First commit of new testbeam software

branches/trunk/Makefile

+BINDIR = bin/
+SRCDIR = src/
+INCLUDE_PATH =	-I core \
+		-I algorithms \
+		-I objs
+
+# Compiler
+CC = g++
+
+# Compiler flags
+ROOTCFLAGS   := $(shell root-config --cflags)
+ROOTLIBS     := $(shell root-config --glibs)
+CFLAGS = -fPIC -w -g -W ${ROOTCFLAGS}
+LFLAGS = -O3 ${ROOTLIBS} -g -lGenVector -lMinuit
+
+# Automatically decide what to compile
+CORE = $(notdir $(wildcard core/*.C))
+OBJS = $(CORE:.C=.o)
+OBJS := $(addprefix ${BINDIR}, ${OBJS})
+
+EXE = ${BINDIR}tbAnalysis
+
+ALGORITHMS = $(notdir $(wildcard algorithms/*.C))
+ALGOBJS = $(ALGORITHMS:.C=.ao)
+ALGOBJS := $(addprefix ${BINDIR}, ${ALGOBJS})
+
+DATAOBJS = $(wildcard ${PWD}/objs/*.h) 
+
+# Compile core, user algorithms and make an executable for each user algorithm
+all :				${OBJS} ${ALGOBJS} ${EXE}
+				@echo "Done"
+
+# Compile core algorithms (everything .C)
+${BINDIR}%.o :			core/%.C core/%.h
+				@echo "Compiling $(notdir $<)"
+				@$(CC) $(CFLAGS) ${INCLUDE_PATH} -c $< -o $@
+
+${BINDIR}%.ao :			algorithms/%.C algorithms/%.h
+				@echo "Compiling $(notdir $<)"
+				@$(CC) $(CFLAGS) ${INCLUDE_PATH} -c $< -o $@
+
+${BINDIR}Steering.o :		core/Steering.C
+				@echo "Compiling steering file"
+				@$(CC) $(CFLAGS) ${INCLUDE_PATH} -c core/Steering.C -o ${BINDIR}Steering.o
+
+${BINDIR}EventDict.o :		${DATAOBJS}
+				@echo "Making event dictionary"
+				@rm -f core/EventDict.C core/EventDict.h
+				@rootcint core/EventDict.C -c ${DATAOBJS} 
+				@$(CC) $(CFLAGS) ${INCLUDE_PATH} -c core/EventDict.C -o ${BINDIR}EventDict.o
+
+${EXE} :			${OBJS} ${ALGOBJS} ${BINDIR}EventDict.o
+				@echo "Making executable tbAnalysis"
+				@$(CC) -o ${BINDIR}tbAnalysis $(OBJS) ${ALGOBJS} $(LFLAGS) 
+
+# Remove all executables and object files
+clean:
+				@rm -f ${BINDIR}*
+				@echo "Cleaned"
+
+

branches/trunk/algorithms/Alignment.C

+#include "Alignment.h"
+
+#include <TVirtualFitter.h>
+
+Alignment::Alignment(bool debugging)
+: Algorithm("Alignment"){
+  debug = debugging;
+}
+
+// Global container declarations
+Timepix3Tracks globalTracks;
+string detectorToAlign;
+Parameters* globalParameters;
+int detNum;
+
+void Alignment::initialise(Parameters* par){
+ 
+  parameters = par;
+  
+}
+
+int Alignment::run(Clipboard* clipboard){
+ 
+  // Get the tracks
+  Timepix3Tracks* tracks = (Timepix3Tracks*)clipboard->get("Timepix3","tracks");
+  if(tracks == NULL){
+    return 1;
+  }
+  
+  // Make a local copy and store it 
+  for(int iTrack=0; iTrack<tracks->size(); iTrack++){
+    Timepix3Track* track = (*tracks)[iTrack];
+    Timepix3Track* alignmentTrack = new Timepix3Track(track);
+    m_alignmenttracks.push_back(alignmentTrack);
+  }
+  
+  return 1;
+
+}
+
+void Alignment::finalise(){
+  
+  // Make the fitting object
+  TVirtualFitter* residualFitter = TVirtualFitter::Fitter(0,50);
+  
+  // Tell it what to minimise
+  residualFitter->SetFCN(SumDistance2);
+  
+  // Set the global parameters
+  globalTracks = m_alignmenttracks;
+  globalParameters = parameters;
+
+  // Set the printout arguments of the fitter
+  Double_t arglist[10];
+  arglist[0] = 3;
+  residualFitter->ExecuteCommand("SET PRINT",arglist,1);
+  
+  // Set some fitter parameters
+  arglist[0] = 1000; // number of function calls
+  arglist[1] = 0.001; // tolerance
+  
+  // Loop over all planes. For each plane, set the plane alignment parameters which will be varied, and
+  // then minimise the track chi2 (sum of biased residuals). This means that tracks are refitted with
+  // each minimisation step.
+  
+  int det = 0;
+  for(int ndet = 0; ndet<parameters->nDetectors; ndet++){
+    // Check if they are a Timepix3
+    string detectorID = parameters->detectors[ndet];
+    if(parameters->detector[detectorID]->type() != "Timepix3") continue;
+    // Do not align the reference plane
+    if(detectorID == parameters->reference) continue;
+    if(detectorID == "W0013_F09") continue;
+    if(detectorID == "W0013_G02") continue;
+    // Say that this is the detector we align
+    detectorToAlign = detectorID;
+    detNum=det;
+    // Add the parameters to the fitter (z displacement not allowed to move!)
+    residualFitter->SetParameter(det*6+0,(detectorID+"_displacementX").c_str(),parameters->detector[detectorID]->displacementX(),0.01,-50,50);
+    residualFitter->SetParameter(det*6+1,(detectorID+"_displacementY").c_str(),parameters->detector[detectorID]->displacementY(),0.01,-50,50);
+    residualFitter->SetParameter(det*6+2,(detectorID+"_displacementZ").c_str(),parameters->detector[detectorID]->displacementZ(),0,-10,500);
+    residualFitter->SetParameter(det*6+3,(detectorID+"_rotationX").c_str(),parameters->detector[detectorID]->rotationX(),0.01,-6.30,6.30);
+    residualFitter->SetParameter(det*6+4,(detectorID+"_rotationY").c_str(),parameters->detector[detectorID]->rotationY(),0.01,-6.30,6.30);
+    residualFitter->SetParameter(det*6+5,(detectorID+"_rotationZ").c_str(),parameters->detector[detectorID]->rotationZ(),0.01,-6.30,6.30);
+    
+    // Fit this plane (minimising global track chi2)
+		residualFitter->ExecuteCommand("MIGRAD",arglist,2);
+    
+    // Now that this device is fitted, set parameter errors to 0 so that they are not fitted again
+    residualFitter->SetParameter(det*6+0,(detectorID+"_displacementX").c_str(),residualFitter->GetParameter(det*6+0),0,-50,50);
+    residualFitter->SetParameter(det*6+1,(detectorID+"_displacementY").c_str(),residualFitter->GetParameter(det*6+1),0,-50,50);
+    residualFitter->SetParameter(det*6+2,(detectorID+"_displacementZ").c_str(),residualFitter->GetParameter(det*6+2),0,-10,500);
+    residualFitter->SetParameter(det*6+3,(detectorID+"_rotationX").c_str(),residualFitter->GetParameter(det*6+3),0,-6.30,6.30);
+    residualFitter->SetParameter(det*6+4,(detectorID+"_rotationY").c_str(),residualFitter->GetParameter(det*6+4),0,-6.30,6.30);
+    residualFitter->SetParameter(det*6+5,(detectorID+"_rotationZ").c_str(),residualFitter->GetParameter(det*6+5),0,-6.30,6.30);
+    // Set the alignment parameters of this plane to be the optimised values from the alignment
+    parameters->detector[detectorID]->displacementX(residualFitter->GetParameter(det*6+0));
+    parameters->detector[detectorID]->displacementY(residualFitter->GetParameter(det*6+1));
+    parameters->detector[detectorID]->displacementZ(residualFitter->GetParameter(det*6+2));
+    parameters->detector[detectorID]->rotationX(residualFitter->GetParameter(det*6+3));
+    parameters->detector[detectorID]->rotationY(residualFitter->GetParameter(det*6+4));
+    parameters->detector[detectorID]->rotationZ(residualFitter->GetParameter(det*6+5));
+    parameters->detector[detectorID]->update();
+    det++;
+  }
+  
+  det = 0;
+  // Now list the new alignment parameters
+  for(int ndet = 0; ndet<parameters->nDetectors; ndet++){
+    // Check if they are a Timepix3
+    string detectorID = parameters->detectors[ndet];
+    if(parameters->detector[detectorID]->type() != "Timepix3") continue;
+    // Do not align the reference plane
+    if(detectorID == parameters->reference) continue;
+    if(detectorID == "W0013_F09") continue;
+    if(detectorID == "W0013_G02") continue;
+    
+    // Get the alignment parameters
+    double displacementX = residualFitter->GetParameter(det*6+0);
+    double displacementY = residualFitter->GetParameter(det*6+1);
+    double displacementZ = residualFitter->GetParameter(det*6+2);
+    double rotationX = residualFitter->GetParameter(det*6+3);
+    double rotationY = residualFitter->GetParameter(det*6+4);
+    double rotationZ = residualFitter->GetParameter(det*6+5);
+
+    tcout<<" Detector "<<detectorID<<" new alignment parameters: T("<<displacementX<<","<<displacementY<<","<<displacementZ<<") R("<<rotationX<<","<<rotationY<<","<<rotationZ<<")"<<endl;
+    
+    det++;
+  }
+  
+  // Write the output alignment file
+  parameters->writeConditions();
+}
+
+void SumDistance2(Int_t &npar, Double_t *grad, Double_t &result, Double_t *par, Int_t flag) {
+  
+//  cout<<"Parameter size "<<par.size()<<endl;
+  // Pick up new alignment conditions
+  globalParameters->detector[detectorToAlign]->displacementX(par[detNum*6 + 0]);
+  globalParameters->detector[detectorToAlign]->displacementY(par[detNum*6 + 1]);
+  globalParameters->detector[detectorToAlign]->displacementZ(par[detNum*6 + 2]);
+  globalParameters->detector[detectorToAlign]->rotationX(par[detNum*6 + 3]);
+  globalParameters->detector[detectorToAlign]->rotationY(par[detNum*6 + 4]);
+  globalParameters->detector[detectorToAlign]->rotationZ(par[detNum*6 + 5]);
+  // Apply new alignment conditions
+  globalParameters->detector[detectorToAlign]->update();
+
+//  cout<<"displacement x "<<par[detNum*6 + 0]<<endl;
+//  cout<<"displacement y "<<par[detNum*6 + 1]<<endl;
+//  cout<<"displacement z "<<par[detNum*6 + 2]<<endl;
+//  cout<<"rotation x "<<par[detNum*6 + 3]<<endl;
+//  cout<<"rotation y "<<par[detNum*6 + 4]<<endl;
+//  cout<<"rotation z "<<par[detNum*6 + 5]<<endl;
+//  cout<<"Updated alignmnet parameters for detector "<<detectorToAlign<<endl;
+  
+  // The chi2 value to be returned
+  result = 0.;
+
+  // Loop over all tracks
+  for(int iTrack=0; iTrack<globalTracks.size(); iTrack++){
+		// Get the track
+    Timepix3Track* track = globalTracks[iTrack];
+    // Get all clusters on the track
+    Timepix3Clusters trackClusters = track->clusters();
+    // Find the cluster that needs to have its position recalculated
+    for(int iTrackCluster=0; iTrackCluster<trackClusters.size(); iTrackCluster++){
+      Timepix3Cluster* trackCluster = trackClusters[iTrackCluster];
+      string detectorID = trackCluster->detectorID();
+      // Recalculate the global position from the local
+      PositionVector3D<Cartesian3D<double> > positionLocal(trackCluster->localX(),trackCluster->localY(),trackCluster->localZ());
+      PositionVector3D<Cartesian3D<double> > positionGlobal = *(globalParameters->detector[detectorID]->m_localToGlobal) * positionLocal;
+      trackCluster->setClusterCentre(positionGlobal.X(), positionGlobal.Y(),positionGlobal.Z());
+    }
+    // Refit the track
+    track->fit();
+    // Add the new chi2
+    result += track->chi2();
+  }
+//  cout<<"Chi2: "<<result<<endl;
+}
+

branches/trunk/algorithms/Alignment.h

+#ifndef ALIGNMENT_H
+#define ALIGNMENT_H 1
+
+#include "Algorithm.h"
+#include "Timepix3Cluster.h"
+#include "Timepix3Track.h"
+
+// Fitting function for minuit
+void SumDistance2(Int_t &, Double_t *, Double_t &, Double_t *, Int_t );
+
+class Alignment : public Algorithm {
+  
+public:
+  // Constructors and destructors
+  Alignment(bool);
+  ~Alignment(){}
+
+  // Functions
+  void initialise(Parameters*);
+  int run(Clipboard*);
+  void finalise();
+  
+  // Member variables
+  Timepix3Tracks m_alignmenttracks;
+  int nIterations;
+
+};
+
+#endif // ALIGNMENT_H

branches/trunk/algorithms/BasicTracking.C

+#include "BasicTracking.h"
+
+BasicTracking::BasicTracking(bool debugging)
+: Algorithm("BasicTracking"){
+  debug = debugging;
+}
+
+
+void BasicTracking::initialise(Parameters* par){
+ 
+  parameters = par;
+  
+  // Set up histograms
+  trackChi2 = new TH1F("trackChi2","trackChi2",150,0,150);
+  
+  // Loop over all Timepix3
+  for(int det = 0; det<parameters->nDetectors; det++){
+    // Check if they are a Timepix3
+    string detectorID = parameters->detectors[det];
+    if(parameters->detector[detectorID]->type() != "Timepix3") continue;
+    string name = "residualsX_"+detectorID;
+    residualsX[detectorID] = new TH1F(name.c_str(),name.c_str(),400,-0.2,0.2);
+    name = "residualsY_"+detectorID;
+    residualsY[detectorID] = new TH1F(name.c_str(),name.c_str(),400,-0.2,0.2);
+  }
+
+}
+
+int BasicTracking::run(Clipboard* clipboard){
+  
+  // Container for all clusters
+  map<string,Timepix3Clusters*> clusters;
+  vector<string> detectors;
+  
+  // Track container
+  Timepix3Tracks* tracks = new Timepix3Tracks();
+
+  // Loop over all Timepix3 and get clusters
+  for(int det = 0; det<parameters->nDetectors; det++){
+    
+    // Check if they are a Timepix3
+    string detectorID = parameters->detectors[det];
+    if(parameters->detector[detectorID]->type() != "Timepix3") continue;
+		
+		// Get the clusters
+    Timepix3Clusters* tempClusters = (Timepix3Clusters*)clipboard->get(detectorID,"clusters");
+    if(tempClusters == NULL){
+      tcout<<"Detector "<<detectorID<<" does not have any clusters on the clipboard"<<endl;
+    }
+    
+    // Store them
+    clusters[detectorID] = tempClusters;
+    detectors.push_back(detectorID);
+    
+  }
+  
+  // Use the first plane as a seeding plane. For something quick, look a cluster in < 100 ns in the next plane, and continue
+  string reference = parameters->reference;
+  map<Timepix3Cluster*, bool> used;
+
+  // Loop over all clusters
+  for(int iSeedCluster=0;iSeedCluster<clusters[reference]->size();iSeedCluster++){
+
+    // Make a new track
+    Timepix3Track* track = new Timepix3Track();
+    // Get the cluster
+    Timepix3Cluster* cluster = (*clusters[reference])[iSeedCluster];
+    // Add the cluster to the track
+    track->addCluster(cluster);
+    used[cluster] = true;
+		// Get the cluster time
+    long long int timestamp = cluster->timestamp();
+    
+    // Loop over each subsequent plane and look for a cluster within 100 ns
+    for(int det=0; det<detectors.size(); det++){
+      if(detectors[det] == reference) continue;
+      Timepix3Cluster* newCluster = getNearestCluster(timestamp, (*clusters[detectors[det]]) );
+      if( ((newCluster->timestamp() - timestamp) / (4096.*40000000.)) > (10./1000000000.) ) continue;
+      // Check if spatially more than 200 um
+      if( abs(cluster->globalX() - newCluster->globalX()) > 0.3 || abs(cluster->globalY() - newCluster->globalY()) > 0.3 ) continue;
+      track->addCluster(newCluster);
+    }
+   
+    // Now should have a track with one cluster from each plane
+    if(track->nClusters() < 5) continue;
+    
+    // Fit the track and save it
+    track->fit();
+    tracks->push_back(track);
+    
+    // Fill histograms
+    trackChi2->Fill(track->chi2());
+    
+    // Make residuals
+    Timepix3Clusters trackClusters = track->clusters();
+    for(int iTrackCluster=0; iTrackCluster<trackClusters.size(); iTrackCluster++){
+      Timepix3Cluster* trackCluster = trackClusters[iTrackCluster];
+      string detectorID = trackCluster->detectorID();
+      ROOT::Math::XYZPoint intercept = track->intercept(trackCluster->globalZ());
+      residualsX[detectorID]->Fill(intercept.X() - trackCluster->globalX());
+      residualsY[detectorID]->Fill(intercept.Y() - trackCluster->globalY());
+    }
+    
+  }
+  
+  tcout<<"Made "<<tracks->size()<<" tracks"<<endl;
+  clipboard->put("Timepix3","tracks",(TestBeamObjects*)tracks);
+
+  return 1;
+}
+  
+Timepix3Cluster* BasicTracking::getNearestCluster(long long int timestamp, Timepix3Clusters clusters){
+  
+  Timepix3Cluster* bestCluster = NULL;
+  // Loop over all clusters and return the one with the closest timestamp
+  for(int iCluster=0;iCluster<clusters.size();iCluster++){
+    Timepix3Cluster* cluster = clusters[iCluster];
+    if(bestCluster == NULL) bestCluster = cluster;
+    if(abs(cluster->timestamp() - timestamp) < abs(bestCluster->timestamp()-timestamp)) bestCluster = cluster;
+  }
+
+  return bestCluster;
+}
+
+void BasicTracking::finalise(){
+  
+  
+}

branches/trunk/algorithms/BasicTracking.h

+#ifndef BASICTRACKING_H
+#define BASICTRACKING_H 1
+
+#include "Algorithm.h"
+#include <iostream>
+#include "TH1F.h"
+#include "TH2F.h"
+#include "TCanvas.h"
+#include "Timepix3Pixel.h"
+#include "Timepix3Cluster.h"
+#include "Timepix3Track.h"
+
+class BasicTracking : public Algorithm {
+  
+public:
+  // Constructors and destructors
+  BasicTracking(bool);
+  ~BasicTracking(){}
+
+  // Functions
+  void initialise(Parameters*);
+  int run(Clipboard*);
+  void finalise();
+  
+  Timepix3Cluster* getNearestCluster(long long int, Timepix3Clusters);
+
+  // Member variables
+  TH1F* trackChi2;
+  map<string,TH1F*> residualsX;
+  map<string,TH1F*> residualsY;
+  
+};
+
+#endif // BASICTRACKING_H

branches/trunk/algorithms/EventDisplay.C

+#include "EventDisplay.h"
+#include "TApplication.h"
+#include "TPolyLine3D.h"
+
+EventDisplay::EventDisplay(bool debugging)
+: Algorithm("EventDisplay"){
+  debug = debugging;
+}
+
+
+void EventDisplay::initialise(Parameters* par){
+ 
+  parameters = par;
+  
+  // Set up histograms
+  eventMap = new TH3F("eventMap","eventMap",100,-5,5,100,-5,5,105,-10,200);
+  
+
+}
+
+int EventDisplay::run(Clipboard* clipboard){
+  
+
+  // Get the tracks
+  Timepix3Tracks* tracks = (Timepix3Tracks*)clipboard->get("Timepix3","tracks");
+  if(tracks == NULL){
+    return 1;
+  }
+  
+  TApplication* rootapp = new TApplication("example",0, 0);
+  TCanvas* canv = new TCanvas();
+  eventMap->DrawCopy("");
+
+  // Loop over all tracks. Add the cluster points to the histogram and draw a line for the tracks
+  for(int iTrack=0; iTrack<tracks->size(); iTrack++){
+    
+    // Get the track
+    Timepix3Track* track = (*tracks)[iTrack];
+    
+    // Get all clusters on the track
+    Timepix3Clusters trackClusters = track->clusters();
+    
+    // Fill the event map
+    for(int iTrackCluster=0; iTrackCluster<trackClusters.size(); iTrackCluster++){
+      Timepix3Cluster* trackCluster = trackClusters[iTrackCluster];
+      eventMap->Fill(trackCluster->globalX(), trackCluster->globalY(), trackCluster->globalZ());
+    }
+    
+    ROOT::Math::XYZPoint linestart = track->intercept(0);
+    ROOT::Math::XYZPoint linestop = track->intercept(200);
+    
+    TPolyLine3D *line = new TPolyLine3D(2);
+    line->SetPoint(0,linestart.X(),linestart.Y(),linestart.Z());
+    line->SetPoint(1,linestop.X(),linestop.Y(),linestop.Z());
+    line->SetLineColor(2);
+    line->Draw("same");
+
+  }
+  
+    eventMap->DrawCopy("same,box");
+		canv->Update();
+    rootapp->Run();
+    return 1;
+}
+  
+
+void EventDisplay::finalise(){
+  
+  
+}

branches/trunk/algorithms/EventDisplay.h

+#ifndef EVENTDISPLAY_H
+#define EVENTDISPLAY_H 1
+
+#include "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"
+
+class EventDisplay : public Algorithm {
+  
+public:
+  // Constructors and destructors
+  EventDisplay(bool);
+  ~EventDisplay(){}
+
+  // Functions
+  void initialise(Parameters*);
+  int run(Clipboard*);
+  void finalise();
+  
+  TH3F* eventMap;
+  
+};
+
+#endif // EVENTDISPLAY_H

branches/trunk/algorithms/EventLoader.C

+#include "EventLoader.h"
+#include "Pixel.h"
+
+#include <dirent.h>
+#include <sstream>
+#include <string>
+
+EventLoader::EventLoader(bool debugging)
+: Algorithm("EventLoader"){
+  
+  debug = debugging;
+  m_inputDirectory = "testDir";
+  m_nFiles = 0;
+  m_fileNumber = 0;
+  
+}
+
+
+void EventLoader::initialise(Parameters* par){
+ 
+  parameters = par;
+  // Open the input directory and store all filenames
+  DIR* directory = opendir(m_inputDirectory.c_str());
+  dirent* file;
+  while (file = readdir(directory)){
+    if (string(file->d_name).find(".txt") != string::npos){
+      m_files.push_back(m_inputDirectory + "/" + (string)file->d_name);
+      m_nFiles++;
+    }
+  }
+  
+  
+  
+  
+}
+
+int EventLoader::run(Clipboard* clipboard){
+
+  cout<<"\rLooping over files: "<<m_fileNumber<<"/"<<m_nFiles<<flush;
+  // If there are no more files to open, finish the event loop
+  if(!m_currentFile.is_open() && (m_fileNumber == m_nFiles)){
+    cout<<endl;
+    return 0;
+  }
+  
+  // If no files are open, look at the next input file
+  if(!m_currentFile.is_open()){
+    m_currentFile.open(m_files[m_fileNumber]);
+    m_fileNumber++;
+  }
+