This class allows to compute stats for dendrites. More...

#include <DendriteCachedStats.h>

Inheritance diagram for nsol::DendriteCachedStats:

Collaboration diagram for nsol::DendriteCachedStats:

Public Member Functions
	DendriteCachedStats (TDendriteType dendriteType_=BASAL)

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

Public Member Functions inherited from nsol::DendriteStats
	DendriteStats (TDendriteType dendriteType_=BASAL)

Public Member Functions inherited from nsol::Dendrite
	Dendrite (TDendriteType dendriteType=BASAL)

TDendriteType &	dendriteType (void)
	Get the type of neurite.

virtual NeuritePtr	clone (void) const final

Public Member Functions inherited from nsol::Neurite
	Neurite (TNeuriteType neuriteType=DENDRITE)
	Default constructor.

TNeuriteType &	neuriteType (void)
	Get the type of neurite.

NeuronMorphologyPtr	morphology (void) const

NeuronMorphologyPtr	morphology (NeuronMorphologyPtr morphology)

bool	hasMorphology (void) const

NeuronMorphologySectionPtr	firstSection (void) const

Sections	sections (void) const

void	computeBranchBifurcations (void)

unsigned int	numBranches (void)

unsigned int	numBifurcations (void)

bool	operator== (Neurite &other)

bool	operator!= (Neurite &other)

Public Member Functions inherited from nsol::NeuriteStats
	NeuriteStats (TNeuriteType neuriteType=DENDRITE)
	Default constructor.

Public Member Functions inherited from nsol::NeuriteCachedStats
	NeuriteCachedStats (TNeuriteType neuriteType=DENDRITE)
	Default constructor.

virtual	~NeuriteCachedStats (void)
	Default destructor.

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

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

virtual void	firstSection (NeuronMorphologySectionPtr section)
	Set dirty all cached stats and propagates dirty to parent neurite.

virtual float	getStat (TNeuriteStat stat, TAggregation agg=TOTAL) const
	Returns the stat given if the cache is clean and if it is dirty then computes the stat and stores the value in the cache. More...

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::Dendrite
enum	TDendriteType { BASAL = 0, APICAL }
	Type of dendrite.

typedef enum nsol::Dendrite::TDendriteType	TDendriteType
	Type of dendrite.

Public Types inherited from nsol::Neurite
enum	TNeuriteType { DENDRITE = 0, AXON }
	Possible types of neurite.

Public Types inherited from nsol::NeuriteStats
enum	TNeuriteStat { SURFACE = 0, VOLUME, LENGTH, BIFURCATIONS, NEURITE_NUM_STATS }
	Enumeration of the stats that can be computed for Neurite.

Protected Member Functions inherited from nsol::Neurite
void	_addBifurcationCount (unsigned int numBifurcations)

void	_addBranchCount (unsigned int numBranches)

void	_clone (NeuritePtr neurite) const

Protected Attributes inherited from nsol::Dendrite
TDendriteType	_dendriteType
	Type of dendrite.

Protected Attributes inherited from nsol::Neurite
TNeuriteType	_neuriteType

NeuronMorphologySectionPtr	_firstSection

NeuronMorphologyPtr	_morphology

unsigned int	_numBranches

unsigned int	_numBifurcations

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 compute stats for dendrites.

Using this class instead of Dendrite when constructing the hierarchy allows to call the method stats from base Dendrite class and get the corresponding volume, surface and length.

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>
void ComputeAndPrintSurface( nsol::NeuronPtr n )
{
  unsigned int i = 0;
  for ( const auto& neurite : n->morphology( )->neurites( ))
  {
    std::cout << "\tDendrite " << i++ << " type: "
              <<  neurite->neuriteType( ) << " ";
    if ( neurite->neuriteType( ) == nsol::Neurite::DENDRITE )
      std::cout << NSOL_DYNAMIC_CAST( nsol::Dendrite, neurite )->dendriteType( );
    std::cout << " surface: ";
    if ( neurite->stats( ))
    {
      std::cout << " " << neurite->stats( )->getStat(
        nsol::NeuriteStats::SURFACE ) << " ";
      const nsol::Sections& sections = neurite->sections( );
      std::cout << "[ ";
      for ( const auto& section : sections )
      {
        std::cout << dynamic_cast< nsol::NeuronMorphologySectionPtr >(
          section )->stats( )->getStat(
            nsol::NeuronMorphologySectionStats::/*TSectionStat::*/SURFACE ) << " ";
      }
      std::cout << "]";
    }
    else
      std::cout << "No stats available";
    std::cout << std::endl;
  }
}
void PrintCachedSurfaceState( nsol::NeuronPtr n )
{
  unsigned int i = 0;
  for ( const auto& neurite : n->morphology( )->neurites( ))
  {
    std::cout << "\tDendrite " << i++ << " type: "
              <<  neurite->neuriteType( ) << " ";
    if ( neurite->neuriteType( ) == nsol::Neurite::DENDRITE )
      std::cout << NSOL_DYNAMIC_CAST( nsol::Dendrite, ( neurite ))
        ->dendriteType( );
    std::cout << " surface: ";
    if ( neurite->stats( ))
    {
      nsol::Cached<> * cached =
        NSOL_DYNAMIC_CAST( nsol::Cached<>, neurite->stats( ));
      if ( cached )
        std::cout << ( !cached->dirty( nsol::NeuriteCachedStats::SURFACE )
                       ? "C" : "D" );
      nsol::Sections sections = neurite->sections( );
      std::cout << " [ ";
      for ( const auto& section : sections )
      {
        cached =
          NSOL_DYNAMIC_CAST(
            nsol::Cached<>, dynamic_cast< nsol::NeuronMorphologySectionPtr >(
              section )->stats( ));
        if ( cached )
          std::cout  <<
            ( ! cached->dirty(
              nsol::NeuronMorphologySectionCachedStats::SURFACE )
              ? "C " : "D " );
      }
      std::cout << "]";
    }
    else
      std::cout << "No stats available";
    std::cout << std::endl;
  }
}
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 without stats" << std::endl;
  nsol::SwcReader readerWithoutStats;
  nsol::NeuronPtr neuron = readerWithoutStats.readNeuron( argv[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 ( ! neuron || ! neuronWithStats || ! neuronWithCachedStats )
  {
    std::cerr << "Could not read neurons" << std::endl;
    return -1;
  }
  std::cout << std::endl;
  std::cout << "Compute and print neuron stats when not available" << std::endl;
  ComputeAndPrintSurface( neuron );
  std::cout << std::endl;
  std::cout << "Compute and print neuron stats when not cacheable" << std::endl;
  ComputeAndPrintSurface( neuronWithStats );
  std::cout << std::endl;
  std::cout << "Print cached stats" << std::endl;
  PrintCachedSurfaceState( neuronWithCachedStats );
  std::cout << std::endl;
  std::cout << "Compute and print cacheable stats" << std::endl;
  ComputeAndPrintSurface( neuronWithCachedStats );
  std::cout << std::endl;
  std::cout << "Print cached stats" << std::endl;
  PrintCachedSurfaceState( neuronWithCachedStats );
  std::cout << std::endl;
  PrintCachedSurfaceState( neuronWithCachedStats );
  std::cout << std::endl;
  ComputeAndPrintSurface( neuronWithCachedStats );
  std::cout << std::endl;
  PrintCachedSurfaceState( neuronWithCachedStats );
  std::cout << std::endl;
  return 0;
}

Definition at line 40 of file DendriteCachedStats.h.

Member Function Documentation

virtual NeuriteStats* nsol::DendriteCachedStats::stats ( void )

inlinevirtual

Returns object as NeuriteStats.

Returns: pointer to NeuriteStats object

Reimplemented from nsol::NeuriteStats.

Definition at line 51 of file DendriteCachedStats.h.

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

DendriteCachedStats.h

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation