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/// \file DicomPartialDetectorConstruction.cc
/// \brief Implementation of the DicomPartialDetectorConstruction class

#include "DicomPartialDetectorConstruction.hh"

#include "G4Box.hh"
#include "G4Colour.hh"
#include "G4Element.hh"
#include "G4LogicalVolume.hh"
#include "G4Material.hh"
#include "G4NistManager.hh"
#include "G4PVParameterised.hh"
#include "G4PVPlacement.hh"
#include "G4PartialPhantomParameterisation.hh"
#include "G4SystemOfUnits.hh"
#include "G4Tubs.hh"
#include "G4UIcommand.hh"
#include "G4VPhysicalVolume.hh"
#include "G4VisAttributes.hh"
#include "G4ios.hh"
#include "G4tgbMaterialMgr.hh"
#include "G4tgbVolumeMgr.hh"
#include "G4tgrMessenger.hh"
#include "globals.hh"

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPartialDetectorConstruction::DicomPartialDetectorConstruction()
  : DicomDetectorConstruction(),
    fPartialPhantomParam(0),
    fNoVoxels(0),
    fDimX(0),
    fDimY(0),
    fDimZ(0),
    fOffsetX(0),
    fOffsetY(0),
    fOffsetZ(0)
{}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
DicomPartialDetectorConstruction::~DicomPartialDetectorConstruction() {}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
G4VPhysicalVolume* DicomPartialDetectorConstruction::Construct()
{
  InitialisationOfMaterials();

  //----- Build world
  G4double worldXDimension = 1. * m;
  G4double worldYDimension = 1. * m;
  G4double worldZDimension = 1. * m;

  G4Box* world_box = new G4Box("WorldSolid", worldXDimension, worldYDimension, worldZDimension);

  fWorld_logic = new G4LogicalVolume(world_box, fAir, "WorldLogical", 0, 0, 0);

  G4VPhysicalVolume* world_phys =
    new G4PVPlacement(0, G4ThreeVector(0, 0, 0), "World", fWorld_logic, 0, false, 0);

  ReadPhantomData();

  ConstructPhantomContainer();
  ConstructPhantom();

  return world_phys;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadPhantomData()
{
  G4String dataFile = "Data.dat";
  std::ifstream finDF(dataFile.c_str());
  G4String fname;
  if (finDF.good() != 1) {
    G4Exception(" DicomPartialDetectorConstruction::ReadPhantomData", "", FatalErrorInArgument,
                " Problem reading data file: Data.dat");
  }

  G4int compression;
  finDF >> compression;  // not used here

  G4int numFiles;
  finDF >> numFiles;  // only 1 file supported for the moment
  if (numFiles != 1) {
    G4Exception("DicomPartialDetectorConstruction::ReadPhantomData", "", FatalErrorInArgument,
                "More than 1 DICOM file is not supported");
  }
  for (G4int i = 0; i < numFiles; i++) {
    finDF >> fname;
    //--- Read one data file
    fname += ".g4pdcm";
    ReadPhantomDataFile(fname);
  }

  finDF.close();
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadPhantomDataFile(const G4String& fname)
{
  //  G4String filename = "phantom.g4pdcm";
#ifdef G4VERBOSE
  G4cout << " DicomDetectorConstruction::ReadPhantomDataFile opening file " << fname << G4endl;
#endif
  std::ifstream fin(fname.c_str(), std::ios_base::in);
  if (!fin.is_open()) {
    G4Exception("DicomPartialDetectorConstruction::ReadPhantomDataFile", "", FatalException,
                G4String("File not found " + fname).c_str());
  }
  G4int nMaterials;
  fin >> nMaterials;
  G4String stemp;
  G4int nmate;
  for (G4int ii = 0; ii < nMaterials; ii++) {
    fin >> nmate >> stemp;
    G4cout << "DicomPartialDetectorConstruction::ReadPhantomData reading nmate " << ii << " = "
           << nmate << " mate " << stemp << G4endl;
    if (ii != nmate)
      G4Exception("DicomPartialDetectorConstruction::ReadPhantomData", "", FatalErrorInArgument,
                  "Material number should be in increasing order: \
                          wrong material number ");
  }

  fin >> fNoVoxelsX >> fNoVoxelsY >> fNoVoxelsZ;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData nVoxel X/Y/Z " << fNoVoxelsX << " "
         << fNoVoxelsY << " " << fNoVoxelsZ << G4endl;
  fin >> fOffsetX >> fDimX;
  fDimX = (fDimX - fOffsetX) / fNoVoxelsX;
  fin >> fOffsetY >> fDimY;
  fDimY = (fDimY - fOffsetY) / fNoVoxelsY;
  fin >> fOffsetZ >> fDimZ;
  fDimZ = (fDimZ - fOffsetZ) / fNoVoxelsZ;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimX " << fDimX << " fOffsetX "
         << fOffsetX << G4endl;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimY " << fDimY << " fOffsetY "
         << fOffsetY << G4endl;
  G4cout << "DicomPartialDetectorConstruction::ReadPhantomData voxelDimZ " << fDimZ << " fOffsetZ "
         << fOffsetZ << G4endl;

  //--- Read voxels that are filled
  fNoVoxels = 0;
  //  G4bool* isFilled = new G4bool[fNoVoxelsX*fNoVoxelsY*fNoVoxelsZ];
  //  fFilledIDs = new size_t[fNoVoxelsZ*fNoVoxelsY+1];
  //?  fFilledIDs.insert(0);
  G4int ifxmin1, ifxmax1;
  for (G4int iz = 0; iz < fNoVoxelsZ; iz++) {
    std::map<G4int, G4int> ifmin, ifmax;
    for (G4int iy = 0; iy < fNoVoxelsY; iy++) {
      fin >> ifxmin1 >> ifxmax1;
      // check coherence ...

      ifmin[iy] = ifxmin1;
      ifmax[iy] = ifxmax1;
      G4int ifxdiff = ifxmax1 - ifxmin1 + 1;
      if (ifxmax1 == -1 && ifxmin1 == -1) ifxdiff = 0;
      fFilledIDs.insert(std::pair<G4int, G4int>(ifxdiff + fNoVoxels - 1, ifxmin1));
      G4cout << "DicomPartialDetectorConstruction::ReadPhantomData insert "
             << " FilledIDs " << ifxdiff + fNoVoxels - 1 << " min " << ifxmin1
             << " N= " << fFilledIDs.size() << G4endl;
      // filledIDs[iz*fNoVoxelsY+iy+1] = ifxmax1-ifxmin1+1;
      for (G4int ix = 0; ix < fNoVoxelsX; ix++) {
        if (ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1)) {
          fNoVoxels++;
        }
        else {
        }
      }
    }
    fFilledMins[iz] = ifmin;
    fFilledMaxs[iz] = ifmax;
  }

  //--- Read material IDs
  G4int mateID1;
  fMateIDs = new size_t[fNoVoxelsX * fNoVoxelsY * fNoVoxelsZ];
  G4int copyNo = 0;
  for (G4int iz = 0; iz < fNoVoxelsZ; iz++) {
    std::map<G4int, G4int> ifmin = fFilledMins[iz];
    std::map<G4int, G4int> ifmax = fFilledMaxs[iz];
    for (G4int iy = 0; iy < fNoVoxelsY; iy++) {
      ifxmin1 = ifmin[iy];
      ifxmax1 = ifmax[iy];
      for (G4int ix = 0; ix < fNoVoxelsX; ix++) {
        if (ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1)) {
          fin >> mateID1;
          if (mateID1 < 0 || mateID1 >= nMaterials) {
            G4Exception("DicomPartialDetectorConstruction::ReadPhantomData", "", FatalException,
                        G4String("Wrong index in phantom file: It should be between 0 and "
                                 + G4UIcommand::ConvertToString(nMaterials - 1) + ", while it is "
                                 + G4UIcommand::ConvertToString(mateID1))
                          .c_str());
          }
          fMateIDs[copyNo] = mateID1;
          copyNo++;
        }
      }
    }
  }

  ReadVoxelDensitiesPartial(fin);

  fin.close();
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ReadVoxelDensitiesPartial(std::ifstream& fin)
{
  std::map<G4int, std::pair<G4double, G4double>> densiMinMax;
  std::map<G4int, std::pair<G4double, G4double>>::iterator mpite;
  for (G4int ii = 0; ii < G4int(fOriginalMaterials.size()); ++ii) {
    densiMinMax[ii] = std::pair<G4double, G4double>(DBL_MAX, -DBL_MAX);
  }

  //----- Define density differences (maximum density difference to create
  // a new material)
  char* part = std::getenv("DICOM_CHANGE_MATERIAL_DENSITY");
  G4double densityDiff = -1.;
  if (part) densityDiff = G4UIcommand::ConvertToDouble(part);
  std::map<G4int, G4double> densityDiffs;
  if (densityDiff != -1.) {
    for (G4int ii = 0; ii < G4int(fOriginalMaterials.size()); ++ii) {
      densityDiffs[ii] = densityDiff;  // currently all materials
      // with same step
    }
  }
  else {
    if (fMaterials.size() == 0) {  // do it only for first slice
      for (unsigned int ii = 0; ii < fOriginalMaterials.size(); ++ii) {
        fMaterials.push_back(fOriginalMaterials[ii]);
      }
    }
  }
  //  densityDiffs[0] = 0.0001; //fAir

  //--- Calculate the average material density for each material/density bin
  std::map<std::pair<G4Material*, G4int>, matInfo*> newMateDens;

  G4double dens1;
  G4int ifxmin1, ifxmax1;

  //---- Read the material densities
  G4int copyNo = 0;
  for (G4int iz = 0; iz < fNoVoxelsZ; ++iz) {
    std::map<G4int, G4int> ifmin = fFilledMins[iz];
    std::map<G4int, G4int> ifmax = fFilledMaxs[iz];
    for (G4int iy = 0; iy < fNoVoxelsY; ++iy) {
      ifxmin1 = ifmin[iy];
      ifxmax1 = ifmax[iy];
      for (G4int ix = 0; ix < fNoVoxelsX; ++ix) {
        if (ix >= G4int(ifxmin1) && ix <= G4int(ifxmax1)) {
          fin >> dens1;
          //--- store the minimum and maximum density for each material
          //(just for printing)
          mpite = densiMinMax.find(G4int(fMateIDs[copyNo]));
          if (dens1 < (*mpite).second.first) (*mpite).second.first = dens1;
          if (dens1 > (*mpite).second.second) (*mpite).second.second = dens1;

          //--- Get material from original list of material in file
          G4int mateID = G4int(fMateIDs[copyNo]);
          G4Material* mate = fOriginalMaterials[mateID];
          //        G4cout << copyNo << " mateID " << mateID << G4endl;
          //--- Check if density is equal to the original material density
          if (std::fabs(dens1 - mate->GetDensity() / g * cm3) < 1.e-9) continue;

          //--- Build material name with fOriginalMaterials name + density
          //        float densityBin = densityDiffs[mateID] *
          //        (G4int(dens1/densityDiffs[mateID])+0.5);
          G4String newMateName = mate->GetName();

          G4int densityBin = 0;
          //        G4cout << " densityBin " << densityBin << " "
          //        << dens1 << " " <<densityDiffs[mateID] << G4endl;

          if (densityDiff != -1.) {
            densityBin = (G4int(dens1 / densityDiffs[mateID]));
            newMateName = mate->GetName() + G4UIcommand::ConvertToString(densityBin);
          }

          //--- Look if it is the first voxel with this material/densityBin
          std::pair<G4Material*, G4int> matdens(mate, densityBin);

          auto mppite = newMateDens.find(matdens);
          if (mppite != newMateDens.cend()) {
            matInfo* mi = (*mppite).second;
            mi->fSumdens += dens1;
            mi->fNvoxels++;
            fMateIDs[copyNo] = fOriginalMaterials.size() - 1 + mi->fId;
            //  G4cout << copyNo << " mat new again "
            //<< fOriginalMaterials.size()-1 + mi->id << " " << mi->id << G4endl;
          }
          else {
            matInfo* mi = new matInfo;
            mi->fSumdens = dens1;
            mi->fNvoxels = 1;
            mi->fId = G4int(newMateDens.size() + 1);
            newMateDens[matdens] = mi;
            fMateIDs[copyNo] = fOriginalMaterials.size() - 1 + mi->fId;
            //          G4cout << copyNo << " mat new first "
            //          << fOriginalMaterials.size()-1 + mi->fId << G4endl;
          }
          copyNo++;
          //        G4cout << ix << " " << iy << " " << iz
          //  << " filling fMateIDs " << copyNo << " = " << atoi(cid)-1 << G4endl;
          //        fMateIDs[copyNo] = atoi(cid)-1;
        }
      }
    }
  }

  //----- Build the list of phantom materials that go to Parameterisation
  //--- Add original materials
  for (auto mimite = fOriginalMaterials.cbegin(); mimite != fOriginalMaterials.cend(); ++mimite) {
    fPhantomMaterials.push_back((*mimite));
  }
  //
  //---- Build and add new materials
  for (auto mppite = newMateDens.cbegin(); mppite != newMateDens.cend(); ++mppite) {
    G4double averdens = (*mppite).second->fSumdens / (*mppite).second->fNvoxels;
    G4double saverdens = G4int(1000.001 * averdens) / 1000.;
    G4cout << "GmReadPhantomGeometry::ReadVoxelDensities AVER DENS " << averdens << " -> "
           << saverdens << " -> " << G4int(1000 * averdens) << " " << G4int(1000 * averdens) / 1000
           << " " << G4int(1000 * averdens) / 1000. << G4endl;

    G4cout << "GmReadPhantomGeometry::ReadVoxelDensities AVER DENS " << averdens << " -> "
           << saverdens << " -> " << G4UIcommand::ConvertToString(saverdens) << " Nvoxels "
           << (*mppite).second->fNvoxels << G4endl;
    G4String mateName =
      ((*mppite).first).first->GetName() + "_" + G4UIcommand::ConvertToString(saverdens);
    fPhantomMaterials.push_back(
      BuildMaterialWithChangingDensity((*mppite).first.first, G4float(averdens), mateName));
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ConstructPhantomContainer()
{
  // build a clinder that encompass the partial phantom built in the example
  //  /dicom/intersectWithUserVolume 0. 0. 0. 0.*deg 0. 0. TUBE 0. 200. 100.
  //---- Extract number of voxels and voxel dimensions

  G4String contname = "PhantomContainer";

  //----- Define the volume that contains all the voxels
  G4Tubs* container_tube = new G4Tubs(contname, 0., 200., 100., 0., 360 * deg);

  fContainer_logic = new G4LogicalVolume(container_tube, fAir, contname, 0, 0, 0);

  G4ThreeVector posCentreVoxels(0., 0., 0.);
  // G4cout << " PhantomContainer posCentreVoxels " << posCentreVoxels << G4endl;
  G4RotationMatrix* rotm = new G4RotationMatrix;

  fContainer_phys = new G4PVPlacement(rotm,  // rotation
                                      posCentreVoxels,
                                      fContainer_logic,  // The logic volume
                                      contname,  // Name
                                      fWorld_logic,  // Mother
                                      false,  // No op. bool.
                                      1);  // Copy number
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
void DicomPartialDetectorConstruction::ConstructPhantom()
{
  G4String OptimAxis = "kXAxis";
  G4bool bSkipEqualMaterials = 0;
  G4int regStructureID = 2;

  G4ThreeVector posCentreVoxels(0., 0., 0.);

  //----- Build phantom
  G4String voxelName = "phantom";
  G4Box* phantom_solid = new G4Box(voxelName, fDimX / 2., fDimY / 2., fDimZ / 2.);
  G4LogicalVolume* phantom_logic = new G4LogicalVolume(phantom_solid, fAir, voxelName, 0, 0, 0);
  G4bool pVis = 0;
  if (!pVis) {
    G4VisAttributes* visAtt = new G4VisAttributes(FALSE);
    phantom_logic->SetVisAttributes(visAtt);
  }

  G4double theSmartless = 0.5;
  //  fContainer_logic->SetSmartless( theSmartless );
  phantom_logic->SetSmartless(theSmartless);

  fPartialPhantomParam = new G4PartialPhantomParameterisation();

  fPartialPhantomParam->SetMaterials(fPhantomMaterials);
  fPartialPhantomParam->SetVoxelDimensions(fDimX / 2., fDimY / 2., fDimZ / 2.);
  fPartialPhantomParam->SetNoVoxels(fNoVoxelsX, fNoVoxelsY, fNoVoxelsZ);
  fPartialPhantomParam->SetMaterialIndices(fMateIDs);

  fPartialPhantomParam->SetFilledIDs(fFilledIDs);

  fPartialPhantomParam->SetFilledMins(fFilledMins);

  fPartialPhantomParam->BuildContainerWalls();

  //  G4cout << " Number of Materials " << fPhantomMaterials.size() << G4endl;
  //  G4cout << " SetMaterialIndices(0) " << fMateIDs[0] << G4endl;

  G4PVParameterised* phantom_phys = 0;
  if (OptimAxis == "kUndefined") {
    phantom_phys = new G4PVParameterised(voxelName, phantom_logic, fContainer_logic, kUndefined,
                                         fNoVoxels, fPartialPhantomParam);
  }
  else if (OptimAxis == "kXAxis") {
    //    G4cout << " optim kX " << G4endl;
    phantom_phys = new G4PVParameterised(voxelName, phantom_logic, fContainer_logic, kXAxis,
                                         fNoVoxels, fPartialPhantomParam);
    fPartialPhantomParam->SetSkipEqualMaterials(bSkipEqualMaterials);
  }
  else {
    G4Exception("GmReadPhantomGeometry::ConstructPhantom", "", FatalErrorInArgument,
                G4String("Wrong argument to parameter \
         GmReadPhantomGeometry:Phantom:OptimAxis: \
         Only allowed 'kUndefined' or 'kXAxis', it is: "
                         + OptimAxis)
                  .c_str());
  }

  phantom_phys->SetRegularStructureId(regStructureID);
}
