Move C++ source to src directory

3 files changed, 0 insertions, 426 deletions

diff --git a/chroma/fileio/root.C b/chroma/fileio/root.C
deleted file mode 100644
index 2b39b1b..0000000
--- a/chroma/fileio/root.C
+++ /dev/null
@@ -1,147 +0,0 @@
-#include <TVector3.h>
-#include <vector>
-#include <TTree.h>
-#include <string>
-
-struct Vertex {
-  std::string particle_name;
-  TVector3 pos;
-  TVector3 dir;
-  TVector3 pol;
-  double ke;
-  double t0;
-
-  ClassDef(Vertex, 1);
-};
-
-struct Photon {
-  double t;
-  TVector3 pos;
-  TVector3 dir;
-  TVector3 pol;
-  double wavelength; // nm
-  unsigned int flag;
-  int last_hit_triangle;
-
-  ClassDef(Photon, 1);
-};
-
-struct Channel {
-  Channel() : id(-1), t(-1e9), q(-1e9) { };
-  int id;
-  double t;
-  double q;
-  unsigned int flag;
-
-  ClassDef(Channel, 1);
-};
-
-struct Event {
-  int id;
-  unsigned int nhit;
-  unsigned int nchannels;
-
-  Vertex primary_vertex;
-
-  std::vector<Vertex> vertices;
-  std::vector<Photon> photons_beg;
-  std::vector<Photon> photons_end;
-  std::vector<Channel> channels;
-
-  ClassDef(Event, 1);
-};
-
-void fill_channels(Event *ev, unsigned int nhit, unsigned int *ids, float *t,
-		   float *q, unsigned int *flags, unsigned int nchannels)
-{
-  ev->nhit = 0;
-  ev->nchannels = nchannels;
-  ev->channels.resize(0);
-
-  Channel ch;
-  unsigned int id;
-  for (unsigned int i=0; i < nhit; i++) {
-      ev->nhit++;
-      id = ids[i];
-      ch.id = id;
-      ch.t = t[id];
-      ch.q = q[id];
-      ch.flag = flags[id];
-      ev->channels.push_back(ch);
-  }
-}
-
-void get_channels(Event *ev, int *hit, float *t, float *q, unsigned int *flags)
-{
-  for (unsigned int i=0; i < ev->nchannels; i++) {
-    hit[i] = 0;
-    t[i] = -1e9f;
-    q[i] = -1e9f;
-    flags[i] = 0;
-  }
-
-  unsigned int id;
-  for (unsigned int i=0; i < ev->channels.size(); i++) {
-    id = ev->channels[i].id;
-
-    if (id < ev->nchannels) {
-      hit[id] = 1;
-      t[id] = ev->channels[i].t;
-      q[id] = ev->channels[i].q;
-      flags[id] = ev->channels[i].flag;
-    }
-  }
-}
-
-void get_photons(const std::vector<Photon> &photons, float *pos, float *dir,
-		 float *pol, float *wavelengths, float *t,
-		 int *last_hit_triangles, unsigned int *flags)
-{
-  for (unsigned int i=0; i < photons.size(); i++) {
-    const Photon &photon = photons[i];
-    pos[3*i] = photon.pos.X();
-    pos[3*i+1] = photon.pos.Y();
-    pos[3*i+2] = photon.pos.Z();
-
-    dir[3*i] = photon.dir.X();
-    dir[3*i+1] = photon.dir.Y();
-    dir[3*i+2] = photon.dir.Z();
-    
-    pol[3*i] = photon.pol.X();
-    pol[3*i+1] = photon.pol.Y();
-    pol[3*i+2] = photon.pol.Z();
-
-    wavelengths[i] = photon.wavelength;
-    t[i] = photon.t;
-    flags[i] = photon.flag;
-    last_hit_triangles[i] = photon.last_hit_triangle;
-  }
-}
-		 
-void fill_photons(std::vector<Photon> &photons,
-		  unsigned int nphotons, float *pos, float *dir,
-		  float *pol, float *wavelengths, float *t,
-		  int *last_hit_triangles, unsigned int *flags)
-{
-  photons.resize(nphotons);
-  
-  for (unsigned int i=0; i < nphotons; i++) {
-    Photon &photon = photons[i];
-    photon.t = t[i];
-    photon.pos.SetXYZ(pos[3*i], pos[3*i + 1], pos[3*i + 2]);
-    photon.dir.SetXYZ(dir[3*i], dir[3*i + 1], dir[3*i + 2]);
-    photon.pol.SetXYZ(pol[3*i], pol[3*i + 1], pol[3*i + 2]);
-    photon.wavelength = wavelengths[i];
-    photon.last_hit_triangle = last_hit_triangles[i];
-    photon.flag = flags[i];
-
-  }
-}
-
-#ifdef __MAKECINT__
-#pragma link C++ class vector<Vertex>;
-#pragma link C++ class vector<Photon>;
-#pragma link C++ class vector<Channel>;
-#endif
-
-
diff --git a/chroma/generator/G4chroma.cc b/chroma/generator/G4chroma.cc
deleted file mode 100644
index 1aba133..0000000
--- a/chroma/generator/G4chroma.cc
+++ /dev/null
@@ -1,230 +0,0 @@
-#include "G4chroma.hh"
-#include <geant4/G4OpticalPhysics.hh>
-#include <geant4/G4EmPenelopePhysics.hh>
-
-ChromaPhysicsList::ChromaPhysicsList():  G4VModularPhysicsList()
-{
-  // default cut value  (1.0mm) 
-  defaultCutValue = 1.0*mm;
-
-  // General Physics
-  RegisterPhysics( new G4EmPenelopePhysics(0) );
-  // Optical Physics
-  G4OpticalPhysics* opticalPhysics = new G4OpticalPhysics();
-  RegisterPhysics( opticalPhysics );
-  opticalPhysics->SetTrackSecondariesFirst(false);
-}
-
-ChromaPhysicsList::~ChromaPhysicsList()
-{
-}
-
-void ChromaPhysicsList::SetCuts(){
-  //  " G4VUserPhysicsList::SetCutsWithDefault" method sets 
-  //   the default cut value for all particle types 
-  SetCutsWithDefault();   
-}
-
-
-PhotonTrackingAction::PhotonTrackingAction()
-{
-}
-
-PhotonTrackingAction::~PhotonTrackingAction()
-{
-}
-
-int PhotonTrackingAction::GetNumPhotons() const
-{
-  return pos.size();
-}
-
-void PhotonTrackingAction::Clear()
-{
-  pos.clear();
-  dir.clear();
-  pol.clear();
-  wavelength.clear();
-  t0.clear();
-}
-
-void PhotonTrackingAction::GetX(double *x) const
-{
-  for (unsigned i=0; i < pos.size(); i++) x[i] = pos[i].x();
-}
-
-void PhotonTrackingAction::GetY(double *y) const
-{
-  for (unsigned i=0; i < pos.size(); i++) y[i] = pos[i].y();
-}
-
-void PhotonTrackingAction::GetZ(double *z) const
-{
-  for (unsigned i=0; i < pos.size(); i++) z[i] = pos[i].z();
-}
-
-void PhotonTrackingAction::GetDirX(double *dir_x) const
-{
-  for (unsigned i=0; i < dir.size(); i++) dir_x[i] = dir[i].x();
-}
-
-void PhotonTrackingAction::GetDirY(double *dir_y) const
-{
-  for (unsigned i=0; i < dir.size(); i++) dir_y[i] = dir[i].y();
-}
-
-void PhotonTrackingAction::GetDirZ(double *dir_z) const
-{
-  for (unsigned i=0; i < dir.size(); i++) dir_z[i] = dir[i].z();
-}
-
-void PhotonTrackingAction::GetPolX(double *pol_x) const
-{
-  for (unsigned i=0; i < pol.size(); i++) pol_x[i] = pol[i].x();
-}
-
-void PhotonTrackingAction::GetPolY(double *pol_y) const
-{
-  for (unsigned i=0; i < pol.size(); i++) pol_y[i] = pol[i].y();
-}
-
-void PhotonTrackingAction::GetPolZ(double *pol_z) const
-{
-  for (unsigned i=0; i < pol.size(); i++) pol_z[i] = pol[i].z();
-}
-
-void PhotonTrackingAction::GetWavelength(double *wl) const
-{
-  for (unsigned i=0; i < wavelength.size(); i++) wl[i] = wavelength[i];
-}
-
-void PhotonTrackingAction::GetT0(double *t) const
-{
-  for (unsigned i=0; i < t0.size(); i++) t[i] = t0[i];
-}
-
-void PhotonTrackingAction::PreUserTrackingAction(const G4Track *track)
-{
-  G4ParticleDefinition *particle = track->GetDefinition();
-  if (particle->GetParticleName() == "opticalphoton") {
-    pos.push_back(track->GetPosition()/m);
-    dir.push_back(track->GetMomentumDirection());
-    pol.push_back(track->GetPolarization());
-    wavelength.push_back( (h_Planck * c_light / track->GetKineticEnergy()) / nanometer );
-    t0.push_back(track->GetGlobalTime() / s);
-    const_cast<G4Track *>(track)->SetTrackStatus(fStopAndKill);
-  }
-}
-
-#include <boost/python.hpp>
-#include <pyublas/numpy.hpp>
-
-using namespace boost::python;
-
-pyublas::numpy_vector<double> PTA_GetX(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetX(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetY(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetY(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetZ(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetZ(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetDirX(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetDirX(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetDirY(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetDirY(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetDirZ(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetDirZ(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetPolX(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetPolX(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetPolY(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetPolY(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetPolZ(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetPolZ(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetWave(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetWavelength(&r[0]);
-  return r;
-}
-
-pyublas::numpy_vector<double> PTA_GetT0(const PhotonTrackingAction *pta)
-{
-  pyublas::numpy_vector<double> r(pta->GetNumPhotons());
-  pta->GetT0(&r[0]);
-  return r;
-}
-
-
-void export_Chroma()
-{
-  class_<ChromaPhysicsList, ChromaPhysicsList*, bases<G4VModularPhysicsList>, boost::noncopyable > ("ChromaPhysicsList", "EM+Optics physics list")
-    .def(init<>())
-    ;
-
-  class_<PhotonTrackingAction, PhotonTrackingAction*, bases<G4UserTrackingAction>,
-	 boost::noncopyable > ("PhotonTrackingAction", "Tracking action that saves photons")
-    .def(init<>())
-    .def("GetNumPhotons", &PhotonTrackingAction::GetNumPhotons)
-    .def("Clear", &PhotonTrackingAction::Clear)
-    .def("GetX", PTA_GetX)
-    .def("GetY", PTA_GetY)
-    .def("GetZ", PTA_GetZ)
-    .def("GetDirX", PTA_GetDirX)
-    .def("GetDirY", PTA_GetDirY)
-    .def("GetDirZ", PTA_GetDirZ)
-    .def("GetPolX", PTA_GetPolX)
-    .def("GetPolY", PTA_GetPolY)
-    .def("GetPolZ", PTA_GetPolZ)
-    .def("GetWavelength", PTA_GetWave)
-    .def("GetT0", PTA_GetT0)
-    ;
-}
-
-BOOST_PYTHON_MODULE(G4chroma)
-{
-  export_Chroma();
-}
diff --git a/chroma/generator/G4chroma.hh b/chroma/generator/G4chroma.hh
deleted file mode 100644
index 4f085aa..0000000
--- a/chroma/generator/G4chroma.hh
+++ /dev/null
@@ -1,49 +0,0 @@
-#ifndef __G4chroma_hh__
-#define __G4chroma_hh__
-
-#include <geant4/G4VModularPhysicsList.hh>
-class ChromaPhysicsList: public G4VModularPhysicsList
-{
-public:
-  ChromaPhysicsList();
-  virtual ~ChromaPhysicsList();
-  virtual void SetCuts();
-};
-
-#include <geant4/G4UserTrackingAction.hh>
-#include <vector>
-#include <geant4/G4ThreeVector.hh>
-
-class PhotonTrackingAction : public G4UserTrackingAction
-{
-public:
-  PhotonTrackingAction();
-  virtual ~PhotonTrackingAction();
-  
-  int GetNumPhotons() const;
-  void Clear();
-  
-  void GetX(double *x) const;
-  void GetY(double *y) const;
-  void GetZ(double *z) const;
-  void GetDirX(double *dir_x) const;
-  void GetDirY(double *dir_y) const;
-  void GetDirZ(double *dir_z) const;
-  void GetPolX(double *pol_x) const;
-  void GetPolY(double *pol_y) const;
-  void GetPolZ(double *pol_z) const;
-
-  void GetWavelength(double *wl) const;
-  void GetT0(double *t) const;
-
-  virtual void PreUserTrackingAction(const G4Track *);
-
-protected:
-  std::vector<G4ThreeVector> pos;
-  std::vector<G4ThreeVector> dir;
-  std::vector<G4ThreeVector> pol;
-  std::vector<double> wavelength;
-  std::vector<double> t0;
-};
-
-#endif