TPC/calibration: Add standalone dEdx calculation class

Detectors/TPC/calibration/CMakeLists.txt

@@ -51,6 +51,7 @@ o2_add_library(TPCCalibration
                        src/CorrectionMapsLoader.cxx
                        src/SACCCDBHelper.cxx
                        src/TPCFastSpaceChargeCorrectionHelper.cxx
+                       src/CalculatedEdx.cxx
                PUBLIC_LINK_LIBRARIES O2::DataFormatsTPC O2::TPCBase
                                      O2::TPCReconstruction ROOT::Minuit
                                      Microsoft.GSL::GSL
@@ -101,7 +102,8 @@ o2_target_root_dictionary(TPCCalibration
                                   include/TPCCalibration/SACDrawHelper.h
                                   include/TPCCalibration/VDriftHelper.h
                                   include/TPCCalibration/SACCCDBHelper.h
-                                  include/TPCCalibration/TPCFastSpaceChargeCorrectionHelper.h)
+                                  include/TPCCalibration/TPCFastSpaceChargeCorrectionHelper.h
+                                  include/TPCCalibration/CalculatedEdx.h)
 
 o2_add_test_root_macro(macro/comparePedestalsAndNoise.C
                        PUBLIC_LINK_LIBRARIES O2::TPCBase

Detectors/TPC/calibration/include/TPCCalibration/CalculatedEdx.h

@@ -0,0 +1,159 @@
+// Copyright 2019-2020 CERN and copyright holders of ALICE O2.
+// See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
+// All rights not expressly granted are reserved.
+//
+// This software is distributed under the terms of the GNU General Public
+// License v3 (GPL Version 3), copied verbatim in the file "COPYING".
+//
+// In applying this license CERN does not waive the privileges and immunities
+// granted to it by virtue of its status as an Intergovernmental Organization
+// or submit itself to any jurisdiction.
+
+///
+/// @file   CalculatedEdx.h
+/// @author Tuba Gündem, [email protected]
+///
+
+#ifndef AliceO2_TPC_CalculatedEdx_H
+#define AliceO2_TPC_CalculatedEdx_H
+
+// o2 includes
+#include "DataFormatsTPC/TrackTPC.h"
+#include "DataFormatsTPC/dEdxInfo.h"
+#include "GPUO2InterfaceRefit.h"
+#include "CalibdEdxContainer.h"
+#include "CorrectionMapsHelper.h"
+#include "CommonUtils/TreeStreamRedirector.h"
+
+#include <vector>
+
+namespace o2::tpc
+{
+
+/// \brief dEdx calculation class
+///
+/// This class is used to calculate dEdx of reconstructed tracks.
+/// Calibration objects are loaded from CCDB with the run number.
+/// For the calculation of dEdx:
+///   different corrections (track topology correction, gain map and residual dEdx correction) can be switched on and off
+///   truncation range can be set for truncated mean calculation
+///
+/// How to use:
+/// Example:
+/// CalculatedEdx c{};
+/// c.loadCalibsFromCCDB(runNumberOrTimeStamp);
+/// start looping over the data
+/// c.setMembers(tpcTrackClIdxVecInput, clusterIndex, tpcTracks); // set the member variables: TrackTPC, TPCClRefElem, o2::tpc::ClusterNativeAccess
+/// c.setRefit(); // set the refit pointer to perform refitting of tracks, otherwise setPropagateTrack to true
+/// start looping over the tracks
+/// c.calculatedEdx(track, output, 0.01, 0.6, CorrectionFlags::TopologyPol | CorrectionFlags::GainFull | CorrectionFlags::GainResidual | CorrectionFlags::dEdxResidual) // this will fill the dEdxInfo output for given track
+
+enum class CorrectionFlags : unsigned short {
+  TopologySimple = 1 << 0, ///< flag for simple analytical topology correction
+  TopologyPol = 1 << 1,    ///< flag for topology correction from polynomials
+  GainFull = 1 << 2,       ///< flag for full gain map from calibration container
+  GainResidual = 1 << 3,   ///< flag for residuals gain map from calibration container
+  dEdxResidual = 1 << 4,   ///< flag for residual dEdx correction
+};
+
+inline CorrectionFlags operator&(CorrectionFlags a, CorrectionFlags b) { return static_cast<CorrectionFlags>(static_cast<unsigned short>(a) & static_cast<unsigned short>(b)); }
+inline CorrectionFlags operator~(CorrectionFlags a) { return static_cast<CorrectionFlags>(~static_cast<unsigned short>(a)); }
+inline CorrectionFlags operator|(CorrectionFlags a, CorrectionFlags b) { return static_cast<CorrectionFlags>(static_cast<unsigned short>(a) | static_cast<unsigned short>(b)); }
+
+class CalculatedEdx
+{
+ public:
+  CalculatedEdx();
+
+  ~CalculatedEdx() = default;
+
+  /// set the member variables
+  /// \param tpcTrackClIdxVecInput TPCClRefElem member variable
+  /// \param clIndex ClusterNativeAccess member variable
+  /// \param vTPCTracksArrayInp vector of tpc tracks
+  void setMembers(std::vector<o2::tpc::TPCClRefElem>* tpcTrackClIdxVecInput, const o2::tpc::ClusterNativeAccess& clIndex, std::vector<o2::tpc::TrackTPC>* vTPCTracksArrayInp);
+
+  /// set the refitter
+  void setRefit();
+
+  /// \param propagate propagate the tracks to extract the track parameters instead of performing a refit
+  void setPropagateTrack(const bool propagate) { mPropagateTrack = propagate; }
+
+  /// \param debug use debug streamer and set debug vectors
+  void setDebug(const bool debug) { mDebug = debug; }
+
+  /// \param field magnetic field in kG, used for track propagation
+  void setField(const float field) { mField = field; }
+
+  /// \param maxMissingCl maximum number of missing clusters for subthreshold check
+  void setMaxMissingCl(int maxMissingCl) { mMaxMissingCl = maxMissingCl; }
+
+  /// set the debug streamer
+  void setStreamer() { mStreamer = std::make_unique<o2::utils::TreeStreamRedirector>("dEdxDebug.root", "recreate"); };
+
+  /// \return returns magnetic field in kG
+  float getField() { return mField; }
+
+  /// \return returns maxMissingCl for subthreshold cluster treatment
+  int getMaxMissingCl() { return mMaxMissingCl; }
+
+  /// fill missing clusters with minimum charge (method=0) or minimum charge/2 (method=1)
+  void fillMissingClusters(int missingClusters[4], float minChargeTot, float minChargeMax, int method);
+
+  /// get the truncated mean for the input track with the truncation range, charge type, region and corrections
+  /// the cluster charge is normalized by effective length*gain, you can turn off the normalization by setting all corrections to false
+  /// \param track input track
+  /// \param output output dEdxInfo
+  /// \param low lower cluster cut
+  /// \param high higher cluster cut
+  /// \param mask to apply different corrections: TopologySimple = simple analytical topology correction, TopologyPol = topology correction from polynomials, GainFull = full gain map from calibration container,
+  ///                                                      GainResidual = residuals gain map from calibration container, dEdxResidual = residual dEdx correction
+  void calculatedEdx(TrackTPC& track, dEdxInfo& output, float low = 0.05f, float high = 0.6f, CorrectionFlags mask = CorrectionFlags::TopologyPol | CorrectionFlags::GainFull | CorrectionFlags::GainResidual | CorrectionFlags::dEdxResidual);
+
+  /// get the truncated mean for the input charge vector and the truncation range low*nCl<nCl<high*nCl
+  /// \param charge input vector
+  /// \param low lower cluster cut (e.g. 0.05)
+  /// \param high higher cluster cut (e.g. 0.6)
+  float getTruncMean(std::vector<float>& charge, float low, float high) const;
+
+  /// get effective track length using simple analytical topology correction
+  /// \param track input track
+  /// \param region pad region
+  /// \return returns simple analytical topology correction
+  float getTrackTopologyCorrection(const o2::tpc::TrackTPC& track, const unsigned int region) const;
+
+  /// get effective track length using topology correction from polynomials
+  /// \param track input track
+  /// \param cl cluster
+  /// \param region pad region
+  /// \param charge total or maximum charge of the cluster, cl
+  /// \param chargeType total or maximum
+  /// \param threshold zero supression threshold
+  /// \return returns topology correction from polynomials
+  float getTrackTopologyCorrectionPol(const o2::tpc::TrackTPC& track, const o2::tpc::ClusterNative& cl, const unsigned int region, const float charge, ChargeType chargeType, const float threshold) const;
+
+  /// load calibration objects from CCDB
+  /// \param runNumberOrTimeStamp run number or time stamp
+  void loadCalibsFromCCDB(long runNumberOrTimeStamp);
+
+ private:
+  std::vector<TrackTPC>* mTracks{nullptr};                       ///< vector containing the tpc tracks which will be processed.
+  std::vector<TPCClRefElem>* mTPCTrackClIdxVecInput{nullptr};    ///< input vector with TPC tracks cluster indicies
+  const o2::tpc::ClusterNativeAccess* mClusterIndex{nullptr};    ///< needed to access clusternative with tpctracks
+  o2::gpu::CorrectionMapsHelper mTPCCorrMapsHelper;              ///< cluster corrections map helper
+  std::unique_ptr<o2::gpu::GPUO2InterfaceRefit> mRefit{nullptr}; ///< TPC refitter used for TPC tracks refit during the reconstruction
+
+  int mMaxMissingCl{2};                                                ///< maximum number of missing clusters for subthreshold check
+  float mField{5};                                                     ///< magnetic field in kG, used for track propagation
+  bool mPropagateTrack{false};                                         ///< propagating the track instead of performing a refit
+  bool mDebug{false};                                                  ///< use the debug streamer
+  CalibdEdxContainer mCalibCont;                                       ///< calibration container
+  std::unique_ptr<o2::utils::TreeStreamRedirector> mStreamer{nullptr}; ///< debug streamer
+
+  std::array<std::vector<float>, 5> mChargeTotROC;
+  std::array<std::vector<float>, 5> mChargeMaxROC;
+};
+
+} // namespace o2::tpc
+
+#endif