TChannel.cxx

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#include "TChannel.h"
 
#include <stdexcept>
#include <fstream>
#include <iostream>
#include <fcntl.h>
#include <unistd.h>
#include <unordered_map>
 
#include <vector>
#include <sstream>
#include <algorithm>
#include <regex>
 
#include "TFile.h"
#include "TKey.h"
#include "TRandom.h"
 
#include "StoppableThread.h"
#include "Globals.h"
#include "TGRSIUtilities.h"
#include "TMnemonic.h"
 
/*
 * Author:  P.C. Bender, <pcbend@gmail.com>
 *
 * Please indicate changes with your initials.
 *
 *
 */
 
// NOTE: The fChannelMap is unordered. The easiest way to order it is using std::map<int, int> ordered(unordered.begin(), unordered.end());
 
std::unordered_map<unsigned int, TChannel*>* TChannel::fChannelMap        = new std::unordered_map<unsigned int, TChannel*>;   // global maps of channels
std::unordered_map<unsigned int, int>*       TChannel::fMissingChannelMap = new std::unordered_map<unsigned int, int>;         // global map of missing channels
std::unordered_map<int, TChannel*>*          TChannel::fChannelNumberMap  = new std::unordered_map<int, TChannel*>;
 
// TClass* TChannel::fMnemonicClass = TMnemonic::Class();
TClassRef TChannel::fMnemonicClass = TClassRef("TMnemonic");
 
std::string TChannel::fFileData;
 
TChannel::TChannel()
{
   Clear();
}   // default constructor need to write to root file.
 
TChannel::~TChannel()
{
   delete fMnemonic.Value();
}
 
TChannel::TChannel(const char* tempName)
{
   Clear();
   // only set name if it's not empty
   if(strlen(tempName) > 0) { SetName(tempName); }
}
 
TChannel::TChannel(const TChannel& chan) : TNamed(chan)
{
   /// Makes a copy of the TChannel.
   Clear();
   *(fMnemonic.Value()) = *(chan.fMnemonic.Value());
   SetAddress(chan.GetAddress());
   SetIntegration(chan.fIntegration);
   SetNumber(chan.fNumber);
   SetStream(chan.fStream);
   SetName(chan.GetName());
   SetDigitizerType(chan.fDigitizerTypeString);
   SetTimeOffset(chan.fTimeOffset);
   SetTimeDrift(chan.fTimeDrift);
   SetAllENGCoefficients(chan.fENGCoefficients);
   SetENGRanges(chan.fENGRanges);
   SetAllENGChi2(chan.fENGChi2);
   SetENGDriftCoefficents(chan.fENGDriftCoefficents);
   SetCFDCoefficients(chan.fCFDCoefficients);
   SetLEDCoefficients(chan.fLEDCoefficients);
   SetTIMECoefficients(chan.fTIMECoefficients);
   SetEFFCoefficients(chan.fEFFCoefficients);
   SetCTCoefficients(chan.fCTCoefficients);
   SetEnergyNonlinearity(chan.fEnergyNonlinearity);
   SetTimeNonlinearity(chan.fTimeNonlinearity);
   SetCFDChi2(chan.fCFDChi2);
   SetLEDChi2(chan.fLEDChi2);
   SetTIMEChi2(chan.fTIMEChi2);
   SetEFFChi2(chan.fEFFChi2);
   SetUseCalFileIntegration(chan.fUseCalFileInt);
   SetWaveParam(chan.GetWaveParam());
   SetDetectorNumber(chan.GetDetectorNumber());
   SetSegmentNumber(chan.GetSegmentNumber());
   SetCrystalNumber(chan.GetCrystalNumber());
 
   SetClassType(chan.GetClassType());
}
 
TChannel::TChannel(TChannel&& chan) noexcept : TNamed(chan)
{
   /// Moves chan to this.
   /// Just a copy of the copy constructor right now, needs to be changed.
   Clear();
   *(fMnemonic.Value()) = *(chan.fMnemonic.Value());
   SetAddress(chan.GetAddress());
   SetIntegration(chan.fIntegration);
   SetNumber(chan.fNumber);
   SetStream(chan.fStream);
   SetName(chan.GetName());
   SetDigitizerType(chan.fDigitizerTypeString);
   SetTimeOffset(chan.fTimeOffset);
   SetTimeDrift(chan.fTimeDrift);
   SetAllENGCoefficients(chan.fENGCoefficients);
   SetENGRanges(chan.fENGRanges);
   SetAllENGChi2(chan.fENGChi2);
   SetENGDriftCoefficents(chan.fENGDriftCoefficents);
   SetCFDCoefficients(chan.fCFDCoefficients);
   SetLEDCoefficients(chan.fLEDCoefficients);
   SetTIMECoefficients(chan.fTIMECoefficients);
   SetEFFCoefficients(chan.fEFFCoefficients);
   SetCTCoefficients(chan.fCTCoefficients);
   SetEnergyNonlinearity(chan.fEnergyNonlinearity);
   SetTimeNonlinearity(chan.fTimeNonlinearity);
   SetCFDChi2(chan.fCFDChi2);
   SetLEDChi2(chan.fLEDChi2);
   SetTIMEChi2(chan.fTIMEChi2);
   SetEFFChi2(chan.fEFFChi2);
   SetUseCalFileIntegration(chan.fUseCalFileInt);
   SetWaveParam(chan.GetWaveParam());
   SetDetectorNumber(chan.GetDetectorNumber());
   SetSegmentNumber(chan.GetSegmentNumber());
   SetCrystalNumber(chan.GetCrystalNumber());
 
   SetClassType(chan.GetClassType());
}
 
TChannel::TChannel(TChannel* chan)
{
   /// Makes a copy of a the TChannel.
   Clear();
   *(fMnemonic.Value()) = *(chan->fMnemonic.Value());
   SetAddress(chan->GetAddress());
   SetIntegration(chan->fIntegration);
   SetNumber(chan->fNumber);
   SetStream(chan->fStream);
   SetName(chan->GetName());
   SetDigitizerType(chan->fDigitizerTypeString);
   SetTimeOffset(chan->fTimeOffset);
   SetTimeDrift(chan->fTimeDrift);
   SetAllENGCoefficients(chan->fENGCoefficients);
   SetENGRanges(chan->fENGRanges);
   SetAllENGChi2(chan->fENGChi2);
   SetENGDriftCoefficents(chan->fENGDriftCoefficents);
   SetCFDCoefficients(chan->fCFDCoefficients);
   SetLEDCoefficients(chan->fLEDCoefficients);
   SetTIMECoefficients(chan->fTIMECoefficients);
   SetEFFCoefficients(chan->fEFFCoefficients);
   SetCTCoefficients(chan->fCTCoefficients);
   SetEnergyNonlinearity(chan->fEnergyNonlinearity);
   SetTimeNonlinearity(chan->fTimeNonlinearity);
   SetCFDChi2(chan->fCFDChi2);
   SetLEDChi2(chan->fLEDChi2);
   SetTIMEChi2(chan->fTIMEChi2);
   SetEFFChi2(chan->fEFFChi2);
   SetUseCalFileIntegration(chan->fUseCalFileInt);
   SetWaveParam(chan->GetWaveParam());
   SetDetectorNumber(chan->GetDetectorNumber());
   SetSegmentNumber(chan->GetSegmentNumber());
   SetCrystalNumber(chan->GetCrystalNumber());
 
   SetClassType(chan->GetClassType());
}
 
TChannel& TChannel::operator=(const TChannel& rhs)
{
   /// copy assignment operator
   /// Simply a copy of the copy constructor code (plus returing *this).
   Clear();
   *(fMnemonic.Value()) = *(rhs.fMnemonic.Value());
   SetAddress(rhs.GetAddress());
   SetIntegration(rhs.fIntegration);
   SetNumber(rhs.fNumber);
   SetStream(rhs.fStream);
   SetName(rhs.GetName());
   SetDigitizerType(rhs.fDigitizerTypeString);
   SetTimeOffset(rhs.fTimeOffset);
   SetTimeDrift(rhs.fTimeDrift);
   SetAllENGCoefficients(rhs.fENGCoefficients);
   SetENGRanges(rhs.fENGRanges);
   SetAllENGChi2(rhs.fENGChi2);
   SetENGDriftCoefficents(rhs.fENGDriftCoefficents);
   SetCFDCoefficients(rhs.fCFDCoefficients);
   SetLEDCoefficients(rhs.fLEDCoefficients);
   SetTIMECoefficients(rhs.fTIMECoefficients);
   SetEFFCoefficients(rhs.fEFFCoefficients);
   SetCTCoefficients(rhs.fCTCoefficients);
   SetEnergyNonlinearity(rhs.fEnergyNonlinearity);
   SetTimeNonlinearity(rhs.fTimeNonlinearity);
   SetCFDChi2(rhs.fCFDChi2);
   SetLEDChi2(rhs.fLEDChi2);
   SetTIMEChi2(rhs.fTIMEChi2);
   SetEFFChi2(rhs.fEFFChi2);
   SetUseCalFileIntegration(rhs.fUseCalFileInt);
   SetWaveParam(rhs.GetWaveParam());
   SetDetectorNumber(rhs.GetDetectorNumber());
   SetSegmentNumber(rhs.GetSegmentNumber());
   SetCrystalNumber(rhs.GetCrystalNumber());
 
   SetClassType(rhs.GetClassType());
 
   return *this;
}
 
TChannel& TChannel::operator=(TChannel&& rhs) noexcept
{
   /// move assignment operator
   /// Doesn't really move anything yet, it's just a copy of the copy assignment operator.
   /// This needs to be changed.
   Clear();
   *(fMnemonic.Value()) = *(rhs.fMnemonic.Value());
   SetAddress(rhs.GetAddress());
   SetIntegration(rhs.fIntegration);
   SetNumber(rhs.fNumber);
   SetStream(rhs.fStream);
   SetName(rhs.GetName());
   SetDigitizerType(rhs.fDigitizerTypeString);
   SetTimeOffset(rhs.fTimeOffset);
   SetTimeDrift(rhs.fTimeDrift);
   SetAllENGCoefficients(rhs.fENGCoefficients);
   SetENGRanges(rhs.fENGRanges);
   SetAllENGChi2(rhs.fENGChi2);
   SetENGDriftCoefficents(rhs.fENGDriftCoefficents);
   SetCFDCoefficients(rhs.fCFDCoefficients);
   SetLEDCoefficients(rhs.fLEDCoefficients);
   SetTIMECoefficients(rhs.fTIMECoefficients);
   SetEFFCoefficients(rhs.fEFFCoefficients);
   SetCTCoefficients(rhs.fCTCoefficients);
   SetEnergyNonlinearity(rhs.fEnergyNonlinearity);
   SetTimeNonlinearity(rhs.fTimeNonlinearity);
   SetCFDChi2(rhs.fCFDChi2);
   SetLEDChi2(rhs.fLEDChi2);
   SetTIMEChi2(rhs.fTIMEChi2);
   SetEFFChi2(rhs.fEFFChi2);
   SetUseCalFileIntegration(rhs.fUseCalFileInt);
   SetWaveParam(rhs.GetWaveParam());
   SetDetectorNumber(rhs.GetDetectorNumber());
   SetSegmentNumber(rhs.GetSegmentNumber());
   SetCrystalNumber(rhs.GetCrystalNumber());
 
   SetClassType(rhs.GetClassType());
 
   return *this;
}
 
void TChannel::SetName(const char* tmpName)
{
   if(strlen(tmpName) == 0) { return; }
   TNamed::SetName(tmpName);
   // do not parse the default name
   if(strcmp(tmpName, "DefaultTChannel") != 0) {
      fMnemonic.Value()->Parse(GetName());
   }
}
 
void TChannel::InitChannelInput()
{
   int channels_found = ParseInputData(fFileData.c_str(), "q", EPriority::kRootFile);
   if(gFile != nullptr) {
      std::cout << "Successfully read " << channels_found << " TChannels from " << CYAN << gFile->GetName() << RESET_COLOR << std::endl;
   } else {
      std::cout << "Successfully read " << channels_found << " TChannels" << std::endl;
   }
}
 
bool TChannel::CompareChannels(const TChannel* chana, const TChannel* chanb)
{
   /// Compares the names of the two TChannels.
   /// Returns true if the name of chana goes lexicographically before the name of chanb.
   std::string namea(chana->GetName());
 
   return namea.compare(chanb->GetName()) < 0;
}
 
void TChannel::DeleteAllChannels()
{
   /// Safely deletes fChannelMap and fChannelNumberMap
   for(auto iter : *fChannelMap) {
      delete iter.second;
      // These maps should point to the same pointers, so this should clear out both
      iter.second = nullptr;
   }
   fChannelMap->clear();
   fChannelNumberMap->clear();
}
 
void TChannel::AddChannel(TChannel* chan, Option_t* opt)
{
   /// Add a TChannel to fChannelMap. If the TChannel doesn't exist, create a new TChannel and add that the fChannelMap.
   /// Options:
   ///        "overwrite" -  The TChannel in the fChannelMap at the same address is overwritten.
   ///                       If this option is not specified, an Error is returned if the TChannel already
   ///                       exists in the fChannelMap.
   ///        "save"      -  The temporary channel is not deleted after being placed in the map.
   if(chan == nullptr) {
      return;
   }
   if(fChannelMap->count(chan->GetAddress()) == 1) {   // if this channel exists
      if(strcmp(opt, "overwrite") == 0) {
         TChannel* oldchan   = GetChannel(chan->GetAddress());
         int       oldNumber = oldchan->GetNumber();
         oldchan->OverWriteChannel(chan);
         // Need to also update the channel number map RD
         if(oldNumber != oldchan->GetNumber()) {
            // channel number has changed so we need to delete the old one and insert the new one
            fChannelNumberMap->erase(oldNumber);
            if((oldchan->GetNumber() != 0) && (fChannelNumberMap->count(oldchan->GetNumber()) == 0)) {
               fChannelNumberMap->insert(std::make_pair(oldchan->GetNumber(), oldchan));
            }
         }
         return;
      }
      std::cout << "Trying to add a channel that already exists!" << std::endl;
      return;
   }
   if((chan->GetAddress() & 0x00ffffff) == 0x00ffffff) {
      // this is the default tigress value for i am not there.
      // we should not imclude it in the map.
      delete chan;
   } else {
      // We need to update the channel maps to correspond to the new channel that has been added.
      fChannelMap->insert(std::make_pair(chan->GetAddress(), chan));
      if((chan->GetNumber() != 0) && (fChannelNumberMap->count(chan->GetNumber()) == 0)) {
         fChannelNumberMap->insert(std::make_pair(chan->GetNumber(), chan));
      }
   }
}
 
void TChannel::OverWriteChannel(TChannel* chan)
{
   /// Overwrites the current TChannel with chan.
   SetAddress(chan->GetAddress());
   SetIntegration(TPriorityValue<int>(chan->GetIntegration(), EPriority::kForce));
   SetNumber(TPriorityValue<int>(chan->GetNumber(), EPriority::kForce));
   SetStream(TPriorityValue<int>(chan->GetStream(), EPriority::kForce));
   SetDigitizerType(TPriorityValue<std::string>(chan->GetDigitizerTypeString(), EPriority::kForce));
   SetName(chan->GetName());
 
   SetAllENGCoefficients(TPriorityValue<std::vector<std::vector<Float_t>>>(chan->GetAllENGCoeff(), EPriority::kForce));
   SetENGRanges(TPriorityValue<std::vector<std::pair<double, double>>>(chan->GetENGRanges(), EPriority::kForce));
   SetAllENGChi2(TPriorityValue<std::vector<double>>(chan->GetAllENGChi2(), EPriority::kForce));
   SetENGDriftCoefficents(TPriorityValue<std::vector<Float_t>>(chan->GetENGDriftCoefficents(), EPriority::kForce));
   SetCFDCoefficients(TPriorityValue<std::vector<double>>(chan->GetCFDCoeff(), EPriority::kForce));
   SetLEDCoefficients(TPriorityValue<std::vector<double>>(chan->GetLEDCoeff(), EPriority::kForce));
   SetTIMECoefficients(TPriorityValue<std::vector<double>>(chan->GetTIMECoeff(), EPriority::kForce));
   SetEFFCoefficients(TPriorityValue<std::vector<double>>(chan->GetEFFCoeff(), EPriority::kForce));
   SetCTCoefficients(TPriorityValue<std::vector<double>>(chan->GetCTCoeff(), EPriority::kForce));
   SetEnergyNonlinearity(TPriorityValue<TGraph>(chan->GetEnergyNonlinearity(), EPriority::kForce));
   SetTimeNonlinearity(TPriorityValue<TGraph>(chan->GetTimeNonlinearity(), EPriority::kForce));
 
   SetCFDChi2(TPriorityValue<double>(chan->GetCFDChi2(), EPriority::kForce));
   SetLEDChi2(TPriorityValue<double>(chan->GetLEDChi2(), EPriority::kForce));
   SetTIMEChi2(TPriorityValue<double>(chan->GetTIMEChi2(), EPriority::kForce));
   SetEFFChi2(TPriorityValue<double>(chan->GetEFFChi2(), EPriority::kForce));
 
   SetUseCalFileIntegration(TPriorityValue<bool>(chan->UseCalFileIntegration(), EPriority::kForce));
 
   SetWaveParam(chan->GetWaveParam());
 
   SetDetectorNumber(chan->GetDetectorNumber());
   SetSegmentNumber(chan->GetSegmentNumber());
   SetCrystalNumber(chan->GetCrystalNumber());
   SetTimeOffset(TPriorityValue<Long64_t>(chan->GetTimeOffset(), EPriority::kForce));
   SetTimeDrift(TPriorityValue<double>(chan->GetTimeDrift(), EPriority::kForce));
   SetClassType(chan->GetClassType());
}
 
void TChannel::AppendChannel(TChannel* chan)
{
   /// Sets the current TChannel to chan
   SetIntegration(chan->fIntegration);
   SetNumber(chan->fNumber);
   SetStream(chan->fStream);
   if(strcmp(chan->GetName(), "DefaultTChannel") != 0) { SetName(chan->GetName()); }   // don't overwrite an existing name by the default name
   SetDigitizerType(chan->fDigitizerTypeString);
   SetTimeOffset(chan->fTimeOffset);
   SetTimeDrift(chan->fTimeDrift);
   SetAllENGCoefficients(chan->fENGCoefficients);
   SetENGRanges(chan->fENGRanges);
   SetAllENGChi2(chan->fENGChi2);
   SetENGDriftCoefficents(chan->fENGDriftCoefficents);
   SetCFDCoefficients(chan->fCFDCoefficients);
   SetLEDCoefficients(chan->fLEDCoefficients);
   SetTIMECoefficients(chan->fTIMECoefficients);
   SetEFFCoefficients(chan->fEFFCoefficients);
   SetCTCoefficients(chan->fCTCoefficients);
   SetEnergyNonlinearity(chan->fEnergyNonlinearity);
   SetTimeNonlinearity(chan->fTimeNonlinearity);
   SetCFDChi2(chan->fCFDChi2);
   SetLEDChi2(chan->fLEDChi2);
   SetTIMEChi2(chan->fTIMEChi2);
   SetEFFChi2(chan->fEFFChi2);
   SetUseCalFileIntegration(chan->fUseCalFileInt);
   SetWaveParam(chan->GetWaveParam());
   SetDetectorNumber(chan->GetDetectorNumber());
   SetSegmentNumber(chan->GetSegmentNumber());
   SetCrystalNumber(chan->GetCrystalNumber());
 
   SetClassType(chan->GetClassType());
}
 
int TChannel::UpdateChannel(TChannel* chan, Option_t*)
{
   /// If there is information in the chan, the current TChannel with the same address is updated with that information.
   if(chan == nullptr) {
      return 0;
   }
   TChannel* oldchan = GetChannel(chan->GetAddress());   // look for already existing channel at this address
   if(oldchan == nullptr) {
      return 0;
   }
   oldchan->AppendChannel(chan);
 
   return 0;
}
 
TChannel* TChannel::GetDefaultChannel()
{
   if(!fChannelMap->empty()) {
      return fChannelMap->begin()->second;
   }
   return nullptr;
}
 
void TChannel::Clear(Option_t*)
{
   /// Clears all fields of a TChannel. There are currently no options to be specified.
   fAddress = 0xffffffff;
   fIntegration.Reset(0);
   fDigitizerTypeString = TPriorityValue<std::string>();
   // fDigitizerType.Reset(EDigitizer::kDefault);
   fNumber.Reset(0);
   fStream.Reset(0);
   fUseCalFileInt.Reset(false);
 
   fDetectorNumber = -1;
   fSegmentNumber  = -1;
   fCrystalNumber  = -1;
   fTimeOffset.Reset(0);
   fTimeDrift.Reset(0);
 
   WaveFormShape = WaveFormShapePar();
 
   // only create a new mnemonic if we do not have one yet (this function is called from the constructor)
   if(fMnemonic.Value() != nullptr) {
      fMnemonic.Value()->Clear();
   } else {
      fMnemonic = TPriorityValue<TMnemonic*>(static_cast<TMnemonic*>(fMnemonicClass->New()), EPriority::kForce);
   }
   SetName("DefaultTChannel");
 
   fENGCoefficients.Reset(std::vector<std::vector<Float_t>>());
   fENGRanges.Reset(std::vector<std::pair<double, double>>());
   fENGChi2.Reset(std::vector<double>());
   fENGDriftCoefficents.Reset(std::vector<Float_t>());
   fCFDCoefficients.Reset(std::vector<double>());
   fCFDChi2.Reset(0.0);
   fLEDCoefficients.Reset(std::vector<double>());
   fLEDChi2.Reset(0.0);
   fTIMECoefficients.Reset(std::vector<double>());
   fTIMEChi2.Reset(0.0);
   fEFFCoefficients.Reset(std::vector<double>());
   fEFFChi2.Reset(0.0);
   fCTCoefficients.Reset(std::vector<double>());
   fEnergyNonlinearity.Reset(TGraph());
   fTimeNonlinearity.Reset(TGraph());
}
 
TChannel* TChannel::GetChannel(unsigned int temp_address, bool warn)
{
   /// Returns the TChannel at the specified address. If the address doesn't exist, returns an empty gChannel.
 
   TChannel* chan = nullptr;
   if(fChannelMap->count(temp_address) == 1) {   // found channel
      chan = fChannelMap->at(temp_address);
   }
   if(warn && chan == nullptr) {
      if(fMissingChannelMap->find(temp_address) == fMissingChannelMap->end()) {
         // if there are threads running we're not in interactive mode, so we print a warning about sorting
         if(StoppableThread::AnyThreadRunning()) {
            std::ostringstream str;
            str << RED << "Failed to find channel for address " << hex(temp_address, 4) << ", this channel won't get sorted properly!" << RESET_COLOR << std::endl;
            std::cerr << str.str();
         }
         fMissingChannelMap->insert(std::pair<unsigned int, int>(temp_address, 0));
      }
      ++(*fMissingChannelMap)[temp_address];
   }
   return chan;
}
 
TChannel* TChannel::GetChannelByNumber(int temp_num)
{
   /// Returns the TChannel based on the channel number and not the channel address.
   TChannel* chan = nullptr;
   try {
      chan = fChannelNumberMap->at(temp_num);
   } catch(const std::out_of_range& oor) {
      return nullptr;
   }
   return chan;
}
 
TChannel* TChannel::FindChannelByName(const char* ccName)
{
   /// Finds the TChannel by the name of the channel
   TChannel* chan = nullptr;
   if(ccName == nullptr) {
      return chan;
   }
 
   std::string name = ccName;
   if(name.empty()) {
      return chan;
   }
 
   for(auto iter : *fChannelMap) {
      chan                    = iter.second;
      std::string channelName = chan->GetName();
      if(channelName.compare(0, name.length(), name) == 0) {
         return chan;
      }
   }
 
   return nullptr;
}
 
std::vector<TChannel*> TChannel::FindChannelByRegEx(const char* ccName)
{
   /// Finds the TChannel by the name of the channel
   std::vector<TChannel*> result;
   if(ccName == nullptr) {
      return result;
   }
 
   std::regex regex(ccName);
 
   TChannel* chan = nullptr;
   for(auto iter : *fChannelMap) {
      chan                    = iter.second;
      std::string channelName = chan->GetName();
      if(std::regex_match(channelName, regex)) {
         result.push_back(chan);
      }
   }
 
   return result;
}
 
void TChannel::SetAddress(unsigned int tmpadd)
{
   /// Sets the address of a TChannel and also overwrites that channel if it is in the channel map
   for(auto iter1 : *fChannelMap) {
      if(iter1.second == this) {
         std::cout << "Channel at address: " << hex(fAddress, 4)
                   << " already exists. Please use AddChannel() or OverWriteChannel() to change this TChannel"
                   << std::dec << std::endl;
         break;
      }
   }
   fAddress = tmpadd;
}
 
void TChannel::DestroyENGCal()
{
   /// Erases the ENGCoefficients vector
   fENGCoefficients.Address()->clear();
   fENGRanges.Address()->clear();
   fENGChi2.Address()->clear();
   fENGDriftCoefficents.Address()->clear();
}
 
void TChannel::DestroyCFDCal()
{
   /// Erases the CFDCoefficients vector
   fCFDCoefficients.Address()->clear();
}
 
void TChannel::DestroyLEDCal()
{
   /// Erases the LEDCoefficients vector
   fLEDCoefficients.Address()->clear();
}
 
void TChannel::DestroyTIMECal()
{
   /// Erases the TimeCal vector
   fTIMECoefficients.Address()->clear();
}
 
void TChannel::DestroyEFFCal()
{
   /// Erases the EffCal vector
   fEFFCoefficients.Address()->clear();
}
 
void TChannel::DestroyCTCal()
{
   // Erases the CTCal vector
   fCTCoefficients.Address()->clear();
}
 
void TChannel::DestroyEnergyNonlinearity()
{
   fEnergyNonlinearity.Address()->Set(0);
}
 
void TChannel::DestroyTimeNonlinearity()
{
   fTimeNonlinearity.Address()->Set(0);
}
 
void TChannel::DestroyCalibrations()
{
   /// Erases all Cal vectors
   DestroyENGCal();
   DestroyCFDCal();
   DestroyLEDCal();
   DestroyTIMECal();
   DestroyEFFCal();
   DestroyCTCal();
}
 
double TChannel::CalibrateENG(int charge, int temp_int) const
{
   /// Returns the calibrated energy of the channel when a charge is passed to it.
   /// This is done by first adding a random number between 0 and 1 to the charge
   /// bin. This is then taken and divided by the integration parameter. The
   /// polynomial energy calibration formula is then applied to get the calibrated
   /// energy.
   if(charge == 0) {
      return 0.0000;
   }
 
   // We need to add a random number between 0 and 1 before calibrating to avoid
   // binning issues.
   return CalibrateENG(static_cast<double>(charge) + gRandom->Uniform(), temp_int);
}
 
double TChannel::CalibrateENG(double charge, int temp_int) const
{
   /// Returns the calibrated energy of the channel when a charge is passed to it.
   /// This is divided by the integration parameter. The
   /// polynomial energy calibration formula is then applied to get the calibrated
   /// energy.
   if(charge == 0) {
      return 0.0000;
   }
 
   if(temp_int == 0) {
      if(fIntegration.Value() != 0) {
         temp_int = fIntegration.Value();
      } else {
         temp_int = 1;
      }
   }
 
   return CalibrateENG((charge) / static_cast<double>(temp_int));
}
 
double TChannel::CalibrateENG(double charge) const
{
   /// Returns the calibrated energy. The polynomial energy calibration formula is
   /// applied to get the calibrated energy. This function does not use the
   /// integration parameter. If multiple ranges are present, the calibration of the
   /// range is used. In overlap regions the range used is chosen randomly.
   if(fENGCoefficients.empty()) {
      return charge;
   }
   // select range to use, they should be sorted
   size_t currentRange = 0;
   if(!fENGRanges.empty()) {
      // we need a boolean to tell us if we found a range as the test
      // currentRange+1 == fENGRanges.size()
      // fails if the charge is in the overlap between the second-to-last and last range
      // and the last range was selected
      bool foundRange = false;
      for(currentRange = 0; currentRange + 1 < fENGRanges.size(); ++currentRange) {
         // check if the current range covers this charge
         if(fENGRanges.Value()[currentRange].first < charge && charge < fENGRanges.Value()[currentRange].second) {
            // check if there is an overlap with the next range in which case we select that one in 50% of the cases
            if(fENGRanges.Value()[currentRange + 1].first < charge && charge < fENGRanges.Value()[currentRange + 1].second &&
               gRandom->Uniform() > 0.5) {
               ++currentRange;
            }
            foundRange = true;
            break;
         }
      }
      if(!foundRange) {
         currentRange = fENGRanges.size() - 1;
         if(charge < fENGRanges[currentRange].first || fENGRanges[currentRange].second < charge) {
            std::cerr << "Charge " << charge << " outside all ranges of calibration (first " << fENGRanges.front().first << " - " << fENGRanges.front().second << ", last " << fENGRanges.back().first << " - " << fENGRanges.back().second << ")" << std::endl;
         }
      }
   }
 
   // apply the drift correction first
   if(!fENGDriftCoefficents.empty()) {
      double corrCharge = -fENGDriftCoefficents[0];   // ILL subtracts the offset instead of adding it
      for(size_t i = 1; i < fENGDriftCoefficents.size(); i++) {
         corrCharge += fENGDriftCoefficents[i] * pow(charge, static_cast<double>(i));
      }
      charge = corrCharge;
   }
   // if we had drift correction charge is now the corrected charge, otherwise it is still the charge
   double cal_chg = fENGCoefficients[currentRange][0];
   for(size_t i = 1; i < fENGCoefficients[currentRange].size(); i++) {
      cal_chg += fENGCoefficients[currentRange][i] * pow((charge), static_cast<double>(i));
   }
   return cal_chg;
}
 
double TChannel::CalibrateCFD(int cfd) const
{
   /// Calibrates the CFD properly.
   return CalibrateCFD(static_cast<double>(cfd) + gRandom->Uniform());
}
 
double TChannel::CalibrateCFD(double cfd) const
{
   /// Returns the calibrated CFD. The polynomial CFD calibration formula is
   /// applied to get the calibrated CFD.
   if(fCFDCoefficients.empty()) {
      return cfd;
   }
 
   double cal_cfd = 0.0;
   // std::cout<<cfd<<":";
   for(size_t i = 0; i < fCFDCoefficients.size(); i++) {
      cal_cfd += fCFDCoefficients[i] * pow(cfd, static_cast<double>(i));
      // std::cout<<" "<<i<<" - "<<fCFDCoefficients[i]<<" = "<<cal_cfd;
   }
   // std::cout<<std::endl;
 
   return cal_cfd;
}
 
double TChannel::CalibrateLED(int led) const
{
   /// Calibrates the LED
   return CalibrateLED(static_cast<double>(led) + gRandom->Uniform());
}
 
double TChannel::CalibrateLED(double led) const
{
   /// Returns the calibrated LED. The polynomial LED calibration formula is
   /// applied to get the calibrated LED.
   if(fLEDCoefficients.empty()) {
      return led;
   }
 
   double cal_led = 0.0;
   for(size_t i = 0; i < fLEDCoefficients.size(); i++) {
      cal_led += fLEDCoefficients[i] * pow(led, static_cast<double>(i));
   }
   return cal_led;
}
 
double TChannel::CalibrateTIME(int chg) const
{
   /// Calibrates the time spectrum
   if(fTIMECoefficients.size() != 3 || (chg < 1)) {
      return 0.0000;
   }
   return CalibrateTIME((CalibrateENG(chg)));
}
 
double TChannel::CalibrateTIME(double energy) const
{
   /// uses the values stored in TIMECOefficients to calculate a
   /// "walk correction" factor.  This function returns the correction
   /// not an adjusted time stamp!   pcb.
   if(fTIMECoefficients.size() != 3 || (energy < 3.0)) {
      return 0.0000;
   }
 
   double timeCorrection = 0.0;
 
   timeCorrection = fTIMECoefficients.at(0) + (fTIMECoefficients.at(1) * pow(energy, fTIMECoefficients.at(2)));
 
   return timeCorrection;
}
 
double TChannel::CalibrateEFF(double) const
{
   /// This needs to be added
   return 1.0;
}
 
void TChannel::SetUseCalFileIntegration(const std::string& mnemonic, bool flag, EPriority prio)
{
   /// Writes this UseCalFileIntegration to all channels in the current TChannel Map
   /// that starts with the mnemonic. Use "" to write to ALL channels
   /// WARNING: This is case sensitive!
   std::unordered_map<unsigned int, TChannel*>::iterator mapit;
   std::unordered_map<unsigned int, TChannel*>*          chanmap = TChannel::GetChannelMap();
   for(mapit = chanmap->begin(); mapit != chanmap->end(); mapit++) {
      if(mnemonic.empty() || (strncmp(mapit->second->GetName(), mnemonic.c_str(), mnemonic.size()) == 0)) {
         mapit->second->SetUseCalFileIntegration(TPriorityValue<bool>(flag, prio));
      }
   }
}
 
void TChannel::SetIntegration(const std::string& mnemonic, int tmpint, EPriority prio)
{
   // Writes this integration to all channels in the current TChannel Map
   // that starts with the mnemonic. Use "" to write to ALL channels
   // WARNING: This is case sensitive!
   std::unordered_map<unsigned int, TChannel*>::iterator mapit;
   std::unordered_map<unsigned int, TChannel*>*          chanmap = TChannel::GetChannelMap();
   for(mapit = chanmap->begin(); mapit != chanmap->end(); mapit++) {
      if(mnemonic.empty() || (strncmp(mapit->second->GetName(), mnemonic.c_str(), mnemonic.size()) == 0)) {
         mapit->second->SetIntegration(TPriorityValue<int>(tmpint, prio));
      }
   }
}
 
void TChannel::SetDigitizerType(const std::string& mnemonic, const char* tmpstr, EPriority prio)
{
   // Writes this digitizer type to all channels in the current TChannel Map
   // that starts with the mnemonic. Use "" to write to ALL channels
   // WARNING: This is case sensitive!
   std::unordered_map<unsigned int, TChannel*>::iterator mapit;
   std::unordered_map<unsigned int, TChannel*>*          chanmap = TChannel::GetChannelMap();
   for(mapit = chanmap->begin(); mapit != chanmap->end(); mapit++) {
      if(mnemonic.empty() || (strncmp(mapit->second->GetName(), mnemonic.c_str(), mnemonic.size()) == 0)) {
         mapit->second->SetDigitizerType(TPriorityValue<std::string>(tmpstr, prio));
      }
   }
}
 
void TChannel::PrintCTCoeffs(Option_t*) const
{
   /// Prints out the current TChannel.
   std::cout << GetName() << "\t{\n";   //,channelname.c_str();
   std::cout << "Name:      " << GetName() << std::endl;
   std::cout << "Number:    " << fNumber << std::endl;
   std::cout << "Address:   " << hex(fAddress, 8) << std::endl;
   for(double fCTCoefficient : fCTCoefficients) {
      std::cout << fCTCoefficient << "\t";
   }
   std::cout << std::endl;
   std::cout << "}\n";
   std::cout << "//====================================//\n";
}
 
void TChannel::Print(Option_t*) const
{
   /// Prints out the current TChannel.
   std::cout << PrintToString();
}
 
std::string TChannel::PrintCTToString(Option_t*) const
{
   std::string buffer;
   buffer.append("\n");
   buffer.append(GetName());
   buffer.append("\t{\n");   //,channelname.c_str();
   buffer.append("Name:      ");
   buffer.append(GetName());
   buffer.append("\n");
   buffer.append(Form("Number:    %d\n", fNumber.Value()));
   buffer.append(Form("Address:   0x%08x\n", fAddress));
   if(!fCTCoefficients.empty()) {
      buffer.append("CTCoeff:  ");
      for(double fCTCoefficient : fCTCoefficients) {
         buffer.append(Form("%f\t", fCTCoefficient));
      }
      buffer.append("\n");
   }
   buffer.append("}\n");
 
   buffer.append("//====================================//\n");
 
   return buffer;
}
 
std::string TChannel::PrintToString(Option_t*) const
{
   std::ostringstream str;
 
   str << GetName() << "\t{" << std::endl;   //,channelname.c_str();
   str << "Type:      ";
   if(GetClassType() != nullptr) {
      str << GetClassType()->GetName() << std::endl;
   } else {
      str << "None" << std::endl;
   }
 
   str << "Name:      " << GetName() << std::endl;
   str << "Number:    " << fNumber << std::endl;
   str << "Address:   " << hex(fAddress, 4) << std::dec << std::endl;
   if(!fDigitizerTypeString.empty()) {
      str << "Digitizer: " << fDigitizerTypeString << std::endl;
   }
   str << "TimeOffset: " << fTimeOffset << std::endl;
   str << "TimeDrift: " << fTimeDrift << std::endl;
   str << "Integration: " << fIntegration << std::endl;
   if(!fENGCoefficients.empty()) {
      for(size_t i = 0; i < fENGCoefficients.size(); ++i) {
         if(fENGCoefficients.size() == 1) {
            str << "ENGCoeff:  ";
         } else {
            str << "ENGCoeff:  range " << i << "\t";
         }
         for(auto coeff : fENGCoefficients[i]) {
            str << coeff << "\t";
         }
         str << std::endl;
      }
   }
   if(!fENGChi2.empty()) {
      for(size_t i = 0; i < fENGChi2.size(); ++i) {
         if(fENGCoefficients.size() == 1) {
            str << "ENGChi2:   " << fENGChi2[i] << std::endl;
         } else {
            str << "ENGChi2:   range " << i << "\t" << fENGChi2[i] << std::endl;
         }
      }
   }
   if(!fENGRanges.empty()) {
      for(size_t i = 0; i < fENGRanges.size(); ++i) {
         str << "ENGRange:   " << i << "\t" << fENGRanges[i].first << " " << fENGRanges[i].second << std::endl;
      }
   }
   if(!fENGDriftCoefficents.empty()) {
      str << "ENGDrift:   ";
      auto oldPrecision = str.precision();
      str.precision(9);
      for(auto coeff : fENGDriftCoefficents) {
         str << coeff << "\t";
      }
      str.precision(oldPrecision);
      str << std::endl;
   }
   if(!fEFFCoefficients.empty()) {
      str << "EFFCoeff:  ";
      for(auto coeff : fEFFCoefficients) {
         str << coeff << "\t";
      }
      str << std::endl;
   }
   if(fEFFChi2 != 0) {
      str << "EFFChi2:   " << fEFFChi2 << std::endl;
   }
   if(!fCFDCoefficients.empty()) {
      str << "CFDCoeff:  ";
      for(auto coeff : fCFDCoefficients) {
         str << coeff << "\t";
      }
      str << std::endl;
   }
   if(fEnergyNonlinearity.Value().GetN() > 0) {
      str << "EnergyNonlinearity:  ";
      double* x = fEnergyNonlinearity.Value().GetX();
      double* y = fEnergyNonlinearity.Value().GetY();
      for(int i = 0; i < fEnergyNonlinearity.Value().GetN(); ++i) {
         str << x[i] << "\t" << y[i] << "\t";
      }
      str << std::endl;
   }
   if(fTimeNonlinearity.Value().GetN() > 0) {
      str << "TimeNonlinearity:  ";
      double* x = fTimeNonlinearity.Value().GetX();
      double* y = fTimeNonlinearity.Value().GetY();
      for(int i = 0; i < fTimeNonlinearity.Value().GetN(); ++i) {
         str << x[i] << "\t" << y[i] << "\t";
      }
      str << std::endl;
   }
   if(!fCTCoefficients.empty()) {
      str << "CTCoeff:  ";
      for(auto coeff : fCTCoefficients) {
         str << coeff << "\t";
      }
      str << std::endl;
   }
   if(!fTIMECoefficients.empty()) {
      str << "TIMECoeff: ";
      for(auto coeff : fTIMECoefficients) {
         str << coeff << "\t";
      }
      str << std::endl;
   }
   if(fUseCalFileInt) {
      str << "FileInt: " << fUseCalFileInt << std::endl;
   }
   if(UseWaveParam()) {
      str << "RiseTime: " << WaveFormShape.TauRise << std::endl;
      str << "DecayTime: " << WaveFormShape.TauDecay << std::endl;
      str << "BaseLine: " << WaveFormShape.BaseLine << std::endl;
   }
   str << "}" << std::endl;
   str << "//====================================//" << std::endl;
   std::string buffer = str.str();
 
   return buffer;
}
 
std::vector<TChannel*> TChannel::SortedChannels()
{
   std::vector<TChannel*> chanVec;
   for(auto iter : *fChannelMap) {
      if(iter.second != nullptr) {
         chanVec.push_back(iter.second);
      }
   }
 
   // This orders channels nicely
   std::sort(chanVec.begin(), chanVec.end(), TChannel::CompareChannels);
 
   return chanVec;
}
 
void TChannel::WriteCalFile(const std::string& outfilename)
{
   /// Prints the context of addresschannelmap formatted correctly to stdout if
   /// no file name is passed to the function.  If a file name is passed to the function
   /// prints the context of addresschannelmap formatted correctly to a file with the given
   /// name. This will earse and rewrite the file if the file already exisits!
 
   std::vector<TChannel*> chanVec = SortedChannels();
 
   if(!outfilename.empty()) {
      std::ofstream calout;
      calout.open(outfilename.c_str());
      for(auto* iter_vec : chanVec) {
         std::string chanstr = iter_vec->PrintToString();
         calout << chanstr.c_str();
         calout << std::endl;
      }
      calout << std::endl;
      calout.close();
   } else {
      for(auto* iter_vec : chanVec) {
         iter_vec->Print();
      }
   }
}
 
void TChannel::WriteCTCorrections(const std::string& outfilename)
{
   std::vector<TChannel*> chanVec = SortedChannels();
 
   if(!outfilename.empty()) {
      std::ofstream calout;
      calout.open(outfilename.c_str());
      for(auto* iter_vec : chanVec) {
         if(iter_vec->fCTCoefficients.empty()) { continue; }
         std::string chanstr = iter_vec->PrintCTToString();
         calout << chanstr.c_str();
         calout << std::endl;
      }
      calout << std::endl;
      calout.close();
   } else {
      for(auto* iter_vec : chanVec) {
         iter_vec->PrintCTCoeffs();
      }
   }
}
 
void TChannel::WriteCalBuffer(Option_t*)
{
   /// writes any TChannels in memory to the internal buffer
   /// fFileData.  Can be used to over write info that is there
   /// or create the buffer if the channels originated from the odb.
 
   std::vector<TChannel*> chanVec = SortedChannels();
 
   std::string data;
 
   for(auto* iter_vec : chanVec) {
      data.append(iter_vec->PrintToString());
   }
   fFileData.clear();
   fFileData = data;
}
 
Int_t TChannel::ReadCalFromCurrentFile(Option_t*)
{
   if(!gFile) {
      return 0;
   }
 
   TFile* tempf = gFile->CurrentFile();
 
   return ReadFile(tempf);
}
 
Int_t TChannel::ReadCalFromFile(TFile* tempf, Option_t*)
{
   /// Reads the TChannel information from a TFile if it has already been written to that File.
   if(tempf == nullptr) {
      return 0;
   }
 
   return ReadFile(tempf);
}
 
Int_t TChannel::ReadCalFromTree(TTree* tree, Option_t*)
{
   /// Reads the TChannel information from a Tree if it has already been written to that Tree.
   if(tree == nullptr) {
      return 0;
   }
 
   TFile* tempf = tree->GetCurrentFile();
 
   return ReadFile(tempf);
}
 
Int_t TChannel::ReadFile(TFile* tempf)
{
   TList* list = tempf->GetListOfKeys();
   TIter  iter(list);
   while(TKey* key = static_cast<TKey*>(iter.Next())) {
      if((key == nullptr) || (strcmp(key->GetClassName(), "TChannel") != 0)) {
         continue;
      }
      key->ReadObj();
      return GetNumberOfChannels();
   }
   return 0;
}
 
Int_t TChannel::ReadCalFile(std::ifstream& infile)
{
   if(!infile.is_open()) {
      std::cout << DRED << "could not open file." << RESET_COLOR << std::endl;
      return -2;
   }
 
   infile.seekg(0, std::ios::end);
   int64_t length = infile.tellg();
   if(length < 1) {
      return -2;
   }
 
   auto* buffer = new char[length + 1];   //+1 for the null character to terminate the string
   infile.seekg(0, std::ios::beg);
   infile.read(buffer, length);
   buffer[length] = '\0';
 
   int channelsFound = ParseInputData(buffer, "q", EPriority::kInputFile);
   delete[] buffer;
 
   SaveToSelf();
 
   fChannelNumberMap->clear();   // This isn't the nicest way to do this but will keep us consistent.
 
   for(auto mapiter : *fChannelMap) {
      fChannelNumberMap->insert(std::make_pair(mapiter.second->GetNumber(), mapiter.second));
   }
 
   return channelsFound;
}
 
Int_t TChannel::ReadCalFile(const char* filename)
{
   /// Makes TChannels from a cal file to be used as the current calibration until grsisort
   /// is closed. Returns the number of channels properly read in.
   std::string infilename(filename);
 
   if(infilename.empty()) {
      return -1;
   }
 
   std::cout << "Reading from calibration file: " << CYAN << filename << RESET_COLOR << ".....";
   std::ifstream infile(infilename.c_str());
 
   auto channelsFound = ReadCalFile(infile);
 
   infile.close();
 
   return channelsFound;
}
 
void TChannel::SaveToSelf()
{
   /// This function saves the current cal-file to fFileData.
   /// For some reason it does the latter not by using WriteCalBuffer ???
   std::ostringstream buffer;
   std::streambuf*    std_out = std::cout.rdbuf(buffer.rdbuf());
   WriteCalFile();
   fFileData.assign(buffer.str());
   std::cout.rdbuf(std_out);
}
 
Int_t TChannel::ParseInputData(const char* inputdata, Option_t* opt, EPriority prio)
{
   std::istringstream infile(inputdata);
 
   TChannel* channel = nullptr;
 
   std::string line;
   int         linenumber  = 0;
   int         newchannels = 0;
 
   // bool creatednewchannel = false;
   bool brace_open = false;
   // int detector = 0;
   std::string name;
 
   // Parse the cal file. This is useful because if the cal file contains something that
   // the parser does not recognize, it just skips it!
   while(std::getline(infile, line)) {
      linenumber++;
      trimWS(line);
      size_t comment = line.find("//");
      if(comment != std::string::npos) {
         line = line.substr(0, comment);
      }
      if(line.empty()) {
         continue;
      }
      size_t openbrace  = line.find('{');
      size_t closebrace = line.find('}');
      size_t colon      = line.find(':');
 
      if(openbrace == std::string::npos && closebrace == std::string::npos && colon == std::string::npos) {
         continue;
      }
 
      //*************************************//
      if(closebrace != std::string::npos) {
         brace_open = false;
         if(channel != nullptr) {
            TChannel* currentchan = GetChannel(channel->GetAddress(), false);
            if(currentchan == nullptr) {
               AddChannel(channel);   // consider using a default option here
               newchannels++;
            } else {
               TChannel::UpdateChannel(channel);
               delete channel;
               newchannels++;
            }
         } else {
            delete channel;
         }
         channel = nullptr;
         name.clear();
      }
      //*************************************//
      if(openbrace != std::string::npos) {
         brace_open = true;
         name       = line.substr(0, openbrace);
         trimWS(name);
         channel = new TChannel("");
         if(!name.empty()) { channel->SetName(name.c_str()); }
      }
      //*************************************//
      if(brace_open) {
         size_t ntype = line.find(':');
         if(ntype != std::string::npos) {
            std::string type = line.substr(0, ntype);
            line             = line.substr(ntype + 1, line.length());
            trimWS(line);
            std::istringstream str(line);
            // transform type to upper case
            std::transform(type.begin(), type.end(), type.begin(), ::toupper);
            if(type == "NAME") {
               channel->SetName(line.c_str());
            } else if(type == "ADDRESS") {
               unsigned int tempadd = 0;
               str >> tempadd;
               if(tempadd == 0) {   // maybe it is in hex...
                  std::stringstream newss;
                  newss << std::hex << line;
                  newss >> tempadd;
               }
               tempadd = tempadd & 0x00ffffff;   // front end number is not included in the odb...
               channel->SetAddress(tempadd);
            } else if(type == "INTEGRATION") {
               int tempint = 0;
               str >> tempint;
               channel->SetIntegration(TPriorityValue<int>(tempint, prio));
            } else if(type == "NUMBER") {
               int tempnum = 0;
               str >> tempnum;
               channel->SetNumber(TPriorityValue<int>(tempnum, prio));
            } else if(type == "TIMEOFFSET") {
               Long64_t tempoff = 0;
               str >> tempoff;
               channel->SetTimeOffset(TPriorityValue<Long64_t>(tempoff, prio));
            } else if(type == "TIMEDRIFT") {
               double tempdrift = 0.;
               str >> tempdrift;
               channel->SetTimeDrift(TPriorityValue<double>(tempdrift, prio));
            } else if(type == "STREAM") {
               int tempstream = 0;
               str >> tempstream;
               channel->SetStream(TPriorityValue<int>(tempstream, prio));
            } else if(type == "DIGITIZER") {
               channel->SetDigitizerType(TPriorityValue<std::string>(line, prio));
            } else if(type == "ENGCHI2") {
               size_t range = line.find("range");
               if(range != std::string::npos) {
                  line = line.substr(range + 5, line.length());
                  trimWS(line);
                  str.str(line);
                  str >> range;
               } else {
                  range = 0;
               }
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetENGChi2(TPriorityValue<double>(tempdbl, prio), range);
            } else if(type == "CFDCHI2") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetCFDChi2(TPriorityValue<double>(tempdbl, prio));
            } else if(type == "LEDCHI2") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetLEDChi2(TPriorityValue<double>(tempdbl, prio));
            } else if(type == "TIMECHI2") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetTIMEChi2(TPriorityValue<double>(tempdbl, prio));
            } else if(type == "EFFCHI2") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetEFFChi2(TPriorityValue<double>(tempdbl, prio));
            } else if(type == "ENGCOEFF") {
               size_t range = line.find("range");
               if(range != std::string::npos) {
                  line = line.substr(range + 5, line.length());
                  trimWS(line);
                  str.str(line);
                  str >> range;
               } else {
                  range = 0;
               }
               if(range == 0) {
                  channel->DestroyENGCal();
                  channel->fENGCoefficients.SetPriority(prio);
               }
               float value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddENGCoefficient(value, range);
               }
            } else if(type == "ENGRANGE") {
               size_t range = 0;
               double low   = 0.;
               double high  = 0.;
               str >> range >> low >> high;
               channel->SetENGRange(std::make_pair(low, high), range);
            } else if(type == "ENGDRIFT") {
               channel->fENGDriftCoefficents.SetPriority(prio);
               float value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddENGDriftCoefficent(value);
               }
            } else if(type == "LEDCOEFF") {
               channel->DestroyLEDCal();
               channel->fLEDCoefficients.SetPriority(prio);
               double value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddLEDCoefficient(value);
               }
            } else if(type == "CFDCOEFF") {
               channel->DestroyCFDCal();
               channel->fCFDCoefficients.SetPriority(prio);
               double value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddCFDCoefficient(value);
               }
            } else if(type == "TIMECOEFF" || type == "WALK") {
               channel->DestroyTIMECal();
               channel->fTIMECoefficients.SetPriority(prio);
               double value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddTIMECoefficient(value);
               }
            } else if(type == "CTCOEFF") {
               channel->DestroyCTCal();
               channel->fCTCoefficients.SetPriority(prio);
               double value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddCTCoefficient(value);
               }
            } else if(type == "ENERGYNONLINEARITY") {
               channel->DestroyEnergyNonlinearity();
               channel->fEnergyNonlinearity.SetPriority(prio);
               double x = 0.;
               double y = 0.;
               while(!(str >> x >> y).fail()) {
                  channel->AddEnergyNonlinearityPoint(x, y);
               }
               channel->SetupEnergyNonlinearity();
            } else if(type == "TIMENONLINEARITY") {
               channel->DestroyTimeNonlinearity();
               channel->fTimeNonlinearity.SetPriority(prio);
               double x = 0.;
               double y = 0.;
               while(!(str >> x >> y).fail()) {
                  channel->AddTimeNonlinearityPoint(x, y);
               }
               channel->SetupTimeNonlinearity();
            } else if(type == "EFFCOEFF") {
               channel->DestroyEFFCal();
               channel->fEFFCoefficients.SetPriority(prio);
               double value = 0.;
               while(!(str >> value).fail()) {
                  channel->AddEFFCoefficient(value);
               }
            } else if(type == "FILEINT") {
               int tempstream = 0;
               str >> tempstream;
               if(tempstream > 0) {
                  channel->SetUseCalFileIntegration(TPriorityValue<bool>(true, prio));
               } else {
                  channel->SetUseCalFileIntegration(TPriorityValue<bool>(false, prio));
               }
            } else if(type == "RISETIME") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetWaveRise(tempdbl);
            } else if(type == "DECAYTIME") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetWaveDecay(tempdbl);
            } else if(type == "BASELINE") {
               double tempdbl = 0.;
               str >> tempdbl;
               channel->SetWaveBaseLine(tempdbl);
            } else {
            }
         }
      }
   }
   if(strcmp(opt, "q") != 0) {
      std::cout << "parsed " << linenumber << " lines." << std::endl;
   }
 
   return newchannels;
}
 
void TChannel::Streamer(TBuffer& R__b)
{
   SetBit(kCanDelete);
   UInt_t R__s = 0;
   UInt_t R__c = 0;
   if(R__b.IsReading()) {   // reading from file
      Version_t R__v = R__b.ReadVersion(&R__s, &R__c);
      if(R__v != 0) {
      }
      TNamed::Streamer(R__b);
      {
         fMnemonicClass->Streamer(R__b);
      }
      if(R__v <= 5) {
         TString R__str;
         R__str.Streamer(R__b);
      }
      {
         TString R__str;
         R__str.Streamer(R__b);
         fFileData.assign(R__str.Data());
      }
      InitChannelInput();
      R__b.CheckByteCount(R__s, R__c, TChannel::IsA());
   } else {   // writing to file
      R__c = R__b.WriteVersion(TChannel::IsA(), true);
      TNamed::Streamer(R__b);
      {
         fMnemonicClass->Streamer(R__b);
      }
      {
         TString R__str = fFileData.c_str();
         R__str.Streamer(R__b);
      }
      R__b.SetByteCount(R__c, true);
   }
}
 
int TChannel::WriteToRoot(TFile* fileptr)
{
   /// Writes Cal File information to the tree
 
   TChannel* chan = GetDefaultChannel();
   // Maintain old gDirectory info
   TDirectory* savdir = gDirectory;
 
   if(chan == nullptr) {
      std::cout << "No TChannels found to write." << std::endl;
      return 0;
   }
   if(fileptr == nullptr) {
      fileptr = gDirectory->GetFile();
   }
 
   // check if we got a file
   if(fileptr == nullptr) {
      std::cout << "Error, no file provided and no file open (gDirectory = " << gDirectory->GetName() << ")!" << std::endl;
      return 0;
   }
   fileptr->cd();
   std::string oldoption = std::string(fileptr->GetOption());
   if(oldoption == "READ") {
      fileptr->ReOpen("UPDATE");
   }
   if(!gDirectory) {   // we don't compare to nullptr here, as ROOT >= 6.24.00 uses the TDirectoryAtomicAdapter structure with a bool() operator
      std::cout << "No file opened to write TChannel to." << std::endl;
   }
   TIter iter(gDirectory->GetListOfKeys());
 
   bool        found         = false;
   std::string defaultName   = "Channel";
   std::string defaultTitle  = "TChannel";
   std::string channelbuffer = fFileData;   // fFileData is the old TChannel information read from file
   WriteCalBuffer();                        // replaces fFileData with the current channels
   std::string savedata = fFileData;
 
   FILE* originalstdout = stdout;
   int   fd             = open("/dev/null", O_WRONLY);   // turn off stdout.
   stdout               = fdopen(fd, "w");
 
   while(TKey* key = static_cast<TKey*>(iter.Next())) {
      if((key == nullptr) || (strcmp(key->GetClassName(), "TChannel") != 0)) {
         continue;
      }
      if(!found) {
         found       = true;
         auto* curCh = static_cast<TChannel*>(key->ReadObj());
         defaultName.assign(curCh->GetName());
         defaultTitle.assign(curCh->GetTitle());
      }
      std::string cname = key->ReadObj()->GetName();
      cname.append(";*");
      gDirectory->Delete(cname.c_str());
      TChannel::DeleteAllChannels();
   }
 
   stdout = originalstdout;   // Restore stdout
 
   ParseInputData(savedata.c_str(), "q", EPriority::kRootFile);
   SaveToSelf();
   TChannel::ParseInputData(channelbuffer.c_str(), "q", EPriority::kRootFile);
   chan = TChannel::GetDefaultChannel();
   chan->SetNameTitle(defaultName.c_str(), defaultTitle.c_str());
   chan->Write("Channel", TObject::kOverwrite);
 
   ParseInputData(savedata.c_str(), "q", EPriority::kRootFile);
   SaveToSelf();
 
   std::cout << "  " << GetNumberOfChannels() << " TChannels saved to " << gDirectory->GetFile()->GetName() << std::endl;
   if(oldoption == "READ") {
      std::cout << "  Returning " << gDirectory->GetFile()->GetName() << " to \"READ\" mode." << std::endl;
      fileptr->ReOpen("READ");
   }
   savdir->cd();   // Go back to original gDirectory
 
   return GetNumberOfChannels();
}
 
int TChannel::GetDetectorNumber() const
{
   if(fDetectorNumber > -1) {   //||fDetectorNumber==0x0fffffff)
      return fDetectorNumber;
   }
 
   fDetectorNumber = static_cast<int32_t>(fMnemonic.Value()->ArrayPosition());
   return fDetectorNumber;
}
 
int TChannel::GetSegmentNumber() const
{
   if(fSegmentNumber > -1) {
      return fSegmentNumber;
   }
 
   std::string name = GetName();
   if(name.length() < 10) {
      fSegmentNumber = 0;
   } else {
      TString str = name[9];
      if(str.IsDigit()) {
         std::string buf;
         buf.clear();
         buf.assign(name, 7, 3);
         fSegmentNumber = static_cast<int32_t>(atoi(buf.c_str()));
      } else {
         fSegmentNumber = static_cast<int32_t>(fMnemonic.Value()->Segment());
      }
   }
 
   return fSegmentNumber;
}
 
int TChannel::GetCrystalNumber() const
{
   if(fCrystalNumber > -1) {
      return fCrystalNumber;
   }
 
   fCrystalNumber = fMnemonic.Value()->NumericArraySubPosition();
 
   return fCrystalNumber;
}
 
double TChannel::GetEnergyNonlinearity(double eng) const
{
   int nPoints = fEnergyNonlinearity.Value().GetN();
   if(nPoints < 1 || eng < fEnergyNonlinearity.Value().GetX()[0] || fEnergyNonlinearity.Value().GetX()[nPoints - 1] < eng) { return 0.; }
   return fEnergyNonlinearity.Value().Eval(eng);
}
 
double TChannel::GetTimeNonlinearity(Long64_t mytimestamp) const
{
   int nPoints = fTimeNonlinearity.Value().GetN();
   if(nPoints < 1 || static_cast<double>(mytimestamp) < fTimeNonlinearity.Value().GetX()[0] || fTimeNonlinearity.Value().GetX()[nPoints - 1] < static_cast<double>(mytimestamp)) { return 0.; }
   return fTimeNonlinearity.Value().Eval(static_cast<double>(mytimestamp));
}
 
void TChannel::SetupEnergyNonlinearity()
{
   fEnergyNonlinearity.Address()->Sort();
   fEnergyNonlinearity.Address()->SetBit(TGraph::kIsSortedX);
   fEnergyNonlinearity.Address()->SetName(Form("EnergyNonlinearity0x%04x", fAddress));
   fEnergyNonlinearity.Address()->SetTitle(Form("Energy nonlinearity of channel 0x%04x", fAddress));
}
 
void TChannel::SetupTimeNonlinearity()
{
   fTimeNonlinearity.Address()->Sort();
   fTimeNonlinearity.Address()->SetBit(TGraph::kIsSortedX);
   fTimeNonlinearity.Address()->SetName(Form("TimeNonlinearity0x%04x", fAddress));
   fTimeNonlinearity.Address()->SetTitle(Form("Time nonlinearity of channel 0x%04x", fAddress));
}
 
void TChannel::ReadEnergyNonlinearities(TFile* file, const char* graphName, bool all)
{
   /// Read energy nonlinearities as TGraphErrors from provided root file using "graphName%x" as names
   TList* list = file->GetListOfKeys();
   TIter  iter(list);
   while(TKey* key = static_cast<TKey*>(iter.Next())) {
      TClass* cls = TClass::GetClass(key->GetClassName());
      if(!cls->InheritsFrom(TGraph::Class()) || strncmp(key->GetName(), graphName, strlen(graphName)) != 0) {
         continue;
      }
      // get address from keys name
      std::stringstream str;
      str << std::hex << key->GetName() + strlen(graphName);
      unsigned int address = 0;
      str >> address;
      if(GetChannel(address) != nullptr) {
         GetChannel(address)->fEnergyNonlinearity.Set(*(static_cast<TGraph*>(key->ReadObj())), EPriority::kRootFile);
         GetChannel(address)->SetupEnergyNonlinearity();
      } else if(all) {
         auto* newChannel = new TChannel("");
         newChannel->SetAddress(address);
         newChannel->fEnergyNonlinearity.Set(*(static_cast<TGraph*>(key->ReadObj())), EPriority::kRootFile);
         newChannel->SetupEnergyNonlinearity();
         AddChannel(newChannel);
      }
   }
}
 
void TChannel::ReadTimeNonlinearities(TFile* file, const char* graphName, bool all)
{
   /// Read Time nonlinearities as TGraphErrors from provided root file using "graphName%x" as names
   TList* list = file->GetListOfKeys();
   TIter  iter(list);
   while(TKey* key = static_cast<TKey*>(iter.Next())) {
      TClass* cls = TClass::GetClass(key->GetClassName());
      if(!cls->InheritsFrom(TGraph::Class()) || strncmp(key->GetName(), graphName, strlen(graphName)) != 0) {
         continue;
      }
      // get address from keys name
      std::stringstream str;
      str << std::hex << key->GetName() + strlen(graphName);
      unsigned int address = 0;
      str >> address;
      if(GetChannel(address) != nullptr) {
         GetChannel(address)->fTimeNonlinearity.Set(*(static_cast<TGraph*>(key->ReadObj())), EPriority::kRootFile);
         GetChannel(address)->SetupTimeNonlinearity();
      } else if(all) {
         auto* newChannel = new TChannel("");
         newChannel->SetAddress(address);
         newChannel->fTimeNonlinearity.Set(*(static_cast<TGraph*>(key->ReadObj())), EPriority::kRootFile);
         newChannel->SetupTimeNonlinearity();
         AddChannel(newChannel);
      }
   }
}
 
void TChannel::SetDigitizerType(const TPriorityValue<std::string>& tmp)
{
   fDigitizerTypeString = tmp;
   if(fMnemonic.Value() != nullptr) {
      fMnemonic.Value()->EnumerateDigitizer(fDigitizerTypeString, fDigitizerType, fTimeStampUnit);
   } else {
      std::cerr << __PRETTY_FUNCTION__ << ": mnemonic not set, can't set digitizer type and timestamp unit from " << fDigitizerTypeString << std::endl;   // NOLINT(cppcoreguidelines-pro-type-const-cast, cppcoreguidelines-pro-bounds-array-to-pointer-decay)
   }
}
 
double TChannel::GetTime(Long64_t timestamp, Float_t cfd, double energy) const
{
   return fMnemonic.Value()->GetTime(timestamp, cfd, energy, this);
}
 
const TMnemonic* TChannel::GetMnemonic() const
{
   return fMnemonic.Value();
}
 
TClass* TChannel::GetClassType() const
{
   return fMnemonic.Value()->GetClassType();
}
 
void TChannel::SetClassType(TClass* cl_type)
{
   fMnemonic.Value()->SetClassType(cl_type);
}