Sample Class Reference

The Sample is the object to simulate. It contains the spins. More...

#include <Sample.h>

Inheritance diagram for Sample:

Collaboration diagram for Sample:

Public Member Functions
	Sample ()
	Sample (const string &file, const int multiple=1)
	Sample (const size_t size)
virtual	~Sample ()
virtual void	Prepare (const std::string &fname="")
void	ClearSpins ()
	delete the spin structure
void	CreateSpins (const size_t size)
	create the spin structure More...
void	CreateSpins (const size_t nprops, const size_t size)
	create the spin structure More...
size_t	GetSize () const
size_t	GetNProps () const
vector< size_t >	GetSampleDims () const
void	SetSampleDims (vector< size_t > d)
const int	GetSampleDimsSize () const
	Dimensions. More...
Sample *	GetSubSample (const int n, const size_t size)
void	GetValues (const size_t l, double *val)
	Get values for spin l and deliver them in val. More...
double *	GetResolution ()
	Get grid resolution. More...
void	InitRandGenerator (int val=1)
	Initialize the randome number generator. More...
void	SetR2Prime (double val)
	Set the random local field fluctuations. More...
void	SetPositionRandomness (double val)
	Set the position randomness in per cent of the cartesian resolution. More...
double	GetDeltaB (size_t pos=-1)
	Get off-resonance of a specific spin. More...
virtual IO::Status	Populate (const string &file)
double *	GetSpinsData ()
void	SetReorderStrategy (string strat)
void	ReorderSample ()
void	DumpRestartInfo (CoilArray *RxCA)
	Utility function for restart: dump information to restart jemris after crash.
void	ReportSpin (int beg, int end, int value)
	Utility function for restart: mark spins which have been calculated.
int	ReadSpinsState ()
	Utility function for restart: Read restart file after crash.
void	ClearSpinsState ()
	Utility function for restart: mark all spins as not simulated.
void	GetScatterVectors (int *sendcount, int *displ, int size)
	utility function to send sample in parallel mode: initial samples are send via mpi_scatterv; get needed vectors to scatter data.
void	GetNextPacket (int &noSpins, int &NextSpinToSend, int SlaveId)
	utility function to send sample in parallel mode: get next spin packet to be sent. (beginning index + no_spins to send)
int	SpinsLeft ()
	Returns No spins which still needs to be calculated.
void	SetTimeInterval (double val)
	Set Time interval in seconds after which new spins are sent (approx. value.)
bool	IsRestart ()
	true if simulation run is from a restart
void	GetHelper (double *target)
double *	GetHelper ()
size_t	GetHelperSize ()
int	GetNoSpinCompartments ()
void	SetNoSpinCompartments (int n)
void	CreateHelper (const size_t l)
void	CreateDims (const size_t l)
void	CopyHelper (double *out)
virtual void	CropEnumerate ()

Protected Member Functions
void	MultiplySample (int multiple)

Protected Attributes
Ensemble< double >	m_ensemble
vector< size_t >	m_index
vector< double >	m_res
vector< double >	m_offset
RNG	m_rng
double	m_r2prime
double	m_pos_rand_perc
SampleReorderStrategyInterface *	m_reorder_strategy
int	m_max_paket_size
int	m_min_paket_size
int	m_next_spin_to_send
vector< char >	m_spin_state
bool	m_is_restart
vector< int >	m_spins_sent
vector< int >	m_last_offset_sent
vector< timeval >	m_last_time
double	m_sent_interval
double	m_total_cpu_time
double	m_no_spins_done
vector< double >	m_helper
int	m_no_spin_compartments

Detailed Description

The Sample is the object to simulate. It contains the spins.

Constructor & Destructor Documentation

Sample() [1/3]

Sample::Sample

(

)

Constructor

Here is the call graph for this function:

Sample() [2/3]

Sample::Sample	(	const string &	file,
		const int	multiple = 1
	)

Constructor

Create a container from binary file

Parameters

file	Sample binary file

Here is the call graph for this function:

Sample() [3/3]

Sample::Sample

(

const size_t

size

)

Constructor

Create a container of requested size initialized with zeros

Parameters

size	Size of the sample

Here is the call graph for this function:

~Sample()

Sample::~Sample ( )

virtual

Destructor

Here is the call graph for this function:

Member Function Documentation

CreateSpins() [1/2]

void Sample::CreateSpins	(	const size_t	nprops,
		const size_t	size
	)

create the spin structure

Parameters

size	Size of the spin structure to create

Here is the call graph for this function:

CreateSpins() [2/2]

void Sample::CreateSpins

(

const size_t

size

)

create the spin structure

Parameters

size	Size of the spin structure to create

Here is the call graph for this function:

GetDeltaB()

double Sample::GetDeltaB

(

size_t

pos = -1

)

Get off-resonance of a specific spin.

The off-resonance is given by the deterministic value, read by Populate from the binary file, plus the random field fluctuation specified by SetR2Prime.

Parameters

pos	Position of the spin. If negative, last acquired spin by GetValues is used.

Returns

The off-resonance in unit [Khz]

Here is the call graph for this function:

GetNProps()

size_t Sample::GetNProps ( ) const

inline

Get number of spin properties including spatial

Returns

Number of spin properties

Here is the call graph for this function:

Here is the caller graph for this function:

GetResolution()

double * Sample::GetResolution ( )

inline

Get grid resolution.

Returns

Grid resolution

GetSampleDims()

vector< size_t > Sample::GetSampleDims ( ) const

inline

Get number of sample dimensions

Returns

number of sample dimensions

Here is the call graph for this function:

Here is the caller graph for this function:

GetSampleDimsSize()

const int Sample::GetSampleDimsSize ( ) const

inline

Dimensions.

Returns

Dimensions of the ensemble

Here is the call graph for this function:

GetSize()

size_t Sample::GetSize

(

)

const

Get size of the sample

Returns

Size of the sample

Here is the call graph for this function:

Here is the caller graph for this function:

GetSpinsData()

double * Sample::GetSpinsData ( )

inline

returns pointer to sample data (needed for MPI send/receive)

Here is the call graph for this function:

GetSubSample()

Sample * Sample::GetSubSample	(	const int	n,
		const size_t	size
	)

Get a subset of this sample

Parameters

n	N-th subset
size	Size of the subset

GetValues()

void Sample::GetValues	(	const size_t	l,
		double *	val
	)

Get values for spin l and deliver them in val.

Parameters

l	Spin number
val	Output container

Here is the call graph for this function:

InitRandGenerator()

void Sample::InitRandGenerator ( int  val = 1 )

inline

Initialize the randome number generator.

Parameters

val	any integer

Here is the caller graph for this function:

Populate()

IO::Status Sample::Populate ( const string &  file )

virtual

Create a container from binary file

Parameters

file	Sample binary file

Here is the call graph for this function:

Here is the caller graph for this function:

Prepare()

void Sample::Prepare ( const std::string &  fname = "" )

virtual

init variables which are same for all constructors

Reimplemented in MultiPoolSample.

Here is the call graph for this function:

Here is the caller graph for this function:

ReorderSample()

void Sample::ReorderSample

(

)

executes sample reordering

Here is the caller graph for this function:

SetPositionRandomness()

void Sample::SetPositionRandomness ( double  val )

inline

Set the position randomness in per cent of the cartesian resolution.

Parameters

val	Percentage width of the Gaussian distribution.

Here is the caller graph for this function:

SetR2Prime()

void Sample::SetR2Prime ( double  val )

inline

Set the random local field fluctuations.

Parameters

val	R2Prime (Shaping parameter of the Lorentz distribution in kHz).

Here is the caller graph for this function:

SetReorderStrategy()

void Sample::SetReorderStrategy

(

string

strat

)

can set a method to reorder the sample (do nothing, shuffle sample,... )

Here is the caller graph for this function:

SetSampleDims()

void Sample::SetSampleDims ( vector< size_t >  d )

inline

Get number of sample dimensions

Returns

number of sample dimensions

Here is the call graph for this function:

Member Data Documentation

m_ensemble

Ensemble<double> Sample::m_ensemble

protected

clones sample 'multiple'-times, e.g. for diffusion simulation

m_is_restart

bool Sample::m_is_restart

protected

keeps track whether spin is not touched (==0), sent (==1) or calculated (==2)

m_last_offset_sent

vector<int> Sample::m_last_offset_sent

protected

no of spins last sent to each slave

m_last_time

vector<timeval> Sample::m_last_time

protected

offset to the last spins sent

m_min_paket_size

int Sample::m_min_paket_size

protected

maximal no of spins to send

m_next_spin_to_send

int Sample::m_next_spin_to_send

protected

minimal no of spins to send

m_offset

vector<double> Sample::m_offset

protected

< Sample resolution [mm]

m_pos_rand_perc

double Sample::m_pos_rand_perc

protected

< R2-Prime == shaping parameter of the Lorentzian distribution

m_r2prime

double Sample::m_r2prime

protected

< random number generator

m_reorder_strategy

SampleReorderStrategyInterface* Sample::m_reorder_strategy

protected

< Percantage (of cartesian resolution) randomness in spin position .

m_res

vector<double> Sample::m_res

protected

< Sample dimensions

m_rng

RNG Sample::m_rng

protected

< Sample offeset to {0,0,0} origin

m_sent_interval

double Sample::m_sent_interval

protected

last timepoint at which spins were sent

m_spins_sent

vector<int> Sample::m_spins_sent

protected

true if simulation run is from a restart

m_total_cpu_time

double Sample::m_total_cpu_time

protected

approx. time in seconds after which new spins are sent

---

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

• /Users/stoeckert/DZNE/workspace/jemris/src/Sample.h
• /Users/stoeckert/DZNE/workspace/jemris/src/Sample.cpp