Computes moments from a windowed profile. More...

#include <MomentWindow.h>

Inheritance diagram for casa::MomentWindow< T >:

Public Types
using	AccumType = typename casacore::NumericTraits< T >::PrecisionType

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

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

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

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

	~MomentWindow ()
	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...

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...

virtual Bool	canHandleNullMask () const
	Can the process function in the derived class handle a null mask? If not, LatticeApply ensures that it'll always pass a filled mask vector, even if the lattice does not have a mask (in that case that mask contains all True values). More...

Private Member Functions
casacore::Bool	getAutoWindow (casacore::uInt &nFailed, casacore::Vector< casacore::Int > &window, const casacore::Vector< T > &x, const casacore::Vector< T > &y, const casacore::Vector< casacore::Bool > &mask, const T peakSNR, const T stdDeviation, const casacore::Bool doFit) const
	Automatically determine the spectral window. More...

casacore::Bool	_getBosmaWindow (casacore::Vector< casacore::Int > &window, const casacore::Vector< T > &y, const casacore::Vector< casacore::Bool > &mask, const T peakSNR, const T stdDeviation) const
	Automatically determine the spectral window via Bosma's algorithm. More...

casacore::Bool	setNSigmaWindow (casacore::Vector< casacore::Int > &window, const T pos, const T width, const casacore::Int nPts, const casacore::Int N) const
	Take the fitted Gaussian parameters and set an N-sigma window. 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

T	stdDeviation_p

T	peakSNR_p

casacore::Bool	doFit_p

casacore::IPosition	sliceShape_p

Additional Inherited Members
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::MomentWindow< T >

Computes moments from a windowed profile.

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 MomentWindow object and passes it to the LatticeApply function lineMultiApply. This function iterates through a given lattice, and invokes the multiProcess member function of MomentWindow on each profile 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.

MomentWindow computes moments from a subset of the pixels selected from the input profile. This subset is a simple index range, or window. The window is selected, for each profile, that is thought to surround the spectral feature of interest. This window can be found from the primary lattice, or from an ancilliary lattice (ImageMoments or MSMoments offers a smoothed version of the primary lattice as the ancilliary lattice). The moments are always computed from primary lattice data.

For each profile, the window can be found either interactively or automatically. There are two interactive methods. Either you just mark the window with the cursor, or you interactively fit a Gaussian to the profile and the +/- 3-sigma window is returned. There are two automatic methods. Either Bosma's converging mean algorithm is used, or an automatically fit Gaussian +/- 3-sigma window is returned.

The constructor takes an MomentsBase object that is actually an ImageMoments or an MSMoments object; the one that is constructing the MomentWindow 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 MomentWindow for consumption.

Note that the ancilliary lattice is only accessed if the pointer to it is non zero.

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. os_P is a casacore::LogIO object.

// Construct desired moment calculator object.  Use it polymorphically via 
// a pointer to the base class.
 
 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;

Motivation

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

Definition at line 140 of file MomentWindow.h.

Member Typedef Documentation

template<class T >

using casa::MomentWindow< T >::AccumType = typename casacore::NumericTraits<T>::PrecisionType

Definition at line 143 of file MomentWindow.h.

template<class T >

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

Definition at line 144 of file MomentWindow.h.

template<class T >

using casa::MomentWindow< T >::MaskIterator = casacore::Vector<casacore::Bool>::const_iterator

Definition at line 145 of file MomentWindow.h.

Constructor & Destructor Documentation

template<class T >

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

Constructor.

The pointer is to a lattice containing the masking lattice (created by ImageMoments or MSMoments). 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 >

casa::MomentWindow< T >::~MomentWindow ( )

Destructor (does nothing).

Member Function Documentation

template<class T >

casacore::Bool casa::MomentWindow< T >::_getBosmaWindow	(	casacore::Vector< casacore::Int > &	window,
		const casacore::Vector< T > &	y,
		const casacore::Vector< casacore::Bool > &	mask,
		const T	peakSNR,
		const T	stdDeviation
	)		const

private

Automatically determine the spectral window via Bosma's algorithm.

template<class T >

casacore::Bool casa::MomentWindow< T >::getAutoWindow	(	casacore::uInt &	nFailed,
		casacore::Vector< casacore::Int > &	window,
		const casacore::Vector< T > &	x,
		const casacore::Vector< T > &	y,
		const casacore::Vector< casacore::Bool > &	mask,
		const T	peakSNR,
		const T	stdDeviation,
		const casacore::Bool	doFit
	)		const

private

Automatically determine the spectral window.

template<class T >

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

virtual

This function is not implemented and throws an exception.

Implements casacore::LineCollapser< T, T >.

template<class T >

casacore::Bool casa::MomentWindow< T >::setNSigmaWindow	(	casacore::Vector< casacore::Int > &	window,
		const T	pos,
		const T	width,
		const casacore::Int	nPts,
		const casacore::Int	N
	)		const

private

Take the fitted Gaussian parameters and set an N-sigma window.

If the window is too small return a Fail condition.

Member Data Documentation

template<class T >

shared_ptr<casacore::Lattice<T> > casa::MomentWindow< T >::_ancilliaryLattice

private

Definition at line 178 of file MomentWindow.h.

template<class T >

casacore::Vector<T> casa::MomentWindow< T >::ancilliarySliceRef_p

private

Definition at line 183 of file MomentWindow.h.

template<class T >

casacore::Bool casa::MomentWindow< T >::doFit_p

private

Definition at line 186 of file MomentWindow.h.

template<class T >

MomentsBase<T>& casa::MomentWindow< T >::iMom_p

private

Definition at line 179 of file MomentWindow.h.

template<class T >

casacore::LogIO casa::MomentWindow< T >::os_p

private

Definition at line 180 of file MomentWindow.h.

template<class T >

T casa::MomentWindow< T >::peakSNR_p

private

Definition at line 185 of file MomentWindow.h.

template<class T >

const casacore::Vector<T>* casa::MomentWindow< T >::pProfileSelect_p

private

Definition at line 182 of file MomentWindow.h.

template<class T >

casacore::Vector<T> casa::MomentWindow< T >::selectedData_p

private

Definition at line 184 of file MomentWindow.h.

template<class T >

casacore::IPosition casa::MomentWindow< T >::sliceShape_p

private

Definition at line 187 of file MomentWindow.h.

template<class T >

T casa::MomentWindow< T >::stdDeviation_p

private

Definition at line 185 of file MomentWindow.h.

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

casa/code/imageanalysis/ImageAnalysis/MomentWindow.h

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class T> class casa::MomentWindow< T >

Intended use:

Review Status

Prerequisite

Synopsis

Example

Motivation

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class T>
class casa::MomentWindow< T >