Adapt relative include paths

Former-commit-id: b4a94e1fcbeb6ad34a01e9a5493e23cb90270cd0

src/algorithms/Alignment.h

@@ -6,12 +6,12 @@
 #include "Math/Functor.h"
 #include "TError.h"
 // Local includes
-#include "Algorithm.h"
-#include "Cluster.h"
-#include "Track.h"
+#include "core/Algorithm.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
 
 class Alignment : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   Alignment(bool);
@@ -21,7 +21,7 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Member variables
   Tracks m_alignmenttracks;
   int nIterations;

src/algorithms/BasicTracking.h

 #ifndef BASICTRACKING_H
 #define BASICTRACKING_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
-#include "Pixel.h"
-#include "Cluster.h"
-#include "Track.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
 
 class BasicTracking : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   BasicTracking(bool);
@@ -21,12 +21,12 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
 //  Cluster* getNearestCluster(Cluster*, map<Cluster*, bool>, Clusters*);
   Cluster* getNearestCluster(long long int, Clusters);
 
   // Member variables
-  
+
   // Histograms
   TH1F* trackChi2;
   TH1F* clustersPerTrack;
@@ -36,13 +36,13 @@ public:
   TH1F* trackAngleY;
   map<string,TH1F*> residualsX;
   map<string,TH1F*> residualsY;
-  
+
   // Cuts for tracking
   double timingCut;
   double spatialCut;
   int minHitsOnTrack;
   double nTracksTotal;
-  
+
 };
 
 #endif // BASICTRACKING_H

src/algorithms/ClicpixAnalysis.h

 #ifndef ClicpixAnalysis_H
 #define ClicpixAnalysis_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include <sstream>
 #include "TH1F.h"
@@ -9,7 +9,7 @@
 #include "TCanvas.h"
 
 class ClicpixAnalysis : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   ClicpixAnalysis(bool);
@@ -28,14 +28,14 @@ public:
   TH2F* hHitPixels;
   TH1F* hColumnHits;
   TH1F* hRowHits;
-  
+
   TH1F* hClusterSizeAll;
   TH1F* hClusterTOTAll;
   TH1F* hClustersPerEvent;
   TH1F* hClustersVersusEventNo;
   TH1F* hClusterWidthRow;
   TH1F* hClusterWidthCol;
-  
+
   // Track histograms
   TH1F* hGlobalTrackDifferenceX;
   TH1F* hGlobalTrackDifferenceY;
@@ -90,8 +90,8 @@ public:
   TH1F* hClusterTOTRatioCol2pix;
   TH2F* hResidualsLocalRow2pixClusterTOT;
   TH2F* hResidualsLocalRow2pixPixelIntercept;
-  
-  
+
+
   // Maps
   TH2F* hTrackIntercepts;
   TH2F* hTrackInterceptsAssociated;
@@ -110,7 +110,7 @@ public:
   TH2F* hInterceptClusterSize2;
   TH2F* hInterceptClusterSize3;
   TH2F* hInterceptClusterSize4;
-  
+
   TH2F* hMapClusterSizeAssociated;
   int m_nBinsX; int m_nBinsY;
   std::map<int, TH1F*> hMapClusterTOTAssociated1pix;
@@ -124,7 +124,7 @@ public:
   double m_proximityCut;
   double m_lostHits;
   bool timepix3Telescope;
-  
+
 };
 
 #endif // ClicpixAnalysis_H

src/algorithms/DUTAnalysis.h

 #ifndef DUTAnalysis_H
 #define DUTAnalysis_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
 
 class DUTAnalysis : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   DUTAnalysis(bool);
@@ -18,7 +18,7 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Histograms
   TH1F* tracksVersusTime;
   TH1F* associatedTracksVersusTime;
@@ -36,7 +36,7 @@ public:
 
   TH1F* tracksVersusPowerOnTime;
   TH1F* associatedTracksVersusPowerOnTime;
-  
+
   // Member variables
   int m_eventNumber;
   int m_nAlignmentClusters;

src/algorithms/DataDump.h

 #ifndef DataDump_H
 #define DataDump_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
-#include "Pixel.h"
-#include "Cluster.h"
-#include "Track.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
 #include <dirent.h>
 #include <sstream>
 #include <fstream>
 #include <stdint.h>
 
 class DataDump : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   DataDump(bool);
@@ -29,7 +29,7 @@ public:
   // Member variables
   int m_eventNumber;
   string m_detector;
-  
+
 };
 
 #endif // DataDump_H

src/algorithms/EventDisplay.h

 #ifndef EVENTDISPLAY_H
 #define EVENTDISPLAY_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TH3F.h"
 #include "TCanvas.h"
-#include "Timepix3Pixel.h"
-#include "Timepix3Cluster.h"
-#include "Timepix3Track.h"
+#include "objects/Timepix3Pixel.h"
+#include "objects/Timepix3Cluster.h"
+#include "objects/Timepix3Track.h"
 
 class EventDisplay : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   EventDisplay(bool);
@@ -22,9 +22,9 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   TH3F* eventMap;
-  
+
 };
 
 #endif // EVENTDISPLAY_H

src/algorithms/FileReader.h

 #ifndef FileReader_H
 #define FileReader_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TTree.h"
 #include "TFile.h"
 
 class FileReader : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   FileReader(bool);
@@ -17,7 +17,7 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Member variables
   int m_eventNumber;
   string m_fileName;
@@ -28,23 +28,23 @@ public:
   bool m_readPixels;
   bool m_readTracks;
   bool m_onlyDUT;
-  
+
   // Map of trees which holds the output objects
   map<string, TTree*> m_inputTrees;
-  
+
   // Objects which the trees will point to (when
   // the branch address is set
   long long int m_time;
   map<string, TestBeamObject*> m_objects;
-  
+
   // List of objects to write out
   vector<string> m_objectList;
-  
+
   // Variables to keep track of time and file reading
   long long int m_currentTime;
   map<string, long long int> m_currentPosition;
   double m_timeWindow;
-  
+
 };
 
 #endif // FileReader_H

src/algorithms/FileWriter.h

 #ifndef FileWriter_H
 #define FileWriter_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TTree.h"
 #include "TFile.h"
 
 class FileWriter : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   FileWriter(bool);
@@ -17,29 +17,29 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Member variables
   int m_eventNumber;
   string m_fileName;
   TFile* m_outputFile;
-  
+
   // Flags for which data types to write out
   bool m_writeClusters;
   bool m_writePixels;
   bool m_writeTracks;
   bool m_onlyDUT;
-  
+
   // Map of trees which holds the output objects
   map<string, TTree*> m_outputTrees;
-  
+
   // Objects which the trees will point to (when
   // the branch address is set
   long long int m_time;
   map<string, TestBeamObject*> m_objects;
-  
+
   // List of objects to write out
   vector<string> m_objectList;
-  
+
 };
 
 #endif // FileWriter_H

src/algorithms/GUI.h

 #ifndef GUI_H
 #define GUI_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
@@ -11,12 +11,12 @@
 #include "TThread.h"
 #include "TApplication.h"
 
-#include "Pixel.h"
-#include "Cluster.h"
-#include "Track.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
 
 class GUI : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   GUI(bool);
@@ -26,24 +26,24 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Plot holders
   vector<TCanvas*> canvases;
   map<TCanvas*,vector<TH1*> > histograms;
   map<TH1*,string> styles;
-  
+
   // Add plots and canvases
   void addPlot(TCanvas*, string, string style = "");
   void addCanvas(TCanvas*);
-  
+
   // Application to allow display of canvases
   TApplication* app;
-  
+
   // Misc. member objects
   int nDetectors;
   int eventNumber;
   int updateNumber;
-  
+
 };
 
 #endif // GUI_H

src/algorithms/OnlineMonitor.h

 #ifndef OnlineMonitor_H
 #define OnlineMonitor_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
-#include "Pixel.h"
-#include "Cluster.h"
-#include "Track.h"
-#include "GuiDisplay.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
+#include "objects/GuiDisplay.h"
 
 // ROOT includes
 #include "TH1F.h"
@@ -24,7 +24,7 @@
 #include "TRootEmbeddedCanvas.h"
 
 class OnlineMonitor : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   OnlineMonitor(bool);
@@ -34,18 +34,18 @@ public:
   void initialise(Parameters*);
   StatusCode run(Clipboard*);
   void finalise();
-  
+
   // Application to allow display persistancy
   TApplication* app;
   GuiDisplay* gui;
-  
+
   void AddHisto(string, string, string style="");
   void AddButton(string, string);
-  
+
   // Member variables
   int eventNumber;
   int updateNumber;
-  
+
 };
 
 #endif // OnlineMonitor_H

src/algorithms/SpatialTracking.h

@@ -10,12 +10,12 @@
 #include "Minuit2/Minuit2Minimizer.h"
 #include "Math/Functor.h"
 // Local includes
-#include "Algorithm.h"
-#include "Cluster.h"
-#include "Track.h"
+#include "core/Algorithm.h"
+#include "objects/Cluster.h"
+#include "objects/Track.h"
 
 class SpatialTracking : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   SpatialTracking(bool);
@@ -35,13 +35,13 @@ public:
   TH1F* trackAngleY;
   map<string,TH1F*> residualsX;
   map<string,TH1F*> residualsY;
-  
+
   // Member variables
   int m_eventNumber;
   double spatialCut;
   int minHitsOnTrack;
   double nTracksTotal;
-  
+
 };
 
 #endif // SpatialTracking_H

src/algorithms/TestAlgorithm.h

 #ifndef TESTALGORITHM_H
 #define TESTALGORITHM_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
-#include "Pixel.h"
-#include "Cluster.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
 
 class TestAlgorithm : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   TestAlgorithm(bool);
@@ -24,12 +24,12 @@ public:
   // Pixel histograms
   map<string, TH2F*> hitmap;
   map<string, TH1F*> eventTimes;
-  
+
   // Cluster histograms
   map<string, TH1F*> clusterSize;
   map<string, TH1F*> clusterTot;
   map<string, TH2F*> clusterPositionGlobal;
-  
+
   // Correlation plots
   map<string, TH1F*> correlationX;
   map<string, TH1F*> correlationY;

src/algorithms/Timepix1Clustering.h

 #ifndef Timepix1Clustering_H
 #define Timepix1Clustering_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
-#include "Cluster.h"
+#include "objects/Cluster.h"
 
 class Timepix1Clustering : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   Timepix1Clustering(bool);
@@ -24,7 +24,7 @@ public:
 
   // Member variables
   int m_eventNumber;
-  
+
 };
 
 #endif // Timepix1Clustering_H

src/algorithms/Timepix1Correlator.h

 #ifndef Timepix1Correlator_H
 #define Timepix1Correlator_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
 
 class Timepix1Correlator : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   Timepix1Correlator(bool);
@@ -26,10 +26,10 @@ public:
   map<string, TH1F*> clustersPerEvent;
   map<string, TH1F*> correlationPlotsX;
   map<string, TH1F*> correlationPlotsY;
-  
+
   // Member variables
   int m_eventNumber;
-  
+
 };
 
 #endif // Timepix1Correlator_H

src/algorithms/Timepix1EventLoader.h

 #ifndef Timepix1EventLoader_H
 #define Timepix1EventLoader_H 1
 
-#include "Algorithm.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
@@ -11,7 +11,7 @@
 #include <string>
 
 class Timepix1EventLoader : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   Timepix1EventLoader(bool);
@@ -23,7 +23,7 @@ public:
   void finalise();
 
   void processHeader(string,string&,long long int&);
-  
+
   // Member variables
   int m_eventNumber;
   string m_inputDirectory;

src/algorithms/Timepix3Clustering.h

 #ifndef TIMEPIX3CLUSTERING_H
 #define TIMEPIX3CLUSTERING_H 1
 
-#include "Pixel.h"
-#include "Cluster.h"
-#include "Algorithm.h"
+#include "objects/Pixel.h"
+#include "objects/Cluster.h"
+#include "core/Algorithm.h"
 #include <iostream>
 #include "TH1F.h"
 #include "TH2F.h"
 #include "TCanvas.h"
 
 class Timepix3Clustering : public Algorithm {
-  
+
 public:
   // Constructors and destructors
   Timepix3Clustering(bool);
@@ -23,7 +23,7 @@ public:
   void calculateClusterCentre(Cluster*);
   bool touching(Pixel*,Cluster*);
   bool closeInTime(Pixel*,Cluster*);
-  
+
   double timingCut;
   long long int timingCutInt;
 

src/algorithms/Timepix3EventLoader.h

 #ifndef TIMEPIX3EVENTLOADER_H
 #define TIMEPIX3EVENTLOADER_H 1
 
-#include "Algorithm.h"
-#include "Pixel.h"