SectionStats Class Reference

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

#include <NeuronMorphologySectionStats.h>

Collaboration diagram for SectionStats:

Detailed Description

This class allows to compute stats for sections.

Using this class instead of Neuron Morphology Section when constructing the hierarchy allows to call the method stats from base Section 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>
#include <stack>


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;
  }


  nsol::NeuronMorphologySectionPtr section =
    neuron->morphology( )->neurites( )[0]->firstSection( );

  nsol::NeuronMorphologySectionPtr sectionWithStats =
    neuronWithStats->morphology( )->neurites()[0]->firstSection( );

  nsol::NeuronMorphologySectionPtr sectionWithCachedStats =
    neuronWithCachedStats->morphology( )->neurites()[0]->firstSection( );

  if ( ! section || ! sectionWithStats || ! sectionWithCachedStats )
  {
    std::cerr << "Could not get sections of first neurite" << std::endl;
    return -1;
  }

  std::cout << std::endl;

  // Section without stats should return nullptr when asking for its stats
  NSOL_CHECK_THROW ( section->stats( ) == nullptr, "stats not null" );

  // Section without stats should return SectionStats pointer
  NSOL_CHECK_THROW ( sectionWithStats->stats( ) != nullptr, "stats null" );

  // Will get the base class to force cache operations
  nsol::NeuronMorphologySectionCachedStats * sectionCached =
    dynamic_cast< nsol::NeuronMorphologySectionCachedStats * >
    ( sectionWithCachedStats->stats( ));
  NSOL_CHECK_THROW( sectionCached, "non cached section" );


#define PRINT_SURFACE_DIRTY_STATE( section )                \
  (( section->dirty(nsol::NeuronMorphologySectionCachedStats::SURFACE) ) ?  \
   "Dirty" : "Clean" )


  std::cout << std::endl;

  std::cout << "Surface of the first section of the first neurite "
            << std::endl;

  std::cout << "\tNon cached section: "
            << sectionWithStats->stats( )->getStat(
              nsol::NeuronMorphologySectionStats::
              /*TNeuronMorphologySectionStat::*/SURFACE ) << std::endl;

  std::cout << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << std::endl;

  // Next code shows how to force dirty on a specific cached value
  sectionCached->setDirty( nsol::NeuronMorphologySectionCachedStats::SURFACE );

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << std::endl;

  // Next code shows how to force dirty on all cached values
  sectionCached->setAndPropagateDirty( );

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << std::endl;

  // Now lets pretend to change something on a segment an see if it propagates
  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << std::endl;

  // Now changind the radius of a node should dirty segment and section
  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << "\tCached section ("
            << PRINT_SURFACE_DIRTY_STATE( sectionCached ) << "): ";
  std::cout << sectionWithCachedStats->stats( )->getStat(
    nsol::NeuronMorphologySectionStats::/*TNeuronMorphologySectionStat::
                                         */SURFACE ) << std::endl;

  std::cout << std::endl;


  // Print stats of each neurite
  int j = 0;
  for ( const auto& neurite : neuronWithCachedStats->morphology( )->neurites( ))
  {
    std::cout << "Neurite " << j << std::endl;

    std::stack< nsol::SectionPtr > sSP;

    nsol::NeuronMorphologySectionPtr neuriteSection = neurite->firstSection( );

    sSP.push( neuriteSection );

    int k = 0;
    while ( !sSP.empty( ))
    {
      neuriteSection = dynamic_cast< nsol::NeuronMorphologySectionPtr >(
        sSP.top( ));
      sSP.pop( );

      std::cout << "  Section " << k << std::endl;
      std::cout << "    Surface " << neuriteSection->stats( )->getStat(
        nsol::NeuronMorphologySectionStats::SURFACE ) << std::endl;
      std::cout << "    Volume " << neuriteSection->stats( )->getStat(
        nsol::NeuronMorphologySectionStats::VOLUME ) << std::endl;
      std::cout << "    Length " << neuriteSection->stats( )->getStat(
        nsol::NeuronMorphologySectionStats::LENGTH ) << std::endl;


      if ( section->children( ).size( ) > 0 )
        for ( const auto& sec : section->children( ))
          sSP.push( sec );
      ++k;
    }

    ++j;
  }

  return 0;

}

---

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

• NeuronMorphologySectionStats.h