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

#include <NeuriteCachedStats.h>

Inheritance diagram for nsol::NeuriteCachedStats:

Collaboration diagram for nsol::NeuriteCachedStats:

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

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

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)

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::NeuriteStats
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.

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

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 neurites.

Using this class instead of Neurite or NeuriteStats when constructing the hierarchy allows to call the method stats from base Neurite 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>
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 44 of file NeuriteCachedStats.h.

Member Function Documentation

float nsol::NeuriteCachedStats::getStat	(	TNeuriteStat	stat,
		TAggregation	agg = `TOTAL`
	)		const

virtual

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.

Only TAggregation::TOTAL caches values, other aggregations are computed

Parameters

stat	stat to compute
agg	aggregation used

Returns: stat value using the aggregation given

Reimplemented from nsol::NeuriteStats.

Definition at line 67 of file NeuriteCachedStats.cpp.

References nsol::NeuriteStats::getStat().

Here is the call graph for this function:

void nsol::NeuriteCachedStats::setAndPropagateDirty ( unsigned int id )

virtual

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

Parameters

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

Reimplemented from nsol::Cached<>.

Definition at line 41 of file NeuriteCachedStats.cpp.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation