Namespaces
	DP3MS

	test

Classes
class	BaselineSelection
	Class containing a few static functions to parse a baseline selection string. More...

class	BdaBuffer

class	ComponentInfo
	Class for visitors that visit model component to extract information. More...

class	const_cursor

class	cursor
	Multi-dimensional iterators. More...

struct	Direction
	A direction on the celestial sphere. More...

class	DPBuffer
	Buffer holding the data of a timeslot/band. More...

class	DPInfo
	General info about DP3 data processing attributes like averaging. More...

class	FlagCounter
	Class to keep counts of nr of flagged points. More...

class	GainCalAlgorithm
	DPPP step class to apply a calibration correction to the data. More...

class	GaussianSource
	Gaussian source model component. More...

class	LogAntennaParseErrors
	RAII object for temporarily overriding MSAntennaParse::thisMSAErrorHandler. More...

class	ModelComponent
	Base class for model components. More...

class	ModelComponentVisitor
	Base class for visitors that visit model component hierarchies. More...

class	ParsetATerms
	Parses the parameter settings (parset) related to the aterm settings in an EveryBeam-acceptable format. More...

class	PointSource
	Point source model component with optional spectral index and rotation measure. More...

class	PredictBuffer

class	PredictModel

class	ProgressMeter
	Visual indication of a tasks progress. More...

class	RcuMode

struct	StManParsetKeys

class	Stokes
	Complex Stokes vector. More...

class	SubtableWriter

class	UVWCalculator
	Class to calculate UVW coordinates. More...

Typedefs
typedef std::pair< size_t, size_t >	Baseline


typedef std::complex< double >	dcomplex

Enumerations
enum class	CalType { kScalar , kScalarAmplitude , kScalarPhase , kDiagonal , kDiagonalAmplitude , kDiagonalPhase , kFullJones , kTec , kTecAndDelay , kTecAndPhase , kTecPhaseAndDelay , kTecScreen , kRotationAndDiagonal , kRotation , kFaradayRotation , kLeakage , kLeakageAmplitude }

enum class	SiscoMode { Full , Diagonal , StokesI }

Functions
template<typename T >
const_cursor< T >	casa_const_cursor (const casacore::Array< T > &array)

template<typename T >
cursor< T >	casa_cursor (casacore::Array< T > &array)

bool	estimate (size_t nDirection, size_t nStation, size_t nBaseline, size_t nChannel, const_cursor< Baseline > baselines, std::vector< const_cursor< std::complex< float >>> data, std::vector< const_cursor< std::complex< double >>> model, const_cursor< bool > flag, const_cursor< float > weight, const_cursor< std::complex< double >> mix, double *unknowns, size_t maxiter=50)

void	Execute (const std::string &parsetName, const std::vector< std::string > &arguments={})

void	ExecuteFromCommandLine (const std::vector< std::string > &arguments)
	Command-line interface. More...

void	ExecuteFromCommandLine (int argc, char *argv[])
	Command-line interface. More...

std::vector< size_t >	GetBaselineSelection (size_t n_antennas, const std::vector< size_t > &bl_idx_sorted, const std::vector< int > &antennas1, const std::vector< int > &antennas2)

std::vector< size_t >	GetBaselinesSortedByLength (const std::vector< int > &antennas1, const std::vector< int > &antennas2, const std::vector< std::array< double, 3 >> &antenna_positions)

dp3::common::Fields	GetChainRequiredFields (std::shared_ptr< steps::Step > first_step)

std::string	GetCompressionString (const StManParsetKeys &st_man_keys)

constexpr size_t	GetNPolarizations (CalType cal_type)

size_t	GetNThreads ()

SiscoMode	GetSiscoMode (const std::string &mode_str)

std::unique_ptr< everybeam::telescope::Telescope >	GetTelescope (const std::string &ms_name, const everybeam::ElementResponseModel element_response_model, bool use_channel_frequency, const std::string &coefficients_file)

bool	IsHomogeneous (const everybeam::telescope::Telescope &telescope)

void	makeIndex (std::size_t n_direction, std::size_t n_station, const Baseline &baseline, unsigned int *index)

std::shared_ptr< steps::InputStep >	MakeMainSteps (const common::ParameterSet &parset)

std::shared_ptr< steps::Step >	MakeSingleStep (const std::string &type, const common::ParameterSet &parset, const std::string &prefix, steps::Step::MsType input_type)

std::shared_ptr< steps::Step >	MakeStepsFromParset (const common::ParameterSet &parset, const std::string &prefix, const std::string &step_names_key, const std::string &input_ms_name, bool terminateChain, steps::Step::MsType initial_step_output)

void	radec2lmn (const Direction &reference, const Direction &direction, double *lmn)

std::string	ReadAntennaSet (const casacore::MeasurementSet &ms)

void	rotateUVW (const Direction &from, const Direction &to, size_t nUVW, double *uvw)

std::vector< size_t >	SelectStationIndices (const everybeam::telescope::Telescope &telescope, const std::vector< std::string > &station_names)

dp3::common::Fields	SetChainProvidedFields (std::shared_ptr< steps::Step > first_step, dp3::common::Fields provided_fields=dp3::common::Fields())

void	SetNThreads (size_t n_threads)

std::vector< int >	SetupUvwSplitting (unsigned int nant, const std::vector< int > &ant1, const std::vector< int > &ant2)

std::vector< int >	SetupUvwSplitting (unsigned int nant, const std::vector< int > &ant1, const std::vector< int > &ant2, const std::vector< std::array< double, 3 >> &antenna_positions)

void	ShowUsage ()

void	simulate (const Direction &reference, const std::shared_ptr< const sky_model::Patch > &patch, size_t nStation, size_t nBaseline, size_t nChannel, const_cursor< Baseline > baselines, const_cursor< double > freq, const_cursor< double > uvw, cursor< std::complex< double >> buffer)

void	SplitUvw (const std::vector< int > &baseline_indices, const std::vector< Baseline > &baselines, const DPBuffer::UvwType &uvw_bl, xt::xtensor< double, 2 > &uvw_ant)

CalType	StringToCalType (const std::string &mode)
	Convert string to a CalType. More...

void	subtract (size_t nBaseline, size_t nChannel, const_cursor< Baseline > baselines, cursor< std::complex< float >> data, const_cursor< std::complex< double >> model, const_cursor< std::complex< double >> weight, float &var_before, float &var_after)

std::string	ToString (CalType caltype)
	Convert CalType to a string. More...

std::string	ToString (SiscoMode mode)


void	apply (size_t nBaseline, size_t nChannel, const_cursor< Baseline > baselines, const_cursor< double > coeff, cursor< std::complex< double >> data)
	Apply station Jones matrices to a set of visibilities. More...

Detailed Description

This code was taken from https://git.astron.nl/RD/aartfaac-tools/-/raw/master/common/aartfaac/aartfaacmode.h?ref_type=heads and adapted to fit into DP3 codebase.

The Receiver Unit Mode, hereafter RCU mode, is the mode in which the receiver units are set in a LOFAR station. The mode determines the amount of frequency ranges the RCU is sensitive towards. The RcuMode class provides the the frequency, bandwidth, antenna type, and a descriptive string of the RCU mode given a mode code. A reference for this modes can be found in https://science.astron.nl/telescopes/lofar/lofar-system-overview/technical-specification/frequency-subband-selection-and-rfi/.

This class is responsible to create ancillary tables such as ANTENNA or SPECTRAL_WINDOW In the future this could be part of the DP3 writer step it was a choice to keep it separate to avoid changing core DP3 functionalities Most of this code was taken from https://git.astron.nl/RD/aartfaac-tools.git and adapted to fit into the DP3 codebase.

Typedef Documentation

◆ Baseline

typedef std::pair<size_t, size_t> dp3::base::Baseline

◆ dcomplex

typedef std::complex<double> dp3::base::dcomplex

Enumeration Type Documentation

◆ CalType

enum dp3::base::CalType

strong

Enumerator
kScalar
kScalarAmplitude
kScalarPhase
kDiagonal
kDiagonalAmplitude
kDiagonalPhase
kFullJones
kTec
kTecAndDelay
kTecAndPhase
kTecPhaseAndDelay
kTecScreen
kRotationAndDiagonal
kRotation
kFaradayRotation
kLeakage
kLeakageAmplitude

◆ SiscoMode

enum dp3::base::SiscoMode

strong

Enumerator
Full
Diagonal
StokesI

Function Documentation

◆ apply()

void dp3::base::apply	(	size_t	nBaseline,
		size_t	nChannel,
		const_cursor< Baseline >	baselines,
		const_cursor< double >	coeff,
		cursor< std::complex< double >>	data
	)

Apply station Jones matrices to a set of visibilities.

Parameters

[in]	nBaseline	Number of baselines.
[in]	nChannel	Number of frequency channels.
[in]	baselines	A cursor for a 1-D buffer of baselines of shape (`nBaseline`).
[in]	coeff	A cursor for a 2-D buffer of Jones matrix coefficients of shape (No. of stations, 8). Each station index contained in `baselines` should be a valid index for the first axis of `coeff`.
[in]	data	A cursor for a 3-D buffer of visibilities of shape (`nBaseline`, `nChannel`, 4).

◆ casa_const_cursor()

template<typename T >

const_cursor<T> dp3::base::casa_const_cursor ( const casacore::Array< T > & array )

◆ casa_cursor()

template<typename T >

cursor<T> dp3::base::casa_cursor ( casacore::Array< T > & array )

◆ estimate()

bool dp3::base::estimate	(	size_t	nDirection,
		size_t	nStation,
		size_t	nBaseline,
		size_t	nChannel,
		const_cursor< Baseline >	baselines,
		std::vector< const_cursor< std::complex< float >>>	data,
		std::vector< const_cursor< std::complex< double >>>	model,
		const_cursor< bool >	flag,
		const_cursor< float >	weight,
		const_cursor< std::complex< double >>	mix,
		double *	unknowns,
		size_t	maxiter = `50`
	)

Estimate Jones matrices for several directions simultaneously. A separate data stream is used for each direction. The mixing coefficients quantify the influence of each direction on each of the other directions (including time and frequency smearing).

Parameters

[in]	nDirection	Number of directions to estimate Jones matrices for.
[in]	nStation	Number of stations.
[in]	nBaseline	Number of baselines.
[in]	nChannel	Number of frequency channels.
[in]	data	Vector of length `nDirection` of cursors for 3-D buffers of observed visiblity data of shape (`nBaseline`, `nChannel`, 4).
[in]	model	Vector of length `nDirection` of cursors for 3-D buffers of simulated visiblity data of shape (`nBaseline`, `nChannel`, 4).
[in]	baselines	A cursor for a 1-D buffer of baselines of shape (`nBaseline`).
[in]	flag	A cursor for a 3-D buffer of observed visibility flags of shape (`nBaseline`, `nChannel`, 4).
[in]	weight	A cursor for a 3-D buffer of observed visibility weights of shape (`nBaseline`, `nChannel`, 4).
[in]	mix	A cursor for a 5-D buffer of mixing weights of shape (`nBaseline`, `nChannel`, 4, `nDirection`, `nDirection`).
[in]	unknowns	A pointer to a buffer of unknowns of size nDirection * nStation * 8.

◆ Execute()

void dp3::base::Execute	(	const std::string &	parsetName,
		const std::vector< std::string > &	arguments = `{}`
	)

Execute the steps defined in the parset file. Possible parameters given at the command line are taken into account.

◆ ExecuteFromCommandLine() [1/2]

void dp3::base::ExecuteFromCommandLine ( const std::vector< std::string > & arguments )

Command-line interface.

◆ ExecuteFromCommandLine() [2/2]

void dp3::base::ExecuteFromCommandLine	(	int	argc,
		char *	argv[]
	)

Command-line interface.

◆ GetBaselineSelection()

std::vector<size_t> dp3::base::GetBaselineSelection	(	size_t	n_antennas,
		const std::vector< size_t > &	bl_idx_sorted,
		const std::vector< int > &	antennas1,
		const std::vector< int > &	antennas2
	)

Helper function for SetupUvwSplitting(). Was put in header so it can be tested.

◆ GetBaselinesSortedByLength()

std::vector<size_t> dp3::base::GetBaselinesSortedByLength	(	const std::vector< int > &	antennas1,
		const std::vector< int > &	antennas2,
		const std::vector< std::array< double, 3 >> &	antenna_positions
	)

Helper function for SetupUvwSplitting(). Was put in header so it can be tested.

◆ GetChainRequiredFields()

dp3::common::Fields dp3::base::GetChainRequiredFields ( std::shared_ptr< steps::Step > first_step )

Go through the steps to define which fields of the measurement set should be read by the input step.

Parameters

first_step The first step of a chain of steps.

Returns: The combined required fields of the step chain.

◆ GetCompressionString()

std::string dp3::base::GetCompressionString ( const StManParsetKeys & st_man_keys )

inline

◆ GetNPolarizations()

constexpr size_t dp3::base::GetNPolarizations ( CalType cal_type )

constexpr

◆ GetNThreads()

size_t dp3::base::GetNThreads ( )

Get the number of threads used in DP3. This function is needed since each library / application has its own aocommon Threadpool object.

◆ GetSiscoMode()

SiscoMode dp3::base::GetSiscoMode ( const std::string & mode_str )

inline

◆ GetTelescope()

std::unique_ptr<everybeam::telescope::Telescope> dp3::base::GetTelescope	(	const std::string &	ms_name,
		const everybeam::ElementResponseModel	element_response_model,
		bool	use_channel_frequency,
		const std::string &	coefficients_file
	)

inline

Retrieve the everybeam telescope from a Measurement Set.

◆ IsHomogeneous()

bool dp3::base::IsHomogeneous ( const everybeam::telescope::Telescope & telescope )

◆ makeIndex()

void dp3::base::makeIndex	(	std::size_t	n_direction,
		std::size_t	n_station,
		const Baseline &	baseline,
		unsigned int *	index
	)

Compute a map that contains the index of the unknowns related to the specified baseline in the list of all unknowns.

Parameters

[in]	n_direction
[in]	n_station
[in]	baseline	A tuple of baseline station ids
[out]	index	A vector of size 48n_direction to store the indices

◆ MakeMainSteps()

std::shared_ptr<steps::InputStep> dp3::base::MakeMainSteps ( const common::ParameterSet & parset )

Create a chain of step objects that are connected together. A writer will be added to the steps if it is not defined, and a terminating NullStep is added.

◆ MakeSingleStep()

std::shared_ptr<steps::Step> dp3::base::MakeSingleStep	(	const std::string &	type,
		const common::ParameterSet &	parset,
		const std::string &	prefix,
		steps::Step::MsType	input_type
	)

Create a step

Parameters

type	Type of the step.
parset	ParameterSet containing the configuration for the step.
prefix	Prefix, including trailing dot ("."), to use for looking up parameters in the ParameterSet.
input_type	Type of input data, BDA or regular.

Returns: Pointer to the newly created step, or a null pointer if the type not recognized.

◆ MakeStepsFromParset()

std::shared_ptr<steps::Step> dp3::base::MakeStepsFromParset	(	const common::ParameterSet &	parset,
		const std::string &	prefix,
		const std::string &	step_names_key,
		const std::string &	input_ms_name,
		bool	terminateChain,
		steps::Step::MsType	initial_step_output
	)

Create a chain of step objects that are connected together. Unlike MakeMainSteps(), this does neither add a writer nor terminate the chain with a NullStep.

Parameters

step_names_key Parset key for getting the step names.

Returns: The first step of the step chain or a null pointer if the chain is empty.

◆ radec2lmn()

void dp3::base::radec2lmn	(	const Direction &	reference,
		const Direction &	direction,
		double *	lmn
	)

inline

Compute LMN coordinates of direction relative to reference.

Parameters

[in]	reference	Reference direction on the celestial sphere.
[in]	direction	Direction of interest on the celestial sphere.
[out]	lmn	Pointer to a buffer of (at least) length three into which the computed LMN coordinates will be written.

\begin{eqnarray*} \ell &= \cos(\delta) \sin(\alpha - \alpha_0) \\ m &= \sin(\delta) \cos(\delta_0) - \cos(\delta) \sin(\delta_0) \cos(\alpha - \alpha_0) \end{eqnarray*}

◆ ReadAntennaSet()

std::string dp3::base::ReadAntennaSet ( const casacore::MeasurementSet & ms )

Read the antenna set (e.g. LBA_OUTER, HBA_DUAL_INNER) from the OBSERVATION table in the MS. This is a LOFAR-specific extension.

Parameters

ms	A measurement set, which may contain the antenna set field.

Returns: The antenna set of the MS, or an empty string if not found.

◆ rotateUVW()

void dp3::base::rotateUVW	(	const Direction &	from,
		const Direction &	to,
		size_t	nUVW,
		double *	uvw
	)

Transform UVW coordinates from phase reference position from to phase reference position to. The transformation is performed in place.

Parameters

[in]	from	Current phase reference position for the UVW coordinates.
[in]	to	New phase reference position for the UVW coordinates.
[in]	nUVW	The number of UVW coordinates to transform.
[in]	uvw	A 2-D buffer of UVW coordinates of shape (`UVW`, 3).

◆ SelectStationIndices()

std::vector<size_t> dp3::base::SelectStationIndices	(	const everybeam::telescope::Telescope &	telescope,
		const std::vector< std::string > &	station_names
	)

Find stations in a telescope by name and return their indices.

Parameters

telescope	The telescope, which contains antennae / stations.
station_names	A list of station names. The order of the names in this list should match the order in which they occur in the telescope.

Returns: The indices corresponding to the station names. Because of the ordering restriction, the list always has increasing indices only.

◆ SetChainProvidedFields()

dp3::common::Fields dp3::base::SetChainProvidedFields	(	std::shared_ptr< steps::Step >	first_step,
		dp3::common::Fields	provided_fields = `dp3::common::Fields()`
	)

Go through a step chain, combine provided fields of non-output steps and call SetFieldsToWrite for all output steps.

Parameters

first_step	The first step of a chain of steps.
provided_fields	The provided fields before the step chain. Steps that have sub-steps should use this argument.

Returns: The remaining provided fields after the last step in the chain.

◆ SetNThreads()

void dp3::base::SetNThreads ( size_t n_threads )

Set the number of threads used in DP3. This function is needed since each library / application has its own aocommon Threadpool object.

◆ SetupUvwSplitting() [1/2]

std::vector<int> dp3::base::SetupUvwSplitting	(	unsigned int	nant,
		const std::vector< int > &	ant1,
		const std::vector< int > &	ant2
	)

Setup the splitting of the baseline UVWs into station UVWs. It returns the indices of the baselines needed to split the baseline UVWs into station UVWs. They are in such an order that the UVW of a station is known before used in another baseline to derive the UVW of the other station. It can handle cases where baselines occur in disjoint station groups like 0-1, 0-2, 1-2 and 3-4, 4-5, 5-6. Note that the first station of a group gets UVW=0. All other station UVWs are relative to it using the baseline UVWs. Also note that nr of groups can be derived from the size of the returned vector (because it contains no entry for the first antenna in a group).

◆ SetupUvwSplitting() [2/2]

std::vector<int> dp3::base::SetupUvwSplitting	(	unsigned int	nant,
		const std::vector< int > &	ant1,
		const std::vector< int > &	ant2,
		const std::vector< std::array< double, 3 >> &	antenna_positions
	)

Same as the other SetupUvwSplitting() overload, except that this version accepts antenna_positions as extra argument. It uses the antenna positions to select the long baselines. This is needed in case of BDA data to prevent loss of information. See UVW splitting of BDA expanded data for details.

◆ ShowUsage()

void dp3::base::ShowUsage ( )

◆ simulate()

void dp3::base::simulate	(	const Direction &	reference,
		const std::shared_ptr< const sky_model::Patch > &	patch,
		size_t	nStation,
		size_t	nBaseline,
		size_t	nChannel,
		const_cursor< Baseline >	baselines,
		const_cursor< double >	freq,
		const_cursor< double >	uvw,
		cursor< std::complex< double >>	buffer
	)

Simulate visibilities for a patch of sources. The computed visibilities are added to vis.

Parameters

[in]	reference	Phase reference position.
[in]	patch	Patch of sources to simulate visibilities for.
[in]	nStation	The number of stations.
[in]	nBaseline	The number of baselines.
[in]	nChannel	The number of frequency channels.
[in]	baselines	A cursor for a 1-D buffer of baselines of shape (`nBaseline`).
[in]	freq	A cursor for a 1-D buffer of channel frequencies of shape (`nChannel`).
[in]	uvw	A cursor for a 2-D buffer of station UVW coordinates of shape (`nStation`, 3).
[in]	buffer	A cursor for a 3-D buffer of shape (`nBaseline`, `nChannel`, 4) into which the simulated visibilities will be written.

◆ SplitUvw()

void dp3::base::SplitUvw	(	const std::vector< int > &	baseline_indices,
		const std::vector< Baseline > &	baselines,
		const DPBuffer::UvwType &	uvw_bl,
		xt::xtensor< double, 2 > &	uvw_ant
	)

Do the actual splitting of baseline UVWs into station UVWs using the index vector generated by SetupUvwSplitting.

◆ StringToCalType()

CalType dp3::base::StringToCalType ( const std::string & mode )

Convert string to a CalType.

◆ subtract()

void dp3::base::subtract	(	size_t	nBaseline,
		size_t	nChannel,
		const_cursor< Baseline >	baselines,
		cursor< std::complex< float >>	data,
		const_cursor< std::complex< double >>	model,
		const_cursor< std::complex< double >>	weight,
		float &	var_before,
		float &	var_after
	)

Subtract visibilities from a buffer after weighting by mixing coefficients.

Parameters

[in]	nBaseline	Number of baselines.
[in]	nChannel	Number of frequency channels.
[in]	baselines	A cursor for a 1-D buffer of baselines of shape (`nBaseline`).
[in]	data	A cursor for a 3-D buffer of observed visibilities of shape (`nBaseline`, `nChannel`, 4).
[in]	model	A cursor for a 3-D buffer of simulated visibilities of shape (`nBaseline`, `nChannel`, 4).
[in]	weight	A cursor for a 3-D buffer of mixing weight of shape (`nBaseline`, `nChannel`, 4).
[out]	var_before	variance before subtraction
[out]	var_after	variance after subtraction

◆ ToString() [1/2]

std::string dp3::base::ToString ( CalType caltype )

Convert CalType to a string.

◆ ToString() [2/2]

std::string dp3::base::ToString ( SiscoMode mode )

inline

Namespaces

Classes

Typedefs

Enumerations

Functions

Detailed Description

Typedef Documentation

◆ Baseline

◆ dcomplex

Enumeration Type Documentation

◆ CalType

◆ SiscoMode

Function Documentation

◆ apply()

◆ casa_const_cursor()

◆ casa_cursor()

◆ estimate()

◆ Execute()

◆ ExecuteFromCommandLine() [1/2]

◆ ExecuteFromCommandLine() [2/2]

◆ GetBaselineSelection()

◆ GetBaselinesSortedByLength()

◆ GetChainRequiredFields()

◆ GetCompressionString()

◆ GetNPolarizations()

◆ GetNThreads()

◆ GetSiscoMode()

◆ GetTelescope()

◆ IsHomogeneous()

◆ makeIndex()

◆ MakeMainSteps()

◆ MakeSingleStep()

◆ MakeStepsFromParset()

◆ radec2lmn()

◆ ReadAntennaSet()

◆ rotateUVW()

◆ SelectStationIndices()

◆ SetChainProvidedFields()

◆ SetNThreads()

◆ SetupUvwSplitting() [1/2]

◆ SetupUvwSplitting() [2/2]

◆ ShowUsage()

◆ simulate()

◆ SplitUvw()

◆ StringToCalType()

◆ subtract()

◆ ToString() [1/2]

◆ ToString() [2/2]