From bb4b71378e8dd6be9aa5b2618d836cd8738a3e92 Mon Sep 17 00:00:00 2001
From: Gleb Lukicov <g.lukicov@ucl.ac.uk>
Date: Sun, 20 Aug 2017 23:01:46 -0500
Subject: [PATCH] General Lines: Complete

---
 mpIIDESY/AlignTracker.cpp         | 3 +--
 mpIIDESY/AlignTracker_methods.cpp | 4 ++--
 mpIIDESY/AlignTracker_methods.h   | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/mpIIDESY/AlignTracker.cpp b/mpIIDESY/AlignTracker.cpp
index 8be4b00..7c79ec1 100644
--- a/mpIIDESY/AlignTracker.cpp
+++ b/mpIIDESY/AlignTracker.cpp
@@ -235,7 +235,7 @@ int main(int argc, char* argv[]){
     TH1F* h_residual_true = new TH1F("h_residual_true", "Residuals for generated tracks", 500, -0.4, 0.4);
     TH1F* h_chi2_true = new TH1F("h_chi2_true", "Chi2 for generated tracks", 40, -1, 100);
     TH1F* h_residual_recon = new TH1F("h_residual_recon", "Residuals for reconstructed tracks", 500, -0.2, 0.2);
-    TH1F* h_chi2_recon = new TH1F("h_chi2_recon", "Chi2 for Reconstructed Tracks", 379, 0, 400);
+    TH1F* h_chi2_recon = new TH1F("h_chi2_recon", "Chi2 for Reconstructed Tracks", 379, 0, 500);
     TH1I* h_hitCount = new TH1I("h_hitCount", "Total Hit count per track", 32 , 0, 32);
     TH1F* h_reconMinusTrue_track = new TH1F("h_reconMinusTrue_line", "Reconstructed - True X position of the lines",  149,  -0.1, 0.1);
     TH1F* h_reconMinusTrue_hits = new TH1F("h_reconMinusTrue_hits", "Reconstructed - True X position of the hits",  169,  -0.1, 0.2);
@@ -683,7 +683,6 @@ int main(int argc, char* argv[]){
     rp1->Draw("noconfint");
     cChi2->Update();
     rp1->GetLowerRefYaxis()->SetTitle("Frac. Error");
-    rp1->GetUpperRefYaxis()->SetTitle("Entries");
     cChi2->Print("FoM_Chi2_recon.C");
     cChi2->Print("FoM_Chi2_recon.png");
     cChi2->Write();
diff --git a/mpIIDESY/AlignTracker_methods.cpp b/mpIIDESY/AlignTracker_methods.cpp
index b81678e..9b8ce01 100644
--- a/mpIIDESY/AlignTracker_methods.cpp
+++ b/mpIIDESY/AlignTracker_methods.cpp
@@ -518,7 +518,7 @@ void Tracker::setGeometry(ofstream& debug_geom,  bool debugBool){
                     cout << mod_lyr_strawIdealPosition[i_module][i_view][i_layer][i_straw]<<" ";
                     debug_geom << mod_lyr_strawIdealPosition[i_module][i_view][i_layer][i_straw] << " ";
                     } // straws 
-                    cout << "  | Z= " << distance[Zcounter] << " [cm]" << endl;  // XXX fix this 
+                    cout << "  | Z= " << distance[Zcounter] << " [cm]" << endl;  // TODO align the cout better 
                     debug_geom << distance[Zcounter] << endl;
                     Zcounter++;
                 } // end of Layers
@@ -672,7 +672,7 @@ void Tracker::misalign(ofstream& debug_mis, ofstream& pede_mis, bool debugBool){
     } // modules
    
    // The Chi2 estimation requires misalignment parameters per layer
-   Chi2_recon_estimated=N-2;  // 2 parameter fit
+   Chi2_recon_estimated=N-2.0;  // 2 parameter fit
    i_totalLayers=0;
     for (int i_module=0; i_module<moduleN; i_module++){
         for (int i_view=0; i_view<viewN; i_view++){
diff --git a/mpIIDESY/AlignTracker_methods.h b/mpIIDESY/AlignTracker_methods.h
index b7addf2..75e491b 100644
--- a/mpIIDESY/AlignTracker_methods.h
+++ b/mpIIDESY/AlignTracker_methods.h
@@ -94,7 +94,7 @@ class Tracker {
 	//initialising physics variables
  	// MF + inhomogeneity, E_loss, MS
 
-    float dispX[8] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0}; // manual misalignment [relative misalignment per module]
+    float dispX[8] = {-0.03, 0.1, 0.0, 0.05, 0.0, 0.02, 0.0}; // manual misalignment [relative misalignment per module]
     
     static constexpr float resolution=0.015;  // 150um = 0.015 cm for hit smearing