MillePedeAlignmentAlgorithm.cc

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#include "Alignment/MillePedeAlignmentAlgorithm/interface/MillePedeAlignmentAlgorithm.h"
//#include "MillePedeAlignmentAlgorithm.h"

#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"

#include "TrackingTools/PatternTools/interface/Trajectory.h"
// in header, too
// end in header, too

#include "Alignment/MillePedeAlignmentAlgorithm/interface/MillePedeMonitor.h"
#include "Alignment/MillePedeAlignmentAlgorithm/interface/MillePedeVariables.h"
#include "Alignment/MillePedeAlignmentAlgorithm/interface/MillePedeVariablesIORoot.h"
#include "Mille.h"       // 'unpublished' interface located in src
#include "PedeSteerer.h" // dito
#include "PedeReader.h" // dito
#include "Alignment/MillePedeAlignmentAlgorithm/interface/PedeLabelerBase.h" // dito
#include "Alignment/MillePedeAlignmentAlgorithm/interface/PedeLabelerPluginFactory.h" // dito

#include "Alignment/ReferenceTrajectories/interface/TrajectoryFactoryBase.h"
#include "Alignment/ReferenceTrajectories/interface/TrajectoryFactoryPlugin.h"

#include "Alignment/CommonAlignmentAlgorithm/interface/AlignmentParameterStore.h"
#include "Alignment/CommonAlignmentAlgorithm/interface/AlignmentIORoot.h"
#include "Alignment/CommonAlignmentAlgorithm/interface/IntegratedCalibrationBase.h"

#include "Alignment/CommonAlignment/interface/AlignmentParameters.h"
#include "Alignment/CommonAlignment/interface/AlignableNavigator.h"
#include "Alignment/CommonAlignment/interface/AlignableDetOrUnitPtr.h"

// includes to make known that they inherit from Alignable:
#include "Alignment/TrackerAlignment/interface/AlignableTracker.h"
#include "Alignment/MuonAlignment/interface/AlignableMuon.h"
#include "Alignment/CommonAlignment/interface/AlignableExtras.h"

#include "DataFormats/CLHEP/interface/AlgebraicObjects.h"
#include "DataFormats/TrackReco/interface/Track.h"
#include "DataFormats/SiStripDetId/interface/SiStripDetId.h"
#include "DataFormats/Alignment/interface/TkFittedLasBeam.h"
#include "Alignment/LaserAlignment/interface/TsosVectorCollection.h"

#include <Geometry/CommonDetUnit/interface/GeomDetUnit.h>
#include <Geometry/CommonDetUnit/interface/GeomDetType.h>
#include "DataFormats/TrackerCommon/interface/TrackerTopology.h"
#include "Geometry/Records/interface/TrackerTopologyRcd.h"
#include "Geometry/Records/interface/IdealGeometryRecord.h"

#include "DataFormats/TrackerRecHit2D/interface/ProjectedSiStripRecHit2D.h"

#include <fstream>
#include <sstream>
#include <algorithm>
#include <sys/stat.h>

#include <TMath.h>
#include <TMatrixDSymEigen.h>
typedef TransientTrackingRecHit::ConstRecHitContainer ConstRecHitContainer;
typedef TransientTrackingRecHit::ConstRecHitPointer   ConstRecHitPointer;
typedef TrajectoryFactoryBase::ReferenceTrajectoryCollection RefTrajColl;

// Includes for PXB survey
#include <iostream>
#include "Alignment/SurveyAnalysis/interface/SurveyPxbImage.h"
#include "Alignment/SurveyAnalysis/interface/SurveyPxbImageLocalFit.h"
#include "Alignment/SurveyAnalysis/interface/SurveyPxbImageReader.h"
#include "Alignment/SurveyAnalysis/interface/SurveyPxbDicer.h"
#include "DataFormats/GeometryVector/interface/LocalPoint.h"
#include "DataFormats/GeometryVector/interface/GlobalPoint.h"

#include "Alignment/CommonAlignmentParametrization/interface/AlignmentParametersFactory.h"

using namespace gbl;


// Constructor ----------------------------------------------------------------
//____________________________________________________
MillePedeAlignmentAlgorithm::MillePedeAlignmentAlgorithm(const edm::ParameterSet &cfg) :
  AlignmentAlgorithmBase(cfg), 
  theConfig(cfg), theMode(this->decodeMode(theConfig.getUntrackedParameter<std::string>("mode"))),
  theDir(theConfig.getUntrackedParameter<std::string>("fileDir")),
  theAlignmentParameterStore(0), theAlignables(), theAlignableNavigator(0),
  theMonitor(0), theMille(0), thePedeLabels(0), thePedeSteer(0),
  theTrajectoryFactory(0),
  theMinNumHits(cfg.getParameter<unsigned int>("minNumHits")),
  theMaximalCor2D(cfg.getParameter<double>("max2Dcorrelation")),
  theLastWrittenIov(0),
  theBinary(0),theGblDoubleBinary(cfg.getParameter<bool>("doubleBinary"))
{
  if (!theDir.empty() && theDir.find_last_of('/') != theDir.size()-1) theDir += '/';// may need '/'
  edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm" << "Start in mode '"
                            << theConfig.getUntrackedParameter<std::string>("mode")
                            << "' with output directory '" << theDir << "'.";
  if (this->isMode(myMilleBit)) {
    theMille = new Mille((theDir + theConfig.getParameter<std::string>("binaryFile")).c_str());// add ', false);' for text output);
    // use same file for GBL
    theBinary = new MilleBinary((theDir + theConfig.getParameter<std::string>("binaryFile")).c_str(), theGblDoubleBinary);
  }
}

// Destructor ----------------------------------------------------------------
//____________________________________________________
MillePedeAlignmentAlgorithm::~MillePedeAlignmentAlgorithm()
{
  delete theAlignableNavigator;
  theAlignableNavigator = 0;
  delete theMille;
  theMille = 0;
  delete theMonitor;
  theMonitor = 0;
  delete thePedeSteer;
  thePedeSteer = 0;
  delete thePedeLabels;
  thePedeLabels = 0;
  delete theTrajectoryFactory;
  theTrajectoryFactory = 0;
}

// Call at beginning of job ---------------------------------------------------
//____________________________________________________
void MillePedeAlignmentAlgorithm::initialize(const edm::EventSetup &setup, 
                                             AlignableTracker *tracker, AlignableMuon *muon, AlignableExtras *extras,
                                             AlignmentParameterStore *store)
{
  if (muon) {
    edm::LogWarning("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::initialize"
                 << "Running with AlignabeMuon not yet tested.";
  }

  //Retrieve tracker topology from geometry
  edm::ESHandle<TrackerTopology> tTopoHandle;
  setup.get<TrackerTopologyRcd>().get(tTopoHandle);
  const TrackerTopology* const tTopo = tTopoHandle.product();

  theAlignableNavigator = new AlignableNavigator(extras, tracker, muon);
  theAlignmentParameterStore = store;
  theAlignables = theAlignmentParameterStore->alignables();

  edm::ParameterSet pedeLabelerCfg(theConfig.getParameter<edm::ParameterSet>("pedeLabeler"));
  edm::VParameterSet RunRangeSelectionVPSet(theConfig.getUntrackedParameter<edm::VParameterSet>("RunRangeSelection"));
  pedeLabelerCfg.addUntrackedParameter<edm::VParameterSet>("RunRangeSelection",
                               RunRangeSelectionVPSet);

  std::string labelerPlugin = "PedeLabeler";
  if (RunRangeSelectionVPSet.size()>0) {
    labelerPlugin = "RunRangeDependentPedeLabeler";
    if (pedeLabelerCfg.exists("plugin")) {
      std::string labelerPluginCfg = pedeLabelerCfg.getParameter<std::string>("plugin");
      if ((labelerPluginCfg!="PedeLabeler" && labelerPluginCfg!="RunRangeDependentPedeLabeler") ||
      pedeLabelerCfg.getUntrackedParameter<edm::VParameterSet>("parameterInstances").size()>0) {
    throw cms::Exception("BadConfig")
      << "MillePedeAlignmentAlgorithm::initialize"
      << "both RunRangeSelection and generic labeler specified in config file. "
      << "Please get rid of either one of them.\n";
      }
    }
  } else {
    if (pedeLabelerCfg.exists("plugin")) {
      labelerPlugin = pedeLabelerCfg.getParameter<std::string>("plugin");
    }
  }
  
  if (!pedeLabelerCfg.exists("plugin")) {
    pedeLabelerCfg.addUntrackedParameter<std::string>("plugin", labelerPlugin);
  }

  edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::initialize"
                << "Using plugin '" << labelerPlugin << "' to generate labels.";
  
  thePedeLabels = PedeLabelerPluginFactory::get()->create(labelerPlugin,
                              PedeLabelerBase::TopLevelAlignables(tracker, muon, extras),
                              pedeLabelerCfg);
  
  // 1) Create PedeSteerer: correct alignable positions for coordinate system selection
  edm::ParameterSet pedeSteerCfg(theConfig.getParameter<edm::ParameterSet>("pedeSteerer"));
  thePedeSteer = new PedeSteerer(tracker, muon, extras,
                 theAlignmentParameterStore, thePedeLabels,
                 pedeSteerCfg, theDir, !this->isMode(myPedeSteerBit));
  
  // 2) If requested, directly read in and apply result of previous pede run,
  //    assuming that correction from 1) was also applied to create the result:
  const std::vector<edm::ParameterSet> mprespset
    (theConfig.getParameter<std::vector<edm::ParameterSet> >("pedeReaderInputs"));
  if (!mprespset.empty()) {
    edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::initialize"
                  << "Apply " << mprespset.end() - mprespset.begin()
                  << " previous MillePede constants from 'pedeReaderInputs'.";
  }

  // FIXME: add selection of run range via 'pedeReaderInputs'
  // Note: Results for parameters of IntegratedCalibration's cannot be treated... 
  RunRange runrange(cond::timeTypeSpecs[cond::runnumber].beginValue,
            cond::timeTypeSpecs[cond::runnumber].endValue);
  for (std::vector<edm::ParameterSet>::const_iterator iSet = mprespset.begin(), iE = mprespset.end();
       iSet != iE; ++iSet) {
    // This read will ignore calibrations as long as they are not yet passed to Millepede
    // during/before initialize(..) - currently addCalibrations(..) is called later in AlignmentProducer
    if (!this->readFromPede((*iSet), false, runrange)) { // false: do not erase SelectionUserVariables
      throw cms::Exception("BadConfig")
    << "MillePedeAlignmentAlgorithm::initialize: Problems reading input constants of "
    << "pedeReaderInputs entry " << iSet - mprespset.begin() << '.';
    }
    theAlignmentParameterStore->applyParameters();
    // Needed to shut up later warning from checkAliParams:
    theAlignmentParameterStore->resetParameters();
  }
  
  // 3) Now create steerings with 'final' start position:
  thePedeSteer->buildSubSteer(tracker, muon, extras);
  
  // After (!) 1-3 of PedeSteerer which uses the SelectionUserVariables attached to the parameters:
  this->buildUserVariables(theAlignables); // for hit statistics and/or pede result

  if (this->isMode(myMilleBit)) {
    if (!theConfig.getParameter<std::vector<std::string> >("mergeBinaryFiles").empty() ||
        !theConfig.getParameter<std::vector<std::string> >("mergeTreeFiles").empty()) {
      throw cms::Exception("BadConfig")
        << "'vstring mergeTreeFiles' and 'vstring mergeBinaryFiles' must be empty for "
        << "modes running mille.";
    }
    const std::string moniFile(theConfig.getUntrackedParameter<std::string>("monitorFile"));
    if (moniFile.size()) theMonitor = new MillePedeMonitor(tTopo, (theDir + moniFile).c_str());

    // Get trajectory factory. In case nothing found, FrameWork will throw...
    const edm::ParameterSet fctCfg(theConfig.getParameter<edm::ParameterSet>("TrajectoryFactory"));
    const std::string fctName(fctCfg.getParameter<std::string>("TrajectoryFactoryName"));
    theTrajectoryFactory = TrajectoryFactoryPlugin::get()->create(fctName, fctCfg);
  }

  if (this->isMode(myPedeSteerBit)) {
    // Get config for survey and set flag accordingly
    const edm::ParameterSet pxbSurveyCfg(theConfig.getParameter<edm::ParameterSet>("surveyPixelBarrel"));
    theDoSurveyPixelBarrel = pxbSurveyCfg.getParameter<bool>("doSurvey");
    if (theDoSurveyPixelBarrel) this->addPxbSurvey(pxbSurveyCfg);
  }
}

//____________________________________________________
bool MillePedeAlignmentAlgorithm::supportsCalibrations() {
  return true;
}

//____________________________________________________
bool MillePedeAlignmentAlgorithm::addCalibrations(const std::vector<IntegratedCalibrationBase*> &iCals)
{
  theCalibrations.insert(theCalibrations.end(), iCals.begin(), iCals.end());
  thePedeLabels->addCalibrations(iCals);
  return true;
}

//_____________________________________________________________________________
bool MillePedeAlignmentAlgorithm::processesEvents()
{
  if (isMode(myMilleBit)) {
    return true;
  } else {
    return false;
  }
}

//____________________________________________________
bool MillePedeAlignmentAlgorithm::setParametersForRunRange(const RunRange &runrange)
{
  if (this->isMode(myPedeReadBit)) {
    // restore initial positions, rotations and deformations
    theAlignmentParameterStore->restoreCachedTransformations();

    // Needed to shut up later warning from checkAliParams:
    theAlignmentParameterStore->resetParameters();
    // To avoid that they keep values from previous IOV if no new one in pede result
    this->buildUserVariables(theAlignables);
    
    if (!this->readFromPede(theConfig.getParameter<edm::ParameterSet>("pedeReader"), true, runrange)) {
      edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::setParametersForRunRange"
                                 << "Problems reading pede result, but applying!";
    }
    theAlignmentParameterStore->applyParameters();

    this->doIO(++theLastWrittenIov); // pre-increment!
  }
  
  return true;
}

// Call at end of job ---------------------------------------------------------
//____________________________________________________
void MillePedeAlignmentAlgorithm::terminate(const edm::EventSetup& iSetup)
{
  terminate();
}
void MillePedeAlignmentAlgorithm::terminate()
{
  delete theMille;// delete to close binary before running pede below (flush would be enough...)
  theMille = 0;

  std::vector<std::string> files;
  if (this->isMode(myMilleBit) || !theConfig.getParameter<std::string>("binaryFile").empty()) {
    files.push_back(theDir + theConfig.getParameter<std::string>("binaryFile"));
  } else {
    const std::vector<std::string> plainFiles(theConfig.getParameter<std::vector<std::string> >("mergeBinaryFiles"));
    files = getExistingFormattedFiles(plainFiles, theDir);
    // Do some logging:
    std::string filesForLogOutput;
    for (const auto& file: files) filesForLogOutput += " " + file + ",";
    if (filesForLogOutput.length() != 0) filesForLogOutput.pop_back();
    edm::LogInfo("Alignment")
      << "Based on the config parameter mergeBinaryFiles, using the following "
      << "files as input (assigned weights are indicated by ' -- <weight>'):"
      << filesForLogOutput;
  }

  // cache all positions, rotations and deformations
  theAlignmentParameterStore->cacheTransformations();

  const std::string masterSteer(thePedeSteer->buildMasterSteer(files));// do only if myPedeSteerBit?
  if (this->isMode(myPedeRunBit)) {
    thePedeSteer->runPede(masterSteer);
  }

  // parameters from pede are not yet applied,
  // so we can still write start positions (but with hit statistics in case of mille):
  this->doIO(0);
  theLastWrittenIov = 0;
}

std::vector<std::string> MillePedeAlignmentAlgorithm::getExistingFormattedFiles(const std::vector<std::string>& plainFiles, const std::string& theDir) {
  std::vector<std::string> files;
  for (const auto& plainFile: plainFiles) {
    std::string theInputFileName = plainFile;
    int theNumber = 0;
    while (true) {
      // Create a formatted version of the filename, with growing numbers
      // If the parameter doesn't contain a formatting directive, it just stays unchanged
      char theNumberedInputFileName[200];
      sprintf(theNumberedInputFileName, theInputFileName.c_str(), theNumber);
      std::string theCompleteInputFileName = theDir + theNumberedInputFileName;
      const auto endOfStrippedFileName = theCompleteInputFileName.rfind(" --");
      const auto strippedInputFileName = theCompleteInputFileName.substr(0, endOfStrippedFileName);
      // Check if the file exists
      struct stat buffer;
      if (stat (strippedInputFileName.c_str(), &buffer) == 0) {
        // If the file exists, add it to the list
        files.push_back(theCompleteInputFileName);
        if (theNumberedInputFileName == theInputFileName) {
          // If the filename didn't contain a formatting directive, no reason to look any further, break out of the loop
          break;
        } else {
          // Otherwise look for the next number
          theNumber++;
        }
      } else {
        // The file doesn't exist, break out of the loop
    edm::LogWarning("Alignment")
      << "The input file '" << strippedInputFileName << "' does not exist.";
        break;
      }
    }
  }
  return files;
}

// Run the algorithm on trajectories and tracks -------------------------------
//____________________________________________________
void MillePedeAlignmentAlgorithm::run(const edm::EventSetup &setup, const EventInfo &eventInfo)
{
  if (!this->isMode(myMilleBit)) return; // no theMille created...
  const ConstTrajTrackPairCollection &tracks = eventInfo.trajTrackPairs();

  if (theMonitor) { // monitor input tracks
    for (ConstTrajTrackPairCollection::const_iterator iTrajTrack = tracks.begin();
     iTrajTrack != tracks.end(); ++iTrajTrack) {
      theMonitor->fillTrack((*iTrajTrack).second);
    }
  }

  const RefTrajColl trajectories(theTrajectoryFactory->trajectories(setup, tracks, eventInfo.beamSpot()));

  // Now loop over ReferenceTrajectoryCollection
  unsigned int refTrajCount = 0; // counter for track monitoring if 1 track per trajectory
  for (RefTrajColl::const_iterator iRefTraj = trajectories.begin(), iRefTrajE = trajectories.end();
       iRefTraj != iRefTrajE; ++iRefTraj, ++refTrajCount) {

    RefTrajColl::value_type refTrajPtr = *iRefTraj; 
    if (theMonitor) theMonitor->fillRefTrajectory(refTrajPtr);

    const std::pair<unsigned int, unsigned int> nHitXy 
      = this->addReferenceTrajectory(setup, eventInfo, refTrajPtr);

    if (theMonitor && (nHitXy.first || nHitXy.second)) {
      // if track used (i.e. some hits), fill monitoring
      // track NULL ptr if trajectories and tracks do not match
      const reco::Track *trackPtr = 
    (trajectories.size() == tracks.size() ? tracks[refTrajCount].second : 0);
      theMonitor->fillUsedTrack(trackPtr, nHitXy.first, nHitXy.second);
    }

  } // end of reference trajectory and track loop
}

//____________________________________________________
std::pair<unsigned int, unsigned int>
MillePedeAlignmentAlgorithm::addReferenceTrajectory(const edm::EventSetup &setup,
                                                    const EventInfo &eventInfo, 
                            const RefTrajColl::value_type &refTrajPtr)
{
  std::pair<unsigned int, unsigned int> hitResultXy(0,0);
  if (refTrajPtr->isValid()) {
    

    // GblTrajectory?
    if (refTrajPtr->gblInput().size() > 0) {
      // by construction: number of GblPoints == number of recHits or == zero !!!
      unsigned int iHit = 0;
      unsigned int numPointsWithMeas = 0;
      std::vector<GblPoint>::iterator itPoint;
      std::vector<std::pair<std::vector<GblPoint>, TMatrixD> > theGblInput = refTrajPtr->gblInput();
      for (unsigned int iTraj = 0; iTraj < refTrajPtr->gblInput().size(); ++iTraj) {
        for (itPoint = refTrajPtr->gblInput()[iTraj].first.begin(); itPoint < refTrajPtr->gblInput()[iTraj].first.end(); ++itPoint) {
          if (this->addGlobalData(setup, eventInfo, refTrajPtr, iHit++, *itPoint) < 0) return hitResultXy;
          if (itPoint->hasMeasurement() >= 1) ++numPointsWithMeas;
        }
      }
      hitResultXy.first = numPointsWithMeas;
      // check #hits criterion
      if (hitResultXy.first == 0 || hitResultXy.first < theMinNumHits) return hitResultXy;
      // construct GBL trajectory
      if (refTrajPtr->gblInput().size() == 1) {
        // from single track
        GblTrajectory aGblTrajectory( refTrajPtr->gblInput()[0].first, refTrajPtr->nominalField() != 0 );
        // GBL fit trajectory
        /*double Chi2;
        int Ndf;
        double lostWeight;
        aGblTrajectory.fit(Chi2, Ndf, lostWeight);
        std::cout << " GblFit: " << Chi2 << ", " << Ndf << ", " << lostWeight << std::endl; */
        // write to MP binary file
        if (aGblTrajectory.isValid() && aGblTrajectory.getNumPoints() >= theMinNumHits) aGblTrajectory.milleOut(*theBinary);
      }
      if (refTrajPtr->gblInput().size() == 2) {
        // from TwoBodyDecay
        GblTrajectory aGblTrajectory( refTrajPtr->gblInput(), refTrajPtr->gblExtDerivatives(), refTrajPtr->gblExtMeasurements(), refTrajPtr->gblExtPrecisions() );
        // write to MP binary file
        if (aGblTrajectory.isValid() && aGblTrajectory.getNumPoints() >= theMinNumHits) aGblTrajectory.milleOut(*theBinary);
      }
    } else {
      // to add hits if all fine:
      std::vector<AlignmentParameters*> parVec(refTrajPtr->recHits().size());
      // collect hit statistics, assuming that there are no y-only hits
      std::vector<bool> validHitVecY(refTrajPtr->recHits().size(), false);
      // Use recHits from ReferenceTrajectory (since they have the right order!):
      for (unsigned int iHit = 0; iHit < refTrajPtr->recHits().size(); ++iHit) {
        const int flagXY = this->addMeasurementData(setup, eventInfo, refTrajPtr, iHit, parVec[iHit]);

        if (flagXY < 0) { // problem
          hitResultXy.first = 0;
          break;
        } else { // hit is fine, increase x/y statistics
          if (flagXY >= 1) ++hitResultXy.first;
          validHitVecY[iHit] = (flagXY >= 2);
        }
      } // end loop on hits

      // add virtual measurements
      for (unsigned int iVirtualMeas = 0; iVirtualMeas < refTrajPtr->numberOfVirtualMeas(); ++iVirtualMeas) {
        this->addVirtualMeas(refTrajPtr, iVirtualMeas);
      }

      // kill or end 'track' for mille, depends on #hits criterion
      if (hitResultXy.first == 0 || hitResultXy.first < theMinNumHits) {
        theMille->kill();
        hitResultXy.first = hitResultXy.second = 0; //reset
      } else {
        theMille->end();
        // add x/y hit count to MillePedeVariables of parVec,
        // returning number of y-hits of the reference trajectory
        hitResultXy.second = this->addHitCount(parVec, validHitVecY);
        //
      }
    }

  } // end if valid trajectory

  return hitResultXy;
}

//____________________________________________________
unsigned int
MillePedeAlignmentAlgorithm::addHitCount(const std::vector<AlignmentParameters*> &parVec,
                     const std::vector<bool> &validHitVecY) const
{
  // Loop on all hit information in the input arrays and count valid y-hits:
  unsigned int nHitY = 0;
  for (unsigned int iHit = 0; iHit < validHitVecY.size(); ++iHit) {
    Alignable *ali = (parVec[iHit] ? parVec[iHit]->alignable() : 0);
    // Loop upwards on hierarchy of alignables to add hits to all levels 
    // that are currently aligned. If only a non-selected alignable was hit,
    // (i.e. flagXY == 0 in addReferenceTrajectory(..)), there is no loop at all...
    while (ali) {
      AlignmentParameters *pars = ali->alignmentParameters();
      if (pars) { // otherwise hierarchy level not selected
    // cast ensured by previous checks:
    MillePedeVariables *mpVar = static_cast<MillePedeVariables*>(pars->userVariables());
    // every hit has an x-measurement, cf. addReferenceTrajectory(..):
    mpVar->increaseHitsX();
    if (validHitVecY[iHit]) {
      mpVar->increaseHitsY();
      if (pars == parVec[iHit]) ++nHitY; // do not count hits twice
    }
      }
      ali = ali->mother();
    }
  }
  
  return nHitY;
}

//____________________________________________________
void MillePedeAlignmentAlgorithm::endRun(const EventInfo &eventInfo, const EndRunInfo &runInfo,
                     const edm::EventSetup &setup)
{
  if(runInfo.tkLasBeams() && runInfo.tkLasBeamTsoses()){
    // LAS beam treatment
    this->addLaserData(eventInfo, *(runInfo.tkLasBeams()), *(runInfo.tkLasBeamTsoses()));
  }
  if(this->isMode(myMilleBit)) theMille->flushOutputFile();
}

// Implementation of endRun that DOES get called. (Because we need it.)
void MillePedeAlignmentAlgorithm::endRun(const EndRunInfo &runInfo, const edm::EventSetup &setup) {
  if(this->isMode(myMilleBit)) theMille->flushOutputFile();
}


//____________________________________________________
int MillePedeAlignmentAlgorithm::addMeasurementData(const edm::EventSetup &setup,
                                                    const EventInfo &eventInfo, 
                            const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
                            unsigned int iHit,
                            AlignmentParameters *&params)
{
  params = 0;
  theFloatBufferX.clear();
  theFloatBufferY.clear();
  theIntBuffer.clear();
 
  const TrajectoryStateOnSurface &tsos = refTrajPtr->trajectoryStates()[iHit];
  const ConstRecHitPointer &recHitPtr = refTrajPtr->recHits()[iHit];
  // ignore invalid hits
  if (!recHitPtr->isValid()) return 0;

  // First add the derivatives from IntegratedCalibration's,
  // should even be OK if problems for "usual" derivatives from Alignables
  this->globalDerivativesCalibration(recHitPtr, tsos, setup, eventInfo, // input
                                     theFloatBufferX, theFloatBufferY, theIntBuffer); // output

  // get AlignableDet/Unit for this hit
  AlignableDetOrUnitPtr alidet(theAlignableNavigator->alignableFromDetId(recHitPtr->geographicalId()));
  
  if (!this->globalDerivativesHierarchy(eventInfo,
                    tsos, alidet, alidet, theFloatBufferX, // 2x alidet, sic!
                    theFloatBufferY, theIntBuffer, params)) {
    return -1; // problem
  } else if (theFloatBufferX.empty()) {
     return 0; // empty for X: no alignable for hit, nor calibrations
  } else { // now even if no alignable, but calibrations!
    return this->callMille(refTrajPtr, iHit, theIntBuffer, theFloatBufferX, theFloatBufferY);
  }
}

//____________________________________________________

int MillePedeAlignmentAlgorithm::addGlobalData(const edm::EventSetup &setup, const EventInfo &eventInfo,
                                                    const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
                                                    unsigned int iHit, GblPoint &gblPoint)
{
  AlignmentParameters* params = 0;
  std::vector<double> theDoubleBufferX, theDoubleBufferY;
  theDoubleBufferX.clear();
  theDoubleBufferY.clear();
  theIntBuffer.clear();
  int iret = 0;

  const TrajectoryStateOnSurface &tsos = refTrajPtr->trajectoryStates()[iHit];
  const ConstRecHitPointer &recHitPtr = refTrajPtr->recHits()[iHit];
  // ignore invalid hits
  if (!recHitPtr->isValid()) return 0;

  // get AlignableDet/Unit for this hit
  AlignableDetOrUnitPtr alidet(theAlignableNavigator->alignableFromDetId(recHitPtr->geographicalId()));

  if (!this->globalDerivativesHierarchy(eventInfo,
                                        tsos, alidet, alidet, theDoubleBufferX, // 2x alidet, sic!
                                        theDoubleBufferY, theIntBuffer, params)) {
    return -1; // problem
  }
  //calibration parameters
  int globalLabel;
  std::vector<IntegratedCalibrationBase::ValuesIndexPair> derivs;
  for (auto iCalib = theCalibrations.begin(); iCalib != theCalibrations.end(); ++iCalib) {
    // get all derivatives of this calibration // const unsigned int num =
    (*iCalib)->derivatives(derivs, *recHitPtr, tsos, setup, eventInfo);
    for (auto iValuesInd = derivs.begin(); iValuesInd != derivs.end(); ++iValuesInd) {
      // transfer label and x/y derivatives
      globalLabel = thePedeLabels->calibrationLabel(*iCalib, iValuesInd->second);
      if (globalLabel > 0 && globalLabel <= 2147483647) {
        theIntBuffer.push_back(globalLabel);
        theDoubleBufferX.push_back(iValuesInd->first.first);
        theDoubleBufferY.push_back(iValuesInd->first.second);
      } else {
        std::cerr << "MillePedeAlignmentAlgorithm::addGlobalData: Invalid label " << globalLabel << " <= 0 or > 2147483647" << std::endl;
      }
    }
  }
  unsigned int numGlobals = theIntBuffer.size();
  if (numGlobals > 0)
  {
    TMatrixD globalDer(2,numGlobals);
    for (unsigned int i = 0; i < numGlobals; ++i) {
      globalDer(0,i) = theDoubleBufferX[i];
      globalDer(1,i) = theDoubleBufferY[i];
    }
    gblPoint.addGlobals( theIntBuffer, globalDer );
    iret = 1;
  }
  return iret;
}
  
//____________________________________________________
bool MillePedeAlignmentAlgorithm
::globalDerivativesHierarchy(const EventInfo &eventInfo,
                 const TrajectoryStateOnSurface &tsos,
                             Alignable *ali, const AlignableDetOrUnitPtr &alidet,
                             std::vector<float> &globalDerivativesX,
                             std::vector<float> &globalDerivativesY,
                             std::vector<int> &globalLabels,
                             AlignmentParameters *&lowestParams) const
{
  // derivatives and labels are recursively attached
  if (!ali) return true; // no mother might be OK

  if (false && theMonitor && alidet != ali) theMonitor->fillFrameToFrame(alidet, ali);

  AlignmentParameters *params = ali->alignmentParameters();

  if (params) {
    if (!lowestParams) lowestParams = params; // set parameters of lowest level

    bool hasSplitParameters = thePedeLabels->hasSplitParameters(ali);
    const unsigned int alignableLabel = thePedeLabels->alignableLabel(ali);
    
    if (0 == alignableLabel) { // FIXME: what about regardAllHits in Markus' code?
      edm::LogWarning("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::globalDerivativesHierarchy"
                                   << "Label not found, skip Alignable.";
      return false;
    }
    
    const std::vector<bool> &selPars = params->selector();
    const AlgebraicMatrix derivs(params->derivatives(tsos, alidet));

    // cols: 2, i.e. x&y, rows: parameters, usually RigidBodyAlignmentParameters::N_PARAM
    for (unsigned int iSel = 0; iSel < selPars.size(); ++iSel) {
      if (selPars[iSel]) {
        globalDerivativesX.push_back(derivs[iSel][kLocalX]
                     /thePedeSteer->cmsToPedeFactor(iSel));
    if (hasSplitParameters==true) {
      globalLabels.push_back(thePedeLabels->parameterLabel(ali, iSel, eventInfo, tsos));
    } else {
      globalLabels.push_back(thePedeLabels->parameterLabel(alignableLabel, iSel));
    }
    globalDerivativesY.push_back(derivs[iSel][kLocalY]
                     /thePedeSteer->cmsToPedeFactor(iSel));
      }
    }
    // Exclude mothers if Alignable selected to be no part of a hierarchy:
    if (thePedeSteer->isNoHiera(ali)) return true;
  }
  // Call recursively for mother, will stop if mother == 0:
  return this->globalDerivativesHierarchy(eventInfo,
                      tsos, ali->mother(), alidet,
                                          globalDerivativesX, globalDerivativesY,
                      globalLabels, lowestParams);
}

//____________________________________________________
bool MillePedeAlignmentAlgorithm
::globalDerivativesHierarchy(const EventInfo &eventInfo,
                             const TrajectoryStateOnSurface &tsos,
                             Alignable *ali, const AlignableDetOrUnitPtr &alidet,
                             std::vector<double> &globalDerivativesX,
                             std::vector<double> &globalDerivativesY,
                             std::vector<int> &globalLabels,
                             AlignmentParameters *&lowestParams) const
{
  // derivatives and labels are recursively attached
  if (!ali) return true; // no mother might be OK

  if (false && theMonitor && alidet != ali) theMonitor->fillFrameToFrame(alidet, ali);

  AlignmentParameters *params = ali->alignmentParameters();

  if (params) {
    if (!lowestParams) lowestParams = params; // set parameters of lowest level

    bool hasSplitParameters = thePedeLabels->hasSplitParameters(ali);
    const unsigned int alignableLabel = thePedeLabels->alignableLabel(ali);

    if (0 == alignableLabel) { // FIXME: what about regardAllHits in Markus' code?
      edm::LogWarning("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::globalDerivativesHierarchy"
                                   << "Label not found, skip Alignable.";
      return false;
    }

    const std::vector<bool> &selPars = params->selector();
    const AlgebraicMatrix derivs(params->derivatives(tsos, alidet));
    int globalLabel;

    // cols: 2, i.e. x&y, rows: parameters, usually RigidBodyAlignmentParameters::N_PARAM
    for (unsigned int iSel = 0; iSel < selPars.size(); ++iSel) {
      if (selPars[iSel]) {
        if (hasSplitParameters==true) {
          globalLabel = thePedeLabels->parameterLabel(ali, iSel, eventInfo, tsos);
        } else {
          globalLabel = thePedeLabels->parameterLabel(alignableLabel, iSel);
        }
        if (globalLabel > 0 && globalLabel <= 2147483647) {
          globalLabels.push_back(globalLabel);
          globalDerivativesX.push_back(derivs[iSel][kLocalX] / thePedeSteer->cmsToPedeFactor(iSel));
          globalDerivativesY.push_back(derivs[iSel][kLocalY] / thePedeSteer->cmsToPedeFactor(iSel));
        } else {
          std::cerr << "MillePedeAlignmentAlgorithm::globalDerivativesHierarchy: Invalid label " << globalLabel << " <= 0 or > 2147483647" << std::endl;
        }
      }
    }
    // Exclude mothers if Alignable selected to be no part of a hierarchy:
    if (thePedeSteer->isNoHiera(ali)) return true;
  }
  // Call recursively for mother, will stop if mother == 0:
  return this->globalDerivativesHierarchy(eventInfo,
                                          tsos, ali->mother(), alidet,
                                          globalDerivativesX, globalDerivativesY,
                                          globalLabels, lowestParams);
}
                      
//____________________________________________________
void MillePedeAlignmentAlgorithm::
globalDerivativesCalibration(const TransientTrackingRecHit::ConstRecHitPointer &recHit,
                             const TrajectoryStateOnSurface &tsos,
                             const edm::EventSetup &setup, const EventInfo &eventInfo,
                             std::vector<float> &globalDerivativesX,
                             std::vector<float> &globalDerivativesY,
                             std::vector<int> &globalLabels) const
{
  std::vector<IntegratedCalibrationBase::ValuesIndexPair> derivs;
  for (auto iCalib = theCalibrations.begin(); iCalib != theCalibrations.end(); ++iCalib) {
    // get all derivatives of this calibration // const unsigned int num =
    (*iCalib)->derivatives(derivs, *recHit, tsos, setup, eventInfo);
    for (auto iValuesInd = derivs.begin(); iValuesInd != derivs.end(); ++iValuesInd) {
      // transfer label and x/y derivatives 
      globalLabels.push_back(thePedeLabels->calibrationLabel(*iCalib, iValuesInd->second));
      globalDerivativesX.push_back(iValuesInd->first.first);
      globalDerivativesY.push_back(iValuesInd->first.second);
    }
  }
}

// //____________________________________________________
// void MillePedeAlignmentAlgorithm
// ::callMille(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
//             unsigned int iTrajHit, MeasurementDirection xOrY,
//             const std::vector<float> &globalDerivatives, const std::vector<int> &globalLabels)
// {
//   const unsigned int xyIndex = iTrajHit*2 + xOrY;
//   // FIXME: here for residuum and sigma we could use KALMAN-Filter results
//   const float residuum =
//     refTrajPtr->measurements()[xyIndex] - refTrajPtr->trajectoryPositions()[xyIndex];
//   const float covariance = refTrajPtr->measurementErrors()[xyIndex][xyIndex];
//   const float sigma = (covariance > 0. ? TMath::Sqrt(covariance) : 0.);

//   const AlgebraicMatrix &locDerivMatrix = refTrajPtr->derivatives();

//   std::vector<float> localDerivs(locDerivMatrix.num_col());
//   for (unsigned int i = 0; i < localDerivs.size(); ++i) {
//     localDerivs[i] = locDerivMatrix[xyIndex][i];
//   }

//   // &(vector[0]) is valid - as long as vector is not empty 
//   // cf. http://www.parashift.com/c++-faq-lite/containers.html#faq-34.3
//   theMille->mille(localDerivs.size(), &(localDerivs[0]),
//        globalDerivatives.size(), &(globalDerivatives[0]), &(globalLabels[0]),
//        residuum, sigma);
//   if (theMonitor) {
//     theMonitor->fillDerivatives(refTrajPtr->recHits()[iTrajHit],localDerivs, globalDerivatives,
//              (xOrY == kLocalY));
//     theMonitor->fillResiduals(refTrajPtr->recHits()[iTrajHit],
//                refTrajPtr->trajectoryStates()[iTrajHit],
//                iTrajHit, residuum, sigma, (xOrY == kLocalY));
//   }
// }

//____________________________________________________
bool MillePedeAlignmentAlgorithm::is2D(const ConstRecHitPointer &recHit) const
{
  // FIXME: Check whether this is a reliable and recommended way to find out...

  if (recHit->dimension() < 2) {
    return false; // some muon and TIB/TOB stuff really has RecHit1D
  } else if (recHit->detUnit()) { // detunit in strip is 1D, in pixel 2D 
    return recHit->detUnit()->type().isTrackerPixel();
  } else { // stereo strips  (FIXME: endcap trouble due to non-parallel strips (wedge sensors)?)
    if (dynamic_cast<const ProjectedSiStripRecHit2D*>(recHit->hit())) { // check persistent hit
      // projected: 1D measurement on 'glued' module
      return false;
    } else {
      return true;
    }
  }
}

//__________________________________________________________________________________________________
bool MillePedeAlignmentAlgorithm::readFromPede(const edm::ParameterSet &mprespset, bool setUserVars,
                           const RunRange &runrange)
{
  bool allEmpty = this->areEmptyParams(theAlignables);

  PedeReader reader(mprespset, *thePedeSteer, *thePedeLabels, runrange);
  std::vector<Alignable*> alis;
  bool okRead = reader.read(alis, setUserVars); // also may set params of IntegratedCalibration's
  bool numMatch = true;
  
  std::stringstream out;
  out << "Read " << alis.size() << " alignables";
  if (alis.size() != theAlignables.size()) {
    out << " while " << theAlignables.size() << " in store";
    numMatch = false; // FIXME: Should we check one by one? Or transfer 'alis' to the store?
  }
  if (!okRead) out << ", but problems in reading"; 
  if (!allEmpty) out << ", possibly overwriting previous settings";
  out << ".";

  if (okRead && allEmpty) {
    if (numMatch) { // as many alignables with result as trying to align
      edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::readFromPede" << out.str();
    } else if (alis.size()) { // dead module do not get hits and no pede result
      edm::LogWarning("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::readFromPede" << out.str();
    } else { // serious problem: no result read - and not all modules can be dead...
      edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::readFromPede" << out.str();
      return false;
    }
    return true;
  }
  // the rest is not OK:
  edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::readFromPede" << out.str();
  return false;
}

//__________________________________________________________________________________________________
bool MillePedeAlignmentAlgorithm::areEmptyParams(const std::vector<Alignable*> &alignables) const
{
  
  for (std::vector<Alignable*>::const_iterator iAli = alignables.begin();
       iAli != alignables.end(); ++iAli) {
    const AlignmentParameters *params = (*iAli)->alignmentParameters();
    if (params) {
      const AlgebraicVector &parVec(params->parameters());
      const AlgebraicMatrix &parCov(params->covariance());
      for (int i = 0; i < parVec.num_row(); ++i) {
        if (parVec[i] != 0.) return false;
        for (int j = i; j < parCov.num_col(); ++j) {
          if (parCov[i][j] != 0.) return false;
        }
      }
    }
  }
  
  return true;
}

//__________________________________________________________________________________________________
unsigned int MillePedeAlignmentAlgorithm::doIO(int loop) const
{
  unsigned int result = 0;

  const std::string outFilePlain(theConfig.getParameter<std::string>("treeFile"));
  if (outFilePlain.empty()) {
    edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO"
                              << "treeFile parameter empty => skip writing for 'loop' " << loop;
    return result;
  }

  const std::string outFile(theDir + outFilePlain);

  AlignmentIORoot aliIO;
  int ioerr = 0;
  if (loop == 0) {
    aliIO.writeAlignableOriginalPositions(theAlignables, outFile.c_str(), loop, false, ioerr);
    if (ioerr) {
      edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO"
                                 << "Problem " << ioerr << " in writeAlignableOriginalPositions";
      ++result;
    }
  } else if (loop == 1) {
    // only for first iov add hit counts, else 2x, 3x,... number of hits in IOV 2, 3,...
    const std::vector<std::string> inFiles
      (theConfig.getParameter<std::vector<std::string> >("mergeTreeFiles"));
    const std::vector<std::string> binFiles
      (theConfig.getParameter<std::vector<std::string> >("mergeBinaryFiles"));
    if (inFiles.size() != binFiles.size()) {
      edm::LogWarning("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO"
                                   << "'vstring mergeTreeFiles' and 'vstring mergeBinaryFiles' "
                                   << "differ in size";
    }
    this->addHitStatistics(0, outFile, inFiles); // add hit info from tree 0 in 'infiles'
  }
  MillePedeVariablesIORoot millePedeIO;
  millePedeIO.writeMillePedeVariables(theAlignables, outFile.c_str(), loop, false, ioerr);
  if (ioerr) {
    edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO"
                               << "Problem " << ioerr << " writing MillePedeVariables";
    ++result;
  }
  
  aliIO.writeOrigRigidBodyAlignmentParameters(theAlignables, outFile.c_str(), loop, false, ioerr);
  if (ioerr) {
    edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO" << "Problem " << ioerr
                   << " in writeOrigRigidBodyAlignmentParameters, " << loop;
    ++result;
  }
  aliIO.writeAlignableAbsolutePositions(theAlignables, outFile.c_str(), loop, false, ioerr);
  if (ioerr) {
    edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::doIO" << "Problem " << ioerr
                               << " in writeAlignableAbsolutePositions, " << loop;
    ++result;
  }

  return result;
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm::buildUserVariables(const std::vector<Alignable*> &alis) const
{
  for (std::vector<Alignable*>::const_iterator iAli = alis.begin(); iAli != alis.end(); ++iAli) {
    AlignmentParameters *params = (*iAli)->alignmentParameters();
    if (!params) {
      throw cms::Exception("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::buildUserVariables"
                                        << "No parameters for alignable";
    }
    MillePedeVariables *userVars = dynamic_cast<MillePedeVariables*>(params->userVariables()); 
    if (userVars) { // Just re-use existing, keeping label and numHits:
      for (unsigned int iPar = 0; iPar < userVars->size(); ++iPar) {
    //  if (params->hierarchyLevel() > 0) {
    //std::cout << params->hierarchyLevel() << "\nBefore: " << userVars->parameter()[iPar];
    //  }
    userVars->setAllDefault(iPar);
    //std::cout << "\nAfter: " << userVars->parameter()[iPar] << std::endl;
      }
    } else { // Nothing yet or erase wrong type:
      userVars = new MillePedeVariables(params->size(), thePedeLabels->alignableLabel(*iAli));
      params->setUserVariables(userVars);
    }
  }
}

//__________________________________________________________________________________________________
unsigned int MillePedeAlignmentAlgorithm::decodeMode(const std::string &mode) const
{
  if (mode == "full") {
    return myMilleBit + myPedeSteerBit + myPedeRunBit + myPedeReadBit;
  } else if (mode == "mille") {
    return myMilleBit; // + myPedeSteerBit; // sic! Including production of steerig file. NO!
  } else if (mode == "pede") {
    return myPedeSteerBit + myPedeRunBit + myPedeReadBit;
  } else if (mode == "pedeSteer") {
    return myPedeSteerBit;
  } else if (mode == "pedeRun") {
    return myPedeSteerBit + myPedeRunBit + myPedeReadBit; // sic! Including steering and reading of result.
  } else if (mode == "pedeRead") {
    return myPedeReadBit;
  }

  throw cms::Exception("BadConfig") 
    << "Unknown mode '" << mode  
    << "', use 'full', 'mille', 'pede', 'pedeRun', 'pedeSteer' or 'pedeRead'.";

  return 0;
}

//__________________________________________________________________________________________________
bool MillePedeAlignmentAlgorithm::addHitStatistics(int fromIov, const std::string &outFile,
                                                   const std::vector<std::string> &inFiles) const
{
  bool allOk = true;
  int ierr = 0;
  MillePedeVariablesIORoot millePedeIO;
  for (std::vector<std::string>::const_iterator iFile = inFiles.begin();
       iFile != inFiles.end(); ++iFile) {
    const std::string inFile(theDir + *iFile); 
    const std::vector<AlignmentUserVariables*> mpVars =
      millePedeIO.readMillePedeVariables(theAlignables, inFile.c_str(), fromIov, ierr);
    if (ierr || !this->addHits(theAlignables, mpVars)) {
      edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::addHitStatistics"
                 << "Error " << ierr << " reading from " << inFile 
                 << ", tree " << fromIov << ", or problems in addHits";
      allOk = false;
    }
    for (std::vector<AlignmentUserVariables*>::const_iterator i = mpVars.begin();
     i != mpVars.end(); ++i) {
      delete *i; // clean created objects
    }
  }

  return allOk;
}

//__________________________________________________________________________________________________
bool MillePedeAlignmentAlgorithm::addHits(const std::vector<Alignable*> &alis,
                                          const std::vector<AlignmentUserVariables*> &mpVars) const
{
  bool allOk = (mpVars.size() == alis.size());
  std::vector<AlignmentUserVariables*>::const_iterator iUser = mpVars.begin();
  for (std::vector<Alignable*>::const_iterator iAli = alis.begin(); 
       iAli != alis.end() && iUser != mpVars.end(); ++iAli, ++iUser) {
    MillePedeVariables *mpVarNew = dynamic_cast<MillePedeVariables*>(*iUser);
    AlignmentParameters *ps = (*iAli)->alignmentParameters();
    MillePedeVariables *mpVarOld = (ps ? dynamic_cast<MillePedeVariables*>(ps->userVariables()) : 0);
    if (!mpVarNew || !mpVarOld || mpVarOld->size() != mpVarNew->size()) {
      allOk = false;
      continue; // FIXME error etc.?
    }

    mpVarOld->increaseHitsX(mpVarNew->hitsX());
    mpVarOld->increaseHitsY(mpVarNew->hitsY());
  }
  
  return allOk;
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm::makeGlobDerivMatrix(const std::vector<float> &globalDerivativesx,
                                                      const std::vector<float> &globalDerivativesy,
                                                      TMatrixF &aGlobalDerivativesM)
{

  for (unsigned int i = 0; i < globalDerivativesx.size(); ++i) {
    aGlobalDerivativesM(0,i) = globalDerivativesx[i];
    aGlobalDerivativesM(1,i) = globalDerivativesy[i]; 
  }
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm::diagonalize
(TMatrixDSym &aHitCovarianceM, TMatrixF &aLocalDerivativesM, TMatrixF &aHitResidualsM,
 TMatrixF &aGlobalDerivativesM) const
{
  TMatrixDSymEigen myDiag(aHitCovarianceM);
  TMatrixD aTranfoToDiagonalSystem = myDiag.GetEigenVectors();
  TMatrixD aTranfoToDiagonalSystemInv = myDiag.GetEigenVectors( );
  TMatrixF aTranfoToDiagonalSystemInvF = myDiag.GetEigenVectors( );
  TMatrixD aMatrix = aTranfoToDiagonalSystemInv.Invert() * aHitCovarianceM * aTranfoToDiagonalSystem;
  // Tranformation of matrix M is done by A^T*M*A, not A^{-1}*M*A.
  // But here A^T == A^{-1}, so we would only save CPU by Transpose()...
  // FIXME this - I guess simply use T(), not Transpose()...
  // TMatrixD aMatrix = aTranfoToDiagonalSystemInv.Transpose() * aHitCovarianceM
  //    * aTranfoToDiagonalSystem;
  aHitCovarianceM = TMatrixDSym(2, aMatrix.GetMatrixArray());
  aTranfoToDiagonalSystemInvF.Invert();
  //edm::LogInfo("Alignment") << "NEW HIT loca in matrix"<<aLocalDerivativesM(0,0);
  aLocalDerivativesM = aTranfoToDiagonalSystemInvF * aLocalDerivativesM;
  
  //edm::LogInfo("Alignment") << "NEW HIT loca in matrix after diag:"<<aLocalDerivativesM(0,0);
  aHitResidualsM      = aTranfoToDiagonalSystemInvF * aHitResidualsM;
  aGlobalDerivativesM = aTranfoToDiagonalSystemInvF * aGlobalDerivativesM;
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm
::addRefTrackVirtualMeas1D(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
               unsigned int iVirtualMeas, TMatrixDSym &aHitCovarianceM,
               TMatrixF &aHitResidualsM, TMatrixF &aLocalDerivativesM)
{
  // This Method is valid for 1D measurements only

  const unsigned int xIndex = iVirtualMeas + refTrajPtr->numberOfHitMeas();
  // Covariance into a TMatrixDSym
  
  //aHitCovarianceM = new TMatrixDSym(1);
  aHitCovarianceM(0,0)=refTrajPtr->measurementErrors()[xIndex][xIndex];
  
  //theHitResidualsM= new TMatrixF(1,1);
  aHitResidualsM(0,0)= refTrajPtr->measurements()[xIndex];
  
  // Local Derivatives into a TMatrixDSym (to use matrix operations)
  const AlgebraicMatrix &locDerivMatrix = refTrajPtr->derivatives();
  //  theLocalDerivativeNumber = locDerivMatrix.num_col();
  
  //theLocalDerivativesM = new TMatrixF(1,locDerivMatrix.num_col());
  for (int i = 0; i < locDerivMatrix.num_col(); ++i) {
    aLocalDerivativesM(0,i) = locDerivMatrix[xIndex][i];
  }
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm
::addRefTrackData2D(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
                    unsigned int iTrajHit, TMatrixDSym &aHitCovarianceM,
                    TMatrixF &aHitResidualsM, TMatrixF &aLocalDerivativesM)
{
  // This Method is valid for 2D measurements only
  
  const unsigned int xIndex = iTrajHit*2;
  const unsigned int yIndex = iTrajHit*2+1;
  // Covariance into a TMatrixDSym

  //aHitCovarianceM = new TMatrixDSym(2);
  aHitCovarianceM(0,0)=refTrajPtr->measurementErrors()[xIndex][xIndex];
  aHitCovarianceM(0,1)=refTrajPtr->measurementErrors()[xIndex][yIndex];
  aHitCovarianceM(1,0)=refTrajPtr->measurementErrors()[yIndex][xIndex];
  aHitCovarianceM(1,1)=refTrajPtr->measurementErrors()[yIndex][yIndex];
  
  //theHitResidualsM= new TMatrixF(2,1);
  aHitResidualsM(0,0)= refTrajPtr->measurements()[xIndex] - refTrajPtr->trajectoryPositions()[xIndex];
  aHitResidualsM(1,0)= refTrajPtr->measurements()[yIndex] - refTrajPtr->trajectoryPositions()[yIndex];
  
  // Local Derivatives into a TMatrixDSym (to use matrix operations)
  const AlgebraicMatrix &locDerivMatrix = refTrajPtr->derivatives();
  //  theLocalDerivativeNumber = locDerivMatrix.num_col();
  
  //theLocalDerivativesM = new TMatrixF(2,locDerivMatrix.num_col());
  for (int i = 0; i < locDerivMatrix.num_col(); ++i) {
    aLocalDerivativesM(0,i) = locDerivMatrix[xIndex][i];
    aLocalDerivativesM(1,i) = locDerivMatrix[yIndex][i];
  }
}

//__________________________________________________________________________________________________
int MillePedeAlignmentAlgorithm
::callMille(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
        unsigned int iTrajHit, const std::vector<int> &globalLabels,
        const std::vector<float> &globalDerivativesX,
        const std::vector<float> &globalDerivativesY)
{    
  const ConstRecHitPointer aRecHit(refTrajPtr->recHits()[iTrajHit]);

  if((aRecHit)->dimension() == 1) {
    return this->callMille1D(refTrajPtr, iTrajHit, globalLabels, globalDerivativesX);
  } else {
    return this->callMille2D(refTrajPtr, iTrajHit, globalLabels,
                 globalDerivativesX, globalDerivativesY);
  }
}


//__________________________________________________________________________________________________
int MillePedeAlignmentAlgorithm
::callMille1D(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
              unsigned int iTrajHit, const std::vector<int> &globalLabels,
              const std::vector<float> &globalDerivativesX)
{
  const ConstRecHitPointer aRecHit(refTrajPtr->recHits()[iTrajHit]);
  const unsigned int xIndex = iTrajHit*2; // the even ones are local x

  // local derivatives
  const AlgebraicMatrix &locDerivMatrix = refTrajPtr->derivatives();
  const int nLocal  = locDerivMatrix.num_col();
  std::vector<float> localDerivatives(nLocal);
  for (unsigned int i = 0; i < localDerivatives.size(); ++i) {
    localDerivatives[i] = locDerivMatrix[xIndex][i];
  }

  // residuum and error
  float residX = refTrajPtr->measurements()[xIndex] - refTrajPtr->trajectoryPositions()[xIndex];
  float hitErrX = TMath::Sqrt(refTrajPtr->measurementErrors()[xIndex][xIndex]);

  // number of global derivatives
  const int nGlobal = globalDerivativesX.size();

  // &(localDerivatives[0]) etc. are valid - as long as vector is not empty
  // cf. http://www.parashift.com/c++-faq-lite/containers.html#faq-34.3
  theMille->mille(nLocal, &(localDerivatives[0]), nGlobal, &(globalDerivativesX[0]),
          &(globalLabels[0]), residX, hitErrX);

  if (theMonitor) {
    theMonitor->fillDerivatives(aRecHit, &(localDerivatives[0]), nLocal,
                &(globalDerivativesX[0]), nGlobal, &(globalLabels[0]));
    theMonitor->fillResiduals(aRecHit, refTrajPtr->trajectoryStates()[iTrajHit],
                  iTrajHit, residX, hitErrX, false);
  }

  return 1;
}

//__________________________________________________________________________________________________
int MillePedeAlignmentAlgorithm
::callMille2D(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr,
              unsigned int iTrajHit, const std::vector<int> &globalLabels,
              const std::vector<float> &globalDerivativesx,
              const std::vector<float> &globalDerivativesy)
{
  const ConstRecHitPointer aRecHit(refTrajPtr->recHits()[iTrajHit]);
  
  if((aRecHit)->dimension() != 2) {
    edm::LogError("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::callMille2D"
                               << "You try to call method for 2D hits for a " 
                               << (aRecHit)->dimension()
                               <<  "D Hit. Hit gets ignored!";
    return -1;
  }

  TMatrixDSym aHitCovarianceM(2);
  TMatrixF aHitResidualsM(2,1);
  TMatrixF aLocalDerivativesM(2, refTrajPtr->derivatives().num_col());
  // below method fills above 3 matrices
  this->addRefTrackData2D(refTrajPtr, iTrajHit, aHitCovarianceM,aHitResidualsM,aLocalDerivativesM);
  TMatrixF aGlobalDerivativesM(2,globalDerivativesx.size());
  this->makeGlobDerivMatrix(globalDerivativesx, globalDerivativesy, aGlobalDerivativesM);
 
  // calculates correlation between Hit measurements
  // FIXME: Should take correlation (and resulting transformation) from original hit, 
  //        not 2x2 matrix from ReferenceTrajectory: That can come from error propagation etc.!
  const double corr = aHitCovarianceM(0,1) / sqrt(aHitCovarianceM(0,0) * aHitCovarianceM(1,1));
  if (theMonitor) theMonitor->fillCorrelations2D(corr, aRecHit);
  bool diag = false; // diagonalise only tracker TID, TEC
  switch(aRecHit->geographicalId().subdetId()) {
  case SiStripDetId::TID:
  case SiStripDetId::TEC:
    if (aRecHit->geographicalId().det() == DetId::Tracker && TMath::Abs(corr) > theMaximalCor2D) {
      this->diagonalize(aHitCovarianceM, aLocalDerivativesM, aHitResidualsM, aGlobalDerivativesM);
      diag = true;
    }
    break;
  default:;
  }

  float newResidX = aHitResidualsM(0,0);
  float newResidY = aHitResidualsM(1,0);
  float newHitErrX = TMath::Sqrt(aHitCovarianceM(0,0));
  float newHitErrY = TMath::Sqrt(aHitCovarianceM(1,1));
  float *newLocalDerivsX = aLocalDerivativesM[0].GetPtr();
  float *newLocalDerivsY = aLocalDerivativesM[1].GetPtr();
  float *newGlobDerivsX  = aGlobalDerivativesM[0].GetPtr();
  float *newGlobDerivsY  = aGlobalDerivativesM[1].GetPtr();
  const int nLocal  = aLocalDerivativesM.GetNcols();
  const int nGlobal = aGlobalDerivativesM.GetNcols();

  if (diag && (newHitErrX > newHitErrY)) { // also for 2D hits?
    // measurement with smaller error is x-measurement (for !is2D do not fill y-measurement):
    std::swap(newResidX, newResidY);
    std::swap(newHitErrX, newHitErrY);
    std::swap(newLocalDerivsX, newLocalDerivsY);
    std::swap(newGlobDerivsX, newGlobDerivsY);
  }

  // &(globalLabels[0]) is valid - as long as vector is not empty 
  // cf. http://www.parashift.com/c++-faq-lite/containers.html#faq-34.3
  theMille->mille(nLocal, newLocalDerivsX, nGlobal, newGlobDerivsX,
          &(globalLabels[0]), newResidX, newHitErrX);

  if (theMonitor) {
    theMonitor->fillDerivatives(aRecHit, newLocalDerivsX, nLocal, newGlobDerivsX, nGlobal,
                &(globalLabels[0]));
    theMonitor->fillResiduals(aRecHit, refTrajPtr->trajectoryStates()[iTrajHit],
                  iTrajHit, newResidX, newHitErrX, false);
  }
  const bool isReal2DHit = this->is2D(aRecHit); // strip is 1D (except matched hits)
  if (isReal2DHit) {
    theMille->mille(nLocal, newLocalDerivsY, nGlobal, newGlobDerivsY,
                    &(globalLabels[0]), newResidY, newHitErrY);
    if (theMonitor) {
      theMonitor->fillDerivatives(aRecHit, newLocalDerivsY, nLocal, newGlobDerivsY, nGlobal,
                  &(globalLabels[0]));
      theMonitor->fillResiduals(aRecHit, refTrajPtr->trajectoryStates()[iTrajHit],
                iTrajHit, newResidY, newHitErrY, true);// true: y
    }
  }

  return (isReal2DHit ? 2 : 1);
}

//__________________________________________________________________________________________________
void MillePedeAlignmentAlgorithm
::addVirtualMeas(const ReferenceTrajectoryBase::ReferenceTrajectoryPtr &refTrajPtr, unsigned int iVirtualMeas)
{
  TMatrixDSym aHitCovarianceM(1);
  TMatrixF aHitResidualsM(1,1);
  TMatrixF aLocalDerivativesM(1, refTrajPtr->derivatives().num_col());
  // below method fills above 3 'matrices'
  this->addRefTrackVirtualMeas1D(refTrajPtr, iVirtualMeas, aHitCovarianceM, aHitResidualsM, aLocalDerivativesM);
  
  // no global parameters (use dummy 0)
  TMatrixF aGlobalDerivativesM(1,1);
  aGlobalDerivativesM(0,0) = 0;
      
  float newResidX = aHitResidualsM(0,0);  
  float newHitErrX = TMath::Sqrt(aHitCovarianceM(0,0));
  float *newLocalDerivsX = aLocalDerivativesM[0].GetPtr();
  float *newGlobDerivsX  = aGlobalDerivativesM[0].GetPtr();
  const int nLocal  = aLocalDerivativesM.GetNcols();
  const int nGlobal = 0;
  
  theMille->mille(nLocal, newLocalDerivsX, nGlobal, newGlobDerivsX,
          &nGlobal, newResidX, newHitErrX);  
}

//____________________________________________________
void MillePedeAlignmentAlgorithm::addLaserData(const EventInfo &eventInfo, 
                           const TkFittedLasBeamCollection &lasBeams,
                           const TsosVectorCollection &lasBeamTsoses)
{
  TsosVectorCollection::const_iterator iTsoses = lasBeamTsoses.begin();
  for(TkFittedLasBeamCollection::const_iterator iBeam = lasBeams.begin(), iEnd = lasBeams.end();
      iBeam != iEnd; ++iBeam, ++iTsoses){ // beam/tsoses parallel!

    edm::LogInfo("Alignment") << "@SUB=MillePedeAlignmentAlgorithm::addLaserData"
                  << "Beam " << iBeam->getBeamId() << " with " 
                  << iBeam->parameters().size() << " parameters and " 
                  << iBeam->getData().size() << " hits.\n There are " 
                  << iTsoses->size() << " TSOSes.";

    this->addLasBeam(eventInfo, *iBeam, *iTsoses);
  }
}

//____________________________________________________
void MillePedeAlignmentAlgorithm::addLasBeam(const EventInfo &eventInfo, 
                         const TkFittedLasBeam &lasBeam,
                         const std::vector<TrajectoryStateOnSurface> &tsoses)
{
  AlignmentParameters *dummyPtr = 0; // for globalDerivativesHierarchy()
  std::vector<float> lasLocalDerivsX; // buffer for local derivatives
  const unsigned int beamLabel = thePedeLabels->lasBeamLabel(lasBeam.getBeamId());// for global par
  
  for (unsigned int iHit = 0; iHit < tsoses.size(); ++iHit) {
    if (!tsoses[iHit].isValid()) continue;
    // clear buffer
    theFloatBufferX.clear();
    theFloatBufferY.clear();
    theIntBuffer.clear();
    lasLocalDerivsX.clear();
    // get alignables and global parameters
    const SiStripLaserRecHit2D &hit = lasBeam.getData()[iHit];
    AlignableDetOrUnitPtr lasAli(theAlignableNavigator->alignableFromDetId(hit.getDetId()));
    this->globalDerivativesHierarchy(eventInfo,
                     tsoses[iHit], lasAli, lasAli, 
                     theFloatBufferX, theFloatBufferY, theIntBuffer, dummyPtr);
    // fill derivatives vector from derivatives matrix
    for (unsigned int nFitParams = 0; 
     nFitParams < static_cast<unsigned int>(lasBeam.parameters().size()); 
     ++nFitParams) {
      const float derivative = lasBeam.derivatives()[iHit][nFitParams];
      if (nFitParams < lasBeam.firstFixedParameter()) { // first local beam parameters
    lasLocalDerivsX.push_back(derivative);
      } else {                                          // now global ones
    const unsigned int numPar = nFitParams - lasBeam.firstFixedParameter();
    theIntBuffer.push_back(thePedeLabels->parameterLabel(beamLabel, numPar));
    theFloatBufferX.push_back(derivative);
      }
    } // end loop over parameters

    const float residual = hit.localPosition().x() - tsoses[iHit].localPosition().x();
    // error from file or assume 0.003
    const float error = 0.003; // hit.localPositionError().xx(); sqrt???
    
    theMille->mille(lasLocalDerivsX.size(), &(lasLocalDerivsX[0]), theFloatBufferX.size(),
            &(theFloatBufferX[0]), &(theIntBuffer[0]), residual, error);
  } // end of loop over hits
  
  theMille->end();
}

void MillePedeAlignmentAlgorithm::addPxbSurvey(const edm::ParameterSet &pxbSurveyCfg)
{
    // do some printing, if requested
    const bool doOutputOnStdout(pxbSurveyCfg.getParameter<bool>("doOutputOnStdout"));
    if (doOutputOnStdout) std::cout << "# Output from addPxbSurvey follows below because doOutputOnStdout is set to True" << std::endl;

    // instantiate a dicer object
    SurveyPxbDicer dicer(pxbSurveyCfg.getParameter<std::vector<edm::ParameterSet> >("toySurveyParameters"), pxbSurveyCfg.getParameter<unsigned int>("toySurveySeed"));
    std::ofstream outfile(pxbSurveyCfg.getUntrackedParameter<std::string>("toySurveyFile").c_str());

    // read data from file
    std::vector<SurveyPxbImageLocalFit> measurements;
    std::string filename(pxbSurveyCfg.getParameter<edm::FileInPath>("infile").fullPath());
    SurveyPxbImageReader<SurveyPxbImageLocalFit> reader(filename, measurements, 800);

    // loop over photographs (=measurements) and perform the fit
    for(std::vector<SurveyPxbImageLocalFit>::size_type i=0; i!=measurements.size(); i++)
    {
        if (doOutputOnStdout) std::cout << "Module " << i << ": ";

        // get the Alignables and their surfaces
        AlignableDetOrUnitPtr mod1(theAlignableNavigator->alignableFromDetId(measurements[i].getIdFirst()));
        AlignableDetOrUnitPtr mod2(theAlignableNavigator->alignableFromDetId(measurements[i].getIdSecond()));
        const AlignableSurface& surf1 = mod1->surface();
        const AlignableSurface& surf2 = mod2->surface();
        
        // the position of the fiducial points in local frame of a PXB module
        const LocalPoint fidpoint0(-0.91,+3.30);
        const LocalPoint fidpoint1(+0.91,+3.30);
        const LocalPoint fidpoint2(+0.91,-3.30);
        const LocalPoint fidpoint3(-0.91,-3.30);
        
        // We choose the local frame of the first module as reference,
        // so take the fidpoints of the second module and calculate their
        // positions in the reference frame
        const GlobalPoint surf2point0(surf2.toGlobal(fidpoint0));
        const GlobalPoint surf2point1(surf2.toGlobal(fidpoint1));
        const LocalPoint fidpoint0inSurf1frame(surf1.toLocal(surf2point0));
        const LocalPoint fidpoint1inSurf1frame(surf1.toLocal(surf2point1));
        
        // Create the vector for the fit
        SurveyPxbImageLocalFit::fidpoint_t fidpointvec;
        fidpointvec.push_back(fidpoint0inSurf1frame);
        fidpointvec.push_back(fidpoint1inSurf1frame);
        fidpointvec.push_back(fidpoint2);
        fidpointvec.push_back(fidpoint3);

        // if toy survey is requested, dice the values now
        if (pxbSurveyCfg.getParameter<bool>("doToySurvey"))
        {
            dicer.doDice(fidpointvec,measurements[i].getIdPair(), outfile);
        }
        
        // do the fit
        measurements[i].doFit(fidpointvec, thePedeLabels->alignableLabel(mod1), thePedeLabels->alignableLabel(mod2));
        SurveyPxbImageLocalFit::localpars_t a; // local pars from fit
        a = measurements[i].getLocalParameters();
        const SurveyPxbImageLocalFit::value_t chi2 = measurements[i].getChi2();

        // do some reporting, if requested
        if (doOutputOnStdout)
        {
          std::cout << "a: " << a[0] << ", " << a[1]  << ", " << a[2] << ", " << a[3]
            << " S= " << sqrt(a[2]*a[2]+a[3]*a[3])
            << " phi= " << atan(a[3]/a[2])
            << " chi2= " << chi2 << std::endl;
        }
        if (theMonitor) 
        {
            theMonitor->fillPxbSurveyHistsChi2(chi2);
            theMonitor->fillPxbSurveyHistsLocalPars(a[0],a[1],sqrt(a[2]*a[2]+a[3]*a[3]),atan(a[3]/a[2]));
        }

        // pass the results from the local fit to mille
        for(SurveyPxbImageLocalFit::count_t j=0; j!=SurveyPxbImageLocalFit::nMsrmts; j++)
        {
            theMille->mille((int)measurements[i].getLocalDerivsSize(),
                measurements[i].getLocalDerivsPtr(j),
                (int)measurements[i].getGlobalDerivsSize(),
                measurements[i].getGlobalDerivsPtr(j),
                measurements[i].getGlobalDerivsLabelPtr(j),
                measurements[i].getResiduum(j),
                measurements[i].getSigma(j));
        }
        theMille->end();
    }
    outfile.close();
}