This class allows to cache the stats for neuronmorphologys. More...

#include <NeuronMorphologyCachedStats.h>

Inheritance diagram for nsol::NeuronMorphologyCachedStats:

Collaboration diagram for nsol::NeuronMorphologyCachedStats:

Public Member Functions
	NeuronMorphologyCachedStats (void)
	Default constructor.

	NeuronMorphologyCachedStats (SomaPtr soma_)

virtual	~NeuronMorphologyCachedStats (void)
	Default destructor.

virtual float	getStat (TNeuronMorphologyStat stat, TAggregation agg=TOTAL) const

virtual void	setAndPropagateDirty (unsigned int id)
	Set dirty a cached stat and propagates dirty to parent neuronmorphology. More...

virtual void	setAndPropagateDirty (void)
	Set dirty all cached stats and propagates dirty to parent neuron morphology.

Public Member Functions inherited from nsol::NeuronMorphologyStats
	NeuronMorphologyStats (SomaPtr soma_)

virtual NeuronMorphologyStats *	stats (void)
	Returns object as NeuronMorphologyStats. More...

Public Member Functions inherited from nsol::NeuronMorphology
	NeuronMorphology (void)
	Default Neuron class constructor. More...

	NeuronMorphology (SomaPtr soma)

SomaPtr	soma (SomaPtr soma)
	Method to set the neuronal soma. More...

NeuritePtr	addNeurite (NeuritePtr neurite)
	Method to add a new neurite to the neuron. More...

Dendrites *	dendrites (void) const
	Method to get all the dendrites in a container. More...

Dendrites *	basalDendrites (void) const
	Method to get all the basal dendrites in a container. More...

Dendrites *	apicalDendrites (void) const
	Method to get all the apical dendrites in a container. More...

DendritePtr	apicalDendrite (void) const
	Method to get the first apical dendrite. More...

Axons *	axons () const
	Method to get all the axons in a container. More...

virtual Neurites &	neurites (void)

const Neurites &	neurites (void) const

virtual Neurons &	parentNeurons (void)

const Neurons &	parentNeurons (void) const

SomaPtr	soma (void)

void	addParentNeuron (NeuronPtr neuron)

virtual NeuronMorphologyPtr	asNeuronMorphology (void)

virtual NeuronMorphologyPtr	clone (void) const

bool	operator== (NeuronMorphology &other)

bool	operator!= (NeuronMorphology &other)

Public Member Functions inherited from nsol::Morphology
Sections &	sections (void)

Public Member Functions inherited from nsol::Object
virtual ColumnPtr	asColumn (void)

virtual MiniColumnPtr	asMiniColumn (void)

virtual NeuronPtr	asNeuron (void)

virtual SectionPtr	asSection (void)

virtual NodePtr	asNode (void)

virtual ObjectWithProperties *	properties (void)

virtual ObjectPtr	create (void)

Public Member Functions inherited from nsol::Cached<>
bool	dirty (unsigned int id_) const

void	setDirty (unsigned int id_)

void	setDirty (void)

void	cacheValue (const unsigned int id_, floatvalue_) const

float	getValue (const unsigned int id_) const

Additional Inherited Members
Public Types inherited from nsol::NeuronMorphologyStats
enum	TNeuronMorphologyStat { DENDRITIC_VOLUME, AXON_VOLUME, NEURITIC_VOLUME, SOMA_VOLUME, VOLUME, DENDRITIC_SURFACE, AXON_SURFACE, NEURITIC_SURFACE, SOMA_SURFACE, SURFACE, DENDRITIC_LENGTH, AXON_LENGTH, NEURITIC_LENGTH, DENDRITIC_BIFURCATIONS, AXON_BIFURCATIONS, NEURITIC_BIFURCATIONS, NEURON_MORPHOLOGY_NUM_STATS }

Protected Attributes inherited from nsol::NeuronMorphology
SomaPtr	_soma

Neurites	_neurites

Neurons	_parentNeurons

Protected Attributes inherited from nsol::Morphology
Sections	_sections
	Morphology sections.

Protected Attributes inherited from nsol::Cached<>
std::map< unsigned int, float >	_values
	Container of the cached values. Is mutable to allow const methods to modify the cache if needed.

Detailed Description

This class allows to cache the stats for neuronmorphologys.

Using this class instead of NeuronMorphology or NeuronMorphologyStats when constructing the hierarchy allows to call the method stats from base NeuronMorphology class and get the corresponding volume, surface and length. If the cached value is dirty then the actual computation process is done. In case is clean the cached value is returned directly.

Example:

/*
 * Copyright (c) 2014-2017 GMRV/URJC.
 *
 * This file is part of nsol <https://github.com/gmrvvis/nsol>
 *
 * This library is free software; you can redistribute it and/or modify it under
 * the terms of the GNU Lesser General Public License version 3.0 as published
 * by the Free Software Foundation.
 *
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
 * details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation, Inc.,
 * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 */
/*
 * Example to show how to use stats and cached stats
 */
#include <nsol/nsol.h>
#ifdef Win32
#include < time.h >
#include <windows.h> //I've omitted this line.
#if defined(_MSC_VER) || defined(_MSC_EXTENSIONS)
  #define DELTA_EPOCH_IN_MICROSECS  11644473600000000Ui64
#else
  #define DELTA_EPOCH_IN_MICROSECS  11644473600000000ULL
#endif
struct timezone
{
  int  tz_minuteswest; /* minutes W of Greenwich */
  int  tz_dsttime;     /* type of dst correction */
};
int gettimeofday(struct timeval *tv, struct timezone *tz)
{
  FILETIME ft;
  unsigned __int64 tmpres = 0;
  static int tzflag;
  if (NULL != tv)
  {
    GetSystemTimeAsFileTime(&ft);
    tmpres |= ft.dwHighDateTime;
    tmpres <<= 32;
    tmpres |= ft.dwLowDateTime;
    /*converting file time to unix epoch*/
    tmpres -= DELTA_EPOCH_IN_MICROSECS;
    tmpres /= 10;  /*convert into microseconds*/
    tv->tv_sec = (long)(tmpres / 1000000UL);
    tv->tv_usec = (long)(tmpres % 1000000UL);
  }
  if (NULL != tz)
  {
    if (!tzflag)
    {
      _tzset();
      tzflag++;
    }
    long seconds;
    _get_timezone( &seconds );
    tz->tz_minuteswest =  seconds / 60;
    int hours;
    _get_daylight( &hours );
    tz->tz_dsttime = hours;
  }
  return 0;
}
#else
#include <sys/time.h>
#endif
void computeNeuronMorphologyStats( nsol::NeuronMorphologyPtr morphology );
void printNeuronMorphologyStats( nsol::NeuronMorphologyPtr morphology );
int main ( int argc, char ** argv )
{
  std::cout << std::endl;
  if ( argc < 2 )
  {
    std::cerr << "Error. Usage: " << argv[0]
              << " swc_input_file" << std::endl;
    return -1;
  }
  std::cout << "Reading neuron with stats" << std::endl;
  nsol::SwcReaderStats readerWithStats;
  nsol::NeuronPtr neuronWithStats = readerWithStats.readNeuron( argv[1] );
  std::cout << "Reading neuron with cached stats" << std::endl;
  nsol::SwcReaderCachedStats readerWithCachedStats;
  nsol::NeuronPtr neuronWithCachedStats =
    readerWithCachedStats.readNeuron( argv[1] );
  if ( ! neuronWithStats || ! neuronWithCachedStats )
  {
    std::cerr << "Could not read neurons" << std::endl;
    return -1;
  }
  std::cout << std::endl;
  std::cout << "Non-cached stats" << std::endl;
  printNeuronMorphologyStats( neuronWithStats->morphology( ));
  std::cout << "Cached stats" << std::endl;
  printNeuronMorphologyStats( neuronWithCachedStats->morphology( ));
  struct timeval startTime, endTime;
  long totalTime;
  gettimeofday(&startTime, NULL);
  for ( int i = 0; i < 10000; i++ )
    computeNeuronMorphologyStats( neuronWithStats->morphology( ));
  gettimeofday(&endTime, NULL);
  totalTime =  (endTime.tv_sec - startTime.tv_sec) * 1000000L;
  totalTime += (endTime.tv_usec - startTime.tv_usec);
  std::cout << "Compute non-cached stats 1000 times. Time elapsed: "
            << (totalTime/1000L) / 1000.0f << std::endl;
  gettimeofday(&startTime, NULL);
  for ( int i = 0; i < 1000; i++ )
    computeNeuronMorphologyStats( neuronWithCachedStats->morphology( ));
  gettimeofday(&endTime, NULL);
  totalTime =  (endTime.tv_sec - startTime.tv_sec) * 1000000L;
  totalTime += (endTime.tv_usec - startTime.tv_usec);
  std::cout << "Compute cached stats 1000 times. Time elapsed: "
            << (totalTime/1000L) / 1000.0f << std::endl;
  std::cout << std::endl;
  return 0;
}
void computeNeuronMorphologyStats( nsol::NeuronMorphologyPtr morphology )
{
  NSOL_DEBUG_CHECK( morphology , "morphology is null" );
  NSOL_DEBUG_CHECK( morphology->stats( ) , "no stats" );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::DENDRITIC_VOLUME );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::AXON_VOLUME );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::NEURITIC_VOLUME );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::SOMA_VOLUME );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::VOLUME );
  // Surface
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::DENDRITIC_SURFACE );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::AXON_SURFACE );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::NEURITIC_SURFACE );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::SOMA_SURFACE );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::SURFACE );
  // Length
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::DENDRITIC_LENGTH );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::AXON_LENGTH );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::NEURITIC_LENGTH
    );
  // Bifurcations
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::DENDRITIC_BIFURCATIONS );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::AXON_BIFURCATIONS );
  morphology->stats( )->getStat(
    nsol::NeuronMorphologyStats::NEURITIC_BIFURCATIONS );
}
void printNeuronMorphologyStats( nsol::NeuronMorphologyPtr morphology )
{
  NSOL_DEBUG_CHECK( morphology , "morphology is null" );
  NSOL_DEBUG_CHECK( morphology->stats( ) , "no stats" );
  #define NMS morphology->stats( )
  std::cout << "\tDendritic surface:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_SURFACE )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_SURFACE,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_SURFACE,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_SURFACE,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
            << std::endl;
  std::cout << "\tAxon surface:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_SURFACE )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_SURFACE,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_SURFACE,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_SURFACE,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tNeuritic surface:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_SURFACE )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_SURFACE,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_SURFACE,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_SURFACE,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tSoma surface:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::SOMA_SURFACE )
            << std::endl;
  std::cout << "\tSurface:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::SURFACE )
             << std::endl;
  std::cout << std::endl;
  std::cout << "\tDendritic volume:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_VOLUME )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_VOLUME,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_VOLUME,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_VOLUME,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
            << std::endl;
  std::cout << "\tAxon volume:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_VOLUME )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_VOLUME,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_VOLUME,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_VOLUME,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tNeuritic volume:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_VOLUME )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_VOLUME,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_VOLUME,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_VOLUME,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tSoma volume:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::SOMA_VOLUME )
            << std::endl;
  std::cout << "\tVolume:\t\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::VOLUME )
             << std::endl;
  std::cout << std::endl;
  std::cout << "\tDendritic length:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_LENGTH )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_LENGTH,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_LENGTH,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::DENDRITIC_LENGTH,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
            << std::endl;
  std::cout << "\tAxon length:\t\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_LENGTH )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_LENGTH,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_LENGTH,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_LENGTH,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tNeuritic length:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_LENGTH )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_LENGTH,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_LENGTH,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_LENGTH,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << std::endl;
  std::cout << "\tDendritic bifurcations:\t"
            << NMS->getStat(
              nsol::NeuronMorphologyStats::DENDRITIC_BIFURCATIONS )
            << " "
            << NMS->getStat(
              nsol::NeuronMorphologyStats::DENDRITIC_BIFURCATIONS,
              nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat(
              nsol::NeuronMorphologyStats::DENDRITIC_BIFURCATIONS,
              nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat(
              nsol::NeuronMorphologyStats::DENDRITIC_BIFURCATIONS,
              nsol::/*TAggregation::*/STD_DEV ) << " "
            << std::endl;
  std::cout << "\tAxon bifurcations:\t"
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_BIFURCATIONS )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_BIFURCATIONS,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_BIFURCATIONS,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::AXON_BIFURCATIONS,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
             << std::endl;
  std::cout << "\tNeuritic bifurcations:\t"
            << NMS->getStat(
              nsol::NeuronMorphologyStats::NEURITIC_BIFURCATIONS )
            << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_BIFURCATIONS,
                             nsol::/*TAggregation::*/MEAN ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_BIFURCATIONS,
                             nsol::/*TAggregation::*/VARIANCE ) << " "
            << NMS->getStat( nsol::NeuronMorphologyStats::NEURITIC_BIFURCATIONS,
                             nsol::/*TAggregation::*/STD_DEV ) << " "
            << std::endl;
  std::cout << std::endl;
}

Definition at line 45 of file NeuronMorphologyCachedStats.h.

Member Function Documentation

virtual void nsol::NeuronMorphologyCachedStats::setAndPropagateDirty ( unsigned int id )

virtual

Set dirty a cached stat and propagates dirty to parent neuronmorphology.

Parameters

id	identifier of the property to set dirty. It also propagates dirty state to parent neuronmorphology. id value has to be one from TNeuronMorphologyCachedValues (checked only on debug compiling).

Reimplemented from nsol::Cached<>.

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

NeuronMorphologyCachedStats.h

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation