Any quantity recorded as a function of pulse phase. More...

#include <Profile.h>

Inheritance diagram for Pulsar::Profile:

Classes
class	Extension
class	Strategies
	Manages the strategies that implement algorithms. More...

Public Types
typedef Functor< std::pair< int, int >(const Profile *) >	Edges

Public Member Functions
	Profile (unsigned nbin=0)
	Default constructor.
	Profile (const Profile &profile)
	copy constructor
	Profile (const Profile *profile)
	copy constructor
	~Profile ()
	destructor
virtual Profile *	clone () const
	returns a pointer to a new copy of self
virtual void	resize (unsigned nbin)
	resize the data area
const Profile &	operator= (const Profile &profile)
	assignment operator
void	copy (const Profile *, bool clone_strategy=true)
	does the work for copy constructor and assignment operator
void	average (const Profile *that)
	set this to the weighted average of this and that
void	sum (const Profile *profile)
	add profile to this
void	diff (const Profile *profile)
	subtract profile from this
const Profile &	operator+= (float offset)
	adds offset to each bin of the profile
const Profile &	operator-= (float offset)
	subtracts offset from each bin of the profile
const Profile &	*operator=** (float scale)
	multiplies each bin of the profile by scale
void	scale (double scale)
	multiplies each bin of the profile by scale
void	offset (double offset)
	offsets each bin of the profile by offset
void	rotate_phase (double phase)
	rotates the profile by phase (in turns)
void	derivative ()
	compute the derivative of profile with respect to index
void	zero ()
	set all amplitudes to zero
void	square_root ()
	calculate the signed sqrt of the absolute value of each bin
void	absolute ()
	calculare the absolute value of each phase bin
void	logarithm (double base=10.0, double threshold=0.0)
	calculate the logarithm of each bin with value greater than threshold
float	max (int bin_start=0, int bin_end=0) const
	Returns the maximum amplitude.
float	min (int bin_start=0, int bin_end=0) const
	Returns the minimum amplitude.
double	sum (int bin_start=0, int bin_end=0) const
	Returns the sum of all amplitudes.
double	sumsq (int bin_start=0, int bin_end=0) const
	Returns the sum of all amplitudes squared.
double	sumfabs (int bin_start=0, int bin_end=0) const
	Returns the sum of the absolute value.
void	stats (double mean, double variance=0, double *varmean=0, int bin_start=0, int bin_end=0) const
	Calculates the mean, variance, and variance of the mean.
void	stats (float phase, double mean, double variance=0, double *varmean=0, float duty_cycle=default_duty_cycle) const
	Convenience interface to stats (start_bin, end_bin)
double	mean (float phase, float duty_cycle=default_duty_cycle) const
	Convenience interface to stats, returns only the mean.
float	find_max_phase (float duty_cycle=default_duty_cycle) const
	Returns the phase of the centre of the region with maximum mean.
float	find_min_phase (float duty_cycle=default_duty_cycle) const
	Returns the phase of the centre of the region with minimum mean.
void	find_transitions (int &highlow, int &lowhigh, int &width) const
	Find the bin numbers at which the mean power transits.
int	find_max_bin (int bin_start=0, int bin_end=0) const
	Returns the bin number with the maximum amplitude.
int	find_min_bin (int bin_start=0, int bin_end=0) const
	Returns the bin number with the minimum amplitude.
void	find_peak_edges (int &rise, int &fall) const
	Find the bin numbers at which the cumulative power crosses thresholds.
Strategies *	get_strategy () const
	Returns the strategy manager.
void	set_strategy (Strategies *)
	Set the strategy manager.
PhaseWeight *	baseline () const
	Return a new PhaseWeight instance with the baseline phase bins masked.
float	snr () const
	Returns the signal to noise ratio of the profile.
void	dedisperse (double dm, double ref_freq, double pfold)
	Rotates the profile to remove dispersion delay.
Estimate< double >	shift (const Profile &std) const
	Returns the shift (in turns) between profile and standard.
std::vector< float >	get_weighted_amps () const
double	get_centre_frequency () const
	get the centre frequency (in MHz)
virtual void	set_centre_frequency (double cfreq)
	set the centre frequency (in MHz)
float	get_weight () const
	get the weight of the profile
virtual void	set_weight (float)
	set the weight of the profile
void	fft_convolve (const Profile *profile)
	convolves this with the given profile (using fft method)
void	convolve (const Profile *profile)
	convolves this with the given profile in time domain
void	correlate (const Profile *profile)
	cross-correlates this with the given profile in time domain
void	correlate_normalized (const Profile *profile)
	cross-correlates and normalizes this with the given profile in time domain
void	pscrunch ()
	some extensions may have to respond to pscrunch
void	bscrunch (unsigned nscrunch)
	integrate neighbouring phase bins in profile
void	bscrunch_to_nbin (unsigned nbin)
	integrate neighbouring phase bins in profile
void	fold (unsigned nfold)
	integrate neighbouring sections of the profile
template<class T>
const T *	get () const
template<class T>
T *	get ()
Public Member Functions inherited from Pulsar::ProfileAmps
	ProfileAmps (unsigned nbin=0)
	Constructor initializes the data array.
virtual	~ProfileAmps ()
	Destructor destroys the data array.
	ProfileAmps (const ProfileAmps &)
	Copy constructor.
unsigned	get_nbin () const
	Return the number of bins.
const float *	get_amps () const
	Return a pointer to the amplitudes array.
float *	get_amps ()
	Return a pointer to the amplitudes array.
template<typename T>
void	set_amps (const T *data)
	set the amplitudes array equal to the contents of the data array
template<typename T>
void	set_amps (const std::vector< T > &data)
	set the amplitudes array equal to the contents of the data array
template<typename T>
void	get_amps (std::vector< T > &data) const
	set the amplitudes array equal to the contents of the data array
void	remove (const std::vector< unsigned > &indeces)
	remove the elements specified in the array of indeces
Public Member Functions inherited from Reference::Able
	Able (const Able &)
Able &	operator= (const Able &)
unsigned	get_reference_count () const
Public Member Functions inherited from Reference::HeapTracked
	HeapTracked (const HeapTracked &)
HeapTracked &	operator= (const HeapTracked &)
bool	__is_on_heap () const

Static Public Member Functions
static unsigned	get_instance_count ()
	returns the number of Profile instances
Static Public Member Functions inherited from Reference::Able
static size_t	get_instance_count ()
Static Public Member Functions inherited from Reference::HeapTracked
static void *	operator new (size_t size, void *ptr=0)
static void	operator delete (void location, void ptr)
static void	operator delete (void *location)
static size_t	get_heap_queue_size ()

Static Public Attributes
static bool	verbose = false
	flag controls the amount output to stderr by Profile methods
static bool	rotate_phase_enabled = true
	Rotation of pulse phase is enabled by default.
static Option< bool >	rotate_in_phase_domain
	When true, Profile::rotate shifts bins in the phase domain.
static Option< float >	transition_duty_cycle
	fractional phase window used to find rise and fall of running mean
static Option< float >	default_duty_cycle
	fractional phase window used in most functions
static Option< Edges >	peak_edges_strategy
	The default implementation of the edge detection algorithm.
Static Public Attributes inherited from Pulsar::ProfileAmps
static bool	no_amps = false
	When true, no memory is allocated for amps.

Friends
class	Integration
	The Integration class may call protected methods.

Extension Interface
Additional algorithms or information can be made available through use of Extension classes.
class	PolnProfile
	centre frequency of profile (in MHz)
class	StandardSNR
	centre frequency of profile (in MHz)
double	centrefreq
	centre frequency of profile (in MHz)
float	weight
	weight of profile
std::vector< Reference::To< Extension > >	extension
	The Extensions added to this Profile instance.
Reference::To< Strategies >	strategy
	The strategy manager.
virtual unsigned	get_nextension () const
	Return the number of extensions available.
virtual const Extension *	get_extension (unsigned iextension) const
	Return a pointer to the specified extension.
virtual Extension *	get_extension (unsigned iextension)
	Return a pointer to the specified extension.
template<class ExtensionType>
const ExtensionType *	get () const
	Template method searches for an Extension of the specified type.
template<class ExtensionType>
ExtensionType *	get ()
	Template method searches for an Extension of the specified type.
virtual void	add_extension (Extension *extension)
	Add an Extension to this instance.
void	convolve (const Profile *profile, int direction)
	does the work for convolve and correlate
void	init ()
	initializes all values to null

Additional Inherited Members
Protected Member Functions inherited from Reference::Able
Handle *	__reference (bool active) const
void	__dereference (bool auto_delete=true) const

Detailed Description

Any quantity recorded as a function of pulse phase.

The Pulsar::Profile class implements a useful, yet minimal, set of functionality required to store, manipulate, and analyse pulsar profiles. Note that:

All methods that change the size of a Profile are protected.
The Integration class is declared as a friend.

This arrangement protects the size of each Profile object from becoming unsynchronized with the Integration in which it is contained. The data in each Profile may still be manipulated through public methods.

Member Function Documentation

◆ add_extension()

void Pulsar::Profile::add_extension ( Extension * ext )

virtual

Add an Extension to this instance.

The derived class must ensure that only one instance of the Extension type is stored.

Derived classes need only define this method, as the non-const version implemented by the Profile base class simply calls this method.

References extension, and verbose.

Referenced by copy().

◆ average()

void Pulsar::Profile::average ( const Profile * profile )

set this to the weighted average of this and that

A series of additions using this operator preserves the relationship:

$\bar{x} = \sum_{i=1}^N W(x_i) x_i / W(\bar{x})$

where $ W(x_i) $ is the weight assigned to $ x_i $ and

$W(\bar{x}) = \sum_{i=1}^N W(x_i)$

References extension, Pulsar::Profile::Extension::integrate(), and Profile().

Referenced by Pulsar::Integration::combine(), Pulsar::FrequencyIntegrate::transform(), and Pulsar::TimeIntegrate::transform().

◆ baseline()

Pulsar::PhaseWeight * Pulsar::Profile::baseline ( ) const

Return a new PhaseWeight instance with the baseline phase bins masked.

Return a PhaseWeight mask with the baseline phase bins enabled.

References baseline(), Pulsar::Profile::Strategies::baseline(), get_strategy(), Pulsar::ProfileWeightFunction::operate(), and verbose.

Referenced by baseline(), Pulsar::FluxPlot::get_flux_error(), Pulsar::AdaptiveSNR::get_snr(), and Pulsar::FortranSNR::get_snr().

◆ dedisperse()

void Pulsar::Profile::dedisperse	(	double	dm,
		double	ref_freq,
		double	pfold )

Rotates the profile to remove dispersion delay.

A convenience interface to Profile::rotate_phase. Rotates the profile in order to remove the dispersion delay with respect to a reference frequency.

Parameters

dm	the dispersion measure (in ${\rm pc\, cm}^{-3}$ )
ref_freq	the reference frequency (in MHz)
pfold	the folding periond (in seconds)

References centrefreq, rotate_phase(), and verbose.

◆ find_max_phase()

float Pulsar::Profile::find_max_phase ( float duty_cycle = default_duty_cycle ) const

Returns the phase of the centre of the region with maximum mean.

Returns the centre phase of the region with maximum mean

Parameters

duty_cycle width of the region over which the mean is calculated

References Pulsar::ProfileAmps::get_amps(), Pulsar::ProfileAmps::get_nbin(), mean(), and verbose.

Referenced by Pulsar::Statistics::get_peak().

◆ find_min_phase()

float Pulsar::Profile::find_min_phase ( float duty_cycle = default_duty_cycle ) const

Returns the phase of the centre of the region with minimum mean.

Returns the centre phase of the region with minimum mean

Parameters

duty_cycle width of the region over which the mean is calculated

References Pulsar::ProfileAmps::get_amps(), Pulsar::ProfileAmps::get_nbin(), mean(), and verbose.

Referenced by Pulsar::find_spike_edges(), Pulsar::NoiseStatistics::get_nfnr(), Pulsar::PhaseSNR::get_snr(), and Pulsar::InfoLabel::plot().

◆ find_transitions()

void Pulsar::Profile::find_transitions	(	int &	hi2lo,
		int &	lo2hi,
		int &	width ) const

Find the bin numbers at which the mean power transits.

Finds the transitions at which the mean power of a sliding window drops below the mean power (high to low) and at which it jumps back above the mean power (low to high). The function is best-suited to detect the transitions of a pulsed calibrator profile, which is usually a square wave with 0.5 duty cycle. The width of the sliding window is given by Pulsar::Profile::transition_duty_cycle.

Return values

hi2lo	bin at which the mean power drops (from left to right)
lo2hi	bin at which the mean power jumps (from left to right)
width	number of bins in the sliding window used to find transitions

References Pulsar::ProfileAmps::get_amps(), Pulsar::ProfileAmps::get_nbin(), stats(), transition_duty_cycle, and verbose.

Referenced by Pulsar::ProfilePlot::draw_transitions(), and Pulsar::SquareWave::get_snr().

◆ get() [1/2]

template<class T>

T * Pulsar::Profile::get ( )

e.g. Profile* profile; MyExtension* ext = profile->get<MyExtension>();

References verbose.

◆ get() [2/2]

template<class T>

const T * Pulsar::Profile::get ( ) const

e.g. const Profile* profile; const MyExtension* ext = profile->get<MyExtension>();

References verbose.

◆ get_extension() [1/2]

Pulsar::Profile::Extension * Pulsar::Profile::get_extension ( unsigned iext )

virtual

Return a pointer to the specified extension.

Simply calls get_extension const

References extension.

◆ get_extension() [2/2]

const Pulsar::Profile::Extension * Pulsar::Profile::get_extension ( unsigned iext ) const

virtual

Return a pointer to the specified extension.

Derived classes need only define this method, as the non-const version implemented by the Profile base class simply calls this method.

References extension.

Referenced by copy().

◆ get_weighted_amps()

vector< float > Pulsar::Profile::get_weighted_amps ( ) const

returns a vector representation of the array of amplitudes, with all zero-weighted points cleaned out

References Pulsar::ProfileAmps::get_amps(), Pulsar::ProfileAmps::get_nbin(), and weight.

Referenced by Pulsar::LinePhasePlot::draw().

◆ mean()

double Pulsar::Profile::mean	(	float	phase,
		float	duty_cycle = default_duty_cycle ) const

Convenience interface to stats, returns only the mean.

Parameters

phase	centre of region
duty_cycle	width of region

Returns: mean of region

References Pulsar::phase(), and stats().

Referenced by correlate_normalized(), find_max_phase(), find_min_phase(), Pulsar::find_spike_edges(), Pulsar::InfoLabel::plot(), stats(), and stats().

◆ operator=()

const Pulsar::Profile & Pulsar::Profile::operator= ( const Profile & input )

assignment operator

Sets all attributes of this Profile equal to that of the input Profile, resizes and copies the amps array.

References copy(), and Profile().

◆ resize()

void Pulsar::Profile::resize ( unsigned nbin )

virtual

resize the data area

Reimplemented from Pulsar::ProfileAmps.

References Pulsar::DataExtension::resize(), and Pulsar::ProfileAmps::resize().

Referenced by bscrunch(), copy(), Pulsar::detect(), fold(), Pulsar::fourier_to_re_im(), Pulsar::StokesFluctPlot::get_profiles(), Pulsar::phase(), and Pulsar::MoreProfiles::resize().

◆ snr()

float Pulsar::Profile::snr ( ) const

Returns the signal to noise ratio of the profile.

This method calls Profile::snr_strategy

References Pulsar::SNRatioEstimator::get_snr(), get_strategy(), Pulsar::Profile::Strategies::snratio(), and verbose.

Referenced by Pulsar::SNRWeight::get_weight().

◆ stats() [1/2]

void Pulsar::Profile::stats	(	double *	mean,
		double *	variance = 0,
		double *	varmean = 0,
		int	istart = 0,
		int	iend = 0 ) const

Calculates the mean, variance, and variance of the mean.

Returns the mean, variance, and variance of the mean over the specified interval.

Return values

mean	the mean of the interval
variance	the variance of the interval
varmean	the variance of the mean of the interval

Parameters

istart	the first bin of the interval
iend	one greater than the last bin of the interval

References Pulsar::ProfileAmps::get_amps(), Pulsar::ProfileAmps::get_nbin(), mean(), and verbose.

Referenced by correlate_normalized(), Pulsar::ProfilePlot::draw_transitions(), find_transitions(), Pulsar::NoiseStatistics::get_nfnr(), Pulsar::PhaseSNR::get_snr(), Pulsar::SquareWave::get_snr(), mean(), Pulsar::InfoLabel::plot(), Pulsar::Archive::rms_baseline(), and stats().

◆ stats() [2/2]

void Pulsar::Profile::stats	(	float	phase,
		double *	mean,
		double *	variance = 0,
		double *	varmean = 0,
		float	duty_cycle = default_duty_cycle ) const

Convenience interface to stats (start_bin, end_bin)

Parameters

phase centre of region

Return values

mean	the mean of the interval
variance	the variance of the interval
varmean	the variance of the mean of the interval

Parameters

phase	centre of region over which statistics will be calculated
duty_cycle	width of region

References Pulsar::ProfileAmps::get_nbin(), mean(), Pulsar::phase(), stats(), and verbose.

Member Data Documentation

◆ default_duty_cycle

Pulsar::Option< float > Pulsar::Profile::default_duty_cycle

static

fractional phase window used in most functions

Default fractional pulse phase window used to calculate statistics related to the baseline.

Referenced by Pulsar::LawnMower::LawnMower(), Pulsar::NoiseStatistics::NoiseStatistics(), and Pulsar::Smooth::Smooth().

◆ peak_edges_strategy

Pulsar::Option< Pulsar::Profile::Edges > Pulsar::Profile::peak_edges_strategy

static

The default implementation of the edge detection algorithm.

The PeakEdgesInterpreter class sets the peak_edges_strategy attribute according to commands specified either in the configuration file or via the psrsh interpreter. It enables convenient experimentation with the peak edges estimation algorithm.

Referenced by find_peak_edges().

◆ rotate_phase_enabled

bool Pulsar::Profile::rotate_phase_enabled = true

static

Rotation of pulse phase is enabled by default.

Rotate the profile by the specified phase. The profile will be rotated such that the power at phase will be found at phase zero. ie.

$t^\prime=t+\phi P$

where $t^\prime$ is the new start time (rising edge of bin 0), $t$ is the original start time, $\phi$ is equal to phase, and $P$ is the period at the time of folding.