This class is a base class for generating moments from an image or a spectral data. More...

#include <MomentCalcBase.h>

Inheritance diagram for casa::MomentsBase< T >:

Public Types
enum	MethodTypes { WINDOW, FIT, NMETHODS }
	The `enum MethodTypes` is provided for use with the `setWinFitMethod` function. More...

enum	MomentTypes { AVERAGE, INTEGRATED, WEIGHTED_MEAN_COORDINATE, WEIGHTED_DISPERSION_COORDINATE, MEDIAN, MEDIAN_COORDINATE, STANDARD_DEVIATION, RMS, ABS_MEAN_DEVIATION, MAXIMUM, MAXIMUM_COORDINATE, MINIMUM, MINIMUM_COORDINATE, NMOMENTS, DEFAULT }
	This `enum MomentTypes` is provided for use with the `setMoments` function. More...

Public Member Functions
virtual	~MomentsBase ()
	Destructor. More...

casacore::Bool	setMoments (const casacore::Vector< casacore::Int > &moments)
	Set the desired moments via an `casacore::Int` array. More...

virtual casacore::Bool	setMomentAxis (casacore::Int)=0
	Set the moment axis (0 relative). More...

casacore::Bool	setWinFitMethod (const casacore::Vector< casacore::Int > &method)
	The method by which you compute the moments is specified by calling (or not calling) the `setWinFitMethod` and `setSmoothMethod` functions. More...

virtual casacore::Bool	setSmoothMethod (const casacore::Vector< casacore::Int > &, const casacore::Vector< casacore::Int > &, const casacore::Vector< casacore::Quantum< casacore::Double > > &)=0
	This function invokes smoothing of the input image. More...

casacore::Bool	setSmoothMethod (const casacore::Vector< casacore::Int > &smoothAxes, const casacore::Vector< casacore::Int > &kernelTypes, const casacore::Vector< casacore::Double > &kernelWidths)

void	setInExCludeRange (const casacore::Vector< T > &include, const casacore::Vector< T > &exclude)
	You may specify a pixel intensity range as either one for which all pixels in that range are included in the moment calculation, or one for which all pixels in that range are excluded from the moment calculations. More...

void	setSnr (const T &peakSNR, const T &stdDeviation)
	This function is used to help assess whether a spectrum along the moment axis is all noise or not. More...

casacore::Bool	setSmoothOutName (const casacore::String &smOut)
	This is the output file name for the smoothed image. More...

void	setVelocityType (casacore::MDoppler::Types type)
	Set Velocity type. More...

void	resetError ()
	Reset argument error condition. More...

casacore::String	errorMessage () const
	Recover last error message. More...

virtual const casacore::CoordinateSystem &	coordinates ()=0
	Get CoordinateSystem. More...

virtual casacore::IPosition	getShape () const =0

casacore::Bool	shouldConvertToVelocity () const

Static Public Member Functions
static casacore::Vector < casacore::Int >	toMethodTypes (const casacore::String &methods)
	Helper function to convert a string containing a list of desired methods to the correct `casacore::Vector<casacore::Int>` required for the `setWinFitMethod` function. More...

Protected Member Functions
	MomentsBase (casacore::LogIO &os, casacore::Bool overWriteOutput=false, casacore::Bool showProgress=true)
	Constructor takes an image and a `casacore::LogIO` object for logging purposes. More...

void	_checkMethod ()
	Check that the combination of methods that the user has requested is valid casacore::List a handy dandy table if not. More...

void	_setIncludeExclude (casacore::Vector< T > &range, casacore::Bool &noInclude, casacore::Bool &noExclude, const casacore::Vector< T > &include, const casacore::Vector< T > &exclude)
	Take the user's data inclusion and exclusion data ranges and generate the range and Booleans to say what sort it is. More...

casacore::Bool	_setOutThings (casacore::String &suffix, casacore::Unit &momentUnits, const casacore::Unit &imageUnits, const casacore::String &momentAxisUnits, const casacore::Int moment, casacore::Bool convertToVelocity)
	Set the output image suffixes and units. More...

casacore::CoordinateSystem	_makeOutputCoordinates (casacore::IPosition &outShape, const casacore::CoordinateSystem &cSysIn, const casacore::IPosition &inShape, casacore::Int momentAxis, casacore::Bool removeAxis)
	Make output Coordinates. More...

Protected Attributes
casacore::LogIO	os_p

casacore::Bool	showProgress_p

casacore::Int	momentAxisDefault_p

T	peakSNR_p

T	stdDeviation_p

T	yMin_p

T	yMax_p

casacore::String	out_p

casacore::String	smoothOut_p

casacore::Bool	goodParameterStatus_p

casacore::Bool	doWindow_p

casacore::Bool	doFit_p

casacore::Bool	doSmooth_p

casacore::Bool	noInclude_p

casacore::Bool	noExclude_p

casacore::Bool	fixedYLimits_p

casacore::Int	momentAxis_p

casacore::Int	worldMomentAxis_p

casacore::Vector< casacore::Int >	kernelTypes_p

casacore::Vector < casacore::Quantity >	kernelWidths_p

casacore::Vector< casacore::Int >	moments_p

casacore::Vector< T >	selectRange_p

casacore::Vector< casacore::Int >	smoothAxes_p

casacore::Bool	overWriteOutput_p

casacore::String	error_p

casacore::Bool	convertToVelocity_p

casacore::MDoppler::Types	velocityType_p

Friends
class	MomentCalcBase< T >
	Note that if I don't put MomentCalcBase as a forward declaration and use instead "friend class MomentCalcBase<T>" The gnu compiler fails with a typedef problem. More...

Detailed Description

template<class T>
class casa::MomentsBase< T >

This class is a base class for generating moments from an image or a spectral data.

Intended use:

Public interface

Review Status

Date Reviewed:: yyyy/mm/dd

Prerequisite

ImageMoments
MSMoments
casacore::LatticeApply
MomentCalcBase

Etymology

This class is an abstract class to compute moments from images or spectral data.

Synopsis

The primary goal of MSMoments, ImageMoments, and MSMoments are to help spectral-line astronomers analyze their multi-dimensional images or spectral data (in the form of casacore::MeasurementSet) by generating moments of a specified axis. ImageMoments is a specialized class to generate moments from images, while MSMoments is designed properly for casacore::MeasurementSet input. MSMoments class is an abstract class that is inherited by the above two concrete classes. MomentsBase provides interface layer to the MomentCalculators so that functionalities in MomentCalculators can be shared with ImageMoments and MSMoments. The word "moment" is used loosely here. It refers to collapsing an axis to one pixel and putting the value of that pixel (for all of the other non-collapsed axes) to something computed from the data values along the moment axis. For example, take an RA-DEC-Velocity cube, collapse the velocity axis by computing the mean intensity at each RA-DEC pixel. This class and its inheritances offer many different moments and a variety of interactive and automatic ways to compute them.

Motivation

MSMoments is defined so that moments can be generated from both images and spectral data (in the form of casacore::MeasurementSet).

Definition at line 34 of file MomentCalcBase.h.

Member Enumeration Documentation

template<class T>

enum casa::MomentsBase::MethodTypes

The enum MethodTypes is provided for use with the setWinFitMethod function.

It gives the allowed moment methods which are available with this function. The use of these methods is described further with the description of this function as well as in the general documentation earlier.

Enumerator
WINDOW	Invokes the spectral windowing method.
FIT	Invokes Gaussian fitting.
NMETHODS

Definition at line 111 of file MomentsBase.h.

template<class T>

enum casa::MomentsBase::MomentTypes

This enum MomentTypes is provided for use with the setMoments function.

It gives the allowed moment types that you can ask for.

Enumerator
AVERAGE	The average intensity.
INTEGRATED	The integrated intensity.
WEIGHTED_MEAN_COORDINATE	The intensity weighted mean coordinate (usually velocity)
WEIGHTED_DISPERSION_COORDINATE	The intensity weighted coordinate (usually velocity) dispersion.
MEDIAN	The median intensity.
MEDIAN_COORDINATE	The median coordinate (usually velocity). Treat the spectrum as a probability distribution, generate the cumulative distribution, and find the coordinate corresponding to the 50% value.
STANDARD_DEVIATION	The standard deviation about the mean of the intensity.
RMS	The rms of the intensity.
ABS_MEAN_DEVIATION	The absolute mean deviation of the intensity.
MAXIMUM	The maximum value of the intensity.
MAXIMUM_COORDINATE	The coordinate (usually velocity) of the maximum value of the intensity.
MINIMUM	The minimum value of the intensity.
MINIMUM_COORDINATE	The coordinate (usually velocity) of the minimum value of the intensity.
NMOMENTS	Total number.
DEFAULT	Default value is the integrated intensity.

Definition at line 123 of file MomentsBase.h.

Constructor & Destructor Documentation

template<class T>

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

virtual

Destructor.

template<class T>

casa::MomentsBase< T >::MomentsBase	(	casacore::LogIO &	os,
		casacore::Bool	overWriteOutput = `false`,
		casacore::Bool	showProgress = `true`
	)

protected

Constructor takes an image and a casacore::LogIO object for logging purposes.

You specify whether output images are automatically overwritten if pre-existing, or whether an intercative choice dialog widget appears (overWriteOutput=F) You may also determine whether a progress meter is displayed or not.

Member Function Documentation

template<class T>

void casa::MomentsBase< T >::_checkMethod ( )

protected

Check that the combination of methods that the user has requested is valid casacore::List a handy dandy table if not.

template<class T>

casacore::CoordinateSystem casa::MomentsBase< T >::_makeOutputCoordinates	(	casacore::IPosition &	outShape,
		const casacore::CoordinateSystem &	cSysIn,
		const casacore::IPosition &	inShape,
		casacore::Int	momentAxis,
		casacore::Bool	removeAxis
	)

protected

Make output Coordinates.

template<class T>

void casa::MomentsBase< T >::_setIncludeExclude	(	casacore::Vector< T > &	range,
		casacore::Bool &	noInclude,
		casacore::Bool &	noExclude,
		const casacore::Vector< T > &	include,
		const casacore::Vector< T > &	exclude
	)

protected

Take the user's data inclusion and exclusion data ranges and generate the range and Booleans to say what sort it is.

template<class T>

casacore::Bool casa::MomentsBase< T >::_setOutThings	(	casacore::String &	suffix,
		casacore::Unit &	momentUnits,
		const casacore::Unit &	imageUnits,
		const casacore::String &	momentAxisUnits,
		const casacore::Int	moment,
		casacore::Bool	convertToVelocity
	)

protected

Set the output image suffixes and units.

template<class T>

virtual const casacore::CoordinateSystem& casa::MomentsBase< T >::coordinates ( )

pure virtual

Get CoordinateSystem.

Implemented in casa::ImageMoments< T >, and casa::ImageMoments< float >.

template<class T>

casacore::String casa::MomentsBase< T >::errorMessage ( ) const

inline

Recover last error message.

Definition at line 273 of file MomentsBase.h.

template<class T>

virtual casacore::IPosition casa::MomentsBase< T >::getShape ( ) const

pure virtual

Implemented in casa::ImageMoments< T >, and casa::ImageMoments< float >.

template<class T>

void casa::MomentsBase< T >::resetError ( )

inline

Reset argument error condition.

If you specify invalid arguments to one of the above functions, an internal flag will be set which will prevent the createMoments function, which is defined in its inheritances, from doing anything (should you have chosen to igmore the Boolean return values of the functions). This function allows you to reset that internal state to good.

Definition at line 270 of file MomentsBase.h.

template<class T>

void casa::MomentsBase< T >::setInExCludeRange	(	const casacore::Vector< T > &	include,
		const casacore::Vector< T > &	exclude
	)

You may specify a pixel intensity range as either one for which all pixels in that range are included in the moment calculation, or one for which all pixels in that range are excluded from the moment calculations.

One or the other of include and exclude must therefore be a zero length vector if you call this function. A return value of false indicates that you have given both an include and an exclude range. If you don't call this function, the default state of the class is to include all pixels.

template<class T>

virtual casacore::Bool casa::MomentsBase< T >::setMomentAxis ( casacore::Int )

pure virtual

Set the moment axis (0 relative).

A return value of false indicates that the axis was not contained in the image. If you don't call this function, the default state of the class is to set the moment axis to the spectral axis if it can find one. Otherwise an error will result.

Implemented in casa::ImageMoments< T >, and casa::ImageMoments< float >.

template<class T>

casacore::Bool casa::MomentsBase< T >::setMoments ( const casacore::Vector< casacore::Int > & moments )

Set the desired moments via an casacore::Int array.

Each casacore::Int specifies a different moment; the allowed values and their meanings are given by the enum MomentTypes. A return value of false indicates you asked for an out of range moment. If you don't call this function, the default state of the class is to request the integrated intensity.

template<class T>

virtual casacore::Bool casa::MomentsBase< T >::setSmoothMethod	(	const casacore::Vector< casacore::Int > &	,
		const casacore::Vector< casacore::Int > &	,
		const casacore::Vector< casacore::Quantum< casacore::Double > > &
	)

pure virtual

This function invokes smoothing of the input image.

Give casacore::Int arrays for the axes (0 relative) to be smoothed and the smoothing kernel types (use the enum KernelTypes) for each axis. Give a casacore::Double array for the widths (full width for BOXCAR and full width at half maximum for GAUSSIAN) in pixels of the smoothing kernels for each axis. For HANNING smoothing, you always get the quarter-half-quarter kernel (no matter what you might ask for). A return value of false indicates that you have given an inconsistent or invalid set of smoothing parameters. If you don't call this function the default state of the class is to do no smoothing. The kernel types are specified with the casacore::VectorKernel::KernelTypes enum

Implemented in casa::ImageMoments< T >, and casa::ImageMoments< float >.

template<class T>

casacore::Bool casa::MomentsBase< T >::setSmoothMethod	(	const casacore::Vector< casacore::Int > &	smoothAxes,
		const casacore::Vector< casacore::Int > &	kernelTypes,
		const casacore::Vector< casacore::Double > &	kernelWidths
	)

template<class T>

casacore::Bool casa::MomentsBase< T >::setSmoothOutName ( const casacore::String & smOut )

This is the output file name for the smoothed image.

It can be useful to have access this to this image when trying to get the pixel include or exclude range correct for the smooth-clip method. The default state of the class is to not output the smoothed image.

template<class T>

void casa::MomentsBase< T >::setSnr	(	const T &	peakSNR,
		const T &	stdDeviation
	)

This function is used to help assess whether a spectrum along the moment axis is all noise or not.

If it is all noise, there is not a lot of point to trying to computing the moment. peakSNR is the signal-to-noise ratio of the peak value in the spectrum below which the spectrum is considered pure noise. stdDeviation is the standard deviation of the noise for the input image.

Default values for one or the other parameter are indicated by giving zero.

The default state of the class then is to set peakSNR=3 and/or to work out the noise level from a Gaussian fit to a histogram (above 25%) of the entire image (it is very hard to get an accurate estimate of the noise a single spectrum).

template<class T>

void casa::MomentsBase< T >::setVelocityType ( casacore::MDoppler::Types type )

Set Velocity type.

This is used for moments for which the moment axis is a spectral axis for which the coordinate is traditionally presented in km/s You can select the velocity definition. The default state of the class is to use the radio definition.

template<class T>

casacore::Bool casa::MomentsBase< T >::setWinFitMethod ( const casacore::Vector< casacore::Int > & method )

The method by which you compute the moments is specified by calling (or not calling) the setWinFitMethod and setSmoothMethod functions.

The default state of the class is to compute directly on all (or some according to setInExClude) of the pixels in the spectrum. Calling these functions modifies the computational state to something more complicated.

The setWinMethod function requires an casacore::Int array as its argument. Each casacore::Int specifies a different method that you can invoke (either separately or in combination). The allowed values and their meanings are given by the enum MethodTypes.

Both the windowing and fitting methods have interactive modes. The windowing method also has a fitting flavour, so if you set both MomentsBase::WINDOW and MomentsBase::FIT, you would be invoking the windowing method but determining the window by fitting Gaussians automatically (as MomentsBase::INTERACTIVE) was not given.

If you don't call this function, then neither the windowing nor fitting methods are invoked. A return value of false indicates that you asked for an illegal method.

template<class T>

casacore::Bool casa::MomentsBase< T >::shouldConvertToVelocity ( ) const

inline

Definition at line 288 of file MomentsBase.h.

template<class T>

static casacore::Vector<casacore::Int> casa::MomentsBase< T >::toMethodTypes ( const casacore::String & methods )

static

Helper function to convert a string containing a list of desired methods to the correct casacore::Vector<casacore::Int> required for the setWinFitMethod function.

This may be usful if your user interface involves strings rather than integers. A new value is added to the output vector (which is resized appropriately) if any of the substrings "window", "fit" or "interactive" (actually "win", "box" and "inter" will do) is present.

Friends And Related Function Documentation

template<class T>

friend class MomentCalcBase< T >

friend

Note that if I don't put MomentCalcBase as a forward declaration and use instead "friend class MomentCalcBase<T>" The gnu compiler fails with a typedef problem.

But I can't solve it with say typedef MomentCalcBase<T> gpp_type; because you can only do a typedef with an actual type, not a T !

Definition at line 104 of file MomentsBase.h.