StatServices Class Reference

The Service class used to manage the StatHandler objects. More...

#include <statservices.h>

Inheritance diagram for StatServices:

Collaboration diagram for StatServices:

Public Types
typedef list< StatHandlerBase * >::const_iterator	stat_it
typedef list< StatRecBase * >::const_iterator	rec_it

Public Member Functions
	StatServices ()
virtual	~StatServices ()
virtual bool	init ()
Metapop *	get_pop_ptr ()
void	set_pop_ptr (Metapop *pop)
void	set (string &str, unsigned int occ)
void	setStatOptions (string &str)
string &	getStatArg ()
unsigned int	getOccurrence ()
void	setOcccurrence (unsigned int value)
void	setOccurrences (map< unsigned int, unsigned int > timeTable)
	Sets the list of generation for which statistics must be recorded during a run. More...
unsigned int	getNumOccurrences ()
	Returns the maximum number of generation records per replicate. More...
unsigned int	getNumOccurrences (unsigned int replicate)
	Returns the number of generation records present in the stat table for a replicate. More...
unsigned int	getCurrentOccurrence ()
	Returns the last generation recorded for current replicate. More...
void	resetCurrentOccurrence ()
	Resets the occurrence iterator to the beginning of the list of generation occurrences. More...
void	printStatHeaders (ofstream &FH)
void	doPrintAverages ()
void	cancelPrintAverages ()
bool	getPrintAveragesOpt ()
void	printStatValue (ofstream &FH, unsigned int repl_idx)
	Prints the stat values to the '.txt' output file. More...
void	printStatAverage (ofstream &FH)
void	setCompactOutputFormat ()
void	setFieldWidth (unsigned int val)
void	setFieldPrecision (unsigned int val)
void	setFieldSeparator (unsigned char c)
void	setDefaultOutputFormat ()
list< StatRecBase * >	getAllStats ()
unsigned int	getNumStats ()
stat_it	getFirst ()
stat_it	getLast ()
vector< double * > *	getReplicateStatRecords (unsigned int replicate)
double *	getGenerationStatValues (unsigned int replicate, unsigned int occurence) const
void	copyGenerationStatValues (unsigned int replicate, unsigned int occurence, double *values, unsigned int size)
void	recordStats (unsigned int gen)
	record stat values in stat table by calling all stat recorders. More...
virtual void	notify ()
virtual void	load (SimComponent *sc)
	tell the SimComponent to load its stat handlers More...
virtual void	attach (Handler *H)
	attach the StatHandler to the current list (_statHandlers) of the StatServices More...
virtual void	reset ()
	clear the list of StatHandler More...
void	reset_stat_table ()
	Deletes the stat tables. More...
Public Member Functions inherited from Service
	Service ()
virtual	~Service ()

Private Attributes
Metapop *	_popPtr
list< StatHandlerBase * >	_statHandlers
	List of stat handlers declared by currently active simulation components. More...
list< StatRecBase * >	_statRecorders
	List of stat recorders. More...
unsigned int	_numRecorders
	Number of stats to record. More...
vector< vector< double * > >	_statValues
	Table containing all recorded stats, replicate x generation x (num recorders + 2) . More...
double *	_currentStatValues
	Pointer to the last recorded stats. More...
string	_statArg
	The string argument of the 'stat' input option. More...
unsigned int	_occurrence
	Deprecated. More...
list< unsigned int >	_occurrences
	List of all generations to record. More...
list< unsigned int >::const_iterator	_current_occurrence
	Iterator pointing to the current generation to record. More...
unsigned int	_width
unsigned int	_precision
unsigned char	_separator
bool	_printAverages

Detailed Description

The Service class used to manage the StatHandler objects.

Member Typedef Documentation

rec_it

typedef list< StatRecBase* >::const_iterator StatServices::rec_it

stat_it

typedef list< StatHandlerBase* >::const_iterator StatServices::stat_it

Constructor & Destructor Documentation

StatServices()

StatServices::StatServices ( )

inline

                   : _popPtr(0), _occurrence(0), _currentStatValues(0), 
  _numRecorders(0), _width(12), _precision(6), _separator('\t'), _printAverages(1)
  { }

~StatServices()

virtual StatServices::~StatServices ( )

inlinevirtual

{ reset_stat_table(); }

Member Function Documentation

attach()

void StatServices::attach ( Handler *  H )

virtual

attach the StatHandler to the current list (_statHandlers) of the StatServices

Parameters

H	the StatHandler

Implements Service.

{
  StatHandlerBase* SH = dynamic_cast<StatHandlerBase*> (H);
  
  _statHandlers.push_back(SH);
  
  SH->set_service(this);
}

References StatHandlerBase::set_service().

Referenced by LCE_Selection_base::loadStatServices(), Metapop::loadStatServices(), TProtoBDMI::loadStatServices(), TProtoDeletMutations_bitstring::loadStatServices(), TProtoDispersal::loadStatServices(), TProtoNeutralGenes::loadStatServices(), TProtoQuanti::loadStatServices(), and TProtoWolbachia::loadStatServices().

cancelPrintAverages()

void StatServices::cancelPrintAverages ( )

inline

{_printAverages = 0;}

Referenced by LCE_StatServiceNotifier::loadStatServices().

copyGenerationStatValues()

void StatServices::copyGenerationStatValues ( unsigned int  replicate, unsigned int  occurence, double *  values, unsigned int  size  )

inline

  {
    assert( _statValues[ replicate-1 ].size() < _occurrences.size() );
    
    assert( size == _numRecorders+2);
    
    double* new_record = new double[size];
    
    memcpy(new_record, values, size*sizeof(double));
    
    _statValues[ replicate-1 ].push_back(new_record);
  }

doPrintAverages()

void StatServices::doPrintAverages ( )

inline

{_printAverages = 1;}

Referenced by LCE_StatServiceNotifier::loadStatServices().

get_pop_ptr()

Metapop* StatServices::get_pop_ptr ( )

inline

{return _popPtr;}

Referenced by StatHandlerBase::get_pop_ptr().

getAllStats()

list< StatRecBase * > StatServices::getAllStats

(

)

{
  list< StatHandlerBase* >::iterator HIT = _statHandlers.begin();
  
  list<StatRecBase*> allStats, stats;
  
  while(HIT != _statHandlers.end()) {
    stats = (*HIT)->getStats();
    allStats.insert(allStats.end(), stats.begin(), stats.end());
    HIT++;
  }
  
  return allStats;
}

Referenced by SimRunner::get_allRegisteredStats().

getCurrentOccurrence()

unsigned int StatServices::getCurrentOccurrence ( )

inline

Returns the last generation recorded for current replicate.

{return *_current_occurrence;}

Referenced by StatHandlerBase::getCurrentOccurrence().

getFirst()

stat_it StatServices::getFirst ( )

inline

{return _statHandlers.begin();}

getGenerationStatValues()

double* StatServices::getGenerationStatValues ( unsigned int  replicate, unsigned int  occurence  ) const

inline

  {
    assert(occurence < _occurrences.size());
    return _statValues[ replicate-1 ][ occurence ];
  }

getLast()

stat_it StatServices::getLast ( )

inline

{return _statHandlers.end();}

getNumOccurrences() [1/2]

unsigned int StatServices::getNumOccurrences ( )

inline

Returns the maximum number of generation records per replicate.

{return _occurrences.size();}

Referenced by StatHandlerBase::getNumOccurrences().

getNumOccurrences() [2/2]

unsigned int StatServices::getNumOccurrences ( unsigned int  replicate )

inline

Returns the number of generation records present in the stat table for a replicate.

Parameters

replicate

the replicate number (not the index in the stat table).

  {
    return _statValues[replicate-1].size();
  }

getNumStats()

unsigned int StatServices::getNumStats ( )

inline

{return _statRecorders.size();}

getOccurrence()

unsigned int StatServices::getOccurrence ( )

inline

{return _occurrence;}

Referenced by LCE_StatServiceNotifier::execute(), and StatHandlerBase::getOccurrence().

getPrintAveragesOpt()

bool StatServices::getPrintAveragesOpt ( )

inline

{return _printAverages;}

Referenced by LCE_StatFH::FHwrite().

getReplicateStatRecords()

vector<double*>* StatServices::getReplicateStatRecords ( unsigned int  replicate )

inline

  {
    return &_statValues[ replicate-1 ];
  }

getStatArg()

string& StatServices::getStatArg ( )

inline

{return _statArg;}

init()

bool StatServices::init ( )

virtual

Implements Service.

{
  stat_it HIT;
  
  HIT = _statHandlers.begin();
  
  //first init the stat handlers -> will define the dims of the stat tables
  while(HIT != _statHandlers.end()) {
    (*HIT)->init();
    HIT++;
  }
  
  istringstream stats(_statArg);
  string arg;
  list<string> args;
  
  //extract the stat options from the string read in the init file
  while(stats>>arg) args.push_back(arg);
        
  list<string>::iterator token = args.begin();
  
  bool is_set = false;
  
  while(token != args.end()) {
    
    HIT = _statHandlers.begin();
    
    is_set = false;
    
    while(HIT != _statHandlers.end() && !is_set) {
      is_set |= (*HIT)->setStatRecorders( (*token) );
      HIT++;
    }
    
    if(!is_set) {
      error("the string \"%s\" is not a valid stat option\n",(*token).c_str());
      return false;
    }
    
    token++;
  }
 
  //---- set the list of stat recorders:
  _statRecorders.clear();
  
  for (HIT = _statHandlers.begin(); HIT != _statHandlers.end(); ++HIT) {
 
    _statRecorders.splice(_statRecorders.end(), (*HIT)->getStats());
    //this removes the recorders from the handler's list (in principle)
    //this means we need to delete the recorders within the StatServices!!
  } 
  
  _numRecorders = _statRecorders.size();
 
  
  //---- set iterator to first generation occurrence to record
  _current_occurrence = _occurrences.begin(); 
  //this is safe as the occurrence list is set before init() is called.
  
//  //reset output option for per-gen mean stats
//  _printAverages = 1;  //this resets user-defined option!!
  
  //---- set the stat table:
  reset_stat_table();
  
  for (unsigned int i = 0; i < SIMenv::getReplicates(); ++i) {
    _statValues.push_back(vector<double*>());
  }
  
  return true;
}

References error(), and SIMenv::getReplicates().

Referenced by SimRunner::init_components().

load()

void StatServices::load ( SimComponent *  sc )

virtual

tell the SimComponent to load its stat handlers

Parameters

sc	the SimComponent

Implements Service.

{
  sc->loadStatServices(this);
}

References SimComponent::loadStatServices().

Referenced by SimRunner::register_component().

notify()

void StatServices::notify ( )

virtual

Implements Service.

{
#ifdef _DEBUG_
  message("StatServices::notify (%i/%i): ", SIMenv::getCurrentGeneration(),
          *_current_occurrence);
  fflush(stdout);
#endif
  
  if( *_current_occurrence == SIMenv::getCurrentGeneration() ) {
    recordStats( *_current_occurrence );
    _current_occurrence++;
  }
  
#ifdef _DEBUG_
  message("\n");
#endif
}

References SIMenv::getCurrentGeneration(), and message().

Referenced by LCE_StatServiceNotifier::execute().

printStatAverage()

void StatServices::printStatAverage

(

ofstream &

FH

)

{
  vector< double > means;
  vector< unsigned int > stat_rep_cntr;
  unsigned int num_repl = SIMenv::getReplicates(), rep_cntr;
  unsigned int num_gen  = getNumOccurrences();
  unsigned int current_gen = 0;
  
  //print the first row with stats headers:
//  FH.setf(ios::left,ios::adjustfield);
  FH << setw(_width) << left <<"generation";
  
  //print the stat names:
  printStatHeaders(FH);
  
  FH<< _separator << setw(_width) << "alive.rpl" << endl;
  
//  FH << setprecision(_precision);
  
  for (unsigned int gen = 0; gen < num_gen; ++gen) {
    
    rep_cntr = 0;
    
    means.assign(_numRecorders,0);
    stat_rep_cntr.assign(_numRecorders, 0);
    
    for (unsigned int rep = 0; rep < num_repl; ++rep) {
      
      //verify if this replicate was not extinct at this generation
      if ( _statValues[ rep ].size() > gen) rep_cntr++;
      else continue; //skip this replicate
 
      for (unsigned int j = 0, pos = 0; j < _numRecorders; ++j) {
        pos = j+2;
        // verify that the value is not NAN
        if( !isnan(_statValues[ rep ][ gen ][pos]) ) {
          means[j] += _statValues[rep][gen][pos]; //two first are replicate and generation
          stat_rep_cntr[j]++;
        }
      }
      current_gen = _statValues[rep][gen][1];
    }
    
    if(rep_cntr != 0) {
      
//      FH.width(_width);
//      FH.setf(ios::left,ios::adjustfield);
      //FH<<_statValues[0][gen][1];
      FH << setw(_width) << left << current_gen;
      
      FH << setprecision(_precision);
      
      for (unsigned int j = 0; j < _numRecorders; ++j) {
        FH << _separator  << setw(_width) << means[j] / stat_rep_cntr[j];
      }
      //print number of alive replicates 'til this generation
      FH << _separator << setw(_width) << rep_cntr;
 
      FH << endl;
    }
    
  }
  
  
}

References SIMenv::getReplicates().

Referenced by LCE_StatFH::PrintStat_byGen().

printStatHeaders()

void StatServices::printStatHeaders

(

ofstream &

FH

)

{
  for (rec_it IT = _statRecorders.begin(); IT != _statRecorders.end(); ++IT) {
    FH << _separator << setw(_width) << (*IT)->getName();
  }
}

printStatValue()

void StatServices::printStatValue	(	ofstream &	FH,
		unsigned int	repl_idx
	)

Prints the stat values to the '.txt' output file.

Parameters

FH	the file output stream
repl_idx	the replicate index in the stat tables

{
  
//  FH.width(_width);
//  FH.setf(ios::left,ios::adjustfield);
 
  if(SIMenv::getCurrentReplicate() == 1) {
        
    //print the first row with stat headers:
    FH << setw(_width) << left <<"replicate"<< _separator << setw(_width) <<"generation";
    
    //print the stat names:
    printStatHeaders(FH);
    
    FH << endl;
  }
    
  for (unsigned int gen = 0, i = 2; gen < _statValues[repl_idx].size(); ++gen) {
    //for all generations recorded, print stuff:
 
    assert( repl_idx + 1 == _statValues[repl_idx][gen][0]); //check if replicate is ok
    
//    FH.width(_width);
    FH << setw(_width) << left << _statValues[repl_idx][gen][0]; //replicate number
    FH << _separator;
    FH << setprecision(16); //to avoid scientific notation for generation number
    FH << setw(_width) << _statValues[repl_idx][gen][1]; //generation recorded
    FH << setprecision(_precision); //this precision is needed only for stat values
    
    i = 2;
    //print all stats on one line
    for (rec_it IT = _statRecorders.begin(); IT != _statRecorders.end(); ++IT) {
      
      FH << _separator << setw(_width) << _statValues[repl_idx][gen][i];
      
      i++;
      
    }
    
    FH<<endl;
    
    assert( i == _numRecorders + 2 );
  }
  
}

References SIMenv::getCurrentReplicate().

Referenced by LCE_StatFH::FHwrite().

recordStats()

void StatServices::recordStats

(

unsigned int

gen

)

record stat values in stat table by calling all stat recorders.

{
  _currentStatValues = new double [ _numRecorders + 2]; //+ replicate + generation
  
  _currentStatValues[0] = SIMenv::getCurrentReplicate();
  _currentStatValues[1] = gen;
  
  unsigned int i = 2, tab_idx = SIMenv::getCurrentReplicate() - 1;
  
  for (rec_it REC = _statRecorders.begin(); REC != _statRecorders.end(); ++REC) 
  {
 
    assert(i < _numRecorders+2 );
    
    _currentStatValues[i++] = (*REC)->setVal( _popPtr->getCurrentAge() ); 
    
  }
  
  _statValues[ tab_idx ].push_back(_currentStatValues);
  
  assert( _statValues[ tab_idx ].size() <= getNumOccurrences() );
}

References SIMenv::getCurrentReplicate().

reset()

void StatServices::reset ( )

virtual

clear the list of StatHandler

Implements Service.

{
#ifdef _DEBUG_
  message("StatServices::reset\n");
#endif
 
  stat_it HIT = _statHandlers.begin();
  
  while(HIT != _statHandlers.end()) {
    (*HIT)->reset();
    HIT++;
  }
  
  _statHandlers.clear();
  
  //the stat recorders must be freed here, they have been removed from the StatHandlers
  rec_it REC = _statRecorders.begin();
  
  for(; REC != _statRecorders.end(); ++REC) delete (*REC);
  
  _statRecorders.clear();
  
  reset_stat_table();
 
#ifdef _DEBUG_
  message("StatServices::reset done\n");
#endif
 
}

References message().

Referenced by SimRunner::reset_services().

reset_stat_table()

void StatServices::reset_stat_table

(

)

Deletes the stat tables.

{
  for (unsigned int i = 0; i < _statValues.size(); ++i) {
    for (unsigned int j = 0; j < _statValues[i].size(); ++j) {
      delete [] _statValues[i][j];
    }
    _statValues[i].clear();
  }
  _statValues.clear();
  
  _currentStatValues = 0;
}

resetCurrentOccurrence()

void StatServices::resetCurrentOccurrence ( )

inline

Resets the occurrence iterator to the beginning of the list of generation occurrences.

{_current_occurrence = _occurrences.begin();}

Referenced by SimRunner::setForFirstGeneration().

set()

void StatServices::set ( string &  str, unsigned int  occ  )

inline

  {_statArg = str; _occurrence = occ;}

set_pop_ptr()

void StatServices::set_pop_ptr ( Metapop *  pop )

inline

{_popPtr=pop;}

Referenced by SimRunner::init_components().

setCompactOutputFormat()

void StatServices::setCompactOutputFormat ( )

inline

{_width = 0; _separator = ' ';}

Referenced by LCE_StatServiceNotifier::setParameters().

setDefaultOutputFormat()

void StatServices::setDefaultOutputFormat ( )

inline

{_width = 12; _precision = 6; _separator = '\t';}

Referenced by LCE_StatServiceNotifier::setParameters().

setFieldPrecision()

void StatServices::setFieldPrecision ( unsigned int  val )

inline

{_precision = val;}

Referenced by LCE_StatServiceNotifier::setParameters().

setFieldSeparator()

void StatServices::setFieldSeparator ( unsigned char  c )

inline

{_separator = c;}

Referenced by LCE_StatServiceNotifier::setParameters().

setFieldWidth()

void StatServices::setFieldWidth ( unsigned int  val )

inline

{_width = val;}

Referenced by LCE_StatServiceNotifier::setParameters().

setOcccurrence()

void StatServices::setOcccurrence ( unsigned int  value )

inline

{_occurrence = value;}

setOccurrences()

void StatServices::setOccurrences

(

map< unsigned int, unsigned int >

timeTable

)

Sets the list of generation for which statistics must be recorded during a run.

Parameters

timeTable

a map containing the generations at which stats must be recorded

{
  map<unsigned int, unsigned int>::const_iterator time = timeTable.begin(), next;
  
  _occurrences.clear();
  _occurrences.push_front(0);
  
  if (time->first == 0 && time->second != 0) { //this is a recursive logtime
    
    unsigned int next_term;
    
    for (;time != timeTable.end(); ++time) {
      
      next = time;
      next++;
      next_term = ( next != timeTable.end() ? 
                   next->first : SIMenv::getGenerations() );
      
      while( _occurrences.back() + time->second < next_term)
      {
        _occurrences.push_back( _occurrences.back() + time->second );
      }
      _occurrences.push_back(next_term);
    }
    
    
  } else if (time->second == 0) { //non-recursive logtime, only records specific times
    
    for (;time != timeTable.end(); ++time) _occurrences.push_back(time->first);
    
  } else { 
    
    fatal("something went wrong while setting stat recording times (first=%i, second=%i)\n",
          time->first, time->second);
  }
  
  //clean up:
  while (_occurrences.back() > SIMenv::getGenerations()) _occurrences.pop_back();
  
  if(_occurrences.back() != SIMenv::getGenerations()) //automatically record last gen
    _occurrences.push_back(SIMenv::getGenerations());
  
  if (_occurrences.front() == 0) _occurrences.pop_front();
  if (_occurrences.front() != 1) _occurrences.push_front(1); //automatically record first gen
}

References fatal(), and SIMenv::getGenerations().

Referenced by LCE_StatServiceNotifier::setOccurence().

setStatOptions()

void StatServices::setStatOptions ( string &  str )

inline

{_statArg = str;}

Referenced by LCE_StatServiceNotifier::loadStatServices().

Member Data Documentation

_current_occurrence

list< unsigned int >::const_iterator StatServices::_current_occurrence

private

Iterator pointing to the current generation to record.

Is incremented once all stats have been recorded for the current generation.

_currentStatValues

double* StatServices::_currentStatValues

private

Pointer to the last recorded stats.

_numRecorders

unsigned int StatServices::_numRecorders

private

Number of stats to record.

_occurrence

unsigned int StatServices::_occurrence

private

Deprecated.

_occurrences

list< unsigned int > StatServices::_occurrences

private

List of all generations to record.

_popPtr

Metapop* StatServices::_popPtr

private

_precision

unsigned int StatServices::_precision

private

_printAverages

bool StatServices::_printAverages

private

_separator

unsigned char StatServices::_separator

private

_statArg

string StatServices::_statArg

private

The string argument of the 'stat' input option.

_statHandlers

list< StatHandlerBase* > StatServices::_statHandlers

private

List of stat handlers declared by currently active simulation components.

_statRecorders

list< StatRecBase *> StatServices::_statRecorders

private

List of stat recorders.

_statValues

vector< vector< double*> > StatServices::_statValues

private

Table containing all recorded stats, replicate x generation x (num recorders + 2) .

_width

unsigned int StatServices::_width

private

---

The documentation for this class was generated from the following files:

• statservices.h
• statservices.cc