nsol  0.4.1
Nsol - Neuroscience Objects Library
Public Types | Public Member Functions | List of all members
nsol::NeuronMorphologyStats Class Reference

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

#include <NeuronMorphologyStats.h>

+ Inheritance diagram for nsol::NeuronMorphologyStats:
+ Collaboration diagram for nsol::NeuronMorphologyStats:

Public Types

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
}
 

Public Member Functions

 NeuronMorphologyStats (SomaPtr soma_)
 
virtual NeuronMorphologyStats * stats (void)
 Returns object as NeuronMorphologyStats. More...
 
virtual float getStat (TNeuronMorphologyStat stat, TAggregation agg=TOTAL) const
 
- 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)
 

Additional Inherited Members

- Protected Attributes inherited from nsol::NeuronMorphology
SomaPtr _soma
 
Neurites _neurites
 
Neurons _parentNeurons
 
- Protected Attributes inherited from nsol::Morphology
Sections _sections
 Morphology sections.
 

Detailed Description

This class allows to compute stats for sections.

Using this class instead of NeuronMorphology when constructing the hierarchy allows to call the method stats from base NeuronMorphology 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>
#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 39 of file NeuronMorphologyStats.h.

Member Function Documentation

virtual NeuronMorphologyStats* nsol::NeuronMorphologyStats::stats ( void  )
virtual

Returns object as NeuronMorphologyStats.

Returns
pointer to NeuronMorphologyStats object

Reimplemented from nsol::NeuronMorphology.

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