FPGATrackSimNNTrackTool.cxx

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/*
   Copyright (C) 2002-2026 CERN for the benefit of the ATLAS collaboration
   */
 
#include "FPGATrackSimAlgorithms/FPGATrackSimNNTrackTool.h"
#include "FPGATrackSimMaps/FPGATrackSimNNMap.h"
#include "FPGATrackSimMaps/IFPGATrackSimMappingSvc.h"
#include "FPGATrackSimObjects/FPGATrackSimFunctions.h"
#include "FPGATrackSimObjects/FPGATrackSimMultiTruth.h"

FPGATrackSimNNTrackTool::FPGATrackSimNNTrackTool(const std::string &algname, const std::string &name, const IInterface *ifc) : FPGATrackSimTrackingToolBase(algname, name, ifc), OnnxRuntimeBase() {}
 
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
StatusCode FPGATrackSimNNTrackTool::initialize() {
    ATH_CHECK(m_FPGATrackSimMapping.retrieve());
    ATH_CHECK(m_tHistSvc.retrieve());
    if (m_useSpacePoints) ATH_CHECK(m_spRoadFilterTool.retrieve(EnableTool{m_spRoadFilterTool}));
 
    if (m_FPGATrackSimMapping->getFakeNNMapString() != "") {
        m_fakeNN_1st.initialize(m_FPGATrackSimMapping->getFakeNNMapString());
    }
    else {
        ATH_MSG_ERROR("Path to 1st stage NN-based fake track removal ONNX file is empty! If you want to run this pipeline, you need to provide an input file.");
        return StatusCode::FAILURE;
    }
 
    if (m_FPGATrackSimMapping->getParamNNMapString() != "") {
        m_paramNN_1st.initialize(m_FPGATrackSimMapping->getParamNNMapString());
    }
    else {
        ATH_MSG_INFO("Path 1st stage to NN-based track parameter estimation ONNX file is empty! Estimation is not run...");
        m_useParamNN_1st = false;
    }
 
    if (m_FPGATrackSimMapping->getFakeNNMap2ndString() != "") {
        m_fakeNN_2nd.initialize(m_FPGATrackSimMapping->getFakeNNMap2ndString());
    }
    else {
        ATH_MSG_ERROR("Path to 2nd stage NN-based fake track 1st stage removal ONNX file is empty! If you want to run this pipeline, you need to provide an input file.");
        return StatusCode::FAILURE;
    }
 
    if (m_FPGATrackSimMapping->getParamNNMap2ndString() != "") {
        m_paramNN_2nd.initialize(m_FPGATrackSimMapping->getParamNNMap2ndString());
    }
    else {
        ATH_MSG_INFO("Path to 2nd stage NN-based track parameter estimation 2nd ONNX file is empty! Estimation is not run...");
        m_useParamNN_2nd = false;
    }
 
    return StatusCode::SUCCESS;
}
 
 
StatusCode FPGATrackSimNNTrackTool::setTrackParameters(std::vector<FPGATrackSimTrack> &tracks, bool isFirst, const FPGATrackSimTrackPars& min, const FPGATrackSimTrackPars& max) {
 
    ATH_MSG_DEBUG("Running NN-based track parameter estimation!");
    std::vector<float> paramNNoutputs;
    if (!m_useParamNN_1st && isFirst) return StatusCode::SUCCESS;
    if (!m_useParamNN_2nd && !isFirst) return StatusCode::SUCCESS;
 
    for (auto &track : tracks) {
      if (!track.passedOR()) continue; 
        std::vector<float> inputTensorValues;
        const auto& hits = track.getFPGATrackSimHitPtrs();
        bool gotSecondSP = false;
        float tmp_xf;
        float tmp_yf;
        float tmp_zf;
    float tmp_rf;
    float tmp_phif;
    
        for (const auto& hit_ptr : hits) {
            if (!hit_ptr) {
                ATH_MSG_ERROR("Null hit pointer in track");
                return StatusCode::FAILURE;
            }
            if (!hit_ptr->isReal()) continue;
            const auto& hit = *hit_ptr;
 
            // Need to rotate hits
            float xf = hit.getX();
            float yf = hit.getY();
            float zf = hit.getZ();
        float rf = std::sqrt(xf*xf+yf*yf);
        float phif = hit.getGPhi();
        
            // Get average of values for strip hit pairs
            // TODO: this needs to be fixed in the future, for this to work for other cases
            if (hit.isStrip()) {
          if (hit.getHitType() != HitType::spacepoint) { // this is a strip but not a SP!
          if (m_useCartesian) {
                    float xf_scaled = (xf) / (getXScale());
                    float yf_scaled = (yf) / (getYScale());
                    float zf_scaled = (zf) / (getZScale());
            
                    // Get average of two hits for strip hits 
                    inputTensorValues.push_back(xf_scaled);
                    inputTensorValues.push_back(yf_scaled);
                    inputTensorValues.push_back(zf_scaled);
 
          }
          else {
            float rf_scaled = (rf) / (getRScale());
            float phif_scaled = (phif) / (getPhiScale());
            float zf_scaled = (zf) / (getZScale());
            // Get average of two hits for strip hits
                    inputTensorValues.push_back(rf_scaled);
                    inputTensorValues.push_back(phif_scaled);
                    inputTensorValues.push_back(zf_scaled);
          }
          }
          else if (!gotSecondSP) {
        tmp_xf = xf;
        tmp_yf = yf;
        tmp_zf = zf;
        tmp_rf = rf;
        tmp_phif = phif;
        gotSecondSP = true;
          }
          else {
        gotSecondSP = false;
        
        if (m_useCartesian) {
                    float xf_scaled = (xf + tmp_xf) / (2.*getXScale());
                    float yf_scaled = (yf + tmp_yf) / (2.*getYScale());
                    float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
            
                    // Get average of two hits for strip hits 
                    inputTensorValues.push_back(xf_scaled);
                    inputTensorValues.push_back(yf_scaled);
                    inputTensorValues.push_back(zf_scaled);
            
        }
        else {
          float rf_scaled = (rf+tmp_rf) / (2.*getRScale());
          float phif_scaled = (phif+tmp_phif) / (2.*getPhiScale());
          float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
          // Get average of two hits for strip hits
          inputTensorValues.push_back(rf_scaled);
          inputTensorValues.push_back(phif_scaled);
          inputTensorValues.push_back(zf_scaled);
        }
          }
            }
            else {
          if (m_useCartesian) {
                float xf_scaled = (xf) / (getXScale());
                float yf_scaled = (yf) / (getYScale());
                float zf_scaled = (zf) / (getZScale());
                inputTensorValues.push_back(xf_scaled);
                inputTensorValues.push_back(yf_scaled);
                inputTensorValues.push_back(zf_scaled);
          }
          else {
        float rf_scaled = (rf) / (getRScale());
        float phif_scaled = (phif) / (getPhiScale());
        float zf_scaled = (zf) / (getZScale());
        // Get average of two hits for strip hits
        inputTensorValues.push_back(rf_scaled);
        inputTensorValues.push_back(phif_scaled);
        inputTensorValues.push_back(zf_scaled);
          }
            }
        }
 
        if (isFirst){
          if (inputTensorValues.size() < 15) {
            inputTensorValues.resize(15, 0.0f); // Resize to 15 and fill with 0.0f
          }
      
      if (m_doGNNTracking) {
       inputTensorValues.resize(m_nInputsGNN * 3);
      }
    }
    else {
          if (inputTensorValues.size() < 39) {
            inputTensorValues.resize(39, 0.0f); // Resize to 39 and fill with 0.0f
          }
          else if (inputTensorValues.size() > 39) {
            inputTensorValues.resize(39); // Resize to 39 and keep the first e9 elements
          }
    }
    
        if (m_doGNNTracking) {
      inputTensorValues.resize(m_nInputsGNN * 3);
    }
    
    
        if (isFirst) paramNNoutputs = m_paramNN_1st.runONNXInference(inputTensorValues);
        else paramNNoutputs = m_paramNN_2nd.runONNXInference(inputTensorValues);
    
        ATH_MSG_DEBUG("Estimated Track Parameters");
        for (unsigned int i = 0; i < paramNNoutputs.size(); i++) {
      ATH_MSG_DEBUG(paramNNoutputs[i]);
        }
 
    
    double qopt = paramNNoutputs[0]*getQoverPtScale();
    double eta = paramNNoutputs[1]*getEtaScale();
    double phi = paramNNoutputs[2]*getPhiScale();
    double d0 = paramNNoutputs[3]*getD0Scale();
    double z0 = paramNNoutputs[4]*getZ0Scale();
 
 
     if (qopt < min[FPGATrackSimTrackPars::IHIP]) qopt = min[FPGATrackSimTrackPars::IHIP];
     if (qopt > max[FPGATrackSimTrackPars::IHIP]) qopt = max[FPGATrackSimTrackPars::IHIP];
     if (eta < min[FPGATrackSimTrackPars::IETA]) eta = min[FPGATrackSimTrackPars::IETA];
     if (eta > max[FPGATrackSimTrackPars::IETA]) eta = max[FPGATrackSimTrackPars::IETA];
     if (phi < min[FPGATrackSimTrackPars::IPHI]) phi = min[FPGATrackSimTrackPars::IPHI];
     if (phi > max[FPGATrackSimTrackPars::IPHI]) phi = max[FPGATrackSimTrackPars::IPHI];
     if (d0 < min[FPGATrackSimTrackPars::ID0]) d0 = min[FPGATrackSimTrackPars::ID0];
     if (d0 > max[FPGATrackSimTrackPars::ID0]) d0 = max[FPGATrackSimTrackPars::ID0];
     if (z0 < min[FPGATrackSimTrackPars::IZ0]) z0 = min[FPGATrackSimTrackPars::IZ0];
     if (z0 > max[FPGATrackSimTrackPars::IZ0]) z0 = max[FPGATrackSimTrackPars::IZ0];
    
        track.setQOverPt(qopt);
        track.setEta(eta);
        track.setPhi(phi);
        track.setD0(d0);
        track.setZ0(z0);
    }
    return StatusCode::SUCCESS;
}
 
 
StatusCode FPGATrackSimNNTrackTool::getTracks_1st(std::vector<FPGATrackSimRoad> &roads, std::vector<FPGATrackSimTrack> &tracks) {
 
    if(m_doGNNTracking) {
        ATH_CHECK(getTracks_GNN(roads, tracks));
        return StatusCode::SUCCESS;
    }
 
    ATH_CHECK(setRoadSectors(roads));
    int n_track = 0;
 
    std::vector<std::vector<float> >inputTensorValuesAll;
 
    // Loop over roads
    for (auto const &iroad : roads) {
 
      double y = iroad.getY();
 
        // Just used to get number of layers considered
        const FPGATrackSimPlaneMap *planeMap = m_FPGATrackSimMapping->PlaneMap_1st(iroad.getSubRegion());
 
        // Get info on layers with missing hits
        int nMissing = 0;
        layer_bitmask_t missing_mask = iroad.getNWCLayers();
    for (unsigned ilayer = 0; ilayer < planeMap->getNLogiLayers(); ilayer++) {
      if ((missing_mask >> ilayer) & 0x1) {
        nMissing++;
        if (planeMap->isPixel(ilayer)) nMissing++; 
      }
    }
    
 
        // Create a template track with common parameters filled already for
        // initializing below
        FPGATrackSimTrack temp;
        temp.setTrackStage(TrackStage::FIRST);
        temp.setNLayers(planeMap->getNLogiLayers());
        temp.setBankID(-1);
        temp.setPatternID(iroad.getPID());
        temp.setFirstSectorID(iroad.getSector());
        temp.setHitMap(missing_mask);
        temp.setNMissing(nMissing);
        temp.setQOverPt(y);
 
        temp.setSubRegion(iroad.getSubRegion());
        temp.setHoughX(iroad.getX());
        temp.setHoughY(iroad.getY());
        temp.setHoughXBin(iroad.getXBin());
        temp.setHoughYBin(iroad.getYBin());
 
        temp.setBinIdx(iroad.getBinIdx());

        // Get a list of indices for all possible combinations given a certain
        // number of layers
        std::vector<std::vector<int>> combs;
        
        combs = getComboIndices(iroad.getNHits_layer());
 
        // Loop over possible combinations for this road
        for (size_t icomb = 0; icomb < combs.size(); icomb++) {
            std::vector<float> inputTensorValues;
            std::vector<std::shared_ptr<const FPGATrackSimHit>> hit_list;
 
            // list of indices for this particular combination
            std::vector<int> const &hit_indices = combs[icomb];
 
            // Loop over all layers
            for (unsigned layer = 0; layer < planeMap->getNLogiLayers(); layer++) {
 
                // Check to see if this is a valid hit
                if (hit_indices[layer] >= 0) {
 
                    std::shared_ptr<const FPGATrackSimHit> hit = iroad.getHitPtrs(layer)[hit_indices[layer]];
                    // Add this hit to the road
                    if (hit->isReal()){
                        hit_list.push_back(std::move(hit));
                    }
                }
            }
 
            // Sort the list by radial distance
            std::sort(hit_list.begin(), hit_list.end(),
                    [](std::shared_ptr<const FPGATrackSimHit> &hit1, std::shared_ptr<const FPGATrackSimHit> &hit2) {
                    double rho1 = std::hypot(hit1->getX(), hit1->getY());
                    double rho2 = std::hypot(hit2->getX(), hit2->getY());
                    return rho1 < rho2;
                    });
 
 
            int index = 1;
            bool flipZ = false;
            double rotateAngle = 0;
            bool gotSecondSP = false;
            float tmp_xf;
            float tmp_yf;
            float tmp_zf;
        float tmp_rf;
        float tmp_phif;
            // Loop over all hits
            for (const auto &hit : hit_list) {
                // Need to rotate hits
                float x0 = hit->getX();
                float y0 = hit->getY();
                float z0 = hit->getZ();
        float r0 = std::sqrt(x0*x0+y0*y0);
        float phi0 = hit->getGPhi();
        float xf = x0;
        float yf = y0;
        float zf = z0;
        float rf = r0;
        float phif = phi0;
        if (m_useCartesian) {
          if (index == 1) {
            if (z0 < 0)
              flipZ = true;
            rotateAngle = std::atan(x0 / y0);
            if (y0 < 0)
              rotateAngle += M_PI;
          }       
          xf = x0 * std::cos(rotateAngle) - y0 * std::sin(rotateAngle);
          yf = x0 * std::sin(rotateAngle) + y0 * std::cos(rotateAngle);
          zf = z0;
          if (flipZ) zf = z0 * -1;
        }
 
                // Get average of values for strip hit pairs
                // TODO: this needs to be fixed in the future, for this to work for other cases
                if (hit->isStrip()) {
          
          if (hit->getHitType() != HitType::spacepoint) { // this is a strip but not a SP!
            if (m_useCartesian) {
              float xf_scaled = (xf) / (getXScale());
              float yf_scaled = (yf) / (getYScale());
              float zf_scaled = (zf) / (getZScale());
              
              // Get average of two hits for strip hits
              inputTensorValues.push_back(xf_scaled);
              inputTensorValues.push_back(yf_scaled);
              inputTensorValues.push_back(zf_scaled);
              
            }
            else {
              float rf_scaled = (rf) / (getRScale());
              float phif_scaled = (phif) / (getPhiScale());
              float zf_scaled = (zf) / (getZScale());
              // Get average of two hits for strip hits
              inputTensorValues.push_back(rf_scaled);
              inputTensorValues.push_back(phif_scaled);
              inputTensorValues.push_back(zf_scaled);
            }
          }         
          else if (!gotSecondSP) {
            tmp_xf = xf;
            tmp_yf = yf;
            tmp_zf = zf;
            tmp_phif = phif;
            tmp_rf = rf;
            gotSecondSP = true;
          }
          else {
            gotSecondSP = false;
            if (m_useCartesian) {
              float xf_scaled = (xf + tmp_xf) / (2.*getXScale());
              float yf_scaled = (yf + tmp_yf) / (2.*getYScale());
              float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
              
              // Get average of two hits for strip hits 
              inputTensorValues.push_back(xf_scaled);
              inputTensorValues.push_back(yf_scaled);
              inputTensorValues.push_back(zf_scaled);
              index++;
            }
            else {
              float rf_scaled = (rf + tmp_rf) / (2.*getRScale());
              float phif_scaled = (phif + tmp_phif) / (2.*getPhiScale());
              float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
              inputTensorValues.push_back(rf_scaled);
              inputTensorValues.push_back(phif_scaled);
              inputTensorValues.push_back(zf_scaled);
            }
          }
                }
                else {
          if (m_useCartesian) {
            float xf_scaled = (xf) / (getXScale());
                    float yf_scaled = (yf) / (getYScale());
                    float zf_scaled = (zf) / (getZScale());
                    inputTensorValues.push_back(xf_scaled);
                    inputTensorValues.push_back(yf_scaled);
                    inputTensorValues.push_back(zf_scaled);
                    index++;
          }
          else {
            float rf_scaled = (rf) / (getRScale());
            float phif_scaled = (phif) / (getPhiScale());
            float zf_scaled = (zf) / (getZScale());
            inputTensorValues.push_back(rf_scaled);
            inputTensorValues.push_back(phif_scaled);
            inputTensorValues.push_back(zf_scaled);
          }
                }
            }
        
            if (inputTensorValues.size() != planeMap->getNLogiLayers()*3) {
                inputTensorValues.resize(planeMap->getNLogiLayers()*3);
            }
            inputTensorValues.resize(15); // Retain only the first 15 values for consistency
        
            inputTensorValuesAll.push_back(inputTensorValues);
            FPGATrackSimTrack track_cand;
        n_track++;
            track_cand.setTrackID(n_track);
            track_cand.setNLayers(planeMap->getNLogiLayers());
        track_cand.setNMissing(nMissing);
            for (unsigned ihit = 0; ihit < hit_list.size(); ihit++) {
              track_cand.setFPGATrackSimHit(ihit, hit_list[ihit]);
            }
            tracks.push_back(std::move(track_cand));
 
            ATH_MSG_DEBUG("NN InputTensorValues:");
            ATH_MSG_DEBUG(inputTensorValues);
        }  // loop over combinations
    }  // loop over roads

    auto NNoutputs = m_fakeNN_1st.runONNXInference(inputTensorValuesAll);
 
    for (unsigned itrack = 0; itrack < NNoutputs.size(); itrack++) {
 
        float nn_val = NNoutputs[itrack][0];
        ATH_MSG_DEBUG("NN output:" << nn_val);
        double chi2 = (1 - nn_val) * (tracks[itrack].getNCoords() - tracks[itrack].getNMissing() - 5);
    //std::cout << "1st stage" <<  chi2 << std::endl;
    tracks[itrack].setOrigChi2(chi2);
        tracks[itrack].setChi2(chi2);
    }
 
    // Add truth info
    for (FPGATrackSimTrack &t : tracks) {
        compute_truth(t);  // match the track to a geant particle using the
        // channel-level geant info in the hit data.
    }
    return StatusCode::SUCCESS;
}
 
 
StatusCode FPGATrackSimNNTrackTool::getTracks_2nd(std::vector<FPGATrackSimRoad> &roads, std::vector<FPGATrackSimTrack> &tracks) {
 
    ATH_CHECK(setRoadSectors(roads));
    int n_track = 0;
    std::vector<std::vector<float> >inputTensorValuesAll;
 
    // Loop over roads
    for (auto const &iroad : roads) {
 
      double y = iroad.getY();
 
      const FPGATrackSimPlaneMap *planeMap = m_FPGATrackSimMapping->PlaneMap_2nd(iroad.getSubRegion());
        // Get info on layers with missing hits
        int nMissing = 0;
        layer_bitmask_t missing_mask = iroad.getNWCLayers();
    layer_bitmask_t hit_mask = 0x0;
    for (unsigned ilayer = 0; ilayer < 13; ilayer++) {
      if ((missing_mask >> ilayer) & 0x1) {
        nMissing++;
        if (planeMap->isPixel(ilayer)) nMissing++; 
      }
      else {
        hit_mask |= (0x1 << ilayer);
      }
    }
        
        // Create a template track with common parameters filled already for
        // initializing below
        FPGATrackSimTrack temp;
        temp.setTrackStage(TrackStage::SECOND);
        temp.setNLayers(13);
        temp.setBankID(-1);
        temp.setPatternID(iroad.getPID());
        temp.setFirstSectorID(iroad.getSector());
        temp.setHitMap(hit_mask);
        temp.setNMissing(nMissing);
        temp.setQOverPt(y);
 
        temp.setSubRegion(iroad.getSubRegion());
        temp.setHoughX(iroad.getX());
        temp.setHoughY(iroad.getY());
        temp.setHoughXBin(iroad.getXBin());
        temp.setHoughYBin(iroad.getYBin());
        // Get a list of indices for all possible combinations given a certain
        // number of layers
        std::vector<std::vector<int>> combs =
            getComboIndices(iroad.getNHits_layer());
 
        // Loop over possible combinations for this road
        for (size_t icomb = 0; icomb < combs.size(); icomb++) {
            std::vector<float> inputTensorValues;
 
            // list of indices for this particular combination
            std::vector<int> const &hit_indices = combs[icomb];
            std::vector<std::shared_ptr<const FPGATrackSimHit>> hit_list;
 
            // Loop over all layers
            for (unsigned layer = 0; layer < 13; layer++) {
 
                // Check to see if this is a valid hit
                if (hit_indices[layer] >= 0) {
 
                    std::shared_ptr<const FPGATrackSimHit> hit = iroad.getHitPtrs(layer)[hit_indices[layer]];
                    // Add this hit to the road
                    if (hit->isReal()){
                        hit_list.push_back(std::move(hit));
                    }
                }
            }
 
            // Sort the list by radial distance
            std::sort(hit_list.begin(), hit_list.end(),
                    [](std::shared_ptr<const FPGATrackSimHit> &hit1, std::shared_ptr<const FPGATrackSimHit> &hit2) {
                    double rho1 = std::hypot(hit1->getX(), hit1->getY());
                    double rho2 = std::hypot(hit2->getX(), hit2->getY());
                    return rho1 < rho2;
                    });
 
 
            int index = 1;
            bool flipZ = false;
            double rotateAngle = 0;
            bool gotSecondSP = false;
            float tmp_xf;
            float tmp_yf;
            float tmp_zf;
        float tmp_rf;
        float tmp_phif;
            // Loop over all hits
            for (const auto &hit : hit_list) {
 
                // Need to rotate hits
                float x0 = hit->getX();
                float y0 = hit->getY();
                float z0 = hit->getZ();
        float r0 = std::sqrt(x0*x0+y0*y0);
                float phi0 = hit->getGPhi();
                float xf = x0;
                float yf = y0;
                float zf = z0;
        float rf = r0;
        float phif = phi0;
        
        if (m_useCartesian) {
          if (index == 1) {
                    if (z0 < 0)
              flipZ = true;
                    rotateAngle = std::atan(x0 / y0);
                    if (y0 < 0)
              rotateAngle += M_PI;
          }       
          xf = x0 * std::cos(rotateAngle) - y0 * std::sin(rotateAngle);
          yf = x0 * std::sin(rotateAngle) + y0 * std::cos(rotateAngle);
          zf = z0;
          
          if (flipZ) zf = z0 * -1;
        }
 
                // Get average of values for strip hit pairs
                // TODO: this needs to be fixed in the future, for this to work for other cases
                if (hit->isStrip()) {
 
          if (hit->getHitType() != HitType::spacepoint) { // this is a strip but not a SP!
            if (m_useCartesian) {
              float xf_scaled = (xf) / (getXScale());
              float yf_scaled = (yf) / (getYScale());
              float zf_scaled = (zf) / (getZScale());
              
              // Get average of two hits for strip hits
              inputTensorValues.push_back(xf_scaled);
              inputTensorValues.push_back(yf_scaled);
              inputTensorValues.push_back(zf_scaled);             
            }
            else {
              float rf_scaled = (rf) / (getRScale());
              float phif_scaled = (phif) / (getPhiScale());
              float zf_scaled = (zf) / (getZScale());
              // Get average of two hits for strip hits
              inputTensorValues.push_back(rf_scaled);
              inputTensorValues.push_back(phif_scaled);
              inputTensorValues.push_back(zf_scaled);
            }
          }
          else if (!gotSecondSP) {
            tmp_xf = xf;
            tmp_yf = yf;
            tmp_zf = zf;
            tmp_rf = rf;
            tmp_phif = phif;
            gotSecondSP = true;
          }
          else {
            gotSecondSP = false;
            if (m_useCartesian) {
              float xf_scaled = (xf + tmp_xf) / (2.*getXScale());
              float yf_scaled = (yf + tmp_yf) / (2.*getYScale());
              float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
              
              // Get average of two hits for strip hits
              inputTensorValues.push_back(xf_scaled);
              inputTensorValues.push_back(yf_scaled);
              inputTensorValues.push_back(zf_scaled);
              index++;
            }
            else {
              float rf_scaled = (rf + tmp_rf) / (2.*getRScale());
              float phif_scaled = (phif + tmp_phif) / (2.*getPhiScale());
              float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
              inputTensorValues.push_back(rf_scaled);
              inputTensorValues.push_back(phif_scaled);
              inputTensorValues.push_back(zf_scaled);
            }
          }
        }
        else {
          if (m_useCartesian) {
                    float xf_scaled = (xf) / (getXScale());
                    float yf_scaled = (yf) / (getYScale());
                    float zf_scaled = (zf) / (getZScale());
                    inputTensorValues.push_back(xf_scaled);
                    inputTensorValues.push_back(yf_scaled);
                    inputTensorValues.push_back(zf_scaled);
                    index++;
          }
          else {
                    float rf_scaled = (rf) / (getRScale());
                    float phif_scaled = (phif) / (getPhiScale());
                    float zf_scaled = (zf) / (getZScale());
                    inputTensorValues.push_back(rf_scaled);
                    inputTensorValues.push_back(phif_scaled);
                    inputTensorValues.push_back(zf_scaled);
          }
        }
        }
        
        
        if (inputTensorValues.size() < 39) {
          inputTensorValues.resize(39, 0.0f); // Resize to 39 and fill with 0.0f
        }
        else if (inputTensorValues.size() > 39) {
          inputTensorValues.resize(39); // Resize to 39 and keep the first 39 elements
        }
            inputTensorValuesAll.push_back(inputTensorValues);
 
            ATH_MSG_DEBUG("NN InputTensorValues:");
            ATH_MSG_DEBUG(inputTensorValues);
 
            n_track++;
            FPGATrackSimTrack track_cand;
            track_cand.setTrackID(n_track);
            track_cand.setNLayers(13);
        track_cand.setNMissing(nMissing);
            for (unsigned ihit = 0; ihit < hit_list.size(); ihit++) {
              track_cand.setFPGATrackSimHit(ihit, hit_list[ihit]);
            }
            tracks.push_back(std::move(track_cand));
 
        }  // loop over combinations
    }  // loop over roads

    auto NNoutputs = m_fakeNN_2nd.runONNXInference(inputTensorValuesAll);
    for (unsigned itrack = 0; itrack < NNoutputs.size(); itrack++) {
 
        float nn_val = NNoutputs[itrack][0];
        ATH_MSG_DEBUG("NN output:" << nn_val);
 
        double chi2 = (1 - nn_val) * (tracks[itrack].getNCoords() - tracks[itrack].getNMissing() - 5);
    
        tracks[itrack].setOrigChi2(chi2);
        tracks[itrack].setChi2(chi2);
    }
 
    // Add truth info
    for (FPGATrackSimTrack &t : tracks) {
        compute_truth(t);  // match the track to a geant particle using the
        // channel-level geant info in the hit data.
    }
 
    return StatusCode::SUCCESS;
}
 
StatusCode FPGATrackSimNNTrackTool::getTracks_GNN(std::vector<FPGATrackSimRoad> &roads, std::vector<FPGATrackSimTrack> &tracks) {
 
    ATH_CHECK(setRoadSectors(roads));
    int n_track = 0;
 
    std::vector<std::vector<float> >inputTensorValuesAll;
 
    // Loop over roads
    for (auto const &iroad : roads) {
        // Just used to get number of layers considered
        const FPGATrackSimPlaneMap *planeMap = m_FPGATrackSimMapping->PlaneMap_1st(iroad.getSubRegion());
 
        double y = iroad.getY();
 
        // Get info on layers with missing hits
        int nMissing = 0;
        //if missing_mask is set to zero, then the condition ""(missing_mask >> ilayer) 
        // & 1U" cannot be true.
        layer_bitmask_t missing_mask = iroad.getNWCLayers();
        layer_bitmask_t hit_mask = 0x0;
        for (unsigned ilayer = 0; ilayer < 13; ilayer++) {
          if ((missing_mask >> ilayer) & 0x1) {
            nMissing++;
            if (planeMap->isPixel(ilayer)) nMissing++;
          }
          else {
            hit_mask |= (0x1 << ilayer);
          }
        }
 
        // Create a template track with common parameters filled already for
        // initializing below
        FPGATrackSimTrack temp;
        temp.setTrackStage(TrackStage::FIRST);
        temp.setNLayers(planeMap->getNLogiLayers());
        temp.setBankID(-1);
        temp.setPatternID(iroad.getPID());
        temp.setFirstSectorID(iroad.getSector());
        temp.setHitMap(hit_mask);
        temp.setNMissing(nMissing);
        temp.setQOverPt(y);
 
        temp.setSubRegion(iroad.getSubRegion());
        temp.setHoughX(iroad.getX());
        temp.setHoughY(iroad.getY());
        temp.setHoughXBin(iroad.getXBin());
        temp.setHoughYBin(iroad.getYBin());

        // Get a list of indices for all possible combinations given a certain
        // number of layers
        std::vector<std::vector<int>> combs;
        std::vector<std::shared_ptr<const FPGATrackSimHit>> all_hits;
 
        std::vector<std::shared_ptr<const FPGATrackSimHit>> all_pixel_hits;
        std::vector<std::shared_ptr<const FPGATrackSimHit>> all_strip_hits;
        size_t pixelCount = 0;
 
        for (unsigned layer = 0; layer < iroad.getNLayers(); ++layer) {
            all_hits.insert(all_hits.end(), iroad.getHitPtrs(layer).begin(), iroad.getHitPtrs(layer).end());
        }
 
        for (const auto& hit : all_hits) {
            if(hit->isPixel()) {
                pixelCount++;
            }
        }
 
        if (pixelCount < 1) continue; // Cannot use a form a track candidate from a road that does not have a pixel hit
 
        std::vector<float> inputTensorValues;
        std::vector<std::shared_ptr<const FPGATrackSimHit>> hit_list;
 
        for (const auto &hit : all_hits) {
            if (hit->isReal()) {
                hit_list.push_back(hit);
            }
        }
 
        if (hit_list.size() < m_minNumberOfRealHitsInATrack) continue;
 
        // Sort the list by radial distance
        std::sort(hit_list.begin(), hit_list.end(),
                [](std::shared_ptr<const FPGATrackSimHit> &hit1, std::shared_ptr<const FPGATrackSimHit> &hit2) {
                double rho1 = std::hypot(hit1->getX(), hit1->getY());
                double rho2 = std::hypot(hit2->getX(), hit2->getY());
                return rho1 < rho2;
                });
 
 
        int index = 1;
        bool flipZ = false;
        double rotateAngle = 0;
        bool gotSecondSP = false;
        float tmp_xf;
        float tmp_yf;
        float tmp_zf;
        float tmp_phif;
        float tmp_rf;       
 
        // Loop over all hits
        for (const auto &hit : hit_list) {
            // Need to rotate hits
            float x0 = hit->getX();
            float y0 = hit->getY();
            float z0 = hit->getZ();
        float r0 = std::sqrt(x0*x0+y0*y0);
        float phi0 = hit->getGPhi();
        float xf = x0;
        float yf = y0;
        float zf = z0;
        float rf = r0;
        float phif = phi0;
        
        if (m_useCartesian) {
          if (index == 1) {
                if (z0 < 0)
          flipZ = true;
                rotateAngle = std::atan(x0 / y0);
                if (y0 < 0)
          rotateAngle += M_PI;
          }       
          xf = x0 * std::cos(rotateAngle) - y0 * std::sin(rotateAngle);
          yf = x0 * std::sin(rotateAngle) + y0 * std::cos(rotateAngle);
          zf = z0;
          
          if (flipZ) zf = z0 * -1;
        }
        
            // Get average of values for strip hit pairs
            // TODO: this needs to be fixed in the future, for this to work for other cases
            if (hit->isStrip()) {
 
          if (hit->getHitType() != HitType::spacepoint) { // this is a strip but not a SP!
        if (m_useCartesian) {
          float xf_scaled = (xf) / (getXScale());
          float yf_scaled = (yf) / (getYScale());
          float zf_scaled = (zf) / (getZScale());
          
          // Get average of two hits for strip hits
          inputTensorValues.push_back(xf_scaled);
          inputTensorValues.push_back(yf_scaled);
          inputTensorValues.push_back(zf_scaled);
          
        }
        else {
          float rf_scaled = (rf) / (getRScale());
          float phif_scaled = (phif) / (getPhiScale());
          float zf_scaled = (zf) / (getZScale());
          // Get average of two hits for strip hits
          inputTensorValues.push_back(rf_scaled);
          inputTensorValues.push_back(phif_scaled);
          inputTensorValues.push_back(zf_scaled);
        }
          }
          else if (!gotSecondSP) {
        tmp_xf = xf;
        tmp_yf = yf;
        tmp_zf = zf;
        tmp_phif = phif;
        tmp_rf = rf;
        gotSecondSP = true;
          }
          else {
        gotSecondSP = false;
        if (m_useCartesian) {
          float xf_scaled = (xf + tmp_xf) / (2.*getXScale());
          float yf_scaled = (yf + tmp_yf) / (2.*getYScale());
          float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
          
          // Get average of two hits for strip hits 
          inputTensorValues.push_back(xf_scaled);
          inputTensorValues.push_back(yf_scaled);
          inputTensorValues.push_back(zf_scaled);
          index++;
        }
        else {
          float rf_scaled = (rf + tmp_rf) / (2.*getRScale());
          float phif_scaled = (phif + tmp_phif) / (2.*getPhiScale());
          float zf_scaled = (zf + tmp_zf) / (2.*getZScale());
          inputTensorValues.push_back(rf_scaled);
          inputTensorValues.push_back(phif_scaled);
          inputTensorValues.push_back(zf_scaled);
        }
          }
            }
            else {
          if (m_useCartesian) {
                float xf_scaled = (xf) / (getXScale());
                float yf_scaled = (yf) / (getYScale());
                float zf_scaled = (zf) / (getZScale());
                inputTensorValues.push_back(xf_scaled);
                inputTensorValues.push_back(yf_scaled);
                inputTensorValues.push_back(zf_scaled);
                index++;
          }
          else {
        float rf_scaled = (rf) / (getRScale());
        float phif_scaled = (phif) / (getPhiScale());
        float zf_scaled = (zf) / (getZScale());
        inputTensorValues.push_back(rf_scaled);
        inputTensorValues.push_back(phif_scaled);
        inputTensorValues.push_back(zf_scaled);
          }
            }
        }
 
        // NN Estimator can either be 5 or 9 spacepoints as inputs
        // Let this be decided by m_nInputsGNN
 
        // NN Estimator needs 9 spacepoints -> 27 inputs
        // If there are more than 9 spacepoints entered, then it accepts the first 9
        // If there are less than 9 spacepoints, then it enters no values for it (although I actually probably need to just reject these)
        inputTensorValues.resize(m_nInputsGNN * 3); 
        
        inputTensorValuesAll.push_back(inputTensorValues);
        FPGATrackSimTrack track_cand;
        track_cand.setTrackID(n_track);
        track_cand.setNLayers(hit_list.size());
        for (unsigned ihit = 0; ihit < hit_list.size(); ihit++) {
          track_cand.setFPGATrackSimHit(ihit, hit_list[ihit]);
        }
        tracks.push_back(std::move(track_cand));
 
 
        ATH_MSG_DEBUG("NN InputTensorValues:");
        ATH_MSG_DEBUG(inputTensorValues);
    }  // loop over roads

    auto NNoutputs = m_fakeNN_1st.runONNXInference(inputTensorValuesAll);
 
    for (unsigned itrack = 0; itrack < NNoutputs.size(); itrack++) {
 
        float nn_val = NNoutputs[itrack][0];
        ATH_MSG_DEBUG("NN output:" << nn_val);
        double chi2 = (1 - nn_val) * (tracks[itrack].getNCoords() - tracks[itrack].getNMissing() - 5);
        tracks[itrack].setOrigChi2(chi2);
        tracks[itrack].setChi2(chi2);
    }
 
    // Add truth info
    for (FPGATrackSimTrack &t : tracks) {
        compute_truth(t);  // match the track to a geant particle using the
        // channel-level geant info in the hit data.
    }
 
    return StatusCode::SUCCESS;
}
 
 
 
 
// Borrowed same code from TrackFitter - probably a nicer way to inherit instead
void FPGATrackSimNNTrackTool::compute_truth(FPGATrackSimTrack &t) const {
    std::vector<FPGATrackSimMultiTruth> mtv;
 
    unsigned nl = (m_do2ndStage ? 13 : 5);
    const auto& hits = t.getFPGATrackSimHitPtrs();
    for (unsigned layer = 0; layer < nl; layer++) {
      if (!(t.getHitMap() & (1 << layer))) continue;
 
      // Sanity check that we have enough hits.
      if (layer < hits.size() && hits[layer])
        mtv.push_back(hits[layer]->getTruth());
      // adjust weight for hits without (and also with) a truth match, so that
      // each is counted with the same weight.
      mtv.back().assign_equal_normalization();
    }
    
    FPGATrackSimMultiTruth mt(std::accumulate(mtv.begin(), mtv.end(), FPGATrackSimMultiTruth(),
                FPGATrackSimMultiTruth::AddAccumulator()));
    // frac is then the fraction of the total number of hits on the track
    // attributed to the barcode.
 
    FPGATrackSimMultiTruth::Barcode tbarcode;
    FPGATrackSimMultiTruth::Weight tfrac;
    const bool ok = mt.best(tbarcode, tfrac);
    if (ok) {
        t.setEventIndex(tbarcode.first);
        t.setBarcode(tbarcode.second);
        t.setBarcodeFrac(tfrac);
    }
}