Computes simple clipped, and masked moments. More...

#include <MomentClip.h>

Inheritance diagram for casa::MomentClip< T >:

Public Member Functions
	MomentClip (shared_ptr< casacore::Lattice< T >> pAncilliaryLattice, MomentsBase< T > &iMom, casacore::LogIO &os, const casacore::uInt nLatticeOut)
	Constructor. More...

virtual	~MomentClip ()
	Destructor (does nothing). More...

virtual void	process (T &out, casacore::Bool &outMask, const casacore::Vector< T > &in, const casacore::Vector< casacore::Bool > &inMask, const casacore::IPosition &pos)
	This function is not implemented and throws an exception. More...

virtual void	multiProcess (casacore::Vector< T > &out, casacore::Vector< casacore::Bool > &outMask, const casacore::Vector< T > &in, const casacore::Vector< casacore::Bool > &inMask, const casacore::IPosition &pos)
	This function returns a vector of numbers from each input vector. More...

virtual casacore::Bool	canHandleNullMask () const
	Can handle null mask. More...

Public Member Functions inherited from casa::MomentCalcBase< T >
virtual	~MomentCalcBase ()

virtual casacore::uInt	nFailedFits () const
	Returns the number of failed fits if doing fitting. More...

Public Member Functions inherited from casacore::LineCollapser< T, T >
virtual	~LineCollapser ()
	Destructor. More...

Private Attributes
shared_ptr< casacore::Lattice < T > >	_ancilliaryLattice

MomentsBase< T > &	iMom_p

casacore::LogIO	os_p

const casacore::Vector< T > *	pProfileSelect_p

casacore::Vector< T >	ancilliarySliceRef_p

casacore::Vector< T >	selectedData_p

casacore::Vector< casacore::Int >	selectedDataIndex_p

casacore::Bool	doInclude_p

casacore::Bool	doExclude_p

casacore::Vector< T >	range_p

casacore::IPosition	sliceShape_p

Additional Inherited Members
Public Types inherited from casa::MomentCalcBase< T >
using	AccumType = typename casacore::NumericTraits< T >::PrecisionType

using	DataIterator = typename casacore::Vector< T >::const_iterator

using	MaskIterator = casacore::Vector< casacore::Bool >::const_iterator

Protected Member Functions inherited from casa::MomentCalcBase< T >
void	accumSums (typename casacore::NumericTraits< T >::PrecisionType &s0, typename casacore::NumericTraits< T >::PrecisionType &s0Sq, typename casacore::NumericTraits< T >::PrecisionType &s1, typename casacore::NumericTraits< T >::PrecisionType &s2, casacore::Int &iMin, casacore::Int &iMax, T &dMin, T &dMax, casacore::Int i, T datum, casacore::Double coord) const
	Accumulate statistical sums from a vector. More...

casacore::uInt	allNoise (T &dMean, const casacore::Vector< T > &data, const casacore::Vector< casacore::Bool > &mask, T peakSNR, T stdDeviation) const
	Determine if the spectrum is pure noise. More...

void	constructorCheck (casacore::Vector< T > &calcMoments, casacore::Vector< casacore::Bool > &calcMomentsMask, const casacore::Vector< casacore::Int > &selectMoments, casacore::uInt nLatticeOut) const
	Check validity of constructor inputs. More...

void	costlyMoments (MomentsBase< T > &iMom, casacore::Bool &doMedianI, casacore::Bool &doMedianV, casacore::Bool &doAbsDev) const
	Find out from the selectMoments array whether we want to compute the more expensive moments. More...

void	doCoordCalc (casacore::Bool &doCoordProfile, casacore::Bool &doCoordRandom, const MomentsBase< T > &iMom) const
	Return the casacore::Bool saying whether we need to compute coordinates or not for the requested moments. More...

casacore::Bool	doFit (const MomentsBase< T > &iMom) const
	Return the casacore::Bool from the ImageMoments or MSMoments object saying whether we are going to fit Gaussians to the profiles or not. More...

casacore::Bool	findNextDatum (casacore::uInt &iFound, const casacore::uInt &n, const casacore::Vector< casacore::Bool > &mask, const casacore::uInt &iStart, const casacore::Bool &findGood) const
	Find the next masked or unmasked point in a vector. More...

casacore::Bool	fitGaussian (casacore::uInt &nFailed, T &peak, T &pos, T &width, T &level, const casacore::Vector< T > &x, const casacore::Vector< T > &y, const casacore::Vector< casacore::Bool > &mask, T peakGuess, T posGuess, T widthGuess, T levelGuess) const
	Fit a Gaussian to x and y arrays given guesses for the gaussian parameters. More...

casacore::Bool	getAutoGaussianFit (casacore::uInt &nFailed, casacore::Vector< T > &gaussPars, const casacore::Vector< T > &x, const casacore::Vector< T > &y, const casacore::Vector< casacore::Bool > &mask, T peakSNR, T stdDeviation) const
	Automatically fit a Gaussian to a spectrum, including finding the starting guesses. More...

casacore::Bool	getAutoGaussianGuess (T &peakGuess, T &posGuess, T &widthGuess, T &levelGuess, const casacore::Vector< T > &x, const casacore::Vector< T > &y, const casacore::Vector< casacore::Bool > &mask) const
	Automatically work out a guess for the Gaussian parameters Returns false if all pixels masked. More...

casacore::Double	getMomentCoord (const MomentsBase< T > &iMom, casacore::Vector< casacore::Double > &pixelIn, casacore::Vector< casacore::Double > &worldOut, casacore::Double momentPixel, casacore::Bool asVelocity=false) const
	Compute the world coordinate for the given moment axis pixel. More...

void	lineSegments (casacore::uInt &nSeg, casacore::Vector< casacore::uInt > &start, casacore::Vector< casacore::uInt > &nPts, const casacore::Vector< casacore::Bool > &mask) const
	Examine a mask and determine how many segments of unmasked points it consists of. More...

casacore::Int &	momentAxis (MomentsBase< T > &iMom) const
	Return the moment axis from the ImageMoments object. More...

casacore::String	momentAxisName (const casacore::CoordinateSystem &, const MomentsBase< T > &iMom) const
	Return the name of the moment/profile axis. More...

T &	peakSNR (MomentsBase< T > &iMom) const
	Return the peak SNR for determination of all noise spectra from the ImageMoments or MSMoments object. More...

void	selectRange (casacore::Vector< T > &pixelRange, casacore::Bool &doInclude, casacore::Bool &doExlude, MomentsBase< T > &iMom) const
	Return the selected pixel intensity range from the ImageMoments or MSMoments object and the Bools describing whether it is inclusion or exclusion. More...

casacore::Vector< casacore::Int >	selectMoments (MomentsBase< T > &iMom) const
	The MomentCalculators compute a vector of all possible moments. More...

void	setCalcMoments (const MomentsBase< T > &iMom, casacore::Vector< T > &calcMoments, casacore::Vector< casacore::Bool > &calcMomentsMask, casacore::Vector< casacore::Double > &pixelIn, casacore::Vector< casacore::Double > &worldOut, casacore::Bool doCoord, casacore::Double integratedScaleFactor, T dMedian, T vMedian, casacore::Int nPts, typename casacore::NumericTraits< T >::PrecisionType s0, typename casacore::NumericTraits< T >::PrecisionType s1, typename casacore::NumericTraits< T >::PrecisionType s2, typename casacore::NumericTraits< T >::PrecisionType s0Sq, typename casacore::NumericTraits< T >::PrecisionType sumAbsDev, T dMin, T dMax, casacore::Int iMin, casacore::Int iMax) const
	Fill the ouput moments array. More...

void	setPosLabel (casacore::String &title, const casacore::IPosition &pos) const
	Fill a string with the position of the cursor. More...

void	setCoordinateSystem (casacore::CoordinateSystem &cSys, MomentsBase< T > &iMom)
	Install casacore::CoordinateSystem and SpectralCoordinate in protected data members. More...

void	setUpCoords (const MomentsBase< T > &iMom, casacore::Vector< casacore::Double > &pixelIn, casacore::Vector< casacore::Double > &worldOut, casacore::Vector< casacore::Double > &sepWorldCoord, casacore::LogIO &os, casacore::Double &integratedScaleFactor, const casacore::CoordinateSystem &cSys, casacore::Bool doCoordProfile, casacore::Bool doCoordRandom) const
	Set up separable moment axis coordinate vector and conversion vectors if not separable. More...

T &	stdDeviation (MomentsBase< T > &iMom) const
	Return standard deviation of image from ImageMoments or MSMoments object. More...

virtual void	init (casacore::uInt nOutPixelsPerCollapse)
	Check if #pixels is indeed 1. More...

Protected Attributes inherited from casa::MomentCalcBase< T >
casacore::CoordinateSystem	cSys_p
	A number of private data members are kept here in the base class as they are common to the derived classes. More...

casacore::Vector< T >	calcMoments_p
	This vector is a container for all the possible moments that can be calculated. More...

casacore::Vector< casacore::Bool >	calcMomentsMask_p

casacore::Vector< casacore::Int >	selectMoments_p
	This vector tells us which elements of the calcMoments_p vector we wish to select. More...

casacore::Bool	doMedianI_p
	Although the general philosophy of these classes is to compute all the posisble moments and then select the ones we want, some of them are too expensive to calculate unless they are really wanted. More...

casacore::Bool	doMedianV_p

casacore::Bool	doAbsDev_p

casacore::Vector < casacore::Double >	pixelIn_p
	These vectors are used to transform coordinates between pixel and world. More...

casacore::Vector < casacore::Double >	worldOut_p

casacore::Bool	doCoordProfile_p
	All computations involving casacore::Coordinate conversions are relatively expensive These Bools signifies whether we need coordinate calculations or not for the full profile, and for some occaisional calculations. More...

casacore::Bool	doCoordRandom_p

casacore::Vector < casacore::Double >	sepWorldCoord_p
	This vector houses the world coordinate values for the profile if it was from a separable axis. More...

casacore::Vector< T >	abcissa_p
	This vector is used to hold the abscissa values. More...

casacore::String	momAxisType_p
	This string tells us the name of the moment axis (VELO or FREQ etc) More...

casacore::uInt	nFailed_p
	This is the number of Gaussian fits that failed. More...

casacore::Double	integratedScaleFactor_p
	This scale factor is the increment along the moment axis applied so that units for the Integrated moment are like Jy/beam.km/s (or whatever is needed for the moment axis units) For non-linear velocities (e.g. More...

Detailed Description

template<class T>
class casa::MomentClip< T >

Computes simple clipped, and masked moments.

Intended use:

Public interface

Review Status

Date Reviewed:: yyyy/mm/dd

Prerequisite

MomentsBase
ImageMoments
MSMoments
casacore::LatticeApply
MomentCalcBase
casacore::LineCollapser

Synopsis

This concrete class is derived from the abstract base class MomentCalcBase which provides an interface layer to the ImageMoments or MSMoments driver class. ImageMoments or MSMoments creates a MomentClip object and passes it to the LatticeApply function, lineMultiApply. This function iterates through a given lattice, and invokes the multiProcess member function of MomentClip on each vector of pixels that it extracts from the input lattice. The multiProcess function returns a vector of moments which are inserted into the output lattices also supplied to the casacore::LatticeApply function.

MomentClip computes moments directly from a vector of pixel intensities extracted from the primary lattice. An optional pixel intensity inclusion or exclusion range can be applied. It can also compute a mask based on the inclusion or exclusion ranges applied to an ancilliary lattice (the ancilliary vector corresponding to the primary vector is extracted). This mask is then applied to the primary vector for moment computation (ImageMoments or MSMoments offers a smoothed version of the primary lattice as the ancilliary lattice)

The constructor takes an MomentsBase object that is actually an ImageMoments or an MSMoments object; the one that is constructing the MomentClip object of course. There is much control information embodied in the state of the ImageMoments or MSMoments object. This information is extracted by the MomentCalcBase class and passed on to MomentClip for consumption.

Note that the ancilliary lattice is only accessed if the ImageMoments or MSMoments object indicates that a pixel inclusion or exclusion range has been given as well as the pointer to the lattice having a non-zero value.

See the MomentsBase, ImageMoments, and MSMoments for discussion about the moments that are available for computation.

Example

This example comes from ImageMoments. outPt is a pointer block holding pointers to the output lattices. The ancilliary masking lattice is just a smoothed version of the input lattice.

// Construct desired moment calculator object.  Use it polymorphically
// via a pointer to the base class.  os_P is a casacore::LogIO object.
 
 MomentCalcBase<T>* pMomentCalculator = 0;
 if (clipMethod || smoothClipMethod) {
 pMomentCalculator = new MomentClip<T>(pSmoothedImage, *this, os_p, outPt.nelements());
 } else if (windowMethod) {
 pMomentCalculator = new MomentWindow<T>(pSmoothedImage, *this, os_p, outPt.nelements());
 } else if (fitMethod) {
 pMomentCalculator = new MomentFit<T>(*this, os_p, outPt.nelements());
 }
 
// Iterate optimally through the image, compute the moments, fill the output lattices
 
 casacore::LatticeApply<T>::lineMultiApply(outPt, *pInImage_p, *pMomentCalculator,
 momentAxis_p, pProgressMeter);
 delete pMomentCalculator;

Tip: Note that there are is assignment operator or copy constructor; Do not use the ones the system would generate either;

Definition at line 123 of file MomentClip.h.

Constructor & Destructor Documentation

template<class T >

casa::MomentClip< T >::MomentClip	(	shared_ptr< casacore::Lattice< T >>	pAncilliaryLattice,
		MomentsBase< T > &	iMom,
		casacore::LogIO &	os,
		const casacore::uInt	nLatticeOut
	)

Constructor.

The pointer is to an ancilliary lattice used as a mask. If no masking lattice is desired, the pointer value must be zero. We also need the ImageMoments or MSMoments object which is calling us, its logger, and the number of output lattices it has created.

template<class T >

virtual casa::MomentClip< T >::~MomentClip ( )

virtual

Destructor (does nothing).

Member Function Documentation

template<class T >

virtual casacore::Bool casa::MomentClip< T >::canHandleNullMask ( ) const

inlinevirtual

Can handle null mask.

Reimplemented from casacore::LineCollapser< T, T >.

Definition at line 157 of file MomentClip.h.

template<class T >

virtual void casa::MomentClip< T >::multiProcess	(	casacore::Vector< T > &	out,
		casacore::Vector< casacore::Bool > &	outMask,
		const casacore::Vector< T > &	in,
		const casacore::Vector< casacore::Bool > &	inMask,
		const casacore::IPosition &	pos
	)

virtual

This function returns a vector of numbers from each input vector.

the output vector contains the moments known to the ImageMoments or MSMoments object passed into the constructor.

Implements casacore::LineCollapser< T, T >.

template<class T >

virtual void casa::MomentClip< T >::process	(	T &	out,
		casacore::Bool &	outMask,
		const casacore::Vector< T > &	in,
		const casacore::Vector< casacore::Bool > &	inMask,
		const casacore::IPosition &	pos
	)