JEditDetector.cc

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#include <iostream>
#include <sstream>
#include <string>
#include <vector>
#include <map>
#include <algorithm>
#include <cctype>

#include "TRandom3.h"

#include "JDetector/JDetector.hh"
#include "JDetector/JDetectorToolkit.hh"
#include "JDetector/JDetectorHeader.hh"
#include "JDetector/JModuleStatus.hh"
#include "JDetector/JModuleRouter.hh"
#include "JDetector/JPMTIdentifier.hh"
#include "JDetector/JPMTPhysicalAddress.hh"
#include "JDetector/JPMTStatus.hh"
#include "JDetector/JModuleAddressMap.hh"
#include "JDetector/JDetectorAddressMap.hh"
#include "JDetector/JDetectorSupportkit.hh"
#include "JGeometry3D/JVector3D.hh"
#include "JMath/JConstants.hh"
#include "JMath/JMath.hh"
#include "JTools/JRange.hh"
#include "JLang/JException.hh"
#include "JLang/JToken.hh"
#include "JLang/JComparator.hh"
#include "JLang/JComparison.hh"
#include "JSupport/JMeta.hh"

#include "Jeep/JeepToolkit.hh"
#include "Jeep/JPrint.hh"
#include "Jeep/JParser.hh"
#include "Jeep/JMessage.hh"


namespace {

  using namespace JPP;

  /**
   * Wild card for string identifier, module identifier or PMT address.
   */
  static const int         WILDCARD    =  -1;

  static const std::string reset_t     = "reset";             //!< Reset    time offset, position and PMT status bit
  static const std::string set_t       = "set";               //!< Set      time offset, position or  PMT status bit
  static const std::string setx_t      = "setx";              //!< Set      x-position
  static const std::string sety_t      = "sety";              //!< Set      y-position
  static const std::string setz_t      = "setz";              //!< Set      z-position
  static const std::string addx_t      = "addx";              //!< Add      x-position
  static const std::string addy_t      = "addy";              //!< Add      y-position
  static const std::string addz_t      = "addz";              //!< Add      z-position
  static const std::string subx_t      = "subx";              //!< Subtract x-position
  static const std::string suby_t      = "suby";              //!< Subtract y-position
  static const std::string subz_t      = "subz";              //!< Subtract z-position
  static const std::string add_t       = "add";               //!< Add      time offset or position
  static const std::string sub_t       = "sub";               //!< Subtract time offset or position
  static const std::string rot_t       = "rot";               //!< Rotate around z-axis by value [rad]
  static const std::string lower_t     = "lower";             //!< Rotate lower hemisphere around z-axis by value [rad]
  static const std::string upper_t     = "upper";             //!< Rotate upper hemisphere around z-axis by value [rad]
  static const std::string mul_t       = "mul";               //!< Multiply z-position by (1 + value)
  static const std::string div_t       = "div";               //!< Divide   z-position by (1 + value)
  static const std::string tilt_t      = "tilt";              //!< Tilt string
  static const std::string swap_t      = "swap";              //!< Swap     PMTs

  static const std::string assign_t    = "assign";            //!< Assign module identifier
  static const std::string locate_t    = "locate";            //!< Locate module identifier
  static const std::string string_t    = "string";            //!< Assign string number

  static const std::string rand_t      = "rand";              //!< Random value(s)
  static const std::string randset_t   =  rand_t + set_t;     //!< Set      time offset or position
  static const std::string randadd_t   =  rand_t + add_t;     //!< Add      time offset or position
  static const std::string randsub_t   =  rand_t + sub_t;     //!< Subtract time offset or position
  static const std::string randrot_t   =  rand_t + rot_t;     //!< Rotate around z-axis by value [rad]
  static const std::string randmul_t   =  rand_t + mul_t;     //!< Multiply z-position by (1 + value)
  static const std::string randdiv_t   =  rand_t + div_t;     //!< Divide   z-position by (1 + value)
  static const std::string randtilt_t  =  rand_t + tilt_t;    //!< Tilt string

  static const std::string RESET_t     = "RESET";             //!< Reset    time offset of piezo/hydrophone and quaternion calibration of compass
  static const std::string SET_t       = "SET";               //!< Set      time offset of piezo/hydrophone or  quaternion calibration of compass
  static const std::string ADD_t       = "ADD";               //!< Add      time offset of piezo/hydrophone or  quaternion calibration of compass
  static const std::string SUB_t       = "SUB";               //!< Subtract time offset of piezo/hydrophone or  quaternion calibration of compass
  static const std::string ROT_t       = "ROT";               //!< Rotate quaternion calibration of compass around z-axis by value [rad]


  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action)
  {
    if        (action == reset_t) {

      // position does not depend on module but may not exactly be at origin

      module.setCalibration(JCalibration());
      module.setStatus(JStatus());
      module.setQuaternion(JQuaternion3D());
      module.set(getModule<JKM3NeT_t>(1).getPosition());

      for (JModule::iterator pmt = module.begin(); pmt != module.end(); ++pmt) {
        pmt->setCalibration(JCalibration());
        pmt->setStatus(JStatus());
      }

    } else if (action == RESET_t) {

      module.setCalibration(JCalibration());
      module.setQuaternion(JQuaternion3D());
      module.setCalibration(getAverage(make_array(module.begin(), module.end(), &JPMT::getT0), 0.0));

    } else {

      return false;
    }

    return true;
  }

    
  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \param  value       value
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action, const double value)
  {
    if        (action == set_t) {                          // actions with fixed values

      module.set(value);

    } else if (action == setx_t) {

      module.set(JVector3D(value, module.getY(), module.getZ()));

    } else if (action == addx_t) {

      module.add(JVector3D(value, 0.0, 0.0));

    } else if (action == subx_t) {

      module.sub(JVector3D(value, 0.0, 0.0));

    } else if (action == sety_t) {

      module.set(JVector3D(module.getX(), value, module.getZ()));

    } else if (action == addy_t) {

      module.add(JVector3D(0.0, value, 0.0));

    } else if (action == suby_t) {

      module.sub(JVector3D(0.0, value, 0.0));

    } else if (action == setz_t) {

      module.set(JVector3D(module.getX(), module.getY(), value));

    } else if (action == addz_t) {

      module.add(JVector3D(0.0, 0.0, value));

    } else if (action == subz_t) {

      module.sub(JVector3D(0.0, 0.0, value));

    } else if (action == add_t) {

      module.add(value);

    } else if (action == sub_t) {

      module.sub(value);

    } else if (action == rot_t) {

      const JVector3D center = module.getPosition();

      module.sub(center);
        
      module.rotate(JRotation3Z(value));

      module.add(center);

    } else if (action == lower_t ||
               action == upper_t) {

      const JVector3D center = module.getPosition();

      module.sub(center);
        
      const JRotation3Z R(value);

      for (JModule::iterator pmt = module.begin(); pmt != module.end(); ++pmt) {
        if ((action == upper_t && pmt->getDZ() > 0.0) ||
            (action == lower_t && pmt->getDZ() < 0.0)) {
          pmt->rotate(R);
        }
      }

      module.add(center);

    } else if (action == mul_t) {

      JVector3D center;

      if (value > 0.0)
        center = JVector3D(module.getPosition().getX(),
                           module.getPosition().getY(),
                           module.getPosition().getZ() * (1.0 + value));
      else
        center = JVector3D(module.getPosition().getX(),
                           module.getPosition().getY(),
                           module.getPosition().getZ() / (1.0 - value));

      module.set(center);

    } else if (action == div_t) {

      JVector3D center;

      if (value > 0.0)
        center = JVector3D(module.getPosition().getX(),
                           module.getPosition().getY(),
                           module.getPosition().getZ() / (1.0 + value));
      else
        center = JVector3D(module.getPosition().getX(),
                           module.getPosition().getY(),
                           module.getPosition().getZ() * (1.0 - value));

      module.set(center);

    } else if (action == SET_t) {

      module.getCalibration().setT0(value);

    } else if (action == ADD_t) {

      module.getCalibration().addT0(value);

    } else if (action == SUB_t) {

      module.getCalibration().subT0(value);

    } else if (action == ROT_t) {

      module.setQuaternion(JQuaternion3Z(value) * module.getQuaternion());

    } else if (action == randadd_t) {                      // actions with random values

      module.add(gRandom->Gaus(0.0, value));

    } else if (action == randsub_t) {
        
      module.sub(gRandom->Gaus(0.0, value));

    } else if (action == randrot_t){

      const JVector3D center = module.getPosition();

      module.sub(center);

      module.rotate(JRotation3Z(gRandom->Gaus(0.0, value)));

      module.add(center);
      
    } else if (action == randmul_t) {

      const JVector3D center(module.getPosition().getX(),
                             module.getPosition().getY(),
                             module.getPosition().getZ() * gRandom->Gaus(1.0, value));
        
      module.set(center);
      
    } else if (action == randdiv_t) {

      const JVector3D center(module.getPosition().getX(),
                             module.getPosition().getY(),
                             module.getPosition().getZ() / gRandom->Gaus(1.0, value));
        
      module.set(center);

    } else if (action == assign_t) {                       // action with assigments

      module.setID((int) value);

    } else if (action == string_t) {

      module.setLocation(JLocation((int) value, module.getFloor()));

    } else {                                               // 
        
      return false;
    }
      
    return true;
  }


  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \param  first       first  value
   * \param  second      second value
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action, const double first, const double second)
  {
    if        (action == tilt_t) {                         // actions with fixed values

      const double Tx = first;
      const double Ty = second;
      const double Tz = sqrt(1.0 - Tx*Tx - Ty*Ty);

      const double x  = Tx * module.getZ()  +  module.getX();
      const double y  = Ty * module.getZ()  +  module.getY();
      const double z  = Tz * module.getZ();

      module.set(JPosition3D(x,y,z));

    } else if (action == locate_t) {

      module.setLocation(JLocation((int) first, (int) second));

    } else if (action == swap_t) {

      std::swap(module[(int) first], module[(int) second]);

    } else {                                               // 

      return false;
    }

    return true;
  }


  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \param  pos         pos
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action, const JVector3D& pos)
  {
    const JVector3D randpos(gRandom->Gaus(0.0, pos.getX()),
                            gRandom->Gaus(0.0, pos.getY()),
                            gRandom->Gaus(0.0, pos.getZ()));

    if      (action == set_t)                          // actions with fixed values
      module.set(pos);
    else if (action == add_t)
      module.add(pos);
    else if (action == sub_t)
      module.sub(pos);
    else if (action == randset_t)                      // actions with random values
      module.set(randpos);
    else if (action == randadd_t)
      module.add(randpos);
    else if (action == randsub_t)
      module.sub(randpos);
    else
      return false;

    return true;
  }


  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \param  Q           quaternion
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action, const JQuaternion3D& Q)
  {
    if      (action == SET_t)
      module.setQuaternion(Q);
    else if (action == ADD_t)
      module.setQuaternion(Q * module.getQuaternion());
    else if (action == SUB_t)
      module.setQuaternion(Q.getConjugate() * module.getQuaternion());
    else
      return false;

    module.getQuaternion().normalise();

    return true;
  }


  /**
   * Apply action to given module.
   *
   * \param  module      module (I/O)
   * \param  action      action
   * \param  value       value
   * \return             true if valid action; else false
   */
  inline bool apply(JModule& module, const std::string& action, const std::string& value)
  {
    try {
      
      if      (action == set_t)
        module.getStatus().set  (getModuleStatusBit(value));
      else if (action == reset_t)
        module.getStatus().reset(getModuleStatusBit(value));
      else
        return false;

      return true;
    }
    catch(const std::exception&) {
      return false;
    }
  }


  /**
   * Apply action to given PMT.
   *
   * \param  pmt         PMT (I/O)
   * \param  action      action
   * \param  value       value
   * \return             true if valid action; else false
   */
  inline bool apply(JPMT& pmt, const std::string& action, const std::string& value)
  {
    try {

      if      (action == set_t)
        pmt.getStatus().set  (getPMTStatusBit(value));
      else if (action == reset_t)
        pmt.getStatus().reset(getPMTStatusBit(value));
      else
        return false;

      return true;
    }
    catch(const std::exception&) {
      return false;
    }
  }


  /**
   * Auxiliary class for module modifications.
   */
  struct JModifier {
    /**
     * Default constructor.
     */
    JModifier()
    {}


    /**
     * Check validity.
     *
     * \return             true if valid modifier; else false
     */
    bool is_valid() const
    {
      return (action != "" && !data.empty());
    }


    /**
     * Apply action to given module depending on number of values.
     *
     * \param  module      module
     * \return             true if valid action; else false
     */
    bool apply(JModule& module) const
    {
      switch (data.size()) {

      case 0:
        return  ::apply(module, action);
          
      case 1:
        return  ::apply(module, action, data[0]);
          
      case 2:
        return  ::apply(module, action, data[0], data[1]);

      case 3:
        return  ::apply(module, action, JVector3D(data[0], data[1], data[2]));

      case 4:
        return  ::apply(module, action, JQuaternion3D(data[0], data[1], data[2], data[3]));

      default:
        return false;
      }
    }


    /**
     * Read modifier from input.
     *
     * \param  in          input stream
     * \param  modifier    modifier
     * \return             input stream
     */
    friend inline std::istream& operator>>(std::istream& in, JModifier& modifier)
    {
      if (in >> modifier.action) {

        modifier.data.clear();

        for (double x; in >> x; ) {
          modifier.data.push_back(x);
        }

        in.clear(std::ios_base::eofbit);
      }

      return in;
    }


    /**
     * Write modifier to output.
     *
     * \param  out         output stream
     * \param  modifier    modifier
     * \return             output stream
     */
    friend inline std::ostream& operator<<(std::ostream& out, const JModifier& modifier)
    {
      out << modifier.action;

      for (std::vector<double>::const_iterator i = modifier.data.begin(); i != modifier.data.end(); ++i) {
        out << ' ' << *i;
      }

      return out;
    }
  

    std::string         action;
    std::vector<double> data;
  };


  /**
   * Get modifier for given string.
   *
   * For actions <tt>ranXXX</tt>, the corresponding action <tt>XXX</tt> is made the same for all modules in the given string.\n
   * For all other options, the input action is maintained.
   *
   * \param  id          string number
   * \param  modifier    modifier
   * \return             modifier
   */
  inline const JModifier& getModifier(const int id, const JModifier& modifier)
  {
    using namespace std;

    static map<int, map<string, map<size_t, JModifier> > > buffer;

    const string::size_type pos = modifier.action.find(rand_t);

    if (pos != string::npos) {

      JModifier& result = buffer[id][modifier.action][modifier.data.size()];

      if (!result.is_valid()) {      

        result.action = modifier.action.substr(pos + rand_t.length());

        for (size_t i = 0; i != modifier.data.size(); ++i) {
          result.data.push_back(gRandom->Gaus(0.0, modifier.data[i]));
        }
      }

      return result;

    } else {

      return modifier;
    }
  }


  /**
   * Auxiliary class for module status modifications.
   */
  struct JModuleModifier {
    /**
     * Default constructor.
     */
    JModuleModifier()
    {}


    /**
     * Apply action to given module.
     *
     * \param  module      module
     * \return             true if valid action; else false
     */
    bool apply(JModule& module) const
    {
      return ::apply(module, action, value);
    }
 

    /**
     * Read module modifier from input.
     *
     * \param  in          input stream
     * \param  modifier    modifier
     * \return             input stream
     */
    friend inline std::istream& operator>>(std::istream& in, JModuleModifier& modifier)
    {
      return in >> modifier.action >> modifier.value;
    }


    /**
     * Write module modifier to output.
     *
     * \param  out         output stream
     * \param  modifier    modifier
     * \return             output stream
     */
    friend inline std::ostream& operator<<(std::ostream& out, const JModuleModifier& modifier)
    {
      out << modifier.action;
      out << ' ';
      out << modifier.value;

      return out;
    }
  

    std::string action;
    std::string value;
  };


  /**
   * Auxiliary class for PMT status modifications.
   */
  struct JPMTModifier {
    /**
     * Default constructor.
     */
    JPMTModifier()
    {}


    /**
     * Apply action to given PMT.
     *
     * \param  pmt         PMT
     * \return             true if valid action; else false
     */
    bool apply(JPMT& pmt) const
    {
      return ::apply(pmt, action, value);
    }
 

    /**
     * Read PMT modifier from input.
     *
     * \param  in          input stream
     * \param  modifier    modifier
     * \return             input stream
     */
    friend inline std::istream& operator>>(std::istream& in, JPMTModifier& modifier)
    {
      return in >> modifier.action >> modifier.value;
    }


    /**
     * Write PMT modifier to output.
     *
     * \param  out         output stream
     * \param  modifier    modifier
     * \return             output stream
     */
    friend inline std::ostream& operator<<(std::ostream& out, const JPMTModifier& modifier)
    {
      out << modifier.action;
      out << ' ';
      out << modifier.value;

      return out;
    }
  

    std::string action;
    std::string value;
  };


  /**
   * Range of string numbers.
   *
   * The input format could be a single number or two numbers separated by JRange_t::SEPARATOR.
   */
  struct JRange_t :
    public JRange<int>
  {
    /**
     * Separator between two identifier values.
     */
    static const char SEPARATOR = '-';

    /**
     * Default constructor.
     */
    JRange_t() :
      JRange(-1, -1)
    {}


    /**
     * Read range from input.
     *
     * \param  in          input stream
     * \param  range       range
     * \return             input stream
     */
    friend inline std::istream& operator>>(std::istream& in, JRange_t& range)
    {
      if (in >> range.first) {

        range.second = range.first;

        if (in.peek() == (int) JRange_t::SEPARATOR) {

          in.get();

          in >> range.second;

        } else {

          in.clear();
        }
      }

      return in;
    }


    /**
     * Write range to output.
     *
     * \param  out         output stream
     * \param  range       range
     * \return             output stream
     */
    friend inline std::ostream& operator<<(std::ostream& out, const JRange_t& range)
    {
      return out << range.first << JRange_t::SEPARATOR << range.second;
    }
  };


  /**
   * Print module modification.
   *
   * \param  out       output stream
   * \param  module    module
   * \param  modifier  modifier
   */
  inline void print(std::ostream& out, const JModule& module, const JModifier& modifier)
  {
    using namespace std;
    using namespace JPP;

    out << "Modifier"                     << ' '
        << getLabel(module.getLocation()) << ' '
        << setw(10)  << module.getID()    << ' '
        << "action " << modifier          << endl;
  }


  /**
   * Print module modification.
   *
   * \param  out       output stream
   * \param  id        module identifier
   * \param  modifier  modifier
   */
  inline void print(std::ostream& out, const JModuleIdentifier& id, const JModuleModifier& modifier)
  {
    using namespace std;
    using namespace JPP;

    out << "module modifier"                    << ' '
        << "(" << setw(10) << id.getID() << ")" << ' '
        << "action" << ' ' << modifier.action << ' ' 
        << "value"  << ' ' << modifier.value  << endl;
  }


  /**
   * Print PMT modification.
   *
   * \param  out       output stream
   * \param  pmt       PMT identifier
   * \param  modifier  modifier
   */
  inline void print(std::ostream& out, const JPMTIdentifier& pmt, const JPMTModifier& modifier)
  {
    using namespace std;
    using namespace JPP;

    out << "PMT modifier"                                                                 << ' '
        << "(" << setw(10) << pmt.getID() << "," << setw(2) << pmt.getPMTAddress() << ")" << ' '
        << "action" << ' ' << modifier.action << ' ' 
        << "value"  << ' ' << modifier.value  << endl;
  }
}


/**
 * \file
 *
 * Auxiliary program to modify detector calibration.
 *
 * Syntax:
 * <pre>
 *     -M     "<module identifier>     (set|add|sub|randset|randadd|randsub) x0 [x1 x2]"
 *     -(S|s) "<string number>         (set|add|sub|randset|randadd|randsub) x0 [x1 x2]"
 *     -M     "<module identifier>     (setx|addx|subx|sety|addy|suby|setz|addz|subz) value"
 *     -(S|s) "<string number>         (setx|addx|subx|sety|addy|suby|setz|addz|subz) value"
 *     -M     "<module identifier>     (rot|randrot|lower|upper) phi"
 *     -(S|s) "<string number>         (rot|randrot) phi"
 *     -M     "<module identifier>     (mul|randmul) factor"
 *     -(S|s) "<string number>         (mul|randmul) factor"
 *     -M     "<module identifier>     (div|randdiv) factor"
 *     -(S|s) "<string number>         (div|randdiv) factor"
 *     -M     "<module identifier>     (reset)"
 *     -(S|s) "<string number>         (reset)"
 *     -M     "<module identifier>     (assign)  identifier"
 *     -M     "<module identifier>     (locate)  <string> <floor>"
 *     -M     "<module identifier>     (swap)    <PMT>    <PMT>"
 *     -M     "<module identifier>     (SET|ADD|SUB|) x0 [x1 x2 x3]"
 *     -(S|s) "<string number>         (SET|ADD|SUB|) x0 [x1 x2 x3]"
 *     -M     "<module identifier>     (ROT) phi"
 *     -(S|s) "<string number>         (ROT) phi"
 *     -(S|s) "<string number>         (tilt|randtilt) Tx Ty"
 *     -R     "<module identifier>     <PMT physical address>"
 *     -W     "<module identifier>     (set|reset)  (MODULE_DISABLE|COMPASS_DISABLE|HYDROPHONE_DISABLE|PIEZO_DISABLE|MODULE_OUT_OF_SYNC)"
 *     -P     "<PMT identifier>        (set|reset)  (PMT_DISABLE|HIGH_RATE_VETO_DISABLE|FIFO_FULL_DISABLE|UDP_COUNTER_DISABLE|UDP_TRAILER_DISABLE|OUT_OF_SYNC)"
 *     -p     "<PMT physical address>  (set|reset)  (PMT_DISABLE|HIGH_RATE_VETO_DISABLE|FIFO_FULL_DISABLE|UDP_COUNTER_DISABLE|UDP_TRAILER_DISABLE|OUT_OF_SYNC)"
 *     -k     "<string number>[-<string number>]"
 *     -r     "<string number>[-<string number>]"
 *     -m     "<module identifier>"
 *     -D     "<string number> <floor>"
 *     -\@    "<key>=<value>[;<key>=<value>"
 * </pre>
 * Options <tt>-M</tt> and <tt>-S</tt> refer to a module and a string, respectively.\n
 * The values provided for a string modification coherently apply to the modules of the specified string number.\n
 * The option <tt>-s</tt> is equivalent to option <tt>-S</tt> except that 
 * the action applies only to the optical modules in the string and not the base module.
 *
 * The options <tt>randxxx</tt> correspond to a randomisation of the specified option.
 *
 * If the module identifier or string number is -1,
 * the action is applied to all modules or strings in the detector, respectively.
 *
 * For options <tt>[rand]set</tt>, <tt>[rand]add</tt> and <tt>[rand]sub</tt>,
 * the number of values apply to position or time calibration in the following way:
 *     -#  time calibration     <tt>(t = x0)</tt>
 *     -#  invalid
 *     -#  position calibration <tt>(x = x0, y = x1, z = x2)</tt>
 *
 * For options <tt>(set|add|sub)(x|y|z)</tt>, the value corresponds to last character of the the quoted action.
 *
 * For options <tt>[rand]rot</tt>,
 * the angle <tt>phi</tt> refers to an anti-clockwise rotation around the z-axis.\n
 * The options <tt>upper</tt> and <tt>lower</tt> refer to a rotation of the PMTs in the upper and lower hemisphere of the module, respectively.\n
 * The rotation angle is defined in radians.
 *
 * For options <tt>[rand]mul</tt> and <tt>[rand]div</tt>,
 * the multiplication/division <tt>factor</tt> (a.k.a.\ "stretching") applies to the z-coordinates of the modules.\n
 * The factor is defined as a fraction; the actual multiplication/division factor is <tt>(1 + factor)</tt>. 
 *
 * For options <tt>SET</tt>, <tt>ADD</tt> and <tt>SUB</tt>,
 * the number of values apply to time or quaternion calibration of the module in the following way:
 *     -#  time calibration of piezo sensor or hydrophone  <tt>(t = x0)</tt>
 *     -#  invalid
 *     -#  invalid
 *     -#  quaternion calibration of compass <tt>(qa = x0, qb = x1, qc = x2, qd = x3)</tt>
 *
 * For options <tt>ROT</tt>,
 * the angle <tt>phi</tt> refers to an anti-clockwise rotation around the z-axis of the quaternion calibration of the compass.\n
 * The rotation angle is defined in radians.
 *
 * Note that to correct the time calibration for the delay time of the piezo sensor and hydrophone,
 * application JDetectorDB.cc can be used (option <tt>-WW</tt>).
 *
 * The units of all positions and time values are <tt>m</tt> and <tt>ns</tt>, respectively.
 *
 * Note that for string modifiers with option <tt>randxxx</tt>,
 * the action is coherently applied to the modules in the specified string.\n
 * Only one type of action (defined by <tt>xxx</tt> and the number of values) is then allowed per string. 
 *
 * The option <tt>-R</tt> can be used to rotate the positions of PMTs within a given ring.\n
 * In this, the position of the physical address of the PMT corresponds to the number of steps of the rotation.
 *
 * The option <tt>-W</tt> can be used to modify the status of a module.
 * The options <tt>-P</tt> and <tt>-p</tt> can be used to modify the status of PMTs.
 *
 * Option <tt>-\@</tt> refers to the header information.\n
 * The list of possible keys can be obtained using JPrintDetector.cc with option <tt>-O header</tt>.
 *
 * Multiple options <tt>-M</tt>, <tt>-S</tt>, <tt>-s</tt> or <tt>-\@</tt> will be processed in order of appearance.
 *
 * Options <tt>-k</tt> and <tt>-r</tt> can be used to keep and remove (a range of) string numbers, respectively.
 *
 * The options <tt>-m</tt> and <tt>-D</tt> can be used to maintain a specific module (and remove all others) and 
 * to delete a floor from a string, respectively.
 *
 * Note finally that if the output file name is the same as the input file name,
 * the original file will be overwritten.
 *
 * \author mdejong
 */
int main(int argc, char **argv)
{
  using namespace std;
  using namespace JPP;

  typedef JToken<';'>  JToken_t;

  string                           inputFile;
  string                           outputFile;
  vector<JToken_t>                 hdr;
  vector< pair<int, JModifier> >   mod;
  vector< pair<int, JModifier> >   str;
  vector< pair<int, JModifier> >   dos;
  vector< pair<int, 
               JModuleModifier> >  wip;
  vector< pair<JPMTIdentifier,
               JPMTModifier> >     pmt;
  vector< pair<JPMTPhysicalAddress,
               JPMTModifier> >     alt;
  multimap<int, 
           JPMTPhysicalAddress>    ring;
  vector<JRange_t>                 keep;
  vector<JRange_t>                 rm;
  vector<int>                      id;
  multimap<int, int>               del;
  int                              option;
  bool                             squash;
  int                              debug;
  
  try { 

    JParser<> zap("Auxiliary program to modify detector.");

    zap['a'] = make_field(inputFile);
    zap['o'] = make_field(outputFile);
    zap['@'] = make_field(hdr,    "header modification")                                    = JPARSER::initialised();
    zap['M'] = make_field(mod,    "module modification")                                    = JPARSER::initialised();
    zap['S'] = make_field(str,    "string modification (optical modules and base modules)") = JPARSER::initialised();
    zap['s'] = make_field(dos,    "string modification (optical modules only)")             = JPARSER::initialised();
    zap['W'] = make_field(wip,    "module status modification")                             = JPARSER::initialised();
    zap['P'] = make_field(pmt,    "PMT status modification by PMT logical address")         = JPARSER::initialised();
    zap['p'] = make_field(alt,    "PMT status modification by PMT physical address")        = JPARSER::initialised();
    zap['R'] = make_field(ring,   "rotate positions of PMTs in ring")                       = JPARSER::initialised();
    zap['k'] = make_field(keep,   "keep string[s]")                                         = JPARSER::initialised();
    zap['r'] = make_field(rm,     "remove string[s]")                                       = JPARSER::initialised();
    zap['m'] = make_field(id,     "maintain module by identifier")                          = JPARSER::initialised();
    zap['D'] = make_field(del,    "remove module by location")                              = JPARSER::initialised();
    zap['O'] = make_field(option, "sort modules: "\
                          "0 -> no sort; 1 -> module identifier; 2 -> module location")     = 0, 1, 2;
    zap['q'] = make_field(squash, "squash meta data");
    zap['d'] = make_field(debug,  "debug level")                                            = 2;

    zap(argc, argv);
  }
  catch(const exception &error) {
    FATAL(error.what() << endl);
  }
   
  gRandom->SetSeed(0);

  const int ns = ((keep.empty() ? 0 : 1)  +
                  (rm  .empty() ? 0 : 1)  +
                  (id  .empty() ? 0 : 1)  +
                  (del .empty() ? 0 : 1));
  
  if (ns > 1) {
    FATAL("Use either option -k, -r, -m or -D." << endl);
  }

  JDetector detector;

  try {
    load(inputFile, detector);
  }
  catch(const JException& error) {
    FATAL(error);
  }

  if (squash) {
    detector.comment.clear();
  }

  detector.comment.add(JMeta(argc,argv));

  if (detector.setToLatestVersion()) {
    NOTICE("Set detector version to " << detector.getVersion() << endl);
  }


  if (!hdr.empty()) {

    int id = -1;

    JProperties helper = detector.getProperties();

    helper["id"] = id;
    
    for (vector<JToken_t>::const_iterator i = hdr.begin(); i != hdr.end(); ++i) {
      
      istringstream is(*i);
      
      is >> helper;
    }

    if (id != -1) {
      detector.setID(id);
    }
  }


  if (ns != 0) {

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ) {

      bool __rm__ = !keep.empty() && rm.empty();

      for (vector<JRange_t>::const_iterator i = keep.begin(); i != keep.end(); ++i) {
        if (module->getString() >= i->first && module->getString() <= i->second) {
          __rm__ = false;
        }
      }

      for (vector<JRange_t>::const_iterator i = rm.begin(); i != rm.end(); ++i) {
        if (module->getString() >= i->first && module->getString() <= i->second) {
          __rm__ = true;
        }
      }

      if (!id.empty()) {
        __rm__ = find(id.begin(), id.end(), module->getID()) == id.end();
      }

      const auto range = del.equal_range(module->getString());

      for (auto i = range.first; i != range.second; ++i) {
        if (i->second == module->getFloor()) {
          __rm__ = true;
        }
      }

      if (__rm__)
        module = detector.erase(module);
      else
        ++module;
    }
  }


  for (vector< pair<int, JModifier> >::const_iterator i = mod.begin(); i != mod.end(); ++i) {

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      if (module->getID() == i->first || i->first == WILDCARD ){

        if (debug >= debug_t) {
          print(cout, *module, i->second);
        }
        
        if (!i->second.apply(*module)) {
          ERROR("No valid action: " << i->first << ' ' << i->second << endl);
        }
      }
    }
  }


  for (vector< pair<int, JModifier> >::const_iterator i = str.begin(); i != str.end(); ++i) {

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      if (module->getString() == i->first || i->first == WILDCARD) {

        const JModifier modifier = getModifier(module->getString(), i->second);

        if (debug >= debug_t) {
          print(cout, *module, i->second);
        }
        
        if (!modifier.apply(*module)) {
          ERROR("No valid action: " << i->first << ' ' << i->second << endl);
        }
      }
    }
  }


  for (vector< pair<int, JModifier> >::const_iterator i = dos.begin(); i != dos.end(); ++i) {

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      if (module->getFloor() != 0) {

        if (module->getString() == i->first || i->first == WILDCARD) {

          const JModifier modifier = getModifier(module->getString(), i->second);

          if (debug >= debug_t) {
            print(cout, *module, i->second);
          }
        
          if (!modifier.apply(*module)) {
            ERROR("No valid action: " << i->first << ' ' << i->second << endl);
          }
        }
      }
    }
  }


  for (vector< pair<int, JModuleModifier> >::const_iterator i = wip.begin(); i != wip.end(); ++i) {

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      if (module->getID() == i->first || i->first == WILDCARD ){

        if (debug >= debug_t) {
          print(cout, *module, i->second);
        }
        
        if (!i->second.apply(*module)) {
          ERROR("No valid action: " << i->first << ' ' << i->second << endl);
        }
      }
    }
  }


  for (vector< pair<JPMTIdentifier, JPMTModifier> >::const_iterator i = pmt.begin(); i != pmt.end(); ++i) {
  
    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      if (module->getID() == i->first.getModuleID() || i->first.getModuleID() == WILDCARD) {

        if (debug >= debug_t) {
          print(cout, i->first, i->second);
        }

        if        (i->first.getPMTAddress() == WILDCARD) {

          for (int pmt = 0; pmt != getNumberOfPMTs(*module); ++pmt) {
            if (!i->second.apply(module->getPMT(pmt))) {
              ERROR("No valid action: " << i->first << ' ' << i->second << endl);
            }
          }

        } else if (i->first.getPMTAddress() >= 0                         &&
                   i->first.getPMTAddress() <  getNumberOfPMTs(*module)  &&
                   !i->second.apply(module->getPMT(i->first.getPMTAddress()))) {
          ERROR("No valid action: " << i->first << ' ' << i->second << endl);
        }
      }
    }
  }


  if (!alt.empty() || !ring.empty()) {

    if (!hasDetectorAddressMap(detector.getID())) {
      FATAL("Invalid detector identifier " << detector.getID() << endl);
    }

    const JDetectorAddressMap& demo = getDetectorAddressMap(detector.getID());

    for (JDetector::iterator module = detector.begin(); module != detector.end(); ++module) {

      const JModuleAddressMap memo = demo.get(module->getID());

      for (vector< pair<JPMTPhysicalAddress, JPMTModifier> >::const_iterator i = alt.begin(); i != alt.end(); ++i) {

        const JPMTIdentifier id(module->getID(), memo.getAddressTranslator(i->first).tdc);

        if (debug >= debug_t) {
          print(cout, id, i->second);
        }

        if (!i->second.apply(module->getPMT(id.getPMTAddress()))) {
          ERROR("No valid action: " << i->first << ' ' << i->second << endl);
        }
      }

      const auto range = ring.equal_range(module->getID());

      for (auto i = range.first; i != range.second; ++i) {

        JPMTPhysicalAddress modifier = i->second;

        modifier.ring = (char) toupper(modifier.ring);

        if (modifier.ring != 'A') {

          map<JPMTPhysicalAddress, JPMT> buffer;

          for (size_t i = 0; i != module->size(); ++i) {

            const JPMTPhysicalAddress& address = memo.getPMTPhysicalAddress(i);

            if (address.ring == modifier.ring) {
              buffer[address] = (*module)[i];
            }
          }

          for (size_t i = 0; i != module->size(); ++i) {

            const JPMTPhysicalAddress& address = memo.getPMTPhysicalAddress(i);

            if (address.ring == modifier.ring) {

              int position = address.position + modifier.position;

              while (position > 6) { position -= 6; }
              while (position < 1) { position += 6; }

              const JPMTPhysicalAddress source(modifier.ring, position);

              DEBUG("Module " << setw(10) << module->getID() << ' ' << address << " <= " << source << endl);

              (*module)[i] = buffer[source];
            }
          }
        }
      }
    }
  }


  switch (option) {
  case 1:
    sort(detector.begin(), detector.end(), make_comparator(&JModule::getID));
    break;

  case 2:
    sort(detector.begin(), detector.end(), make_comparator(&JModule::getLocation));
    break;

  default:
    break;
  };


  try {
    store(outputFile, detector);
  }
  catch(const JException& error) {
    FATAL(error);
  }
}