sPHENIXSeedFinder.cpp

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#include "sPHENIXSeedFinder.h"

#include "CylinderKalman.h"
#include "Pincushion.h"
#include "SimpleTrack3D.h"
#include "vector_math_inline.h"

#include <Eigen/Core>
#include <Eigen/Dense>
#include <Eigen/LU>

#include <algorithm>
#include <cfloat>
#include <cmath>
#include <cstddef>
#include <iostream>
#include <sys/time.h>
#include <utility>
#include <xmmintrin.h>

class HelixResolution;

#define LogDebug(exp)   std::cout<<"DEBUG: "  <<__FILE__<<": "<<__LINE__<<": "<< exp
#define LogError(exp)   std::cout<<"ERROR: "  <<__FILE__<<": "<<__LINE__<<": "<< exp
#define LogWarning(exp) std::cout<<"WARNING: "<<__FILE__<<": "<<__LINE__<<": "<< exp

using namespace std;
using namespace Eigen;
using namespace SeamStress;

class hit_triplet {
public:
  hit_triplet(unsigned int h1, unsigned int h2, unsigned int h3,
      unsigned int t, float c) :
      hit1(h1), hit2(h2), hit3(h3), track(t), chi2(c) {
  }
  ~hit_triplet() {
  }

  bool operator<(const hit_triplet& other) const {
    return (hit1 < other.hit1)
        || ((hit2 < other.hit2) && (hit1 == other.hit1))
        || ((hit3 < other.hit3) && (hit1 == other.hit1)
            && (hit2 == other.hit2));
  }

  bool operator==(const hit_triplet& other) const {
    return ((hit1 == other.hit1) && (hit2 == other.hit2)
        && (hit3 == other.hit3));
  }

  unsigned int hit1, hit2, hit3, track;
  float chi2;
};

class hitTriplet {
public:
  hitTriplet(unsigned int h1, unsigned int h2, unsigned int h3,
      unsigned int t, float c) :
      hit1(h1), hit2(h2), hit3(h3), track(t), chi2(c) {
  }
  ~hitTriplet() {
  }

  bool operator<(const hitTriplet& other) const {
    return (hit1 < other.hit1)
        || ((hit2 < other.hit2) && (hit1 == other.hit1))
        || ((hit3 < other.hit3) && (hit1 == other.hit1)
            && (hit2 == other.hit2));
  }

  bool operator==(const hitTriplet& other) const {
    return ((hit1 == other.hit1) && (hit2 == other.hit2)
        && (hit3 == other.hit3));
  }

  unsigned int hit1, hit2, hit3, track;
  float chi2;
};

void sPHENIXSeedFinder::tripletRejection(vector<SimpleTrack3D>& input,
           vector<SimpleTrack3D>& /*output*/, vector<bool>& usetrack,
    vector<float>& next_best_chi2) {

  vector<hitTriplet> trips;
  for (unsigned int i = 0; i < input.size(); ++i) {
    for (unsigned int h1 = 0; h1 < input[i].hits.size(); ++h1) {
      for (unsigned int h2 = (h1 + 1); h2 < input[i].hits.size(); ++h2) {
        for (unsigned int h3 = (h2 + 1); h3 < input[i].hits.size(); ++h3) {
          //if (cut_on_dca == false)
          {
            trips.push_back(hitTriplet(
                    input[i].hits[h1].get_id(), input[i].hits[h2].get_id(),
                    input[i].hits[h3].get_id(), i, track_states[i].chi2));
          }
        }
      }
    }
  }
  if (trips.size() == 0) {
    return;
  }
  sort(trips.begin(), trips.end());
  unsigned int pos = 0;
  // unsigned int cur_h1 = trips[pos].hit1;
  // unsigned int cur_h2 = trips[pos].hit2;
  while (pos < trips.size()) {
    unsigned int next_pos = pos + 1;
    if (next_pos >= trips.size()) {
      break;
    }
    while (trips[pos] == trips[next_pos]) {
      next_pos += 1;
      if (next_pos >= trips.size()) {
        break;
      }
    }
    if ((next_pos - pos) > 1) {
      float best_chi2 = trips[pos].chi2;
      float next_chi2 = trips[pos + 1].chi2;
      unsigned int best_pos = pos;
      for (unsigned int i = (pos + 1); i < next_pos; ++i) {
        if (input[trips[i].track].hits.size() <
            input[trips[best_pos].track].hits.size()) {
          continue;
        } else if ((input[trips[i].track].hits.size() >
                input[trips[best_pos].track].hits.size()) ||
            (input[trips[i].track].hits.back().get_layer() >
                input[trips[best_pos].track].hits.back().get_layer())) {
          next_chi2 = best_chi2;
          best_chi2 = trips[i].chi2;
          best_pos = i;
          continue;
        }
        if ((trips[i].chi2 < best_chi2) ||
            (usetrack[trips[best_pos].track] == false)) {
          next_chi2 = best_chi2;
          best_chi2 = trips[i].chi2;
          best_pos = i;
        } else if (trips[i].chi2 < next_chi2) {
          next_chi2 = trips[i].chi2;
        }
      }
      for (unsigned int i = pos; i < next_pos; ++i) {
        if (i != best_pos) {
          usetrack[trips[i].track] = false;
        } else {
          next_best_chi2[trips[i].track] = next_chi2;
        }
      }
    }
    pos = next_pos;
    // cur_h1 = trips[pos].hit1;
    // cur_h2 = trips[pos].hit2;
  }
}

sPHENIXSeedFinder::sPHENIXSeedFinder(unsigned int n_phi, unsigned int n_d,
                               unsigned int n_k, unsigned int n_dzdl,
                               unsigned int n_z0,
                               HelixResolution& min_resolution,
                               HelixResolution& max_resolution,
                               HelixRange& range, vector<float>& material,
                               vector<float>& radius, float Bfield)
    : HelixHough(n_phi, n_d, n_k, n_dzdl, n_z0, min_resolution, max_resolution,
                 range),
      fast_chi2_cut_par0(12.),
      fast_chi2_cut_par1(0.),
      fast_chi2_cut_max(FLT_MAX),
      chi2_cut(3.),
      chi2_removal_cut(1.),
      n_removal_hits(0),
      seeding(false),
      verbosity(0),
      cut_on_dca(false),
      dca_cut(0.01),
      vertex_x(0.),
      vertex_y(0.),
      vertex_z(0.),
      required_layers(0),
      reject_ghosts(false),
      nfits(0),
      findtracksiter(0),
      prev_max_k(0.),
      prev_max_dzdl(0.),
      prev_p_inv(0.),
      seed_layer(0),
      ca_chi2_cut(2.0),
      cosang_cut(0.985) {
  vector<float> detector_material;

  for (unsigned int i = 0; i < radius.size(); ++i) {
    detector_radii.push_back(radius[i]);
  }
  for (unsigned int i = 0; i < material.size(); ++i) {
    detector_scatter.push_back(1.41421356237309515 * 0.0136 *
                               sqrt(3. * material[i]));
    detector_material.push_back(3. * material[i]);
  }

  detector_B_field = Bfield;

  integrated_scatter.assign(detector_scatter.size(), 0.);
  float total_scatter_2 = 0.;
  for (unsigned int l = 0; l < detector_scatter.size(); ++l) {
    total_scatter_2 += detector_scatter[l] * detector_scatter[l];
    integrated_scatter[l] = sqrt(total_scatter_2);
  }

  kalman =
      new CylinderKalman(detector_radii, detector_material, detector_B_field);

  vector<SimpleHit3D> one_layer;
  layer_sorted.assign(n_layers, one_layer);
  for (unsigned int i = 0; i < 4; ++i) {
    layer_sorted_1[i].assign(n_layers, one_layer);
  }
  temp_comb.assign(n_layers, 0);
}

sPHENIXSeedFinder::sPHENIXSeedFinder(vector<vector<unsigned int> >& zoom_profile,
                               unsigned int minzoom, HelixRange& range,
                               vector<float>& material, vector<float>& radius,
                               float Bfield, bool parallel,
                               unsigned int num_threads)
    : HelixHough(zoom_profile, minzoom, range),
      fast_chi2_cut_par0(12.),
      fast_chi2_cut_par1(0.),
      fast_chi2_cut_max(FLT_MAX),
      chi2_cut(3.),
      chi2_removal_cut(1.),
      n_removal_hits(0),
      seeding(false),
      verbosity(0),
      cut_on_dca(false),
      dca_cut(0.01),
      vertex_x(0.),
      vertex_y(0.),
      vertex_z(0.),
      required_layers(0),
      reject_ghosts(false),
      nfits(0),
      findtracksiter(0),
      prev_max_k(0.),
      prev_max_dzdl(0.),
      prev_p_inv(0.),
      seed_layer(0),
      nthreads(num_threads),
      vssp(NULL),
      pins(NULL),
      is_parallel(parallel),
      is_thread(false),
      ca_chi2_cut(2.0),
      cosang_cut(0.985) {
  vector<float> detector_material;

  for (unsigned int i = 0; i < radius.size(); ++i) {
    detector_radii.push_back(radius[i]);
  }
  for (unsigned int i = 0; i < material.size(); ++i) {
    detector_scatter.push_back(
        1.41421356237309515 * 0.0136 * sqrt(3. * material[i]));
    detector_material.push_back(3. * material[i]);
  }

  detector_B_field = Bfield;

  integrated_scatter.assign(detector_scatter.size(), 0.);
  float total_scatter_2 = 0.;
  for (unsigned int l = 0; l < detector_scatter.size(); ++l) {
    total_scatter_2 += detector_scatter[l] * detector_scatter[l];
    integrated_scatter[l] = sqrt(total_scatter_2);
  }

  kalman = new CylinderKalman(detector_radii, detector_material,
      detector_B_field);

  vector<SimpleHit3D> one_layer;
  layer_sorted.assign(n_layers, one_layer);
  for (unsigned int i = 0; i < 4; ++i) {
    layer_sorted_1[i].assign(n_layers, one_layer);
  }
  temp_comb.assign(n_layers, 0);

  if (is_parallel == true) {
    Seamstress::init_vector(num_threads, vss);

    vssp = new vector<Seamstress*>();
    for (unsigned int i = 0; i < vss.size(); i++) {
      vssp->push_back(&(vss[i]));
    }

    pins = new Pincushion<sPHENIXSeedFinder>(this, vssp);

    vector<vector<unsigned int> > zoom_profile_new;
    for (unsigned int i = 1; i < zoom_profile.size(); ++i) {
      zoom_profile_new.push_back(zoom_profile[i]);
    }

    for (unsigned int i = 0; i < nthreads; ++i) {
      thread_trackers.push_back(
          new sPHENIXSeedFinder(zoom_profile, minzoom, range,
              material, radius, Bfield));
      thread_trackers.back()->setThread();
      thread_trackers.back()->setStartZoom(1);
      thread_tracks.push_back(vector<SimpleTrack3D>());
      thread_ranges.push_back(HelixRange());
      thread_hits.push_back(vector<SimpleHit3D>());
      split_output_hits.push_back(new vector<vector<SimpleHit3D> >());
      split_ranges.push_back(new vector<HelixRange>());
      split_input_hits.push_back(vector<SimpleHit3D>());
    }
  }
}

sPHENIXSeedFinder::~sPHENIXSeedFinder() {
  if (kalman != NULL)
    delete kalman;
  for (unsigned int i = 0; i < vss.size(); i++) {
    vss[i].stop();
  }
  for (unsigned int i = 0; i < thread_trackers.size(); ++i) {
    delete thread_trackers[i];
    delete split_output_hits[i];
    delete split_ranges[i];
  }

  if (pins != NULL)
    delete pins;
  if (vssp != NULL)
    delete vssp;
}

float sPHENIXSeedFinder::kappaToPt(float kappa) {
  return detector_B_field / 333.6 / kappa;
}

float sPHENIXSeedFinder::ptToKappa(float pt) {
  return detector_B_field / 333.6 / pt;
}

// hel should be +- 1
// static void xyTangent(SimpleHit3D& hit1, SimpleHit3D& hit2, float kappa,
//    float hel, float& ux_out, float& uy_out, float& ux_in, float& uy_in) {
//  float x = hit2.get_x() - hit1.get_x();
//  float y = hit2.get_y() - hit1.get_y();
//  float D = sqrt(x * x + y * y);
//  float ak = 0.5 * kappa * D;
//  float D_inv = 1. / D;
//  float hk = sqrt(1. - ak * ak);

//  float kcx = (ak * x + hel * hk * y) * D_inv;
//  float kcy = (ak * y - hel * hk * x) * D_inv;
//  float ktx = -(kappa * y - kcy);
//  float kty = kappa * x - kcx;
//  float norm = 1. / sqrt(ktx * ktx + kty * kty);
//  ux_out = ktx * norm;
//  uy_out = kty * norm;

//  ktx = kcy;
//  kty = -kcx;
//  norm = 1. / sqrt(ktx * ktx + kty * kty);
//  ux_in = ktx * norm;
//  uy_in = kty * norm;
// }

// hel should be +- 1
// static float cosScatter(SimpleHit3D& hit1, SimpleHit3D& hit2, SimpleHit3D& hit3,
//    float kappa, float hel) {
//  float ux_in = 0.;
//  float uy_in = 0.;
//  float ux_out = 0.;
//  float uy_out = 0.;

//  float temp1 = 0.;
//  float temp2 = 0.;

//  xyTangent(hit1, hit2, kappa, hel, ux_in, uy_in, temp1, temp2);
//  xyTangent(hit2, hit3, kappa, hel, temp1, temp2, ux_out, uy_out);

//  return ux_in * ux_out + uy_in * uy_out;
// }

// static float dzdsSimple(SimpleHit3D& hit1, SimpleHit3D& hit2, float k) {
//  float x = hit2.get_x() - hit1.get_x();
//  float y = hit2.get_y() - hit1.get_y();
//  float D = sqrt(x * x + y * y);
//  float s = 0.;
//  float temp1 = k * D * 0.5;
//  temp1 *= temp1;
//  float temp2 = D * 0.5;
//  s += 2. * temp2;
//  temp2 *= temp1;
//  s += temp2 / 3.;
//  temp2 *= temp1;
//  s += (3. / 20.) * temp2;
//  temp2 *= temp1;
//  s += (5. / 56.) * temp2;

//  return (hit2.get_z() - hit1.get_z()) / s;
// }

float sPHENIXSeedFinder::dcaToVertexXY(SimpleTrack3D& track, float vx,
    float vy) {
  float d_out = 0.;

  // find point at the dca to 0
  float x0 = track.d * cos(track.phi);
  float y0 = track.d * sin(track.phi);

  // change variables so x0,y0 -> 0,0
  float phi2 = atan2(
      (1. + track.kappa * track.d) * sin(track.phi) - track.kappa * y0,
      (1. + track.kappa * track.d) * cos(track.phi) - track.kappa * x0);

  // translate so that (0,0) -> (x0 - vx , y0 - vy)
  float cosphi = cos(phi2);
  float sinphi = sin(phi2);
  float tx = cosphi + track.kappa * (x0 - vx);
  float ty = sinphi + track.kappa * (y0 - vy);
  float dk = sqrt(tx * tx + ty * ty) - 1.;
  if (track.kappa == 0.) {
    d_out = (x0 - vx) * cosphi + (y0 - vy) * sinphi;
  } else {
    d_out = dk / track.kappa;
  }
  return fabs(d_out);
}

void sPHENIXSeedFinder::finalize(vector<SimpleTrack3D>& input,
    vector<SimpleTrack3D>& output) {

  if (is_thread == true) {
    for (unsigned int i = 0; i < input.size(); ++i) {
      output.push_back(input[i]);
    }
    return;
  }

  unsigned int nt = input.size();
  vector<bool> usetrack;
  usetrack.assign(input.size(), true);
  vector<float> next_best_chi2;
  next_best_chi2.assign(input.size(), 99999.);

  //LogDebug("input size: ")<<input.size()<<endl;

  if (reject_ghosts == true) {
    tripletRejection(input, output, usetrack, next_best_chi2);
  }

  vector<HelixKalmanState> states_new;

  for (unsigned int i = 0; i < nt; ++i) {
    if (usetrack[i] == true) {
      if (!(track_states[i].chi2 == track_states[i].chi2)) {
        continue;
      }

      output.push_back(input[i]);
      output.back().index = (output.size() - 1);
      states_new.push_back(track_states[i]);
      isolation_variable.push_back(next_best_chi2[i]);
    }
  }

  //LogDebug("output size: ")<<output.size()<<endl;

  track_states = states_new;
  if (smooth_back == true) {
    for (unsigned int i = 0; i < output.size(); ++i) {

      HelixKalmanState state = track_states[i];

      track_states[i].C *= 3.;
      track_states[i].chi2 = 0.;
      track_states[i].x_int = 0.;
      track_states[i].y_int = 0.;
      track_states[i].z_int = 0.;
      //       track_states[i].position = output[i].hits.size();
      track_states[i].position = 0;
      for (int h = (output[i].hits.size() - 1); h >= 0; --h) {
        SimpleHit3D hit = output[i].hits[h];
        float err_scale = 1.;
        int layer = hit.get_layer();
        if ((layer >= 0) && (layer < (int) (hit_error_scale.size()))) {
          err_scale = hit_error_scale[layer];
        }
        err_scale *= 3.0; // fudge factor, like needed due to non-gaussian errors

        // \todo location of a rescale fudge factor

        kalman->addHit(hit, track_states[i]);
        track_states[i].position = h;
      }

      //       track_states[i].C = state.C;
      track_states[i].chi2 = state.chi2;
      track_states[i].C *= 2. / 3.;

      output[i].phi = track_states[i].phi;
      output[i].d = track_states[i].d;
      output[i].kappa = track_states[i].kappa;
      output[i].z0 = track_states[i].z0;
      output[i].dzdl = track_states[i].dzdl;
    }
  }

  if (verbosity > 0) {
    cout << "# fits = " << nfits << endl;
    cout << "findTracks called " << findtracksiter << " times" << endl;
    cout << "CAtime = " << CAtime << endl;
    cout << "KALime = " << KALtime << endl;
  }
}

void sPHENIXSeedFinder::findTracks(vector<SimpleHit3D>& hits,
    vector<SimpleTrack3D>& tracks, const HelixRange& range) {

  findtracksiter += 1;
  findTracksBySegments(hits, tracks, range);
}

bool sPHENIXSeedFinder::breakRecursion(const vector<SimpleHit3D>& hits,
               const HelixRange& /*range*/) {
  if (seeding == true) {
    return false;
  }
  unsigned int layer_mask[4] = { 0, 0, 0, 0 };
  for (unsigned int i = 0; i < hits.size(); ++i) {
    if (hits[i].get_layer() < 32) {
      layer_mask[0] = layer_mask[0] | (1 << hits[i].get_layer());
    } else if (hits[i].get_layer() < 64) {
      layer_mask[1] = layer_mask[1] | (1 << (hits[i].get_layer() - 32));
    } else if (hits[i].get_layer() < 96) {
      layer_mask[2] = layer_mask[2] | (1 << (hits[i].get_layer() - 64));
    } else if (hits[i].get_layer() < 128) {
      layer_mask[3] = layer_mask[3] | (1 << (hits[i].get_layer() - 96));
    }
  }
  unsigned int nlayers = __builtin_popcount(layer_mask[0])
      + __builtin_popcount(layer_mask[1])
      + __builtin_popcount(layer_mask[2])
      + __builtin_popcount(layer_mask[3]);

  return (nlayers < required_layers);
}

float sPHENIXSeedFinder::phiError(SimpleHit3D& hit, float  /*min_k*/, float max_k,
          float min_d, float max_d, float /*min_z0*/, float /*max_z0*/, float /*min_dzdl*/,
    float max_dzdl, bool pairvoting) {
  float Bfield_inv = 1. / detector_B_field;
  float p_inv = 0.;

  if ((prev_max_k == max_k) && (prev_max_dzdl == max_dzdl)) {
    p_inv = prev_p_inv;
  } else {
    prev_max_k = max_k;
    prev_max_dzdl = max_dzdl;
    prev_p_inv = 3.33333333333333314e+02 * max_k * Bfield_inv
        * sqrt(1. - max_dzdl * max_dzdl);
    p_inv = prev_p_inv;
  }
  float total_scatter_2 = 0.;
  for (int i = seed_layer + 1; i <= (hit.get_layer()); ++i) {
    float this_scatter = detector_scatter[i - 1]
        * (detector_radii[i] - detector_radii[i - 1])
        / detector_radii[i];
    total_scatter_2 += this_scatter * this_scatter;
  }
  float angle = p_inv * sqrt(total_scatter_2) * 1.0;
  float dsize = 0.5 * (max_d - min_d);
  float angle_from_d = dsize / detector_radii[hit.get_layer()];
  float returnval = 0.;
  if (pairvoting == false) {
    if (angle_from_d > angle) {
      returnval = 0.;
    } else {
      returnval = (angle - angle_from_d);
    }
  } else {
    returnval = angle;
  }

  return returnval;
}

float sPHENIXSeedFinder::dzdlError(SimpleHit3D& hit, float /*min_k*/, float max_k,
           float /*min_d*/, float /*max_d*/, float min_z0, float max_z0, float /*min_dzdl*/,
    float max_dzdl, bool pairvoting) {
  float Bfield_inv = 1. / detector_B_field;
  float p_inv = 0.;

  if ((prev_max_k == max_k) && (prev_max_dzdl == max_dzdl)) {
    p_inv = prev_p_inv;
  } else {
    prev_max_k = max_k;
    prev_max_dzdl = max_dzdl;
    prev_p_inv = 3.33333333333333314e+02 * max_k * Bfield_inv
        * sqrt(1. - max_dzdl * max_dzdl);
    p_inv = prev_p_inv;
  }
  float total_scatter_2 = 0.;
  for (int i = seed_layer + 1; i <= (hit.get_layer()); ++i) {
    float this_scatter = detector_scatter[i - 1]
        * (detector_radii[i] - detector_radii[i - 1])
        / detector_radii[i];
    total_scatter_2 += this_scatter * this_scatter;
  }
  float angle = p_inv * sqrt(total_scatter_2) * 1.0;
  float z0size = 0.5 * (max_z0 - min_z0);
  float angle_from_z0 = z0size / detector_radii[hit.get_layer()];
  float returnval = 0.;
  if (pairvoting == false) {
    if (angle_from_z0 > angle) {
      returnval = 0.;
    } else {
      returnval = (angle - angle_from_z0);
    }
  } else {
    returnval = angle;
  }

  return returnval;
}

void sPHENIXSeedFinder::setRangeFromSeed(HelixRange& range,
    SimpleTrack3D& seed) {
  HelixKalmanState* state = &(seed_states[seed.index]);

  float dphi = 2. * sqrt(state->C(0, 0));
  float dd = 2. * sqrt(state->C(1, 1));
  float dk = 2. * state->C(2, 2);
  float dz0 = 2. * sqrt(state->C(3, 3));
  float ddzdl = 2. * sqrt(state->C(4, 4));

  range.min_phi = seed.phi - dphi;
  range.max_phi = seed.phi + dphi;
  if (range.min_phi < 0.) {
    range.min_phi = 0.;
  }
  if (range.max_phi > 2. * M_PI) {
    range.max_phi = 2. * M_PI;
  }
  range.min_d = seed.d - dd;
  range.max_d = seed.d + dd;
  range.min_k = seed.kappa - dk;
  range.max_k = seed.kappa + dk;
  if (range.min_k < 0.) {
    range.min_k = 0.;
  }

  range.min_k = range.min_k * range.min_k;
  range.max_k = range.max_k * range.max_k;

  range.min_dzdl = seed.dzdl - ddzdl;
  range.max_dzdl = seed.dzdl + ddzdl;
  range.min_z0 = seed.z0 - dz0;
  range.max_z0 = seed.z0 + dz0;
}

float sPHENIXSeedFinder::fitTrack(SimpleTrack3D& track) {
  vector<float> chi2_hit;
  return sPHENIXSeedFinder::fitTrack(track, chi2_hit);
}

float sPHENIXSeedFinder::fitTrack(SimpleTrack3D& track,
    vector<float>& chi2_hit) {
  chi2_hit.clear();
  vector<float> xyres;
  vector<float> xyres_inv;
  vector<float> zres;
  vector<float> zres_inv;
  for (unsigned int i = 0; i < track.hits.size(); i++) {


    xyres.push_back(
        sqrt(
            (0.5 * sqrt(12.) * sqrt(track.hits[i].get_size(0, 0)))
                * (0.5 * sqrt(12.)
                    * sqrt(track.hits[i].get_size(0, 0)))
                + (0.5 * sqrt(12.)
                    * sqrt(track.hits[i].get_size(1, 1)))
                    * (0.5 * sqrt(12.)
                        * sqrt(
                            track.hits[i].get_size(
                                1, 1)))));
    xyres_inv.push_back(1. / xyres.back());
    zres.push_back((0.5 * sqrt(12.) * sqrt(track.hits[i].get_size(2, 2))));
    zres_inv.push_back(1. / zres.back());
  }

  chi2_hit.resize(track.hits.size(), 0.);

  MatrixXf y = MatrixXf::Zero(track.hits.size(), 1);
  for (unsigned int i = 0; i < track.hits.size(); i++) {
    y(i, 0) =
        (pow(track.hits[i].get_x(), 2) + pow(track.hits[i].get_y(), 2));
    y(i, 0) *= xyres_inv[i];
  }

  MatrixXf X = MatrixXf::Zero(track.hits.size(), 3);
  for (unsigned int i = 0; i < track.hits.size(); i++) {
    X(i, 0) = track.hits[i].get_x();
    X(i, 1) = track.hits[i].get_y();
    X(i, 2) = -1.;
    X(i, 0) *= xyres_inv[i];
    X(i, 1) *= xyres_inv[i];
    X(i, 2) *= xyres_inv[i];
  }

  MatrixXf Xt = X.transpose();

  MatrixXf prod = Xt * X;

  MatrixXf Xty = Xt * y;
  MatrixXf beta = prod.ldlt().solve(Xty);

  float cx = beta(0, 0) * 0.5;
  float cy = beta(1, 0) * 0.5;
  float r = sqrt(cx * cx + cy * cy - beta(2, 0));

  float phi = atan2(cy, cx);
  float d = sqrt(cx * cx + cy * cy) - r;
  float k = 1. / r;

  MatrixXf diff = y - (X * beta);
  MatrixXf chi2 = (diff.transpose()) * diff;

  float dx = d * cos(phi);
  float dy = d * sin(phi);

  MatrixXf y2 = MatrixXf::Zero(track.hits.size(), 1);
  for (unsigned int i = 0; i < track.hits.size(); i++) {
    y2(i, 0) = track.hits[i].get_z();
    y2(i, 0) *= zres_inv[i];
  }

  MatrixXf X2 = MatrixXf::Zero(track.hits.size(), 2);
  for (unsigned int i = 0; i < track.hits.size(); i++) {
    float D = sqrt(
        pow(dx - track.hits[i].get_x(), 2)
            + pow(dy - track.hits[i].get_y(), 2));
    float s = 0.0;

    if (0.5 * k * D > 0.1) {
      float v = 0.5 * k * D;
      if (v >= 0.999999) {
        v = 0.999999;
      }
      s = 2. * asin(v) / k;
    } else {
      float temp1 = k * D * 0.5;
      temp1 *= temp1;
      float temp2 = D * 0.5;
      s += 2. * temp2;
      temp2 *= temp1;
      s += temp2 / 3.;
      temp2 *= temp1;
      s += (3. / 20.) * temp2;
      temp2 *= temp1;
      s += (5. / 56.) * temp2;
    }

    X2(i, 0) = s;
    X2(i, 1) = 1.0;

    X2(i, 0) *= zres_inv[i];
    X2(i, 1) *= zres_inv[i];
  }

  MatrixXf Xt2 = X2.transpose();
  MatrixXf prod2 = Xt2 * X2;

  MatrixXf Xty2 = Xt2 * y2;
  MatrixXf beta2 = prod2.ldlt().solve(Xty2);

  MatrixXf diff2 = y2 - (X2 * beta2);
  MatrixXf chi2_z = (diff2.transpose()) * diff2;

  float z0 = beta2(1, 0);
  float dzdl = beta2(0, 0) / sqrt(1. + beta2(0, 0) * beta2(0, 0));

  track.phi = phi;
  track.d = d;
  track.kappa = k;
  track.dzdl = dzdl;
  track.z0 = z0;

  if (track.kappa != 0.) {
    r = 1. / track.kappa;
  } else {
    r = 1.0e10;
  }

  cx = (track.d + r) * cos(track.phi);
  cy = (track.d + r) * sin(track.phi);

  float chi2_tot = 0.;
  for (unsigned int h = 0; h < track.hits.size(); h++) {
    float dx1 = track.hits[h].get_x() - cx;
    float dy1 = track.hits[h].get_y() - cy;

    float dx2 = track.hits[h].get_x() + cx;
    float dy2 = track.hits[h].get_y() + cy;

    float xydiff1 = sqrt(dx1 * dx1 + dy1 * dy1) - r;
    float xydiff2 = sqrt(dx2 * dx2 + dy2 * dy2) - r;
    float xydiff = xydiff2;
    if (fabs(xydiff1) < fabs(xydiff2)) {
      xydiff = xydiff1;
    }

    float ls_xy = xyres[h];

    chi2_hit[h] = 0.;
    chi2_hit[h] += xydiff * xydiff / (ls_xy * ls_xy);
    chi2_hit[h] += diff2(h, 0) * diff2(h, 0);

    chi2_tot += chi2_hit[h];
  }

  unsigned int deg_of_freedom = 2 * track.hits.size() - 5;

  return (chi2_tot) / ((float) (deg_of_freedom));
}

void sPHENIXSeedFinder::calculateKappaTangents(float* x1_a, float* y1_a,
    float* z1_a, float* x2_a, float* y2_a, float* z2_a, float* x3_a,
    float* y3_a, float* z3_a, float* dx1_a, float* dy1_a, float* dz1_a,
    float* dx2_a, float* dy2_a, float* dz2_a, float* dx3_a, float* dy3_a,
    float* dz3_a, float* kappa_a, float* dkappa_a, float* ux_mid_a,
    float* uy_mid_a, float* ux_end_a, float* uy_end_a, float* dzdl_1_a,
    float* dzdl_2_a, float* ddzdl_1_a, float* ddzdl_2_a) {
  static const __m128 two = { 2., 2., 2., 2. };

  __m128 x1 = _mm_load_ps(x1_a);
  __m128 x2 = _mm_load_ps(x2_a);
  __m128 x3 = _mm_load_ps(x3_a);
  __m128 y1 = _mm_load_ps(y1_a);
  __m128 y2 = _mm_load_ps(y2_a);
  __m128 y3 = _mm_load_ps(y3_a);
  __m128 z1 = _mm_load_ps(z1_a);
  __m128 z2 = _mm_load_ps(z2_a);
  __m128 z3 = _mm_load_ps(z3_a);

  __m128 dx1 = _mm_load_ps(dx1_a);
  __m128 dx2 = _mm_load_ps(dx2_a);
  __m128 dx3 = _mm_load_ps(dx3_a);
  __m128 dy1 = _mm_load_ps(dy1_a);
  __m128 dy2 = _mm_load_ps(dy2_a);
  __m128 dy3 = _mm_load_ps(dy3_a);
  __m128 dz1 = _mm_load_ps(dz1_a);
  __m128 dz2 = _mm_load_ps(dz2_a);
  __m128 dz3 = _mm_load_ps(dz3_a);

  __m128 D12 = _mm_sub_ps(x2, x1);
  D12 = _mm_mul_ps(D12, D12);
  __m128 tmp1 = _mm_sub_ps(y2, y1);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D12 = _mm_add_ps(D12, tmp1);
  D12 = _vec_sqrt_ps(D12);

  __m128 D23 = _mm_sub_ps(x3, x2);
  D23 = _mm_mul_ps(D23, D23);
  tmp1 = _mm_sub_ps(y3, y2);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D23 = _mm_add_ps(D23, tmp1);
  D23 = _vec_sqrt_ps(D23);

  __m128 D31 = _mm_sub_ps(x1, x3);
  D31 = _mm_mul_ps(D31, D31);
  tmp1 = _mm_sub_ps(y1, y3);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D31 = _mm_add_ps(D31, tmp1);
  D31 = _vec_sqrt_ps(D31);

  __m128 k = _mm_mul_ps(D12, D23);
  k = _mm_mul_ps(k, D31);
  k = _vec_rec_ps(k);
  tmp1 = (D12 + D23 + D31) * (D23 + D31 - D12) * (D12 + D31 - D23)
      * (D12 + D23 - D31);
  tmp1 = _vec_sqrt_ps(tmp1);
  k *= tmp1;

  __m128 tmp2 = _mm_cmpgt_ps(tmp1, zero);
  tmp1 = _mm_and_ps(tmp2, k);
  tmp2 = _mm_andnot_ps(tmp2, zero);
  k = _mm_xor_ps(tmp1, tmp2);

  _mm_store_ps(kappa_a, k);
  __m128 k_inv = _vec_rec_ps(k);

  __m128 D12_inv = _vec_rec_ps(D12);
  __m128 D23_inv = _vec_rec_ps(D23);
  __m128 D31_inv = _vec_rec_ps(D31);

  __m128 dr1 = dx1 * dx1 + dy1 * dy1;
  dr1 = _vec_sqrt_ps(dr1);
  __m128 dr2 = dx2 * dx2 + dy2 * dy2;
  dr2 = _vec_sqrt_ps(dr2);
  __m128 dr3 = dx3 * dx3 + dy3 * dy3;
  dr3 = _vec_sqrt_ps(dr3);

  __m128 dk1 = (dr1 + dr2) * D12_inv * D12_inv;
  __m128 dk2 = (dr2 + dr3) * D23_inv * D23_inv;
  __m128 dk = dk1 + dk2;
  _mm_store_ps(dkappa_a, dk);

  __m128 ux12 = (x2 - x1) * D12_inv;
  __m128 uy12 = (y2 - y1) * D12_inv;
  __m128 ux23 = (x3 - x2) * D23_inv;
  __m128 uy23 = (y3 - y2) * D23_inv;
  __m128 ux13 = (x3 - x1) * D31_inv;
  __m128 uy13 = (y3 - y1) * D31_inv;

  __m128 cosalpha = ux12 * ux13 + uy12 * uy13;
  __m128 sinalpha = ux13 * uy12 - ux12 * uy13;

  __m128 ux_mid = ux23 * cosalpha - uy23 * sinalpha;
  __m128 uy_mid = ux23 * sinalpha + uy23 * cosalpha;
  _mm_store_ps(ux_mid_a, ux_mid);
  _mm_store_ps(uy_mid_a, uy_mid);

  __m128 ux_end = ux23 * cosalpha + uy23 * sinalpha;
  __m128 uy_end = uy23 * cosalpha - ux23 * sinalpha;

  _mm_store_ps(ux_end_a, ux_end);
  _mm_store_ps(uy_end_a, uy_end);

  // asin(x) = 2*atan( x/( 1 + sqrt( 1 - x*x ) ) )
  __m128 v = one - sinalpha * sinalpha;
  v = _vec_sqrt_ps(v);
  v += one;
  v = _vec_rec_ps(v);
  v *= sinalpha;
  __m128 s2 = _vec_atan_ps(v);
  s2 *= two;
  s2 *= k_inv;
  tmp1 = _mm_cmpgt_ps(k, zero);
  tmp2 = _mm_and_ps(tmp1, s2);
  tmp1 = _mm_andnot_ps(tmp1, D23);
  s2 = _mm_xor_ps(tmp1, tmp2);

  // dz/dl = (dz/ds)/sqrt(1 + (dz/ds)^2)
  // = dz/sqrt(s^2 + dz^2)
  __m128 del_z_2 = z3 - z2;
  __m128 dzdl_2 = s2 * s2 + del_z_2 * del_z_2;
  dzdl_2 = _vec_rsqrt_ps(dzdl_2);
  dzdl_2 *= del_z_2;
  __m128 ddzdl_2 = (dz2 + dz3) * D23_inv;
  _mm_store_ps(dzdl_2_a, dzdl_2);
  _mm_store_ps(ddzdl_2_a, ddzdl_2);

  sinalpha = ux13 * uy23 - ux23 * uy13;
  v = one - sinalpha * sinalpha;
  v = _vec_sqrt_ps(v);
  v += one;
  v = _vec_rec_ps(v);
  v *= sinalpha;
  __m128 s1 = _vec_atan_ps(v);
  s1 *= two;
  s1 *= k_inv;
  tmp1 = _mm_cmpgt_ps(k, zero);
  tmp2 = _mm_and_ps(tmp1, s1);
  tmp1 = _mm_andnot_ps(tmp1, D12);
  s1 = _mm_xor_ps(tmp1, tmp2);

  __m128 del_z_1 = z2 - z1;
  __m128 dzdl_1 = s1 * s1 + del_z_1 * del_z_1;
  dzdl_1 = _vec_rsqrt_ps(dzdl_1);
  dzdl_1 *= del_z_1;
  __m128 ddzdl_1 = (dz1 + dz2) * D12_inv;
  _mm_store_ps(dzdl_1_a, dzdl_1);
  _mm_store_ps(ddzdl_1_a, ddzdl_1);
}

void sPHENIXSeedFinder::calculateKappaTangents(float* x1_a, float* y1_a,
    float* z1_a, float* x2_a, float* y2_a, float* z2_a, float* x3_a,
    float* y3_a, float* z3_a, float* dx1_a, float* dy1_a, float* dz1_a,
    float* dx2_a, float* dy2_a, float* dz2_a, float* dx3_a, float* dy3_a,
    float* dz3_a, float* kappa_a, float* dkappa_a, float* ux_mid_a,
    float* uy_mid_a, float* ux_end_a, float* uy_end_a, float* dzdl_1_a,
    float* dzdl_2_a, float* ddzdl_1_a, float* ddzdl_2_a, float sinang_cut,
    float cosang_diff_inv, float* cur_kappa_a, float* cur_dkappa_a,
    float* cur_ux_a, float* cur_uy_a, float* cur_chi2_a, float* chi2_a) {
  static const __m128 two = { 2., 2., 2., 2. };

  __m128 x1 = _mm_load_ps(x1_a);
  __m128 x2 = _mm_load_ps(x2_a);
  __m128 x3 = _mm_load_ps(x3_a);
  __m128 y1 = _mm_load_ps(y1_a);
  __m128 y2 = _mm_load_ps(y2_a);
  __m128 y3 = _mm_load_ps(y3_a);
  __m128 z1 = _mm_load_ps(z1_a);
  __m128 z2 = _mm_load_ps(z2_a);
  __m128 z3 = _mm_load_ps(z3_a);

  __m128 dx1 = _mm_load_ps(dx1_a);
  __m128 dx2 = _mm_load_ps(dx2_a);
  __m128 dx3 = _mm_load_ps(dx3_a);
  __m128 dy1 = _mm_load_ps(dy1_a);
  __m128 dy2 = _mm_load_ps(dy2_a);
  __m128 dy3 = _mm_load_ps(dy3_a);
  __m128 dz1 = _mm_load_ps(dz1_a);
  __m128 dz2 = _mm_load_ps(dz2_a);
  __m128 dz3 = _mm_load_ps(dz3_a);

  __m128 D12 = _mm_sub_ps(x2, x1);
  D12 = _mm_mul_ps(D12, D12);
  __m128 tmp1 = _mm_sub_ps(y2, y1);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D12 = _mm_add_ps(D12, tmp1);
  D12 = _vec_sqrt_ps(D12);

  __m128 D23 = _mm_sub_ps(x3, x2);
  D23 = _mm_mul_ps(D23, D23);
  tmp1 = _mm_sub_ps(y3, y2);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D23 = _mm_add_ps(D23, tmp1);
  D23 = _vec_sqrt_ps(D23);

  __m128 D31 = _mm_sub_ps(x1, x3);
  D31 = _mm_mul_ps(D31, D31);
  tmp1 = _mm_sub_ps(y1, y3);
  tmp1 = _mm_mul_ps(tmp1, tmp1);
  D31 = _mm_add_ps(D31, tmp1);
  D31 = _vec_sqrt_ps(D31);

  __m128 k = _mm_mul_ps(D12, D23);
  k = _mm_mul_ps(k, D31);
  k = _vec_rec_ps(k);
  tmp1 = (D12 + D23 + D31) * (D23 + D31 - D12) * (D12 + D31 - D23)
      * (D12 + D23 - D31);
  tmp1 = _vec_sqrt_ps(tmp1);
  k *= tmp1;

  __m128 tmp2 = _mm_cmpgt_ps(tmp1, zero);
  tmp1 = _mm_and_ps(tmp2, k);
  tmp2 = _mm_andnot_ps(tmp2, zero);
  k = _mm_xor_ps(tmp1, tmp2);

  _mm_store_ps(kappa_a, k);
  __m128 k_inv = _vec_rec_ps(k);

  __m128 D12_inv = _vec_rec_ps(D12);
  __m128 D23_inv = _vec_rec_ps(D23);
  __m128 D31_inv = _vec_rec_ps(D31);

  __m128 dr1 = dx1 * dx1 + dy1 * dy1;
  dr1 = _vec_sqrt_ps(dr1);
  __m128 dr2 = dx2 * dx2 + dy2 * dy2;
  dr2 = _vec_sqrt_ps(dr2);
  __m128 dr3 = dx3 * dx3 + dy3 * dy3;
  dr3 = _vec_sqrt_ps(dr3);

  __m128 dk1 = (dr1 + dr2) * D12_inv * D12_inv;
  __m128 dk2 = (dr2 + dr3) * D23_inv * D23_inv;
  __m128 dk = dk1 + dk2;
  _mm_store_ps(dkappa_a, dk);

  __m128 ux12 = (x2 - x1) * D12_inv;
  __m128 uy12 = (y2 - y1) * D12_inv;
  __m128 ux23 = (x3 - x2) * D23_inv;
  __m128 uy23 = (y3 - y2) * D23_inv;
  __m128 ux13 = (x3 - x1) * D31_inv;
  __m128 uy13 = (y3 - y1) * D31_inv;

  __m128 cosalpha = ux12 * ux13 + uy12 * uy13;
  __m128 sinalpha = ux13 * uy12 - ux12 * uy13;

  __m128 ux_mid = ux23 * cosalpha - uy23 * sinalpha;
  __m128 uy_mid = ux23 * sinalpha + uy23 * cosalpha;
  _mm_store_ps(ux_mid_a, ux_mid);
  _mm_store_ps(uy_mid_a, uy_mid);

  __m128 ux_end = ux23 * cosalpha + uy23 * sinalpha;
  __m128 uy_end = uy23 * cosalpha - ux23 * sinalpha;

  _mm_store_ps(ux_end_a, ux_end);
  _mm_store_ps(uy_end_a, uy_end);

  // asin(x) = 2*atan( x/( 1 + sqrt( 1 - x*x ) ) )
  __m128 v = one - sinalpha * sinalpha;
  v = _vec_sqrt_ps(v);
  v += one;
  v = _vec_rec_ps(v);
  v *= sinalpha;
  __m128 s2 = _vec_atan_ps(v);
  s2 *= two;
  s2 *= k_inv;
  tmp1 = _mm_cmpgt_ps(k, zero);
  tmp2 = _mm_and_ps(tmp1, s2);
  tmp1 = _mm_andnot_ps(tmp1, D23);
  s2 = _mm_xor_ps(tmp1, tmp2);

  // dz/dl = (dz/ds)/sqrt(1 + (dz/ds)^2)
  // = dz/sqrt(s^2 + dz^2)
  __m128 del_z_2 = z3 - z2;
  __m128 dzdl_2 = s2 * s2 + del_z_2 * del_z_2;
  dzdl_2 = _vec_rsqrt_ps(dzdl_2);
  dzdl_2 *= del_z_2;
  __m128 ddzdl_2 = (dz2 + dz3) * D23_inv;
  _mm_store_ps(dzdl_2_a, dzdl_2);
  _mm_store_ps(ddzdl_2_a, ddzdl_2);

  sinalpha = ux13 * uy23 - ux23 * uy13;
  v = one - sinalpha * sinalpha;
  v = _vec_sqrt_ps(v);
  v += one;
  v = _vec_rec_ps(v);
  v *= sinalpha;
  __m128 s1 = _vec_atan_ps(v);
  s1 *= two;
  s1 *= k_inv;
  tmp1 = _mm_cmpgt_ps(k, zero);
  tmp2 = _mm_and_ps(tmp1, s1);
  tmp1 = _mm_andnot_ps(tmp1, D12);
  s1 = _mm_xor_ps(tmp1, tmp2);

  __m128 del_z_1 = z2 - z1;
  __m128 dzdl_1 = s1 * s1 + del_z_1 * del_z_1;
  dzdl_1 = _vec_rsqrt_ps(dzdl_1);
  dzdl_1 *= del_z_1;
  __m128 ddzdl_1 = (dz1 + dz2) * D12_inv;
  _mm_store_ps(dzdl_1_a, dzdl_1);
  _mm_store_ps(ddzdl_1_a, ddzdl_1);

  __m128 c_dk = _mm_load_ps(cur_dkappa_a);
  __m128 c_k = _mm_load_ps(cur_kappa_a);
  __m128 c_ux = _mm_load_ps(cur_ux_a);
  __m128 c_uy = _mm_load_ps(cur_uy_a);
  __m128 c_chi2 = _mm_load_ps(cur_chi2_a);
  __m128 sinang = _mm_load1_ps(&sinang_cut);
  __m128 cosdiff = _mm_load1_ps(&cosang_diff_inv);

  __m128 kdiff = c_k - k;
  __m128 n_dk = c_dk + dk + sinang * k;
  __m128 chi2_k = kdiff * kdiff / (n_dk * n_dk);
  __m128 cos_scatter = c_ux * ux_mid + c_uy * uy_mid;
  __m128 chi2_ang = (one - cos_scatter) * (one - cos_scatter) * cosdiff
      * cosdiff;
  tmp1 = dzdl_1 * sinang;
  _vec_fabs_ps(tmp1);
  __m128 chi2_dzdl = (dzdl_1 - dzdl_2) / (ddzdl_1 + ddzdl_2 + tmp1);
  chi2_dzdl *= chi2_dzdl;
  chi2_dzdl *= one_o_2;

  __m128 n_chi2 = c_chi2 + chi2_ang + chi2_k + chi2_dzdl;
  _mm_store_ps(chi2_a, n_chi2);
}

struct TempComb {
  TempComb() {
  }
  HelixKalmanState state;
  SimpleTrack3D track;

  inline bool operator<(const TempComb& other) const {
    if (track.hits.size() > other.track.hits.size()) {
      return true;
    } else if (track.hits.size() == other.track.hits.size()) {
      return state.chi2 < other.state.chi2;
    } else {
      return false;
    }
  }
};

void sPHENIXSeedFinder::initDummyHits(vector<SimpleHit3D>& dummies,
    const HelixRange& range, HelixKalmanState& init_state) {
  SimpleTrack3D dummy_track;
  dummy_track.hits.push_back(SimpleHit3D());
  dummy_track.kappa = 0.5 * (range.min_k + range.max_k);
  dummy_track.phi = 0.5 * (range.min_phi + range.max_phi);
  dummy_track.d = 0.5 * (range.min_d + range.max_d);
  dummy_track.dzdl = 0.5 * (range.min_dzdl + range.max_dzdl);
  dummy_track.z0 = 0.5 * (range.min_z0 + range.max_z0);

  init_state.kappa = dummy_track.kappa;
  init_state.nu = sqrt(dummy_track.kappa);
  init_state.phi = dummy_track.phi;
  init_state.d = dummy_track.d;
  init_state.dzdl = dummy_track.dzdl;
  init_state.z0 = dummy_track.z0;

  init_state.C = Matrix<float, 5, 5>::Zero(5, 5);
  init_state.C(0, 0) = pow(range.max_phi - range.min_phi, 2.);
  init_state.C(1, 1) = pow(range.max_d - range.min_d, 2.);
  init_state.C(2, 2) = pow(10. * sqrt(range.max_k - range.min_k), 2.);
  init_state.C(3, 3) = pow(range.max_z0 - range.min_z0, 2.);
  init_state.C(4, 4) = pow(range.max_dzdl - range.min_dzdl, 2.);
  init_state.chi2 = 0.;
  init_state.position = 0;
  init_state.x_int = 0.;
  init_state.y_int = 0.;
  init_state.z_int = 0.;

  for (unsigned int i = 0; i < n_layers; ++i) {
    float x, y, z;
    projectToLayer(dummy_track, i, x, y, z);
    dummies[i].set_x(x);
    dummies[i].set_y(x);
    dummies[i].set_z(x);
    dummies[i].set_layer(i);
  }
}

// static void triplet_rejection(vector<SimpleTrack3D>& input,
//    vector<float>& chi2s, vector<bool>& usetrack) {
//  vector<hit_triplet> trips;
//  for (unsigned int i = 0; i < input.size(); ++i) {
//    for (unsigned int h1 = 0; h1 < input[i].hits.size(); ++h1) {
//      for (unsigned int h2 = (h1 + 1); h2 < input[i].hits.size(); ++h2) {
//        for (unsigned int h3 = (h2 + 1); h3 < input[i].hits.size();
//            ++h3) {
//          trips.push_back(
//              hit_triplet(input[i].hits[h1].get_id(),
//                  input[i].hits[h2].get_id(),
//                  input[i].hits[h3].get_id(), i, chi2s[i]));
//        }
//      }
//    }
//  }
//  if (trips.size() == 0) {
//    return;
//  }
//  sort(trips.begin(), trips.end());
//  unsigned int pos = 0;
//  unsigned int cur_h1 = trips[pos].hit1;
//  unsigned int cur_h2 = trips[pos].hit2;
//  while (pos < trips.size()) {
//    unsigned int next_pos = pos + 1;
//    if (next_pos >= trips.size()) {
//      break;
//    }
//    while (trips[pos] == trips[next_pos]) {
//      next_pos += 1;
//      if (next_pos >= trips.size()) {
//        break;
//      }
//    }
//    if ((next_pos - pos) > 1) {
//      float best_chi2 = trips[pos].chi2;
//      float next_chi2 = trips[pos + 1].chi2;
//      unsigned int best_pos = pos;
//      for (unsigned int i = (pos + 1); i < next_pos; ++i) {
//        if (input[trips[i].track].hits.size()
//            < input[trips[best_pos].track].hits.size()) {
//          continue;
//        } else if ((input[trips[i].track].hits.size()
//            > input[trips[best_pos].track].hits.size())
//            || (input[trips[i].track].hits.back().get_layer()
//                > input[trips[best_pos].track].hits.back().get_layer())) {
//          next_chi2 = best_chi2;
//          best_chi2 = trips[i].chi2;
//          best_pos = i;
//          continue;
//        }
//        if ((trips[i].chi2 < best_chi2)
//            || (usetrack[trips[best_pos].track] == false)) {
//          next_chi2 = best_chi2;
//          best_chi2 = trips[i].chi2;
//          best_pos = i;
//        } else if (trips[i].chi2 < next_chi2) {
//          next_chi2 = trips[i].chi2;
//        }
//      }
//      for (unsigned int i = pos; i < next_pos; ++i) {
//        if (i != best_pos) {
//          usetrack[trips[i].track] = false;
//        }
//      }
//    }
//    pos = next_pos;
//    cur_h1 = trips[pos].hit1;
//    cur_h2 = trips[pos].hit2;
//  }
// }

void sPHENIXSeedFinder::findTracksBySegments(vector<SimpleHit3D>& hits,
               vector<SimpleTrack3D>& tracks, const HelixRange& /*range*/) {

  vector<TrackSegment>* cur_seg = &segments1;
  vector<TrackSegment>* next_seg = &segments2;
  unsigned int curseg_size = 0;
  unsigned int nextseg_size = 0;

  vector<TrackSegment> complete_segments;

  unsigned int allowed_missing = n_layers - req_layers;
  for (unsigned int l = 0; l < n_layers; ++l) {
    layer_sorted[l].clear();
  }
  for (unsigned int i = 0; i < hits.size(); ++i) {
    unsigned int min = (hits[i].get_layer() - allowed_missing);
    if (allowed_missing > (unsigned int) hits[i].get_layer()) {
      min = 0;
    }
    for (int l = min; l <= hits[i].get_layer(); l += 1) {
      layer_sorted[l].push_back(hits[i]);
    }
  }
  for (unsigned int l = 0; l < n_layers; ++l) {
    if (layer_sorted[l].size() == 0) {
      return;
    }
  }

  timeval t1, t2;
  double time1 = 0.;
  double time2 = 0.;

  gettimeofday(&t1, NULL);

  float cosang_diff = 1. - cosang_cut;
  float cosang_diff_inv = 1. / cosang_diff;
  float sinang_cut = sqrt(1. - cosang_cut * cosang_cut);
  float easy_chi2_cut = ca_chi2_cut;

  vector<float> inv_layer;
  inv_layer.assign(n_layers, 1.);
  for (unsigned int l = 3; l < n_layers; ++l) {
    inv_layer[l] = 1. / (((float) l) - 2.);
  }

  unsigned int hit_counter = 0;
  float x1_a[4] __attribute__((aligned(16)));
  float x2_a[4] __attribute__((aligned(16)));
  float x3_a[4] __attribute__((aligned(16)));
  float y1_a[4] __attribute__((aligned(16)));
  float y2_a[4] __attribute__((aligned(16)));
  float y3_a[4] __attribute__((aligned(16)));
  float z1_a[4] __attribute__((aligned(16)));
  float z2_a[4] __attribute__((aligned(16)));
  float z3_a[4] __attribute__((aligned(16)));

  float dx1_a[4] __attribute__((aligned(16)));
  float dx2_a[4] __attribute__((aligned(16)));
  float dx3_a[4] __attribute__((aligned(16)));
  float dy1_a[4] __attribute__((aligned(16)));
  float dy2_a[4] __attribute__((aligned(16)));
  float dy3_a[4] __attribute__((aligned(16)));
  float dz1_a[4] __attribute__((aligned(16)));
  float dz2_a[4] __attribute__((aligned(16)));
  float dz3_a[4] __attribute__((aligned(16)));

  float kappa_a[4] __attribute__((aligned(16)));
  float dkappa_a[4] __attribute__((aligned(16)));

  float ux_mid_a[4] __attribute__((aligned(16)));
  float uy_mid_a[4] __attribute__((aligned(16)));
  float ux_end_a[4] __attribute__((aligned(16)));
  float uy_end_a[4] __attribute__((aligned(16)));

  float dzdl_1_a[4] __attribute__((aligned(16)));
  float dzdl_2_a[4] __attribute__((aligned(16)));
  float ddzdl_1_a[4] __attribute__((aligned(16)));
  float ddzdl_2_a[4] __attribute__((aligned(16)));

  float cur_kappa_a[4] __attribute__((aligned(16)));
  float cur_dkappa_a[4] __attribute__((aligned(16)));
  float cur_ux_a[4] __attribute__((aligned(16)));
  float cur_uy_a[4] __attribute__((aligned(16)));
  float cur_chi2_a[4] __attribute__((aligned(16)));
  float chi2_a[4] __attribute__((aligned(16)));

  unsigned int hit1[4];
  unsigned int hit2[4];
  unsigned int hit3[4];

  TrackSegment temp_segment;
  temp_segment.hits.assign(n_layers, 0);
  // make segments out of first 3 layers
  for (unsigned int i = 0, sizei = layer_sorted[0].size(); i < sizei; ++i) {
    for (unsigned int j = 0, sizej = layer_sorted[1].size(); j < sizej;
        ++j) {
      for (unsigned int k = 0, sizek = layer_sorted[2].size(); k < sizek;
          ++k) {
        if ((layer_sorted[0][i].get_layer()
            >= layer_sorted[1][j].get_layer())
            || (layer_sorted[1][j].get_layer()
                >= layer_sorted[2][k].get_layer())) {
          continue;
        }

        x1_a[hit_counter] = layer_sorted[0][i].get_x();
        y1_a[hit_counter] = layer_sorted[0][i].get_y();
        z1_a[hit_counter] = layer_sorted[0][i].get_z();


        dx1_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[0][i].get_size(0, 0));
        dy1_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[0][i].get_size(1, 1));
        dz1_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[0][i].get_size(2, 2));

        x2_a[hit_counter] = layer_sorted[1][j].get_x();
        y2_a[hit_counter] = layer_sorted[1][j].get_y();
        z2_a[hit_counter] = layer_sorted[1][j].get_z();

        dx2_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[1][j].get_size(0, 0));
        dy2_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[1][j].get_size(1, 1));
        dz2_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[1][j].get_size(2, 2));

        x3_a[hit_counter] = layer_sorted[2][k].get_x();
        y3_a[hit_counter] = layer_sorted[2][k].get_y();
        z3_a[hit_counter] = layer_sorted[2][k].get_z();

        dx3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[2][k].get_size(0, 0));
        dy3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[2][k].get_size(1, 1));
        dz3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[2][k].get_size(2, 2));

        hit1[hit_counter] = i;
        hit2[hit_counter] = j;
        hit3[hit_counter] = k;

        hit_counter += 1;

        if (hit_counter == 4) {
          calculateKappaTangents(x1_a, y1_a, z1_a, x2_a, y2_a, z2_a,
              x3_a, y3_a, z3_a, dx1_a, dy1_a, dz1_a, dx2_a, dy2_a,
              dz2_a, dx3_a, dy3_a, dz3_a, kappa_a, dkappa_a,
              ux_mid_a, uy_mid_a, ux_end_a, uy_end_a, dzdl_1_a,
              dzdl_2_a, ddzdl_1_a, ddzdl_2_a);

          for (unsigned int h = 0; h < hit_counter; ++h) {
            temp_segment.chi2 = (dzdl_1_a[h] - dzdl_2_a[h])
                / (ddzdl_1_a[h] + ddzdl_2_a[h]
                    + fabs(dzdl_1_a[h] * sinang_cut));
            temp_segment.chi2 *= temp_segment.chi2;
            if (temp_segment.chi2 > 2.0) {
              continue;
            }
            temp_segment.ux = ux_end_a[h];
            temp_segment.uy = uy_end_a[h];
            temp_segment.kappa = kappa_a[h];
            if (temp_segment.kappa > top_range.max_k) {
              continue;
            }
            temp_segment.dkappa = dkappa_a[h];
            temp_segment.hits[0] = hit1[h];
            temp_segment.hits[1] = hit2[h];
            temp_segment.hits[2] = hit3[h];
            temp_segment.n_hits = 3;
            unsigned int outer_layer =
                layer_sorted[2][temp_segment.hits[2]].get_layer();
            if ((outer_layer - 2) > allowed_missing) {
              continue;
            }
            if ((n_layers - 3) <= allowed_missing) {
              complete_segments.push_back(temp_segment);
            }
            if (next_seg->size() == nextseg_size) {
              next_seg->push_back(temp_segment);
              nextseg_size += 1;
            } else {
              (*next_seg)[nextseg_size] = temp_segment;
              nextseg_size += 1;
            }
          }

          hit_counter = 0;
        }
      }
    }
  }
  if (hit_counter != 0) {
    calculateKappaTangents(x1_a, y1_a, z1_a, x2_a, y2_a, z2_a, x3_a, y3_a,
        z3_a, dx1_a, dy1_a, dz1_a, dx2_a, dy2_a, dz2_a, dx3_a, dy3_a,
        dz3_a, kappa_a, dkappa_a, ux_mid_a, uy_mid_a, ux_end_a,
        uy_end_a, dzdl_1_a, dzdl_2_a, ddzdl_1_a, ddzdl_2_a);

    for (unsigned int h = 0; h < hit_counter; ++h) {
      temp_segment.chi2 = (dzdl_1_a[h] - dzdl_2_a[h])
          / (ddzdl_1_a[h] + ddzdl_2_a[h]
              + fabs(dzdl_1_a[h] * sinang_cut));
      temp_segment.chi2 *= temp_segment.chi2;
      if (temp_segment.chi2 > 2.0) {
        continue;
      }
      temp_segment.ux = ux_end_a[h];
      temp_segment.uy = uy_end_a[h];
      temp_segment.kappa = kappa_a[h];
      if (temp_segment.kappa > top_range.max_k) {
        continue;
      }
      temp_segment.dkappa = dkappa_a[h];
      temp_segment.hits[0] = hit1[h];
      temp_segment.hits[1] = hit2[h];
      temp_segment.hits[2] = hit3[h];
      temp_segment.n_hits = 3;
      unsigned int outer_layer =
          layer_sorted[2][temp_segment.hits[2]].get_layer();
      if ((outer_layer - 2) > allowed_missing) {
        continue;
      }
      if ((n_layers - 3) <= allowed_missing) {
        complete_segments.push_back(temp_segment);
      }
      if (next_seg->size() == nextseg_size) {
        next_seg->push_back(temp_segment);
        nextseg_size += 1;
      } else {
        (*next_seg)[nextseg_size] = temp_segment;
        nextseg_size += 1;
      }
    }

    hit_counter = 0;
  }

  swap(cur_seg, next_seg);
  swap(curseg_size, nextseg_size);

  // add hits to segments layer-by-layer, cutting out bad segments
  unsigned int whichseg[4];
  for (unsigned int l = 3; l < n_layers; ++l) {
    if (l == (n_layers - 1)) {
      easy_chi2_cut *= 0.25;
    }
    nextseg_size = 0;
    for (unsigned int i = 0, sizei = curseg_size; i < sizei; ++i) {
      for (unsigned int j = 0, sizej = layer_sorted[l].size(); j < sizej;
          ++j) {
        if ((layer_sorted[l - 1][(*cur_seg)[i].hits[l - 1]].get_layer()
            >= layer_sorted[l][j].get_layer())) {
          continue;
        }

        x1_a[hit_counter] =
            layer_sorted[l - 2][(*cur_seg)[i].hits[l - 2]].get_x();
        y1_a[hit_counter] =
            layer_sorted[l - 2][(*cur_seg)[i].hits[l - 2]].get_y();
        z1_a[hit_counter] =
            layer_sorted[l - 2][(*cur_seg)[i].hits[l - 2]].get_z();
        x2_a[hit_counter] =
            layer_sorted[l - 1][(*cur_seg)[i].hits[l - 1]].get_x();
        y2_a[hit_counter] =
            layer_sorted[l - 1][(*cur_seg)[i].hits[l - 1]].get_y();
        z2_a[hit_counter] =
            layer_sorted[l - 1][(*cur_seg)[i].hits[l - 1]].get_z();
        x3_a[hit_counter] = layer_sorted[l][j].get_x();
        y3_a[hit_counter] = layer_sorted[l][j].get_y();
        z3_a[hit_counter] = layer_sorted[l][j].get_z();

        dx1_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 2][(*cur_seg)[i].hits[l
                        - 2]].get_size(0, 0));
        dy1_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 2][(*cur_seg)[i].hits[l
                        - 2]].get_size(1, 1));
        dz1_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 2][(*cur_seg)[i].hits[l
                        - 2]].get_size(2, 2));
        dx2_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 1][(*cur_seg)[i].hits[l
                        - 1]].get_size(0, 0));
        dy2_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 1][(*cur_seg)[i].hits[l
                        - 1]].get_size(1, 1));
        dz2_a[hit_counter] =
            0.5 * sqrt(12.0)
                * sqrt(
                    layer_sorted[l - 1][(*cur_seg)[i].hits[l
                        - 1]].get_size(2, 2));
        dx3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[l][j].get_size(0, 0));
        dy3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[l][j].get_size(1, 1));
        dz3_a[hit_counter] = 0.5 * sqrt(12.0)
            * sqrt(layer_sorted[l][j].get_size(2, 2));

        cur_kappa_a[hit_counter] = (*cur_seg)[i].kappa;
        cur_dkappa_a[hit_counter] = (*cur_seg)[i].dkappa;
        cur_ux_a[hit_counter] = (*cur_seg)[i].ux;
        cur_uy_a[hit_counter] = (*cur_seg)[i].uy;
        cur_chi2_a[hit_counter] = (*cur_seg)[i].chi2;

        whichseg[hit_counter] = i;
        hit1[hit_counter] = j;

        hit_counter += 1;
        if (hit_counter == 4) {
          calculateKappaTangents(x1_a, y1_a, z1_a, x2_a, y2_a, z2_a,
              x3_a, y3_a, z3_a, dx1_a, dy1_a, dz1_a, dx2_a, dy2_a,
              dz2_a, dx3_a, dy3_a, dz3_a, kappa_a, dkappa_a,
              ux_mid_a, uy_mid_a, ux_end_a, uy_end_a, dzdl_1_a,
              dzdl_2_a, ddzdl_1_a, ddzdl_2_a, sinang_cut,
              cosang_diff_inv, cur_kappa_a, cur_dkappa_a,
              cur_ux_a, cur_uy_a, cur_chi2_a, chi2_a);

          for (unsigned int h = 0; h < hit_counter; ++h) {
            if ((chi2_a[h]) * inv_layer[l] < easy_chi2_cut) {
              temp_segment.chi2 = chi2_a[h];
              temp_segment.ux = ux_end_a[h];
              temp_segment.uy = uy_end_a[h];
              temp_segment.kappa = kappa_a[h];
              if (temp_segment.kappa > top_range.max_k) {
                continue;
              }
              temp_segment.dkappa = dkappa_a[h];
              for (unsigned int ll = 0; ll < l; ++ll) {
                temp_segment.hits[ll] =
                    (*cur_seg)[whichseg[h]].hits[ll];
              }
              temp_segment.hits[l] = hit1[h];
              unsigned int outer_layer =
                  layer_sorted[l][temp_segment.hits[l]].get_layer();
              temp_segment.n_hits = l + 1;
              if ((n_layers - (l + 1)) <= allowed_missing) {
                complete_segments.push_back(temp_segment);
              }
              if ((outer_layer - l) > allowed_missing) {
                continue;
              }
              if (next_seg->size() == nextseg_size) {
                next_seg->push_back(temp_segment);
                nextseg_size += 1;
              } else {
                (*next_seg)[nextseg_size] = temp_segment;
                nextseg_size += 1;
              }
            }
          }
          hit_counter = 0;
        }
      }
    }
    if (hit_counter != 0) {
      calculateKappaTangents(x1_a, y1_a, z1_a, x2_a, y2_a, z2_a, x3_a,
          y3_a, z3_a, dx1_a, dy1_a, dz1_a, dx2_a, dy2_a, dz2_a, dx3_a,
          dy3_a, dz3_a, kappa_a, dkappa_a, ux_mid_a, uy_mid_a,
          ux_end_a, uy_end_a, dzdl_1_a, dzdl_2_a, ddzdl_1_a,
          ddzdl_2_a, sinang_cut, cosang_diff_inv, cur_kappa_a,
          cur_dkappa_a, cur_ux_a, cur_uy_a, cur_chi2_a, chi2_a);

      for (unsigned int h = 0; h < hit_counter; ++h) {
        if ((chi2_a[h]) * inv_layer[l] < easy_chi2_cut) {
          temp_segment.chi2 = chi2_a[h];
          temp_segment.ux = ux_end_a[h];
          temp_segment.uy = uy_end_a[h];
          temp_segment.kappa = kappa_a[h];
          if (temp_segment.kappa > top_range.max_k) {
            continue;
          }

          temp_segment.dkappa = dkappa_a[h];
          for (unsigned int ll = 0; ll < l; ++ll) {
            temp_segment.hits[ll] =
                (*cur_seg)[whichseg[h]].hits[ll];
          }
          temp_segment.hits[l] = hit1[h];
          unsigned int outer_layer =
              layer_sorted[l][temp_segment.hits[l]].get_layer();
          temp_segment.n_hits = l + 1;
          if ((n_layers - (l + 1)) <= allowed_missing) {
            complete_segments.push_back(temp_segment);
          }
          if ((outer_layer - l) > allowed_missing) {
            continue;
          }
          if (next_seg->size() == nextseg_size) {
            next_seg->push_back(temp_segment);
            nextseg_size += 1;
          } else {
            (*next_seg)[nextseg_size] = temp_segment;
            nextseg_size += 1;
          }
        }
      }
      hit_counter = 0;
    }
    swap(cur_seg, next_seg);
    swap(curseg_size, nextseg_size);
  }

  for (unsigned int i = 0; i < complete_segments.size(); ++i) {
    if (cur_seg->size() == curseg_size) {
      cur_seg->push_back(complete_segments[i]);
      curseg_size += 1;
    } else {
      (*cur_seg)[curseg_size] = complete_segments[i];
      curseg_size += 1;
    }
  }

  gettimeofday(&t2, NULL);
  time1 = ((double) (t1.tv_sec) + (double) (t1.tv_usec) / 1000000.);
  time2 = ((double) (t2.tv_sec) + (double) (t2.tv_usec) / 1000000.);
  CAtime += (time2 - time1);
  SimpleTrack3D temp_track;
  temp_track.hits.assign(n_layers, SimpleHit3D());
  vector<SimpleHit3D> temp_hits;
  for (unsigned int i = 0, sizei = curseg_size; i < sizei; ++i) {
    temp_track.hits.assign((*cur_seg)[i].n_hits, SimpleHit3D());

    temp_comb.assign((*cur_seg)[i].n_hits, 0);
    for (unsigned int l = 0; l < (*cur_seg)[i].n_hits; ++l) {
      temp_comb[l] = layer_sorted[l][(*cur_seg)[i].hits[l]].get_id();
    }
    sort(temp_comb.begin(), temp_comb.end());
    set<vector<unsigned int> >::iterator it = combos.find(temp_comb);
    if (it != combos.end()) {
      continue;
    }
    if (combos.size() > 10000) {
      combos.clear();
    }
    combos.insert(temp_comb);

    for (unsigned int l = 0; l < (*cur_seg)[i].n_hits; ++l) {
      temp_track.hits[l] = layer_sorted[l][(*cur_seg)[i].hits[l]];
    }

    gettimeofday(&t1, NULL);

    // unsigned int layer_out = temp_track.hits.size()-1;
    // unsigned int layer_mid = layer_out/2;
    // temp_track_3hits.hits[0] = temp_track.hits[0];
    // temp_track_3hits.hits[1] = temp_track.hits[layer_mid];
    // temp_track_3hits.hits[2] = temp_track.hits[layer_out];

    float init_chi2 = fitTrack(temp_track);

    if (init_chi2 > fast_chi2_cut_max) {
      if (init_chi2
          > fast_chi2_cut_par0
              + fast_chi2_cut_par1
                  / kappaToPt(temp_track.kappa)) {
        gettimeofday(&t2, NULL);
        time1 =
            ((double) (t1.tv_sec) + (double) (t1.tv_usec) / 1000000.);
        time2 =
            ((double) (t2.tv_sec) + (double) (t2.tv_usec) / 1000000.);
        KALtime += (time2 - time1);
        continue;
      }
    }
    HelixKalmanState state;
    state.phi = temp_track.phi;
    if (state.phi < 0.) {
      state.phi += 2. * M_PI;
    }
    state.d = temp_track.d;
    state.kappa = temp_track.kappa;
    state.nu = sqrt(state.kappa);
    state.z0 = temp_track.z0;
    state.dzdl = temp_track.dzdl;
    state.C = Matrix<float, 5, 5>::Zero(5, 5);
    state.C(0, 0) = pow(0.01, 2.);
    state.C(1, 1) = pow(0.01, 2.);
    state.C(2, 2) = pow(0.01 * state.nu, 2.);
    state.C(3, 3) = pow(0.05, 2.);
    state.C(4, 4) = pow(0.05, 2.);
    state.chi2 = 0.;
    state.position = 0;
    state.x_int = 0.;
    state.y_int = 0.;
    state.z_int = 0.;

    for (unsigned int h = 0; h < temp_track.hits.size(); ++h) {
      kalman->addHit(temp_track.hits[h], state);
      nfits += 1;
    }

    // fudge factor for non-gaussian hit sizes
    state.C *= 3.;
    state.chi2 *= 6.;

    gettimeofday(&t2, NULL);
    time1 = ((double) (t1.tv_sec) + (double) (t1.tv_usec) / 1000000.);
    time2 = ((double) (t2.tv_sec) + (double) (t2.tv_usec) / 1000000.);
    KALtime += (time2 - time1);

    if (!(temp_track.kappa == temp_track.kappa)) {
      continue;
    }
    if (temp_track.kappa > top_range.max_k) {
      continue;
    }
    if (!(state.chi2 == state.chi2)) {
      continue;
    }
    if (state.chi2 / (2. * ((float) (temp_track.hits.size())) - 5.)
        > chi2_cut) {
      continue;
    }

    if (cut_on_dca == true) {
      if (fabs(temp_track.d) > dca_cut) {
        continue;
      }
      if (fabs(temp_track.z0) > dca_cut) {
        continue;
      }
    }

    /*
    cout << "   add track with hits size " << temp_track.hits.size() 
         << " z0 " << temp_track.z0
         << endl;
    for (unsigned int i = 0; i < temp_track.hits.size(); ++i) 
      {
        cout << " temp_track.hits.get_id() " << temp_track.hits[i].get_id() << endl;
      }
    */

    tracks.push_back(temp_track);
    track_states.push_back(state);
    if ((remove_hits == true) && (state.chi2 < chi2_removal_cut)
        && (temp_track.hits.size() >= n_removal_hits)) {
      for (unsigned int i = 0; i < temp_track.hits.size(); ++i) {
        (*hit_used)[temp_track.hits[i].get_id()] = true;
      }
    }
  }
}

static inline double sign(double x) {
  return ((double) (x > 0.)) - ((double) (x < 0.));
}

void sPHENIXSeedFinder::projectToLayer(SimpleTrack3D& seed, unsigned int layer,
    float& x, float& y, float& z) {
  float phi = seed.phi;
  float d = seed.d;
  float k = seed.kappa;
  float z0 = seed.z0;
  float dzdl = seed.dzdl;

  float hitx = seed.hits.back().get_x();
  float hity = seed.hits.back().get_y();

  float rad_det = detector_radii[layer];

  float cosphi = cos(phi);
  float sinphi = sin(phi);

  k = fabs(k);

  float kd = (d * k + 1.);
  float kcx = kd * cosphi;
  float kcy = kd * sinphi;
  float kd_inv = 1. / kd;
  float R2 = rad_det * rad_det;
  float a = 0.5 * (k * R2 + (d * d * k + 2. * d)) * kd_inv;
  float tmp1 = a * kd_inv;
  float P2x = kcx * tmp1;
  float P2y = kcy * tmp1;

  float h = sqrt(R2 - a * a);

  float ux = -kcy * kd_inv;
  float uy = kcx * kd_inv;

  float x1 = P2x + ux * h;
  float y1 = P2y + uy * h;
  float x2 = P2x - ux * h;
  float y2 = P2y - uy * h;
  float diff1 = (x1 - hitx) * (x1 - hitx) + (y1 - hity) * (y1 - hity);
  float diff2 = (x2 - hitx) * (x2 - hitx) + (y2 - hity) * (y2 - hity);
  float signk = 0.;
  if (diff1 < diff2) {
    signk = 1.;
  } else {
    signk = -1.;
  }
  x = P2x + signk * ux * h;
  y = P2y + signk * uy * h;

  double sign_dzdl = sign(dzdl);
//  double onedzdl2_inv = 1. / (1. - dzdl * dzdl);
  double startx = d * cosphi;
  double starty = d * sinphi;
  double D = sqrt((startx - x) * (startx - x) + (starty - y) * (starty - y));
//  double D_inv = 1. / D;
  double v = 0.5 * k * D;
  z = 0.;
  if (v > 0.1) {
    if (v >= 0.999999) {
      v = 0.999999;
    }
    double s = 2. * asin(v) / k;
//    double s_inv = 1. / s;
//    double sqrtvv = sqrt(1 - v * v);
    double dz = sqrt(s * s * dzdl * dzdl / (1. - dzdl * dzdl));
    z = z0 + sign_dzdl * dz;
  } else {
    double s = 0.;
    double temp1 = k * D * 0.5;
    temp1 *= temp1;
    double temp2 = D * 0.5;
    s += 2. * temp2;
    temp2 *= temp1;
    s += temp2 / 3.;
    temp2 *= temp1;
    s += (3. / 20.) * temp2;
    temp2 *= temp1;
    s += (5. / 56.) * temp2;
//    double s_inv = 1. / s;
    double dz = sqrt(s * s * dzdl * dzdl / (1. - dzdl * dzdl));
    z = z0 + sign_dzdl * dz;
  }
}

void sPHENIXSeedFinder::initSplitting(vector<SimpleHit3D>& hits,
              unsigned int min_hits, unsigned int /*max_hits*/) {
  initEvent(hits, min_hits);
  (*(hits_vec[0])) = hits;
  zoomranges.clear();
  for (unsigned int z = 0; z <= max_zoom; z++) {
    zoomranges.push_back(top_range);
  }
}

void sPHENIXSeedFinder::findHelicesParallelOneHelicity(
  vector<SimpleHit3D>& hits, unsigned int /*min_hits*/, unsigned int /*max_hits*/,
    vector<SimpleTrack3D>& /*tracks*/) {
  unsigned int hits_per_thread = (hits.size() + 2 * nthreads) / nthreads;
  unsigned int pos = 0;
  while (pos < hits.size()) {
    for (unsigned int i = 0; i < nthreads; ++i) {
      if (pos >= hits.size()) {
        break;
      }
      for (unsigned int j = 0; j < hits_per_thread; ++j) {
        if (pos >= hits.size()) {
          break;
        }
        split_input_hits[i].push_back(hits[pos]);
        pos += 1;
      }
    }
  }
  for (unsigned int i = 0; i < nthreads; ++i) {
    thread_trackers[i]->setTopRange(top_range);
    thread_trackers[i]->initSplitting(split_input_hits[i], thread_min_hits,
        thread_max_hits);
  }
  pins->sewStraight(&sPHENIXSeedFinder::splitHitsParallelThread, nthreads);
  thread_ranges.clear();
  thread_hits.clear();

  unsigned int nbins = split_output_hits[0]->size();
  for (unsigned int b = 0; b < nbins; ++b) {
    thread_ranges.push_back((*(split_ranges[0]))[b]);
    thread_hits.push_back(vector<SimpleHit3D>());
    for (unsigned int i = 0; i < nthreads; ++i) {
      for (unsigned int j = 0; j < (*(split_output_hits[i]))[b].size();
          ++j) {
        thread_hits.back().push_back((*(split_output_hits[i]))[b][j]);
      }
    }
  }

  pins->sewStraight(&sPHENIXSeedFinder::findHelicesParallelThread, nthreads);
}

void sPHENIXSeedFinder::findHelicesParallel(vector<SimpleHit3D>& hits,
    unsigned int min_hits, unsigned int max_hits,
    vector<SimpleTrack3D>& tracks) {
  thread_min_hits = min_hits;
  thread_max_hits = max_hits;

  for (unsigned int i = 0; i < nthreads; ++i) {
    thread_tracks[i].clear();
    thread_trackers[i]->clear();
    if (cluster_start_bin != 0) {
      thread_trackers[i]->setClusterStartBin(cluster_start_bin - 1);
    } else {
      thread_trackers[i]->setClusterStartBin(0);
    }
  }

  initSplitting(hits, min_hits, max_hits);

  if (separate_by_helicity == true) {
    for (unsigned int i = 0; i < nthreads; ++i) {
      thread_trackers[i]->setSeparateByHelicity(true);
      thread_trackers[i]->setOnlyOneHelicity(true);
      thread_trackers[i]->setHelicity(true);
      split_output_hits[i]->clear();
      split_input_hits[i].clear();
    }
    findHelicesParallelOneHelicity(hits, min_hits, max_hits, tracks);

    for (unsigned int i = 0; i < nthreads; ++i) {
      thread_trackers[i]->setSeparateByHelicity(true);
      thread_trackers[i]->setOnlyOneHelicity(true);
      thread_trackers[i]->setHelicity(false);
      split_output_hits[i]->clear();
      split_input_hits[i].clear();
    }
    findHelicesParallelOneHelicity(hits, min_hits, max_hits, tracks);
  } else {
    for (unsigned int i = 0; i < nthreads; ++i) {
      thread_trackers[i]->setSeparateByHelicity(false);
      thread_trackers[i]->setOnlyOneHelicity(false);
      split_output_hits[i]->clear();
      split_input_hits[i].clear();
    }

    findHelicesParallelOneHelicity(hits, min_hits, max_hits, tracks);
  }

  vector<SimpleTrack3D> temp_tracks;
  for (unsigned int i = 0; i < nthreads; ++i) {
    vector<HelixKalmanState>* states =
        &(thread_trackers[i]->getKalmanStates());
    for (unsigned int j = 0; j < thread_tracks[i].size(); ++j) {
      track_states.push_back((*states)[j]);
      temp_tracks.push_back(thread_tracks[i][j]);
    }
  }
  finalize(temp_tracks, tracks);
}

void sPHENIXSeedFinder::splitHitsParallelThread(void* arg) {
  unsigned long int w = (*((unsigned long int*) arg));
  thread_trackers[w]->splitIntoBins(thread_min_hits, thread_max_hits,
      *(split_ranges[w]), *(split_output_hits[w]), 0);
}

void sPHENIXSeedFinder::findHelicesParallelThread(void* arg) {
  unsigned long int w = (*((unsigned long int*) arg));

  for (unsigned int i = w; i < thread_ranges.size(); i += nthreads) {
    if (thread_hits[i].size() == 0) {
      continue;
    }
    thread_trackers[w]->setTopRange(thread_ranges[i]);
    thread_trackers[w]->findHelices(thread_hits[i], thread_min_hits,
        thread_max_hits, thread_tracks[w]);
  }
}