DM
zy|hwz{b2p5fo1eWZ^Jhcx~lT-5WzReiUg25F7!*C&5fK?5T%_WH^6t<Lzyg5Xm+`B
z^jBTObCD~nr+H&u)%g@5n3!I1VIK7OaV#*Q2hYi+MWST%w99}VS!mTjIWQCSYa;cI
z?DHUZ?C137?#J7qEO=IX0fiIjWrb-44$-zkUw#>jp#+m(x8eyDd~bbu%JLE7whxtM
zXZblLIh`x_&&J!B#%W6FV$N&Zv2R?hL_4Kxn5uZ22z5ZjoY#9Gi_Olt^zta<pC;?}
z=HJ+eywTbl*ONaJeujV2UT*G+<#yO4H9V5dqklh5YII|rlH<vimpc;-LO=UC{kb2j
z6StE|P{+lLK?T>vuKFFa_*<k$gwKfL4=mraIxHrcPXnV-kMIa8U<Q(;op_&2vgQwr
z)fmR_p=py6;{8n;@e~n9qpI7E$<f6KDJf))0*n5!BITS$gL4NX2Oh%`hcgx?;cBYo
z?)@++4p5g7<HWJW<mD!pJ1Qm^4!1QiOTv53?va$C*s%-QEeEwJsPt=iACnHwuqo%_
z5!LbCv4L9xMM4!=b&6w@#`YY7$kx$mxZ|mK(mz=nV_Km!#q-Br0#C%$mv6!<xQ~@=
zazE60v=`w57voq6E9%H*anvWb*zpOo;-c$aqwu}sr+;(b+0Stp-EUD?rl&?(jRUuD
z4oMnSdgysVNXBPZf2B&vp*Lh^vCM*b8$AQs+dar|R&$wUl@64MJWUTwp7-a+2+i$$
z)xLootgKBrd7dCR3g|m-OznwAMfX!Fd)DI&TS9du@8KQJv^O)i`GT_`eS;;iZ-|Zs
z6N45?591nt(KQ~zfVZnWpwyDtiqN5dq<3uoY~QP$V%mTgs;R)^fBu>rn+~<Oe!M1Z
zJxp$9>USUWE?FmSDuZt4gWhmG_YLNrVz&|K@#j8zSD|P7A(As!DgSGxGwxWMU)wtj
z{BHg=K8p%GUNz!=DdeefERvEg<fr1;dBtqeP(6aXEb2Bo(zk!tc;{KwlRBYoKaHlE
z3*KGJ@ab`bIT3zi#^~HK%0VK1SA|_>kQdra@C<SOSgWbkL&Pb?opxBtD{?3HE8h6}
zJj)V+?&&(BH;dx|Ht&J9?>W*P%=lU^GP;1z;M&rBYGB;<YnKI~DEeJ4E7}wEYSc$7
z1SWf_L)^Ec#dV?})7ZA9YG*MuvbdKO_<oI{*!;LRhVFS(k##vIcKbp+3Q9bWDXU-6
zI;0en3<kkz<tF)a)PfimQv>qJOMuZXs&X#Lm>8>xE2m8-?)VjGHPx{VF-O73xu_0b
z0)8)E7$$(<VS0y+UI7mpu|ZavnMVG1|87E<F)g&3=o`GprI5ejYfJ7RgdBmn5*r68
z5I8S2^joj7us?sPedgOF1qHHVB|Bkw0NJ(fpG5qE9Ub6uCR|mNuC8;f0$M0=T~oO0
zds?A>coXtL$uEi_%V+<`bZBVIqDqxiw*0ttH?6ffVU&(KmzmUUoZyBU_Y5<cyt&vJ
zTW(ea`Ltot$VLL3;H6Odddtp&y3cx~6lOsb_>9j$alfbmSHYZx(8qi`j?A5n6>^lE
zh`Y>NG5&beqP6lhAe2?RO}&8ucwu<Sp;(j3Jh6z(bB)<S3I!L<rw%>3h$$CmS6@9L
zdF3T?6kSOaXKptVi8H1M5hG02WY)ZsNO6H*auCAnl=uQlPx%-eCtAkZWD)5-ttpXt
zg7t;e4z?ST0`;AQ5eKzl25_{hGtaF1Ogf4l5IF=|Eu5>zZ6zdh_rzxqY{$C|p7*1j
zdkrJ4vl)9oP>wa}%%6#%hNnU3QG84DUdBI&`PJFvKEMkbT`p)M5UR8nuJ!|vBaRnq
zYi9+aS`G9i-6@mAc1VvfWD13rj%uPxRJ3Nii@i*1FzIwPGl`up(dZD+BxyMZ!Y1!o
z3WEkN<P*fEmo#*v6B1&XE~tMb4XL)ua!}<Loxk(hHm?;J$(c_9y8S8AmC#w4y&y^N
zeR2>v<YN-1K_TOI*(8t_I$d<*1S!=GI@xu>B-9yJRfawVC~aLP9Ve^gs8U8@6LSlc
z(A<~Wx_~6S(f|0o>|jVti&0!JR*9OIqf!g$ViY#D2b{1;FiCip-{n%~37)RJxlXH=
zP4T)8^(9WIfVM|gp4fqlib^A}C3D&%Rel#ZbhhgYkR|I6@)Vkuc_ld*F0fKrTCo;a
z&gW0<eaebRe?~tAS|r&!K;786`7s?Az<nF>Ml;cGOC@nPil#sHpg+`DP*4-t3&lnv
z8LQgPKY1vJHbBb4Z>@ZS8Qb!DeMF<gGz>@cM!CaNi26=<5gLI{RBsUFm~TZoyqEET
zR?*ARohsJ9r|KnDLbo?lS%6M7V&{^q{>baPEwV-^hdT8Br3_thUGS0p8FdTrmhX|T
z-;GOTqzXHLWyXmX0PmERvNZ6?8yGf;Cx2d&%YTT=I0^l&bYR2`XHCUF>}>Dit%zKP
zQBnu+zX*(YT`k=z@8%y?pPZ~f+bA=7*`HB%HC2K>gE#xC4v`2pWR*xYl~0e<d8)I3
zqO#r1@X}5Tn*az)sA+l0wTrV3dkkPG8?nTWj5-uf=oCI$NASs!4jQyu^b;##w&FfH
z!ip?8gOXVeb;+}Qc`>(d0W15Cvow8~$5@DfOUUA~$kTef*XuFbD_Q1HG*y@iI#*8`
zoh1jK<)3kRw0;JkDGSFs3P;KZJ~%xEKD#WcWiOh0sDZI~74~%V=mcYx19K$ps4bSQ
zBtD&8h%6e_#m+~X2ufeF_{`RL{g!sk#>Il_FLM|7_#9LsUi2EREOc^3W(hSJUdS~n
zNO35iIB=m}TuT>P?OTr4V1u_2bHfYKSSne6+aQ(C3~hpRcaZb6&h)ja!L@)i&bEHU
z5xP{}1vr7z<vq<UKiq)0FUqU9>6|CVa=tqg9Og5gaR<u2dpO9MdIe5Pka{m_8>@;Q
zrw4bGZfx`vS>|7HUFT5q;TPgXe(S4ZqAso@auy!Apg$HE4u~Wi%GDD2ze_7()g<kA
z$w|A1Q^#f-U3Y(>s-iuLFvPGF_O$()Y@j7B>+L0x;tE84gz?h{eP&`N;DdKruk?q&
zn>_yDOV97GOiQe9crqIkm)hp&Mu$T<`(cz;QJ~)(>cOhbSEGSyD<7BZUzu>!>(e8q
zPbQ<1aYAHV`?MrtfJ15A`OD|1TYz};T=y+NCQtqYkh^adG!h92y=@FWrVHAH2^o7$
zwiphB$%i!9@*>2|2%F-I{R$`Rxqs|1W72(UMv*=|g6W=PHtUJ$TY|Z@(dw@ILY+oC
zYo7Dc|7KzK<q~aH*ZS3K{Vbz3$)T$jWSKktywv9me}6obKP<on0-$#oB%(!cw~x<6
zGjA3<@5OA|$(uH?YQ(S=(eRlx@R7u$ZGkJeMJW1X0}Qry_-C)0pLvZq8XksVjyM(#
zAGY9+Y{G~iH&!5v8LT#t|E_TpJ5l%u45V3<2$n5({;kTdXar94skA&sYQGUx7y^dW
zWsG|a^VbgntnKXLdhUo34^J%37c(n92}4(&=ufeIJ@>h;Kw_yTH!D)wuTd*2!cThN
zID)S4L4uiYU)-T-*Vk))9A}(XGhaThFWhggTRwcZ4_}@eU2@;=XV7v`v9-~g>+1u)
zA@_P2nAP4_K8ZMjmmg$nyRhFcx!>hcK0Y0<vbPDHMSTe%lF&4ib^llAn+yC4W;Ioo
z76=IO^dGT`sQX{Bit`_(>Sy);6048}Z5_>Rj5Yo@wF>e-LVty-5=5YGqJM-cwQ#m%
zYXBc+0Y!uoG%2aPQbt*eM3Gw=Y_Y%Dyk8t8iFkz2QGP->hf$RgzG2wZy_3ic#|#Gv
z5#{yx`aREVYmck<>^tPjv&QolV5_(L+53CBdD*$TS~$*Ea0fs%)lBfi66r@oka<@q
z`3G3Q&4#v13~Nj2lxy1>`&CnYb8|fp@x%IXAoS0dmnq+V_a`S1eEQ(=Mw2_59E2_?
z?%m9CVZ>RYn=P>LUR1Il9XUJ6BsUw-V89^yYqR4!RMSI8>FYx=RMxn3UGJ5B^qJ`D
z!_*{Epj{r^{@WSHnYX0~@9o*z@!Pa@z4x1*OSP{nx|q1{`f?EO+wE<dcHDK}>EroG
zB3w_RwcAdqCH|jZjzuV)h4tI%TtU`_E4~#CTUFz*@6ox%&j1ts?-_!ENku%J>D`5(
zS>}sWmdh^lny}9TEUS8Fh%wwm+{mocFfE90Sak_z2W-#d(k|fxG;gi?BRt&p)AF;`
zW8t`W1}DIi_IVsOyS=Y;0=>iLZ0r~mE8(-$q)+`X>Uhh7Ppg6{+;*-7aEK(T_)0Rz
zEEIxBt#r+H7Awz#nGep^zC1*ZLKXCRMbdb|Z>0<Z9}o`bAxVT>cVb9g`kvZPL=Jjn
zz9FYWVsg$6!inae96oHuL`N~iqko!d9uA2P)N&kQ|1ABE>6c$6xYIu{!$^YEu@{aZ
zV&BX`55@_Py2oQ#9V4XBSOsS$$i($rkuXJEtu_!L^V%DuYp<z%_kn9z5N)w+J0pJY
ze}$_A<O)7r+MsgO@HJ?|(`CLhgRd^*7lF&75wG7|&JZ(Nj4gY)({*#guSVSF4+IR1
zrTp-A)f$9)C;KQ%cOkhrcSO%luZs1aMqi>`cc`x&yEBVv19>XO>teKYWq2As>uPer
zALQ+=f`1pRUOBGQ8ge8?aHWyjZ!scyI=x*Ng5@;K?GRKlh=zI^kLN4uRv6_)Dy+Q*
zC5?MbZtEH_K~zUk-Z$CQFjD4elhMqHsM6wVwR~@iPd2k8x7?1XB3MYgCbEh@Y}x#f
z!{cj^sbRn&6D6Fqd%BX#Um9DxQ&yBNMpTE^worzgiX&C&*vo>!PB*MYgW2qjk?IJO
zeIa5oQpq)*5OpTFmoC@ONaABkOfj~FQ4}?qYaYfwj*B~8bN-y${B5LR$>eEbEmFeY
z6u)nc#l+@4olb@mCFO3IPQXWN6hYV7=^IMM6w)h|h_M|ObtMp5lGQv$fsilERYpL(
zA9VU>DPpXxR)uUbPIN?i0L`HQmg%B0mmF8u5B5Hk$rMe3Kydx3Mj;S`Nu~G4j|qH{
z5R~&H^sOEfM3px@XzD(lBlGKLReVER?S#^gcCMB8m_3(;AtcYlR4o%r+>x!kefale
zU{CEmtH$CK!&>9@SK$Q{{o1WZ7>ilxde`g;VO&Gii)5Q7o;ydlr#sJ8Z4aqIyq1E`
z=}*R$1vy8`t4^e+E>}mlY;Igng#+Blud%_LyjYp+Lim;aJ*QX60FWoOm*uMKo)Dgn
z-O4O9SN&Lv2HTQ$vZtxpGpvXxfj6O3w8s$rqG#4%og7b~(<PoPnn9(a<ERt(Z6slj
zF1djaXzZf*S$tPCDv=Itpj4X7Sf>T3hOZE<B3sw0*+0I~4~N~wcgyr~yys$9xX&m>
zaLRnxaN(jFqc!i#vIcP~NsiAyLkKV18)j2V2#Pj6Pm+e9erIIvAHf%p&eJ&ih=thv
z&Zu$n|2j<<)12<!?QF+3PYCvKCrTIl#A7^{1ke^KSe+#;#1c1qX$Cc4dlZ#SGsd#~
z6tMu)ZqX@+DbGoGrAEghTGDt=D`h|`_lVhVF0_oV$iQeVU;{3{KVzw7mLxFFs;w?r
zM5j!0zM5<diB~Xbp5u9CR?rDPPzhxrCav0u3#esP*m!Pw_Cgbl5RM*RFvJyGwHD#g
zy#=GJ?3k@uJqSX%U8wRWp(R0ZwElGzM%4a!w_`kuM)K2_-PVAVkYo6HJuRIl0aTdh
zKEjn?wWswXJe(#$I^rmJzL!{izdyWkhPx|keezyFT?~!k%LL0AL0qbNlPmcm?m?Wy
z=uy*~r2Fbrt4$V4JU&<g1a~3+z<%3&2Lx9<#aJ})8ecTw3Eld>!i0o!ydvzASzw-q
zCp>}Wa7Fs`lQZc$a&xvdS!0aDu+`Aat^Ha3V%aE1LzZ>a23XFwP7%M8Y7ji=XRE&I
zNwcK2YewDVhru(9D%XXEh0TsJZB#aFwyOw4Y~3&C?t~8$xC^J0NQ{Kq(HZLkkm5!<
zJ@W4|!Gkga7o|Bd)+ERkB!%}-lO>T0hIMp(i%t|Sv{WZ;<e$SX5z7&Ni%3?!AIq%6
zVF8!uOO4^Vm37{mmARMC4(_5M2{VAl@RcXt+Zs1P#1`#TbCsTp5NpqZ1E(Sx{Y<k1
zR?HbgtLktDd^!^YOSLvj<t(NaJm^R<m#(ntNWot`&m{&hr#ji=^Rp`nC`@^G);uj)
zaOt#ij+mNC0m)o=$9ngD+TBvM@>Vlx?NaN%Kr`vzW7ynQ4DL(9OA=L+>ddEjoX4U=
zq}>Nwy|nQS7L+|L#nBzD*8a4zjJxBpLS>~WxK{L!C@A>W8v?OzaVpqc)InlDU**HU
zk{T9{h2-kjd#%W|TjhIHfU|BO>2Av<g~CDbec4&4hru<fvnE)XR@K_{<Or9IzU}Nm
zlHD)X`S^NV)y?Bp<-X_fdSSzyTZ9hC$Q~GKkLe^%gFn~JQ0Q13Juaw`vu-TbYl2!<
zJ`49CXGAyi$HHsV7V1^^j}3gbHrBhO_^dO1uB$1gBmUxkXI}=3!lSH~AI0iM-!HTc
zs24dI3RH%&s_LoUdo<x^P=N_Sr@2}W%<Uq7>Ar_jWASleqh&|0)Ux<|R$DhbM30U@
z$5u5cww|Z4*GKj-nr3pcitUe8kwmL@avh3jaqfbvh((2T>4hKHjyXgP?Q)XxHF%x5
z_b?osR(o2u)Ui;*N~wk+%hmFQ;p3L{YR{X2<{LBZRMDOvnoo1E#<#bpLG2{zV5P^9
z^g>@uv>vK=OTxfrqQ{7&&uLz!LK!8Bc&Pwh*P~&Y#*ES>i3!H1-NN$uF(N>lZ~0SZ
zPc1IJBDI4A114$e2&Xn9bO@uC{LmUo3`P8pf@xL%hi!fNoGa#bYhy=I38cPGPY8wQ
zsi7CTuVkYgHPZH5Q&uFC<uF?*N})9_1fwdTU5ZN#%rQwqq$rn4uLUUaOkv4Cy-0lt
zE>J)1*2a3P<Mr)@bKqcnvl=ALXPh?5Iz80<?YZ`J({4aDg!d9+B=ja&Pq<|6lgTTC
zjjb-v^%t)T1K(l(6PTh?%b8N>uwg^fg~aP03aJBR6Lx&KksuJJ%B+*v*nvnYW0Wq&
zEwb0*?p|u%HX<^|#$xRKgL5&<JwAOWVIhJ2)n|;?PMsH{Y_Tr3^y|?6ME6uiJ7nDu
zHgbE)lV6z6!m;AMP@GaV-g6cTo}cd`W1T-WY^^=+%)VvqKB{@vT%&yP-hlzWwV%Sm
z2uY=G{5wV8<X~(T%iHooKeD4_f4j|-&e9<Gm5FDO53%#6NYL8&wLRfl?<%3XwKeYh
zk233q*)B@yQjY`&Vg4dPIVd8uw_G@UwR9pF{{l=e0VgEVS%2k!11V^<jKboS`;iwA
z?JqhC-Y5ZHmy{8d-HrrXw49D{xMu;miT4DUI$o1>oM{pPs@N%<kLWZ3O7DHBz|JLc
zCU>6!L&r>F?+GeWcwFG8gr&ywFRwezXGEs-@u4>z4J8`74%9|j_nMU5ZKzDaEZvxs
z*@VB`^H@Bi!Hg~?)Q>wE;Tpz7LE!y>jdW2<Y5y4W&+N@tYZYe3-9JgVZRvxL@f3}8
zdl&q0=w+$xerrPA8uH-e@V*LdT~9g8T0jhH)jl*t<Bi<OZvAB4k7$k~r$6j=t)V+W
zJw)|?WpwkM@aXUeAU=SZo>Mf~4EP`~_jfqo1Afj})cg<wy}(Y5p(h5BFIBP5%K{!6
zBiTn(_9S4^(gK7;3-qUS*Ebt($=PW_;L-%==UMx4wvu2#Cr6f=QqcPe#EvOL2IBL_
zcg>)_^`px@=(kM>Q=v!DlTAXkq6vlv)q6{6!6kL=(ks=U_|5NQBER0jz7Xg+PsH(p
z;pa?`lkt)MPS^LZ+Xt7Yz;0nfS4s}L3+38yBHiK--rAt}mZvVmC^}Mdn(>RZPoFLT
zH<v4S+&{;sG?C-bW2Jw2k}Zo+FV`_mh0S&G{*}VK94eayExItRo5#uYq?07Yyf_A6
z`>3)D!D>}e=-5UsD?c^K-H-=vj(CtS$Cr^iA3mb@C5CB^4m7}%F_tT3>JU?&20p9#
z*5Wsz59x66ch--U%=g)xy6jj+&*S|~tld8N^UVAhbx1lOPhZn&Xs$GL4pE+?P?-%5
z>ur>0>nBW}ylgR_z9cR)8BXJ!r*!bhwJX*vH3EO4{TJS#5x<$oxOXWX7ea<<8Y|{2
zmB9V@$1J*<W?p(3g~y~BeiKbcWm=XutVWio3mRQZU<zlXp*Ald&-oD&z$ik|w50%-
z`7O%SG*6@mFg^N>Ev1AZ?i<wdP7glit;4_WdVfi-PB`bIHnw!-_p`~=w8zEM5&}1Y
ze5L0OYi^gIh3KRO)=BADT?7s}&#_rrYEPfa2||pei-satM&$NFtC)PQxfH{MTNhqi
zHsUg-jO2H#-R&TH?LpqVmHnga68i}qH6ca`Jy=4Ka+3T5FM+vcaeMkKP(q@zdcXrD
z0jYXC)tW6(dB4SjWEN{2xZt&}A}NTw;qA<-u%^G4Ng4SJGy2${Nzf#<v)?rg%G0+}
zpm(mlA)Ag$egz5p8mSLp6r&hSDVeB#4zB#b$A;W;VIHNmYBUfNdT*uLq>z3cS{{XE
z4SaIbURP{E2cVBCxq2I8h;sMvI^51)sB-PsSgPonAlBsr%e9q6el83QlzeT-W^5tC
zpCT`QDV|f~H!Bc%_28wn6M3N8SHrj?Q+9dy%qcV6_1Gsq+xVWxu%MsT1s(ktMtP3U
zXf)i$AUu+ga3}5obB4&9PaZaC4;yRtBa=rc4+o4PPsr%MXOEAju@$=VU4_F(6MjQH
z;EfYRuw(Jt+JSrn2HWQ}k*g$^H9)!zb%2wpKm7AO@;ODFfH25o#kk)beqj9ZF!8Sz
z((_tFITuiZDDhk9&!dOvTNFbVSJ#J>@|5}WK1kT-)paHzs0YEoHCuH(D557$((no)
z>Q^i(k)TtLsJ6u<3cy<iQ)y{G$muieGZ0nM*l|8ll(X2*_C|V(IjB$4&EVH9+im3#
z=gO-MpkhX@gtg)|EuZnc_p4?!bdUcAtD_$-=j)yTds1A|cFjKbm!{&jd)@Qgp<&>#
zKR9sQQ8TtecT#|yndF!+2i*JpGT?GxSHf=NqQZXpN#&2-Ms;~;X}H7sy3I&^;`c?$
zb6m2N6ZCbz#yKl)buufVX2P`d0HE2OO+28l7ADa8KnR3s^~KTppt=R@1hDnI(0=PS
z>LONuZ_It-V}D(XkNa-NvDN8+e6{#04aF5Ertv*~i_Z}u9wCB#Z)Sb_e!bc<Y<Y#*
z9&Ilx9-)9L!b&kR4EOz?oEu%n8+uPz>eGLljs6N9B%c2Y9shO={nLU3WCX4xW$x$%
ztLWrltZ!}XAZ}w~i!5a8Y+&V1U}bJ&X>9cO;pp^N?wEi9@+A2ycPwda+Ty69@^L+_
zg<o<y?|HS53iACVH#cCDBP}+*U{?V(*E*9v^I{&qxQgPLzKG)ag}rW_PyLvmOw~i3
zA0Z+30e&My3Kjr#2uz}b2m;j)iqJ*yh(t)3yv^Zi!ri#q?7A5+)O_W&(e3E_?6u)I
z%K?Dk=@Jm8LW~$ePtp&BzV;1L$cO})tWxjin0<n(-Y&g__(Rb#3CYv;luVZ=n*8-v
zNbd!|jW&1A^6Jv^ac6{>X8Ex>xtJJwqK^ZsJlijoo<Cg8Rt5=(T#P&~q{KjaOl7E0
z4i}kQC_kZ}nn`ie)wtP5v8eId@5#lTWPOm4p2-#lJra|L$8h4@0uj_Dh66}~eA=OP
znElEohL(1%NI~alF$5Q44(~u{wmvl#0qG;?Sj`(yY@1CCIfn@-G_`-bNch>lEC-8n
z3*+n$Oawj48dkGs6V~QZIw+_G1xaZFKWWL=;S2d3Z$fDfWKz<VZkTe@)6_yz;2<st
zsd>Vl1A_F&<-OpT22ky|@NS@Rc9&zi$#b$Axz+-^)IFzuQ&n;07SFF_8P^ilDU4Oa
z2KFq6)@mlpA>Y<{A;dYfuky&iROnGw`@)|b=91?EKQ`36jc78D5R~qzNK<z6G~Z~_
z=C%bz{C252^NAw}(|QBEB3{eZ`12wao|SWhF|0-rp@uYnH{MB$h$_WxDtp1F`=aKw
zW`7gplWwqyVy4#TcHhde;7~Yc5)zK(HFx5`wU{8S3nc&Lo`|zIa)$fXwk7k0igSZM
zlr+5!`7QA@4Qx_AqcLUnr6!W)>}AW_tx{8Gm}#=6SasgT+u;n>V_W&_lJ}9ng^^IW
z?Wr?_=nx<<@kvP|W*$&%gtMQRXI|GNGgrEd@7#zZ;;$b5z*Lo@V?WI>HN)fXb8Fk{
zPVau?DWHfjr1)YZNV{kYBmLgUY^+a-2X>~QHbmZ~X3Gi#<%P&gn>UEN?`t5G9l~Tn
zW)9Rv72(BB8jxpb!2Il1m(^i={>MNC=H{KmqBLb8R`m<S93q}lPxheyC`*-Qvl1|&
z(r1@qxujPjm=+Ut2b`eZoR4(kU$6gK#ggQeBFyWlzzkbg&5S90j5}N4`Zk+0=!f-|
zE9i?hW5l()5fwg`@eR44&p6>XZ74APq34(Dw#RGBq@iVRsU5LffL|AWfoMpl;Yb^d
zbVn@mImD>rRPm=^Ky7z)hB56O5<BAEbKTB&#9sUDMAmS7Pam!T0eiydvpfA=3LS!k
z`shotX!lZBK7aIX<Crn{o$E!MZTH)X9}E{H{0Gx-?FoPP2N%KH6S&<!JxLg5CqR}b
zjwW_6G84OyTVIe+snDsn;O8f)8SO)r0qqYCQ^ic?Zk=RWoEh*^LV_(=$}dfdJk(_R
z#md#nPWmy9)|v{|)gxx=qvwBA%m%9RF{&kHFog~=j-k!n6f<pR`mv+R4Tzc2`gYRw
zM&#I<(1q6@rCTtDcSFVsR{$cW<f_?mHLv(QgMwI#@8}Pq%pTu!G|~J{dgjb~?zIUa
zt-p&HvkzzUyz|dCTm&v!cjIBoZzb2^qjP^_-sjB4p19%Mliln@<Cnl+63A`3!7I<-
zxM&~UxVgZCvM!Lm)rr=GH-}yuoRTd_X`ck)?rWoWx%W?UxCcJDH(CwDuz)+YS92A?
zqg4=0zvwgt(sx`!zM=WmSx0VrD2jCukwhD-vloeFG+)j|Tq(018AL4QBMbaq!l=AV
z7$6(0GLXhk;c>KNZ#Bq@n0rW=bE1)4ATUUusJ>5WMWl_X$fSV4dc=bLIa%S@z`8U*
zh{{R16<yO9_b4k1Qa*Fbin{7IU<iLDwbCYBC2dXDh#a4H@>Zj??`URa+ulN3J{`PG
zHj(zY9%BTKt~dhSOTF|~?N<-ZwT+l4wqSq^D3rfo6W5bc3VSl#%HV(aEqJ-tnMq3|
z&S-XWe&T=Qaw3gsN0RLZj8^?{!M^!jbSwF=8A7M*6zq=MvCO>!?6fo99Ru%br<;$b
zWmzydTSTmov5i69?;2c+AZ-AncXqL$vVRch6Sf^gg=;wI0l}iWcOkZxA_NQ$+V3bR
zoo~&a){((AM9fS~@^j*G%mUMPXzN5<3@ffqFL)&a(eu@Ym_+R2C91}g4|{O<N>!4b
zqPZ^_TqgZi%PsC!PGk?))v#$L+C2P8qiPZ9@25sS)IZ&i5A78Fb_s(z={!h$jwG;p
zJ0Q5f5E^@S7wKbW@K)z@uy?z<uHr}Q9n3M6Yt#1XSf_^=+)grHH6fAzNoC$vVWdJg
zaou?AE*?EK2~n<EU5Csr8SnNk`|}UJ{CbLkIr27^P%^~j8`TwdpB7r$<hOMiHHhP(
zVSg7E3?m5~bNS(mlS&xqQxYb{!dI9Zt6|SYTBxyl%JlDAnhanA-mQ{q@Ln!gpxYdb
z5o7;eQqBh@G#{=(Nu~Qbfz-OAMBq?d#G5KWVx&yVswoeRH#LsB>pkMO15E$MFly^^
zaqYw_$s~bBSiDVK2%9ma!xw5ooPKu;lg1tK!qV{>%T|jjjj2B488TH=z713oDGpEi
zp;>Q027B5dbn5w!Zh~RjftIyhhbtA>&JHffN-><w(wddk3C8hP{&ke-%AcN^1<sKG
zs-F%-lMB{Aj8(EVx?Ko*&ReBhZN`z+9X=`cj9gVoTtH6UpcOXxSPx3Hgm?BKn=y-a
zKJ=3Cr2+242VI3Wl7_A%Jxc>VvL0Suz+6SU9Rw5a>D-00eZqI={rntfbHuu}oVy8@
zHH3I6_<BJ$m3cwLJ>F&3lD^^)>8xQkY-Zn%ZJvMEQS{|bgFLUQB~kxGpi-+srcu?Q
zp#?~@jWGx~@W!(UwA*!U=V%+?#nKSrU($n-*%kZ44U(LZF_(}NUN`SN-}62x6jA?v
zNEIJ+78c7LPvF&?UE~p`4~@n5B>M{Bn1ymU^3VRL!f&ug$;;GHt_@Y`i&;IEUzKa2
z^-l1>{}rbnMGG*VzhNc+Iexhv_@uPiQthYxo&TbapgfWn%jt-<HO<H`qr$}Prktl-
z@yoSs9)A$GEhBwUlG7H#(nH-O7%J=cX55NTGjWuCFAd9uFgE*BIL8gAxtr!s_yg8`
z{j6p;M|NEfY_PcqS!!W9E=GqMuRD-*cGL?(6~q_d%CVBG#UFjLxxA6_j1{x{ARpas
zRM&AKt+nGyIkOhSb<_7^pDl@!Ss-ZmQmxvK{*R!Xd4Tv_=$Q9#&(ZW<rxe_2o74<#
zc-XVG)^0*Zab13cgvUTMx7-QkLh9o#QUMis@dCcWUj+$!*O`S0o^$@m-``|Z`s7ZK
zx)0H~&+Pld2jb#;xjLY)MQSanVuS1VMC)2IU9&xXF>f~=fWg{Df4bqC*OD)pKRLA=
zTQ+VV9m?8qjnL~*dNM#@I66YubVbg93gvkM^m~S+_Kwn?A*>9)-5WDYwFb!zl4$}3
zj$$%4n;Z@nPH+}e3bAn61NHM`eg(F70Twg`*3!iwmO&hB>DQE1SpVkJhFD?c82bkE
zwT&-Dp)0B=7gC&ctO<vxy*LwsAmrr9_E2w!2=03Frn*?wd<gjkjypuNdAaqJ-G?1c
zj#PJQh~a4h58>avY0dgsy%p*U6aE;_-TObRk$pk%u;*deMSjZ0#5N6#F~$4Uz4lE)
zXF=14WtSme?`<_aq<C+$kW|vFd$Cq#!K83(D>a&|R7T)svJ#)m^NU`A!ihRtJ~sL6
zE#BUS@0ZG)?*A;!Wp{rAvt`?42XYC7{{V9w@4!MZe*IHBpR~)68}h5zoDN0Tx{CmE
zKJk_D!P&6L>Z@a%-*={#h#c!mI?uu<`MVo*^h#X8U2$r~+3%B%dogY^&o1`@f=jW0
zAXCSRVBw(_U*`?a?4&>MTS(Um;z9r3gy1X~pTV;u&{Mgi(l}>w`PRi-?_;G&aRHFs
z5G`B0kAg``T0c6LZk-b=fwSbPc&+$~RORoQe5i<@GsQ|K2L6VyT(i&e_vgRspV}vo
z*MFu2f1CUNO$q)xhY0@81OWp2|7rIBf3Lp&-CN>c?$H0q{oi92f76-&7Wcn(UdCEi
ImL#D60f1~qpa1{>

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 7cdfb47..ad23225 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,9 +6,7 @@ foreach(app
 	Projections
 	SigmaVariation
 	LikelihoodScan
-  SigmaVariation2D
   Variations
-  Variations2D
       )
       
     add_executable(${app} ${app}.cpp)
diff --git a/src/SigmaVariation2D.cpp b/src/SigmaVariation2D.cpp
deleted file mode 100644
index 4b659f6..0000000
--- a/src/SigmaVariation2D.cpp
+++ /dev/null
@@ -1,111 +0,0 @@
-#include <iostream>
-#include <chrono>
-#include <iomanip>
-#include <vector>
-
-#include <TH2D.h>
-#include <THStack.h>
-#include <TStyle.h>
-#include <TCanvas.h>
-#include <TRint.h>
-#include <TLegend.h>
-#include <TColor.h>
-#include <TMath.h>
-
-#include "mcmc/mcmc.h"
-#include "samplePDFDUNE/MaCh3DUNEFactory.h"
-#include "samplePDFDUNE/StructsDUNE.h"
-
-int main(int argc, char * argv[]) {
-  if(argc == 1){
-    MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
-    return 1;
-  }
-  manager* FitManager = new manager(argv[1]);
-
-  //###############################################################################################################################
-
-  //DB Sigma variations in units of each parameters Sigma
-  std::vector<double> sigmaVariations = {-3, -1, 0, 1, 3};
-
-  //###############################################################################################################################
-  //Create samplePDFFD objects
-  
-  covarianceXsec* xsec = nullptr;
-  covarianceOsc* osc = nullptr;
-
-  std::vector<samplePDFFDBase*> DUNEPdfs;
-  MakeMaCh3DuneInstance(FitManager, DUNEPdfs, xsec, osc);
-
-  //###############################################################################################################################
-  //Perform reweight and print total integral
-
-  MACH3LOG_INFO("=======================================================");
-  for(samplePDFFDBase* Sample: DUNEPdfs){
-    Sample->reweight();
-    MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get2DHist()->Integral());
-  }
-  
-  //###############################################################################################################################
-  //DB Can't use the core sigma variations as it's entirely set up around the concept of multiple selections per samplePDF object
-  //   Thats not the case in the FD code, which has one selection per samplePDF object
-  //   Consequently have to write out own code
-  
-  std::vector<covarianceBase*> CovObjs;
-  CovObjs.emplace_back(xsec);
-  CovObjs.emplace_back(osc);
-
-  MACH3LOG_INFO("=======================================================");
-
-  std::string OutputFileName = FitManager->raw()["General"]["OutputFile"].as<std::string>();
-  TFile* File = TFile::Open(OutputFileName.c_str(),"RECREATE");
-  
-  for (covarianceBase* CovObj: CovObjs) {
-    MACH3LOG_INFO("Starting Variations for covarianceBase Object: {}",CovObj->getName());
-    
-    int nPars = CovObj->getNpars();
-    for (int iPar=0;iPar<nPars;iPar++) {
-      std::string ParName = CovObj->GetParName(iPar);
-      double VarInit = CovObj->getParInit(iPar);
-      double VarSigma = CovObj->getDiagonalError(iPar);
-      
-      MACH3LOG_INFO("\tParameter : {:<30} - Variations around value : {:<10.7f} , in units of 1 Sigma : {:<10.7f}",ParName,VarInit,VarSigma);
-
-      File->cd();
-      File->mkdir(ParName.c_str());
-      File->cd(ParName.c_str());
-      
-      for (size_t iSigVar=0;iSigVar<sigmaVariations.size();iSigVar++) {
-	double VarVal = VarInit + sigmaVariations[iSigVar]*VarSigma;
-	if (VarVal < CovObj->GetLowerBound(iPar)) VarVal = CovObj->GetLowerBound(iPar);
-	if (VarVal > CovObj->GetUpperBound(iPar)) VarVal = CovObj->GetUpperBound(iPar);
-	
-	MACH3LOG_INFO("\t\tVariation {:<5.3f} - Parameter Value : {:<10.7f}",sigmaVariations[iSigVar],VarVal);
-	CovObj->setParProp(iPar,VarVal);
-
-	for (size_t iSample=0;iSample<DUNEPdfs.size();iSample++) {
-	  std::string SampleName = DUNEPdfs[iSample]->GetName();
-	  
-	  File->cd(ParName.c_str());
-	  if (iSigVar == 0) {
-	    File->mkdir((ParName+"/"+SampleName).c_str());
-	  }
-	  File->cd((ParName+"/"+SampleName).c_str());
-	  
-	  DUNEPdfs[iSample]->reweight();
-	  TH2* Hist = DUNEPdfs[iSample]->get2DHist();
-	  MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
-	  
-	  Hist->Write(Form("Variation_%i",(int)iSigVar));
-	}
-      }
-
-      CovObj->setParProp(iPar,VarInit);
-    }
-
-    MACH3LOG_INFO("=======================================================");
-  }
-
-  File->Close();
-  
-}
diff --git a/src/Variations.cpp b/src/Variations.cpp
index 043eb19..039b1a8 100644
--- a/src/Variations.cpp
+++ b/src/Variations.cpp
@@ -4,6 +4,7 @@
 #include <vector>
 
 #include <TH1D.h>
+#include <TH2D.h>
 #include <THStack.h>
 #include <TStyle.h>
 #include <TCanvas.h>
@@ -104,7 +105,10 @@ int main(int argc, char * argv[]) {
 	            File->cd((ParName+"/"+SampleName).c_str());
 	  
 	            DUNEPdfs[iSample]->reweight();
-	            TH1* Hist = DUNEPdfs[iSample]->get1DHist();
+              if(Sample->GetNDim() == 1)
+	              TH1* Hist = DUNEPdfs[iSample]->get1DHist();
+              else if(Sample->GetNDim() == 2)
+                TH2* Hist = DUNEPdfs[iSample]->get2DHist();
 	            MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
 	  
 	            Hist->Write(Form("Variation_%.2e",VarVal));
diff --git a/src/Variations2D.cpp b/src/Variations2D.cpp
deleted file mode 100644
index 2d10cba..0000000
--- a/src/Variations2D.cpp
+++ /dev/null
@@ -1,124 +0,0 @@
-#include <iostream>
-#include <chrono>
-#include <iomanip>
-#include <vector>
-
-#include <TH2D.h>
-#include <THStack.h>
-#include <TStyle.h>
-#include <TCanvas.h>
-#include <TRint.h>
-#include <TLegend.h>
-#include <TColor.h>
-#include <TMath.h>
-
-#include "mcmc/mcmc.h"
-#include "samplePDFDUNE/MaCh3DUNEFactory.h"
-#include "samplePDFDUNE/StructsDUNE.h"
-
-int main(int argc, char * argv[]) {
-  if(argc == 1){
-    MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
-    return 1;
-  }
-  manager* FitManager = new manager(argv[1]);
-
-  
-  //###############################################################################################################################
-  //Create samplePDFFD objects
-  
-  covarianceXsec* xsec = nullptr;
-  covarianceOsc* osc = nullptr;
-
-  std::vector<samplePDFFDBase*> DUNEPdfs;
-  MakeMaCh3DuneInstance(FitManager, DUNEPdfs, xsec, osc);
-
-  std::vector<double> oscpars = FitManager->raw()["General"]["OscillationParameters"].as<std::vector<double>>();
-
-  //###############################################################################################################################
-  //Perform reweight and print total integral
-
-  MACH3LOG_INFO("=======================================================");
-  for(samplePDFFDBase* Sample: DUNEPdfs){
-    Sample->reweight();
-    MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get2DHist()->Integral());
-  }
-  
-  //###############################################################################################################################
-  //DB Can't use the core sigma variations as it's entirely set up around the concept of multiple selections per samplePDF object
-  //   Thats not the case in the FD code, which has one selection per samplePDF object
-  //   Consequently have to write out own code
-  
-  std::vector<covarianceBase*> CovObjs;
-  CovObjs.emplace_back(xsec);
-  CovObjs.emplace_back(osc);
-
-  MACH3LOG_INFO("=======================================================");
-
-  std::string OutputFileName = FitManager->raw()["General"]["OutputFile"].as<std::string>();
-  TFile* File = TFile::Open(OutputFileName.c_str(),"RECREATE");
-
-  
-  for (covarianceBase* CovObj: CovObjs) {
-    MACH3LOG_INFO("Starting Variations for covarianceBase Object: {}",CovObj->getName());
-    
-    int nPars = CovObj->getNpars();
-
-    for (int iPar=0;iPar<nPars;iPar++) {
-      std::string ParName = CovObj->GetParName(iPar);
-
-      for (auto const &param : FitManager->raw()["General"]["Variations"]) {
-
-        std::string VarName = (param["Parameter"]["Name"].as<std::string>());
-
-        if(ParName == VarName) {
-
-          MACH3LOG_INFO("\tParameter : {:<30}",ParName);
-
-          if(!param["Parameter"]["OscParDefault"]){ //if specific default values not specified for the parameter then use global default ones
-            CovObj->setParameters(oscpars);
-          }
-          else {
-            CovObj->setParameters((param["Parameter"]["OscParDefault"].as<std::vector<double>>()));
-          }
-
-          std::vector<double> valVariations = (param["Parameter"]["VarValues"].as<std::vector<double>>());
-
-          File->cd();
-          File->mkdir(ParName.c_str());
-          File->cd(ParName.c_str());
-      
-          for (size_t iSigVar=0;iSigVar<valVariations.size();iSigVar++) {
-	          double VarVal = valVariations[iSigVar];
-	
-	          MACH3LOG_INFO("\t\tParameter Value : {:<10.7f}",VarVal);
-            CovObj->setParProp(iPar,VarVal);
-
-	          for (size_t iSample=0;iSample<DUNEPdfs.size();iSample++) {
-	            std::string SampleName = DUNEPdfs[iSample]->GetName();
-	  
-	            File->cd(ParName.c_str());
-	            if (iSigVar == 0) {
-	              File->mkdir((ParName+"/"+SampleName).c_str());
-	            }
-	            File->cd((ParName+"/"+SampleName).c_str());
-	  
-	            DUNEPdfs[iSample]->reweight();
-	            TH2* Hist = DUNEPdfs[iSample]->get2DHist();
-	            MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
-	  
-	            Hist->Write(Form("Variation_%.2e",VarVal));
-	          }
-          }
-
-        }
-      }
-    }
-
-    MACH3LOG_INFO("=======================================================");
-  }
-  
-
-  File->Close();
-  
-}

From da9a0668b4f6edc50feaba6cf9c598bcfcb3b51e Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Mon, 10 Feb 2025 10:43:13 -0600
Subject: [PATCH 6/9] Oopsie, forgot about that file

---
 src/Variations.cpp | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Variations.cpp b/src/Variations.cpp
index 039b1a8..75aac8c 100644
--- a/src/Variations.cpp
+++ b/src/Variations.cpp
@@ -105,10 +105,12 @@ int main(int argc, char * argv[]) {
 	            File->cd((ParName+"/"+SampleName).c_str());
 	  
 	            DUNEPdfs[iSample]->reweight();
-              if(Sample->GetNDim() == 1)
-	              TH1* Hist = DUNEPdfs[iSample]->get1DHist();
-              else if(Sample->GetNDim() == 2)
-                TH2* Hist = DUNEPdfs[iSample]->get2DHist();
+              TH1* Hist;
+              if(DUNEPdfs[iSample]->GetNDim() == 1)
+	              Hist = DUNEPdfs[iSample]->get1DHist();
+              else if(DUNEPdfs[iSample]->GetNDim() == 2)
+                Hist = DUNEPdfs[iSample]->get2DHist();
+
 	            MACH3LOG_INFO("\t\t\tSample : {:<30} - Integral : {:<10}",SampleName,Hist->Integral());
 	  
 	            Hist->Write(Form("Variation_%.2e",VarVal));

From 28140813c20d7c3d3f77f723905a31b06956e489 Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Mon, 10 Feb 2025 11:46:04 -0600
Subject: [PATCH 7/9] For some reason this wasn't tracked anymore

---
 .../Atmospherics/ExampleAtmosphericBinning.root | Bin 0 -> 12719 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 inputs/Atmospherics/ExampleAtmosphericBinning.root

diff --git a/inputs/Atmospherics/ExampleAtmosphericBinning.root b/inputs/Atmospherics/ExampleAtmosphericBinning.root
new file mode 100644
index 0000000000000000000000000000000000000000..f15c313db1f578d6ceb1651dc46b4ca264785be6
GIT binary patch
literal 12719
zcmbt*V~{3Yux7ibjcMEVv^j0twr$(CZQHgvt+#F4#?JTcjlKJ4_ukm8h^)%UbIx;~
z`cV;;Pv&v3wRHjlx*r1q0x|*uVyyjZ#(#Z@zXtr*^uYe!{su@=fPi3s0s+5tU+^NH
zBVBb7anU>l^j!ZP{cl}aK>q+~*;n-;0sa0L`R{H(K;TLu=2pgd!fyK3c2>sxPS&=L
zc4o#7=7s|1Ha6xqrgRSf(EG2(fx!R4{TCYusOvAR-e3C{9|(w{{J$cNT>TF>3jKfA
z^Zvu_pBD!*0#g!W6hacVF?KL@=XW!A{0~a7|1&~BA!@8bsUh{l1Q|%50>};cGR>Vm
z*}HYr_MZF7IwsCNM=-NFOoB2=R45D@6^@EB9JZK=rHnhFoH?}s7?moS$!G=<fypEX
z%CwQ^+I{=E3*bESJ-P-sY+Qb;-hQ**?!NZaeHIYV=j!(h@?-6f0Lzz}lh;);B>17i
z>zJz@%Kaf7<NliA@%rNS>Sj03lmKn%x=N`qsSf4wW__<&#`}w3c5_+yaituO1(F|Z
z>BN<YADVcj+<l&pg*+|hGVh7B%p5Zyp5Vj;9W7a<c)1SymYq^T1g78^d+L1=mDGZm
z&7u{2Fq|h6ulv0~@ONLf>_sq@xSf8yD#*Ut`1mM+KBLSP=XjRlHbg7hy{mZaY8Mat
zZvWof&v1V`JYV@SwJJ{yGopi5Q^cHNCQ38u8G)nn**9+_oVY_2b9-4ej2!G0tMz0$
z7<w@9Cy7(@{>c1max7k;E}Cxp-Hd9|E|0qXkrWlkv6wjTAxAUvgCN^+Sri_acEWyT
zDsY4y=ehlvEFR;VBcuK6#}DG0CopnZ>llUu`JvYwV-f)!my#8z67o3PI{xLwe4sns
zrm{w!svr;^-%neoOSv1J*O{gqwywrkLZVJnuq~EhA+=3z;OlN_@=xm1-Ot4`RV+&|
zFZRr@?x8SrXz*5bDV#3oVDqfi`Bu`M!Xr)6$qvn%+sl48K0M=>gA<h+;oBhD{T8ck
zoz|UuQpZFtds?}on&ay)9}X1n_}MrNrvQ4qfox}Fz%Dgt=Rq>u(hZCK+SXbw*l<X%
z0lST+puO|{=s<)S1=N~JujU6;5|xT8qx(kCd<5;6Ip(RH$;CJciz29T>H#aBRC#Da
zObhj^W#$ex=^^BGt;!2pr{D}r3usR>{j+-k0Q4{<diMD2J&#-F=1la+i~_%j6Ro%$
z7&XNd_si}B0`>GYWO4w3pY$`y%n|~MD!aMlddXDau(BI2H0|4u%3;kCG@7w&Z97ej
zT_?DLKENM;kW#MNA?B)V5wa{M3o6;Y8>-?Rfk|}*@H^UBQ|Km)dXc;NcrolMKx00&
zjO<WQ&J*l~2&Oc@<?YlsLX*M^koxl?=P=+Ja7>GLcH#z}Fe#Zg^NaflkDO;QdB%>1
z1rYd_+=I00@0rJ2pIN>mOvKF434somBpB%WC>4zSi&@F~q1KfxNMxe(&oUUknba@t
z6~$zDz89I;gPe>Ye1F{!qGZ;-Sly!X%Vf5^@&3~y4Lv?))RO6G%8cKQV`@F308_J;
zuf(1yw;vg^e(7JvjAlNYSSgFf5Yxn_ybYM1gSr)ttj;2tJM^)IaL<%yH>wJ`qJ304
zFO@ccIgvnqGeVY}q&fP~lxW|&hgvTP+Ff1xqf_mW6z*TQYMaD!OzDoJ(xdPi&FHWi
z&(|CsuDS3{Te3dM9+C(eTo%57@3~M`OdS#!Oo7bvHAG2E=q6Gyv=9*tLCs6YmJN`g
z+ykA-cyq-UbK;+c6^0Oe#JJQh?uz@hWCqCwhI2E7tqV;jculp(ZgIQUu$QKgBBZD<
z`JaZ(@=DHxP7KFE(?PhQ@b^Ut-kcV5NLX}gfO!zy>!%L2p%H%aZs#}24Y2G=>I?&9
zK0(tJ6~bA}UnewGjZF4lFxpk?vtdTq0;$6HnS{GEC!E*3DhH*&+PYke3Kds^Y|lBH
z<W2{9>lJMFlfy<QF+6hB+!Roo#vGfhTT^p`liZ$7_vjC5)<?1{>hL`BYzKFlx&pHH
zrTU?YL?3(eEqhgP!MZ8_R~jvzJAl_&AI-_CT>$#sYhsGW+~k$Rufs&dhc$6FoO3nE
z?(s_^m8q|}bx(kd$`jrL=0zvFwF-i_{#o(1i-UmfDuby<7}5j1r;R<+FytH0XSr)a
z=3K70d+CZ61ZWc%0W1X{=9bq96Rg$dpPVN}U<iSi-dNk|V1Lo;2-=7${k$tX9gt!;
zh;-xJM;=~?z>K9+viU5Awoj>#;z@A^jC}mnnF7$jbnX7PuWS9fX`!B9eefY-0ErrK
zmw~v`zIf;UQT>xS&iZgU84QUYbvtryq>zb`?h9gOy|lVLV;)_g!L!!f-l&FP{o~ck
z9L7rq9OF?6uhSo}$D%48ubF)}W1&q}=yVwIxf}!fPq-pD&ePdRHvM8rt$l)9feZ<`
zPmU&2KSV^Za%?U10_DLSUZy{&Fr1s3u*GCU{*=kNCyLQye9GMmvy4EAm?k|(YBdBf
zW-F4Euq$G$Ykqm%bkIc=Pgq+@$@$fDey`554eMpqvXfE=V~@}lEt6~)1m5NiZpNPy
zGkonSCVh9qW8m{rH5681ku9ngsYiMHh4XALHm4X53|;nF$uB6SnaMMjK6m{{+}oDy
zEDX?}-<@i?n*wEU7d|$1$%c_iX~q#FW$i~XeRy!^08MMCqI6z0f>4Z~RBVpb=vS%_
z#h2V;O*``F>glmVm$Jo4b=z<SDk+Q#6#$p*a}syU@3v?EIHC(zUB!jztp@WBD+7DM
zy|hwz{b2p5fo1eWZ^Jhcx~lT-5WzReiUg25F7!*C&5fK?5T%_WH^6t<Lzyg5Xm+`B
z^jBTObCD~nr+H&u)%g@5n3!I1VIK7OaV#*Q2hYi+MWST%w99}VS!mTjIWQCSYa;cI
z?DHUZ?C137?#J7qEO=IX0fiIjWrb-44$-zkUw#>jp#+m(x8eyDd~bbu%JLE7whxtM
zXZblLIh`x_&&J!B#%W6FV$N&Zv2R?hL_4Kxn5uZ22z5ZjoY#9Gi_Olt^zta<pC;?}
z=HJ+eywTbl*ONaJeujV2UT*G+<#yO4H9V5dqklh5YII|rlH<vimpc;-LO=UC{kb2j
z6StE|P{+lLK?T>vuKFFa_*<k$gwKfL4=mraIxHrcPXnV-kMIa8U<Q(;op_&2vgQwr
z)fmR_p=py6;{8n;@e~n9qpI7E$<f6KDJf))0*n5!BITS$gL4NX2Oh%`hcgx?;cBYo
z?)@++4p5g7<HWJW<mD!pJ1Qm^4!1QiOTv53?va$C*s%-QEeEwJsPt=iACnHwuqo%_
z5!LbCv4L9xMM4!=b&6w@#`YY7$kx$mxZ|mK(mz=nV_Km!#q-Br0#C%$mv6!<xQ~@=
zazE60v=`w57voq6E9%H*anvWb*zpOo;-c$aqwu}sr+;(b+0Stp-EUD?rl&?(jRUuD
z4oMnSdgysVNXBPZf2B&vp*Lh^vCM*b8$AQs+dar|R&$wUl@64MJWUTwp7-a+2+i$$
z)xLootgKBrd7dCR3g|m-OznwAMfX!Fd)DI&TS9du@8KQJv^O)i`GT_`eS;;iZ-|Zs
z6N45?591nt(KQ~zfVZnWpwyDtiqN5dq<3uoY~QP$V%mTgs;R)^fBu>rn+~<Oe!M1Z
zJxp$9>USUWE?FmSDuZt4gWhmG_YLNrVz&|K@#j8zSD|P7A(As!DgSGxGwxWMU)wtj
z{BHg=K8p%GUNz!=DdeefERvEg<fr1;dBtqeP(6aXEb2Bo(zk!tc;{KwlRBYoKaHlE
z3*KGJ@ab`bIT3zi#^~HK%0VK1SA|_>kQdra@C<SOSgWbkL&Pb?opxBtD{?3HE8h6}
zJj)V+?&&(BH;dx|Ht&J9?>W*P%=lU^GP;1z;M&rBYGB;<YnKI~DEeJ4E7}wEYSc$7
z1SWf_L)^Ec#dV?})7ZA9YG*MuvbdKO_<oI{*!;LRhVFS(k##vIcKbp+3Q9bWDXU-6
zI;0en3<kkz<tF)a)PfimQv>qJOMuZXs&X#Lm>8>xE2m8-?)VjGHPx{VF-O73xu_0b
z0)8)E7$$(<VS0y+UI7mpu|ZavnMVG1|87E<F)g&3=o`GprI5ejYfJ7RgdBmn5*r68
z5I8S2^joj7us?sPedgOF1qHHVB|Bkw0NJ(fpG5qE9Ub6uCR|mNuC8;f0$M0=T~oO0
zds?A>coXtL$uEi_%V+<`bZBVIqDqxiw*0ttH?6ffVU&(KmzmUUoZyBU_Y5<cyt&vJ
zTW(ea`Ltot$VLL3;H6Odddtp&y3cx~6lOsb_>9j$alfbmSHYZx(8qi`j?A5n6>^lE
zh`Y>NG5&beqP6lhAe2?RO}&8ucwu<Sp;(j3Jh6z(bB)<S3I!L<rw%>3h$$CmS6@9L
zdF3T?6kSOaXKptVi8H1M5hG02WY)ZsNO6H*auCAnl=uQlPx%-eCtAkZWD)5-ttpXt
zg7t;e4z?ST0`;AQ5eKzl25_{hGtaF1Ogf4l5IF=|Eu5>zZ6zdh_rzxqY{$C|p7*1j
zdkrJ4vl)9oP>wa}%%6#%hNnU3QG84DUdBI&`PJFvKEMkbT`p)M5UR8nuJ!|vBaRnq
zYi9+aS`G9i-6@mAc1VvfWD13rj%uPxRJ3Nii@i*1FzIwPGl`up(dZD+BxyMZ!Y1!o
z3WEkN<P*fEmo#*v6B1&XE~tMb4XL)ua!}<Loxk(hHm?;J$(c_9y8S8AmC#w4y&y^N
zeR2>v<YN-1K_TOI*(8t_I$d<*1S!=GI@xu>B-9yJRfawVC~aLP9Ve^gs8U8@6LSlc
z(A<~Wx_~6S(f|0o>|jVti&0!JR*9OIqf!g$ViY#D2b{1;FiCip-{n%~37)RJxlXH=
zP4T)8^(9WIfVM|gp4fqlib^A}C3D&%Rel#ZbhhgYkR|I6@)Vkuc_ld*F0fKrTCo;a
z&gW0<eaebRe?~tAS|r&!K;786`7s?Az<nF>Ml;cGOC@nPil#sHpg+`DP*4-t3&lnv
z8LQgPKY1vJHbBb4Z>@ZS8Qb!DeMF<gGz>@cM!CaNi26=<5gLI{RBsUFm~TZoyqEET
zR?*ARohsJ9r|KnDLbo?lS%6M7V&{^q{>baPEwV-^hdT8Br3_thUGS0p8FdTrmhX|T
z-;GOTqzXHLWyXmX0PmERvNZ6?8yGf;Cx2d&%YTT=I0^l&bYR2`XHCUF>}>Dit%zKP
zQBnu+zX*(YT`k=z@8%y?pPZ~f+bA=7*`HB%HC2K>gE#xC4v`2pWR*xYl~0e<d8)I3
zqO#r1@X}5Tn*az)sA+l0wTrV3dkkPG8?nTWj5-uf=oCI$NASs!4jQyu^b;##w&FfH
z!ip?8gOXVeb;+}Qc`>(d0W15Cvow8~$5@DfOUUA~$kTef*XuFbD_Q1HG*y@iI#*8`
zoh1jK<)3kRw0;JkDGSFs3P;KZJ~%xEKD#WcWiOh0sDZI~74~%V=mcYx19K$ps4bSQ
zBtD&8h%6e_#m+~X2ufeF_{`RL{g!sk#>Il_FLM|7_#9LsUi2EREOc^3W(hSJUdS~n
zNO35iIB=m}TuT>P?OTr4V1u_2bHfYKSSne6+aQ(C3~hpRcaZb6&h)ja!L@)i&bEHU
z5xP{}1vr7z<vq<UKiq)0FUqU9>6|CVa=tqg9Og5gaR<u2dpO9MdIe5Pka{m_8>@;Q
zrw4bGZfx`vS>|7HUFT5q;TPgXe(S4ZqAso@auy!Apg$HE4u~Wi%GDD2ze_7()g<kA
z$w|A1Q^#f-U3Y(>s-iuLFvPGF_O$()Y@j7B>+L0x;tE84gz?h{eP&`N;DdKruk?q&
zn>_yDOV97GOiQe9crqIkm)hp&Mu$T<`(cz;QJ~)(>cOhbSEGSyD<7BZUzu>!>(e8q
zPbQ<1aYAHV`?MrtfJ15A`OD|1TYz};T=y+NCQtqYkh^adG!h92y=@FWrVHAH2^o7$
zwiphB$%i!9@*>2|2%F-I{R$`Rxqs|1W72(UMv*=|g6W=PHtUJ$TY|Z@(dw@ILY+oC
zYo7Dc|7KzK<q~aH*ZS3K{Vbz3$)T$jWSKktywv9me}6obKP<on0-$#oB%(!cw~x<6
zGjA3<@5OA|$(uH?YQ(S=(eRlx@R7u$ZGkJeMJW1X0}Qry_-C)0pLvZq8XksVjyM(#
zAGY9+Y{G~iH&!5v8LT#t|E_TpJ5l%u45V3<2$n5({;kTdXar94skA&sYQGUx7y^dW
zWsG|a^VbgntnKXLdhUo34^J%37c(n92}4(&=ufeIJ@>h;Kw_yTH!D)wuTd*2!cThN
zID)S4L4uiYU)-T-*Vk))9A}(XGhaThFWhggTRwcZ4_}@eU2@;=XV7v`v9-~g>+1u)
zA@_P2nAP4_K8ZMjmmg$nyRhFcx!>hcK0Y0<vbPDHMSTe%lF&4ib^llAn+yC4W;Ioo
z76=IO^dGT`sQX{Bit`_(>Sy);6048}Z5_>Rj5Yo@wF>e-LVty-5=5YGqJM-cwQ#m%
zYXBc+0Y!uoG%2aPQbt*eM3Gw=Y_Y%Dyk8t8iFkz2QGP->hf$RgzG2wZy_3ic#|#Gv
z5#{yx`aREVYmck<>^tPjv&QolV5_(L+53CBdD*$TS~$*Ea0fs%)lBfi66r@oka<@q
z`3G3Q&4#v13~Nj2lxy1>`&CnYb8|fp@x%IXAoS0dmnq+V_a`S1eEQ(=Mw2_59E2_?
z?%m9CVZ>RYn=P>LUR1Il9XUJ6BsUw-V89^yYqR4!RMSI8>FYx=RMxn3UGJ5B^qJ`D
z!_*{Epj{r^{@WSHnYX0~@9o*z@!Pa@z4x1*OSP{nx|q1{`f?EO+wE<dcHDK}>EroG
zB3w_RwcAdqCH|jZjzuV)h4tI%TtU`_E4~#CTUFz*@6ox%&j1ts?-_!ENku%J>D`5(
zS>}sWmdh^lny}9TEUS8Fh%wwm+{mocFfE90Sak_z2W-#d(k|fxG;gi?BRt&p)AF;`
zW8t`W1}DIi_IVsOyS=Y;0=>iLZ0r~mE8(-$q)+`X>Uhh7Ppg6{+;*-7aEK(T_)0Rz
zEEIxBt#r+H7Awz#nGep^zC1*ZLKXCRMbdb|Z>0<Z9}o`bAxVT>cVb9g`kvZPL=Jjn
zz9FYWVsg$6!inae96oHuL`N~iqko!d9uA2P)N&kQ|1ABE>6c$6xYIu{!$^YEu@{aZ
zV&BX`55@_Py2oQ#9V4XBSOsS$$i($rkuXJEtu_!L^V%DuYp<z%_kn9z5N)w+J0pJY
ze}$_A<O)7r+MsgO@HJ?|(`CLhgRd^*7lF&75wG7|&JZ(Nj4gY)({*#guSVSF4+IR1
zrTp-A)f$9)C;KQ%cOkhrcSO%luZs1aMqi>`cc`x&yEBVv19>XO>teKYWq2As>uPer
zALQ+=f`1pRUOBGQ8ge8?aHWyjZ!scyI=x*Ng5@;K?GRKlh=zI^kLN4uRv6_)Dy+Q*
zC5?MbZtEH_K~zUk-Z$CQFjD4elhMqHsM6wVwR~@iPd2k8x7?1XB3MYgCbEh@Y}x#f
z!{cj^sbRn&6D6Fqd%BX#Um9DxQ&yBNMpTE^worzgiX&C&*vo>!PB*MYgW2qjk?IJO
zeIa5oQpq)*5OpTFmoC@ONaABkOfj~FQ4}?qYaYfwj*B~8bN-y${B5LR$>eEbEmFeY
z6u)nc#l+@4olb@mCFO3IPQXWN6hYV7=^IMM6w)h|h_M|ObtMp5lGQv$fsilERYpL(
zA9VU>DPpXxR)uUbPIN?i0L`HQmg%B0mmF8u5B5Hk$rMe3Kydx3Mj;S`Nu~G4j|qH{
z5R~&H^sOEfM3px@XzD(lBlGKLReVER?S#^gcCMB8m_3(;AtcYlR4o%r+>x!kefale
zU{CEmtH$CK!&>9@SK$Q{{o1WZ7>ilxde`g;VO&Gii)5Q7o;ydlr#sJ8Z4aqIyq1E`
z=}*R$1vy8`t4^e+E>}mlY;Igng#+Blud%_LyjYp+Lim;aJ*QX60FWoOm*uMKo)Dgn
z-O4O9SN&Lv2HTQ$vZtxpGpvXxfj6O3w8s$rqG#4%og7b~(<PoPnn9(a<ERt(Z6slj
zF1djaXzZf*S$tPCDv=Itpj4X7Sf>T3hOZE<B3sw0*+0I~4~N~wcgyr~yys$9xX&m>
zaLRnxaN(jFqc!i#vIcP~NsiAyLkKV18)j2V2#Pj6Pm+e9erIIvAHf%p&eJ&ih=thv
z&Zu$n|2j<<)12<!?QF+3PYCvKCrTIl#A7^{1ke^KSe+#;#1c1qX$Cc4dlZ#SGsd#~
z6tMu)ZqX@+DbGoGrAEghTGDt=D`h|`_lVhVF0_oV$iQeVU;{3{KVzw7mLxFFs;w?r
zM5j!0zM5<diB~Xbp5u9CR?rDPPzhxrCav0u3#esP*m!Pw_Cgbl5RM*RFvJyGwHD#g
zy#=GJ?3k@uJqSX%U8wRWp(R0ZwElGzM%4a!w_`kuM)K2_-PVAVkYo6HJuRIl0aTdh
zKEjn?wWswXJe(#$I^rmJzL!{izdyWkhPx|keezyFT?~!k%LL0AL0qbNlPmcm?m?Wy
z=uy*~r2Fbrt4$V4JU&<g1a~3+z<%3&2Lx9<#aJ})8ecTw3Eld>!i0o!ydvzASzw-q
zCp>}Wa7Fs`lQZc$a&xvdS!0aDu+`Aat^Ha3V%aE1LzZ>a23XFwP7%M8Y7ji=XRE&I
zNwcK2YewDVhru(9D%XXEh0TsJZB#aFwyOw4Y~3&C?t~8$xC^J0NQ{Kq(HZLkkm5!<
zJ@W4|!Gkga7o|Bd)+ERkB!%}-lO>T0hIMp(i%t|Sv{WZ;<e$SX5z7&Ni%3?!AIq%6
zVF8!uOO4^Vm37{mmARMC4(_5M2{VAl@RcXt+Zs1P#1`#TbCsTp5NpqZ1E(Sx{Y<k1
zR?HbgtLktDd^!^YOSLvj<t(NaJm^R<m#(ntNWot`&m{&hr#ji=^Rp`nC`@^G);uj)
zaOt#ij+mNC0m)o=$9ngD+TBvM@>Vlx?NaN%Kr`vzW7ynQ4DL(9OA=L+>ddEjoX4U=
zq}>Nwy|nQS7L+|L#nBzD*8a4zjJxBpLS>~WxK{L!C@A>W8v?OzaVpqc)InlDU**HU
zk{T9{h2-kjd#%W|TjhIHfU|BO>2Av<g~CDbec4&4hru<fvnE)XR@K_{<Or9IzU}Nm
zlHD)X`S^NV)y?Bp<-X_fdSSzyTZ9hC$Q~GKkLe^%gFn~JQ0Q13Juaw`vu-TbYl2!<
zJ`49CXGAyi$HHsV7V1^^j}3gbHrBhO_^dO1uB$1gBmUxkXI}=3!lSH~AI0iM-!HTc
zs24dI3RH%&s_LoUdo<x^P=N_Sr@2}W%<Uq7>Ar_jWASleqh&|0)Ux<|R$DhbM30U@
z$5u5cww|Z4*GKj-nr3pcitUe8kwmL@avh3jaqfbvh((2T>4hKHjyXgP?Q)XxHF%x5
z_b?osR(o2u)Ui;*N~wk+%hmFQ;p3L{YR{X2<{LBZRMDOvnoo1E#<#bpLG2{zV5P^9
z^g>@uv>vK=OTxfrqQ{7&&uLz!LK!8Bc&Pwh*P~&Y#*ES>i3!H1-NN$uF(N>lZ~0SZ
zPc1IJBDI4A114$e2&Xn9bO@uC{LmUo3`P8pf@xL%hi!fNoGa#bYhy=I38cPGPY8wQ
zsi7CTuVkYgHPZH5Q&uFC<uF?*N})9_1fwdTU5ZN#%rQwqq$rn4uLUUaOkv4Cy-0lt
zE>J)1*2a3P<Mr)@bKqcnvl=ALXPh?5Iz80<?YZ`J({4aDg!d9+B=ja&Pq<|6lgTTC
zjjb-v^%t)T1K(l(6PTh?%b8N>uwg^fg~aP03aJBR6Lx&KksuJJ%B+*v*nvnYW0Wq&
zEwb0*?p|u%HX<^|#$xRKgL5&<JwAOWVIhJ2)n|;?PMsH{Y_Tr3^y|?6ME6uiJ7nDu
zHgbE)lV6z6!m;AMP@GaV-g6cTo}cd`W1T-WY^^=+%)VvqKB{@vT%&yP-hlzWwV%Sm
z2uY=G{5wV8<X~(T%iHooKeD4_f4j|-&e9<Gm5FDO53%#6NYL8&wLRfl?<%3XwKeYh
zk233q*)B@yQjY`&Vg4dPIVd8uw_G@UwR9pF{{l=e0VgEVS%2k!11V^<jKboS`;iwA
z?JqhC-Y5ZHmy{8d-HrrXw49D{xMu;miT4DUI$o1>oM{pPs@N%<kLWZ3O7DHBz|JLc
zCU>6!L&r>F?+GeWcwFG8gr&ywFRwezXGEs-@u4>z4J8`74%9|j_nMU5ZKzDaEZvxs
z*@VB`^H@Bi!Hg~?)Q>wE;Tpz7LE!y>jdW2<Y5y4W&+N@tYZYe3-9JgVZRvxL@f3}8
zdl&q0=w+$xerrPA8uH-e@V*LdT~9g8T0jhH)jl*t<Bi<OZvAB4k7$k~r$6j=t)V+W
zJw)|?WpwkM@aXUeAU=SZo>Mf~4EP`~_jfqo1Afj})cg<wy}(Y5p(h5BFIBP5%K{!6
zBiTn(_9S4^(gK7;3-qUS*Ebt($=PW_;L-%==UMx4wvu2#Cr6f=QqcPe#EvOL2IBL_
zcg>)_^`px@=(kM>Q=v!DlTAXkq6vlv)q6{6!6kL=(ks=U_|5NQBER0jz7Xg+PsH(p
z;pa?`lkt)MPS^LZ+Xt7Yz;0nfS4s}L3+38yBHiK--rAt}mZvVmC^}Mdn(>RZPoFLT
zH<v4S+&{;sG?C-bW2Jw2k}Zo+FV`_mh0S&G{*}VK94eayExItRo5#uYq?07Yyf_A6
z`>3)D!D>}e=-5UsD?c^K-H-=vj(CtS$Cr^iA3mb@C5CB^4m7}%F_tT3>JU?&20p9#
z*5Wsz59x66ch--U%=g)xy6jj+&*S|~tld8N^UVAhbx1lOPhZn&Xs$GL4pE+?P?-%5
z>ur>0>nBW}ylgR_z9cR)8BXJ!r*!bhwJX*vH3EO4{TJS#5x<$oxOXWX7ea<<8Y|{2
zmB9V@$1J*<W?p(3g~y~BeiKbcWm=XutVWio3mRQZU<zlXp*Ald&-oD&z$ik|w50%-
z`7O%SG*6@mFg^N>Ev1AZ?i<wdP7glit;4_WdVfi-PB`bIHnw!-_p`~=w8zEM5&}1Y
ze5L0OYi^gIh3KRO)=BADT?7s}&#_rrYEPfa2||pei-satM&$NFtC)PQxfH{MTNhqi
zHsUg-jO2H#-R&TH?LpqVmHnga68i}qH6ca`Jy=4Ka+3T5FM+vcaeMkKP(q@zdcXrD
z0jYXC)tW6(dB4SjWEN{2xZt&}A}NTw;qA<-u%^G4Ng4SJGy2${Nzf#<v)?rg%G0+}
zpm(mlA)Ag$egz5p8mSLp6r&hSDVeB#4zB#b$A;W;VIHNmYBUfNdT*uLq>z3cS{{XE
z4SaIbURP{E2cVBCxq2I8h;sMvI^51)sB-PsSgPonAlBsr%e9q6el83QlzeT-W^5tC
zpCT`QDV|f~H!Bc%_28wn6M3N8SHrj?Q+9dy%qcV6_1Gsq+xVWxu%MsT1s(ktMtP3U
zXf)i$AUu+ga3}5obB4&9PaZaC4;yRtBa=rc4+o4PPsr%MXOEAju@$=VU4_F(6MjQH
z;EfYRuw(Jt+JSrn2HWQ}k*g$^H9)!zb%2wpKm7AO@;ODFfH25o#kk)beqj9ZF!8Sz
z((_tFITuiZDDhk9&!dOvTNFbVSJ#J>@|5}WK1kT-)paHzs0YEoHCuH(D557$((no)
z>Q^i(k)TtLsJ6u<3cy<iQ)y{G$muieGZ0nM*l|8ll(X2*_C|V(IjB$4&EVH9+im3#
z=gO-MpkhX@gtg)|EuZnc_p4?!bdUcAtD_$-=j)yTds1A|cFjKbm!{&jd)@Qgp<&>#
zKR9sQQ8TtecT#|yndF!+2i*JpGT?GxSHf=NqQZXpN#&2-Ms;~;X}H7sy3I&^;`c?$
zb6m2N6ZCbz#yKl)buufVX2P`d0HE2OO+28l7ADa8KnR3s^~KTppt=R@1hDnI(0=PS
z>LONuZ_It-V}D(XkNa-NvDN8+e6{#04aF5Ertv*~i_Z}u9wCB#Z)Sb_e!bc<Y<Y#*
z9&Ilx9-)9L!b&kR4EOz?oEu%n8+uPz>eGLljs6N9B%c2Y9shO={nLU3WCX4xW$x$%
ztLWrltZ!}XAZ}w~i!5a8Y+&V1U}bJ&X>9cO;pp^N?wEi9@+A2ycPwda+Ty69@^L+_
zg<o<y?|HS53iACVH#cCDBP}+*U{?V(*E*9v^I{&qxQgPLzKG)ag}rW_PyLvmOw~i3
zA0Z+30e&My3Kjr#2uz}b2m;j)iqJ*yh(t)3yv^Zi!ri#q?7A5+)O_W&(e3E_?6u)I
z%K?Dk=@Jm8LW~$ePtp&BzV;1L$cO})tWxjin0<n(-Y&g__(Rb#3CYv;luVZ=n*8-v
zNbd!|jW&1A^6Jv^ac6{>X8Ex>xtJJwqK^ZsJlijoo<Cg8Rt5=(T#P&~q{KjaOl7E0
z4i}kQC_kZ}nn`ie)wtP5v8eId@5#lTWPOm4p2-#lJra|L$8h4@0uj_Dh66}~eA=OP
znElEohL(1%NI~alF$5Q44(~u{wmvl#0qG;?Sj`(yY@1CCIfn@-G_`-bNch>lEC-8n
z3*+n$Oawj48dkGs6V~QZIw+_G1xaZFKWWL=;S2d3Z$fDfWKz<VZkTe@)6_yz;2<st
zsd>Vl1A_F&<-OpT22ky|@NS@Rc9&zi$#b$Axz+-^)IFzuQ&n;07SFF_8P^ilDU4Oa
z2KFq6)@mlpA>Y<{A;dYfuky&iROnGw`@)|b=91?EKQ`36jc78D5R~qzNK<z6G~Z~_
z=C%bz{C252^NAw}(|QBEB3{eZ`12wao|SWhF|0-rp@uYnH{MB$h$_WxDtp1F`=aKw
zW`7gplWwqyVy4#TcHhde;7~Yc5)zK(HFx5`wU{8S3nc&Lo`|zIa)$fXwk7k0igSZM
zlr+5!`7QA@4Qx_AqcLUnr6!W)>}AW_tx{8Gm}#=6SasgT+u;n>V_W&_lJ}9ng^^IW
z?Wr?_=nx<<@kvP|W*$&%gtMQRXI|GNGgrEd@7#zZ;;$b5z*Lo@V?WI>HN)fXb8Fk{
zPVau?DWHfjr1)YZNV{kYBmLgUY^+a-2X>~QHbmZ~X3Gi#<%P&gn>UEN?`t5G9l~Tn
zW)9Rv72(BB8jxpb!2Il1m(^i={>MNC=H{KmqBLb8R`m<S93q}lPxheyC`*-Qvl1|&
z(r1@qxujPjm=+Ut2b`eZoR4(kU$6gK#ggQeBFyWlzzkbg&5S90j5}N4`Zk+0=!f-|
zE9i?hW5l()5fwg`@eR44&p6>XZ74APq34(Dw#RGBq@iVRsU5LffL|AWfoMpl;Yb^d
zbVn@mImD>rRPm=^Ky7z)hB56O5<BAEbKTB&#9sUDMAmS7Pam!T0eiydvpfA=3LS!k
z`shotX!lZBK7aIX<Crn{o$E!MZTH)X9}E{H{0Gx-?FoPP2N%KH6S&<!JxLg5CqR}b
zjwW_6G84OyTVIe+snDsn;O8f)8SO)r0qqYCQ^ic?Zk=RWoEh*^LV_(=$}dfdJk(_R
z#md#nPWmy9)|v{|)gxx=qvwBA%m%9RF{&kHFog~=j-k!n6f<pR`mv+R4Tzc2`gYRw
zM&#I<(1q6@rCTtDcSFVsR{$cW<f_?mHLv(QgMwI#@8}Pq%pTu!G|~J{dgjb~?zIUa
zt-p&HvkzzUyz|dCTm&v!cjIBoZzb2^qjP^_-sjB4p19%Mliln@<Cnl+63A`3!7I<-
zxM&~UxVgZCvM!Lm)rr=GH-}yuoRTd_X`ck)?rWoWx%W?UxCcJDH(CwDuz)+YS92A?
zqg4=0zvwgt(sx`!zM=WmSx0VrD2jCukwhD-vloeFG+)j|Tq(018AL4QBMbaq!l=AV
z7$6(0GLXhk;c>KNZ#Bq@n0rW=bE1)4ATUUusJ>5WMWl_X$fSV4dc=bLIa%S@z`8U*
zh{{R16<yO9_b4k1Qa*Fbin{7IU<iLDwbCYBC2dXDh#a4H@>Zj??`URa+ulN3J{`PG
zHj(zY9%BTKt~dhSOTF|~?N<-ZwT+l4wqSq^D3rfo6W5bc3VSl#%HV(aEqJ-tnMq3|
z&S-XWe&T=Qaw3gsN0RLZj8^?{!M^!jbSwF=8A7M*6zq=MvCO>!?6fo99Ru%br<;$b
zWmzydTSTmov5i69?;2c+AZ-AncXqL$vVRch6Sf^gg=;wI0l}iWcOkZxA_NQ$+V3bR
zoo~&a){((AM9fS~@^j*G%mUMPXzN5<3@ffqFL)&a(eu@Ym_+R2C91}g4|{O<N>!4b
zqPZ^_TqgZi%PsC!PGk?))v#$L+C2P8qiPZ9@25sS)IZ&i5A78Fb_s(z={!h$jwG;p
zJ0Q5f5E^@S7wKbW@K)z@uy?z<uHr}Q9n3M6Yt#1XSf_^=+)grHH6fAzNoC$vVWdJg
zaou?AE*?EK2~n<EU5Csr8SnNk`|}UJ{CbLkIr27^P%^~j8`TwdpB7r$<hOMiHHhP(
zVSg7E3?m5~bNS(mlS&xqQxYb{!dI9Zt6|SYTBxyl%JlDAnhanA-mQ{q@Ln!gpxYdb
z5o7;eQqBh@G#{=(Nu~Qbfz-OAMBq?d#G5KWVx&yVswoeRH#LsB>pkMO15E$MFly^^
zaqYw_$s~bBSiDVK2%9ma!xw5ooPKu;lg1tK!qV{>%T|jjjj2B488TH=z713oDGpEi
zp;>Q027B5dbn5w!Zh~RjftIyhhbtA>&JHffN-><w(wddk3C8hP{&ke-%AcN^1<sKG
zs-F%-lMB{Aj8(EVx?Ko*&ReBhZN`z+9X=`cj9gVoTtH6UpcOXxSPx3Hgm?BKn=y-a
zKJ=3Cr2+242VI3Wl7_A%Jxc>VvL0Suz+6SU9Rw5a>D-00eZqI={rntfbHuu}oVy8@
zHH3I6_<BJ$m3cwLJ>F&3lD^^)>8xQkY-Zn%ZJvMEQS{|bgFLUQB~kxGpi-+srcu?Q
zp#?~@jWGx~@W!(UwA*!U=V%+?#nKSrU($n-*%kZ44U(LZF_(}NUN`SN-}62x6jA?v
zNEIJ+78c7LPvF&?UE~p`4~@n5B>M{Bn1ymU^3VRL!f&ug$;;GHt_@Y`i&;IEUzKa2
z^-l1>{}rbnMGG*VzhNc+Iexhv_@uPiQthYxo&TbapgfWn%jt-<HO<H`qr$}Prktl-
z@yoSs9)A$GEhBwUlG7H#(nH-O7%J=cX55NTGjWuCFAd9uFgE*BIL8gAxtr!s_yg8`
z{j6p;M|NEfY_PcqS!!W9E=GqMuRD-*cGL?(6~q_d%CVBG#UFjLxxA6_j1{x{ARpas
zRM&AKt+nGyIkOhSb<_7^pDl@!Ss-ZmQmxvK{*R!Xd4Tv_=$Q9#&(ZW<rxe_2o74<#
zc-XVG)^0*Zab13cgvUTMx7-QkLh9o#QUMis@dCcWUj+$!*O`S0o^$@m-``|Z`s7ZK
zx)0H~&+Pld2jb#;xjLY)MQSanVuS1VMC)2IU9&xXF>f~=fWg{Df4bqC*OD)pKRLA=
zTQ+VV9m?8qjnL~*dNM#@I66YubVbg93gvkM^m~S+_Kwn?A*>9)-5WDYwFb!zl4$}3
zj$$%4n;Z@nPH+}e3bAn61NHM`eg(F70Twg`*3!iwmO&hB>DQE1SpVkJhFD?c82bkE
zwT&-Dp)0B=7gC&ctO<vxy*LwsAmrr9_E2w!2=03Frn*?wd<gjkjypuNdAaqJ-G?1c
zj#PJQh~a4h58>avY0dgsy%p*U6aE;_-TObRk$pk%u;*deMSjZ0#5N6#F~$4Uz4lE)
zXF=14WtSme?`<_aq<C+$kW|vFd$Cq#!K83(D>a&|R7T)svJ#)m^NU`A!ihRtJ~sL6
zE#BUS@0ZG)?*A;!Wp{rAvt`?42XYC7{{V9w@4!MZe*IHBpR~)68}h5zoDN0Tx{CmE
zKJk_D!P&6L>Z@a%-*={#h#c!mI?uu<`MVo*^h#X8U2$r~+3%B%dogY^&o1`@f=jW0
zAXCSRVBw(_U*`?a?4&>MTS(Um;z9r3gy1X~pTV;u&{Mgi(l}>w`PRi-?_;G&aRHFs
z5G`B0kAg``T0c6LZk-b=fwSbPc&+$~RORoQe5i<@GsQ|K2L6VyT(i&e_vgRspV}vo
z*MFu2f1CUNO$q)xhY0@81OWp2|7rIBf3Lp&-CN>c?$H0q{oi92f76-&7Wcn(UdCEi
ImL#D60f1~qpa1{>

literal 0
HcmV?d00001


From 31376f47436015c52a924ec7eca7982088446d22 Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Tue, 11 Feb 2025 04:28:24 -0600
Subject: [PATCH 8/9] Fixed TH2D casting to be TH1D instead

---
 src/LikelihoodScan.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/LikelihoodScan.cpp b/src/LikelihoodScan.cpp
index d38516b..94ef3d5 100644
--- a/src/LikelihoodScan.cpp
+++ b/src/LikelihoodScan.cpp
@@ -45,7 +45,7 @@ int main(int argc, char * argv[]) {
 
     MACH3LOG_INFO("Event rate for {} : {:<5.2f}", Sample->GetName(), Sample->get1DHist()->Integral());
     if (Sample->GetNDim() == 1)
-      Sample->addData((TH2D*)DUNEHists.back());
+      Sample->addData((TH1D*)DUNEHists.back());
     else if (Sample->GetNDim() == 2)
       Sample->addData((TH2D*)DUNEHists.back());
   }

From aea6dfb9405ae9e803a6c22ea314bf34bf7a5a73 Mon Sep 17 00:00:00 2001
From: "camille.sironneau" <sironneau@apc.in2p3.fr>
Date: Wed, 12 Feb 2025 06:35:48 -0600
Subject: [PATCH 9/9] Modifications to yaml structure for Variations app

---
 configs/Variations_Atmospherics.yaml | 74 +++++++++++++++-------------
 src/Variations.cpp                   | 19 +++++--
 2 files changed, 55 insertions(+), 38 deletions(-)

diff --git a/configs/Variations_Atmospherics.yaml b/configs/Variations_Atmospherics.yaml
index cc729de..d954768 100644
--- a/configs/Variations_Atmospherics.yaml
+++ b/configs/Variations_Atmospherics.yaml
@@ -1,7 +1,7 @@
 General:
-  OutputFile: "parameter_study_sterile/test_2d_var/test_var_sterile_all param_thetav1_AllMC_trueE_trueCos.root"
+  OutputFile: "parameter_study_sterile/test_2d_var/test_var_sterile_all_param_thetav1_dm41_1e-3_nue_numu_selec_recoE_recoCos.root"
 
-  DUNESamples: ["configs/Samples/AtmSample_AllMC.yaml"]
+  DUNESamples: ["configs/Samples/AtmSample_nueselec.yaml", "configs/Samples/AtmSample_numuselec.yaml"]
 
   #Nu-FIT
   #OscillationParameters: [0.310, 0.582, 0.224, 7.39E-5, 2.5254E-3, -2.498, 25]
@@ -13,37 +13,6 @@ General:
 
   #T2K-like best-fit
   #OscillationParameters: [0.307, 0.528, 0.0218, 7.53e-5, 2.509e-3, -1.601, 25]
-
-  Variations:
-    - Parameter: 
-        Name: sin2th_14
-        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
-        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
-
-    - Parameter: 
-        Name: sin2th_24
-        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
-        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
-
-    - Parameter: 
-        Name: sin2th_34
-        #OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.]
-        VarValues: [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
-
-    - Parameter:
-        Name: delm2_14
-        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
-        VarValues: [0., 0.00001, 0.0001, 0.001, 0.01, 0.1, 1.]
-
-    - Parameter:
-        Name: delta_14
-        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
-        VarValues: [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265]
-
-    - Parameter:
-        Name: delta_24
-        OscParDefault: [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.]
-        VarValues: [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265]
   
   Systematics:
     XsecCovFile: ["configs/CovObjs/xsec_covariance_DUNE_systs_2022a_FD_v3.yaml"]
@@ -68,6 +37,45 @@ General:
   Seed: 0
   Debug: No
 
+"Variations": [
+    {
+      "Name": "sin2th_14",
+      #"OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.],
+      "VarValues": [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5],
+    },
+
+    {
+      "Name": "sin2th_24",
+      #"OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.],
+      "VarValues": [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5],
+    },
+
+    {
+      "Name": "sin2th_34",
+      #"OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0., 0., 0., 0.001, 0., 0.],
+      "VarValues": [0., 0.001, 0.005, 0.01, 0.05, 0.1, 0.5],
+    },
+
+    {
+      "Name": "delm2_14",
+      "OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.],
+      "VarValues": [0., 0.00001, 0.0001, 0.001, 0.01, 0.1, 1.],
+    },
+
+    {
+      "Name": "delta_14",
+      "OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.],
+      "VarValues": [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265],
+    },
+
+    {
+      "Name": "delta_24",
+      "OscParDefault": [0.303, 0.451, 0.02225, 7.41E-5, 2.45E-3, -2.233, 0.03, 0.06, 0.05, 0.001, 0., 0.],
+      "VarValues": [-2.35619449019, -1.57079632679, -0.78539816339, 0., 0.78539816339, 1.57079632679, 2.35619449019, 3.14159265],
+    }
+
+]
+
 "Projections": [
   {
     "Name": "RecoNuEnergy", 
diff --git a/src/Variations.cpp b/src/Variations.cpp
index 75aac8c..7f2c7be 100644
--- a/src/Variations.cpp
+++ b/src/Variations.cpp
@@ -17,6 +17,15 @@
 #include "samplePDFDUNE/MaCh3DUNEFactory.h"
 #include "samplePDFDUNE/StructsDUNE.h"
 
+//CS YAML "Variations" node expects to be given each parameter to vary with :
+// - "Name": name of the parameter as written in the CovObjs YAML file 
+// - "OscParDefault" array: values that oscillation parameters should be given as a default for this specific parameter variation 
+//    ex : put sterile mixing angles to non zero values to test variations of sterile cp phases
+//    If "OscParDefault" not given, will use the "OscillationParameters" values specified in "General" node 
+// - "VarValues" array: values we want the parameter to take
+
+//TODO: Consider merging with SigmaVariations app at some point
+
 int main(int argc, char * argv[]) {
   if(argc == 1){
     MACH3LOG_ERROR("Usage: bin/EventRatesDUNEBeam config.cfg");
@@ -68,22 +77,22 @@ int main(int argc, char * argv[]) {
     for (int iPar=0;iPar<nPars;iPar++) {
       std::string ParName = CovObj->GetParName(iPar);
 
-      for (auto const &param : FitManager->raw()["General"]["Variations"]) {
+      for (auto const &param : FitManager->raw()["Variations"]) {
 
-        std::string VarName = (param["Parameter"]["Name"].as<std::string>());
+        std::string VarName = (param["Name"].as<std::string>());
 
         if(ParName == VarName) {
 
           MACH3LOG_INFO("\tParameter : {:<30}",ParName);
 
-          if(!param["Parameter"]["OscParDefault"]){ //if specific default values not specified for the parameter then use global default ones
+          if(!param["OscParDefault"]){ //if specific default values not specified for the parameter then use global default ones
             CovObj->setParameters(oscpars);
           }
           else {
-            CovObj->setParameters((param["Parameter"]["OscParDefault"].as<std::vector<double>>()));
+            CovObj->setParameters((param["OscParDefault"].as<std::vector<double>>()));
           }
 
-          std::vector<double> valVariations = (param["Parameter"]["VarValues"].as<std::vector<double>>());
+          std::vector<double> valVariations = (param["VarValues"].as<std::vector<double>>());
 
           File->cd();
           File->mkdir(ParName.c_str());