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

#include <NeuriteStats.h>

Inheritance diagram for nsol::NeuriteStats:

Collaboration diagram for nsol::NeuriteStats:

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

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

Public Member Functions
	NeuriteStats (TNeuriteType neuriteType=DENDRITE)
	Default constructor.

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

virtual float	getStat (TNeuriteStat stat, TAggregation agg=TOTAL) const
	Computes the stat given. More...

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

virtual void	firstSection (NeuronMorphologySectionPtr section)

Sections	sections (void) const

void	computeBranchBifurcations (void)

unsigned int	numBranches (void)

unsigned int	numBifurcations (void)

virtual NeuritePtr	clone (void) const

bool	operator== (Neurite &other)

bool	operator!= (Neurite &other)

Additional Inherited Members
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::Neurite
TNeuriteType	_neuriteType

NeuronMorphologySectionPtr	_firstSection

NeuronMorphologyPtr	_morphology

unsigned int	_numBranches

unsigned int	_numBifurcations

Detailed Description

This class allows to compute stats for neurites.

Using this class instead of Neurite when constructing the hierarchy allows to call the method stats from base Neurite 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;
}