//# SpectralElement.h: Describes (a set of related) spectral lines
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//# $Id: GaussianMultipletSpectralElement.h 21451 2014-06-10 07:48:08Z gervandiepen $

#ifndef COMPONENTS_GAUSSIANMULTIPLETSPECTRALELEMENT_H
#define COMPONENTS_GAUSSIANMULTIPLETSPECTRALELEMENT_H

#include <casa/Arrays/Matrix.h>
#include <components/SpectralComponents/CompiledSpectralElement.h>

namespace casa { //# NAMESPACE CASA - BEGIN

	class GaussianSpectralElement;

// <summary>
// Describes a multiplet of Gaussian shaped spectral lines
// </summary>

// <use visibility=export>

// <reviewed reviewer="" date="yyyy/mm/dd" tests="tSpectralFit" demos="">
// </reviewed>

// <prerequisite>
//   <li> <linkto class=SpectralElement>SpectralElement</linkto> module
//   <li> <linkto class=GaussianSpectralElement>GaussianSpectralElement</linkto> module
//   <li> <linkto class=CompiledSpectralElement>CompiledSpectralElement</linkto> module
// </prerequisite>
//
// <etymology>
// From Gaussian and multiplet and spectral line and element
// </etymology>
//
// <synopsis>
// The GaussianMultipletSpectralElement class describes a multiplet
// of Gaussian shaped spectral lines for describing spectral profile.
//
// Relationships between Gaussians in the multiplet must be specified.
// Any combination of one or more of fixed relationships between line
// center offsets, line amplitude ratios, and/or line width ratios can
// be specified between a single reference line in the multiplet and
// other (non-reference) lines in the multiplet. The constructor
// takes a Vector of GaussianSpectralElements which describes the estimates
// of the n Gaussians in the multiplet. These objects themselves are not
// used in the fitting, but are used only to create the function that describes
// the multiplet. The first element in this Vector represents the reference line
// to which parameters of the other lines are constrained. In addition, the
// constructor takes an n-1 x 3 Matrix<Double> describing the fixed relationships
// between the reference line and the other lines in the multiplet. Each ith row
// describes the fixed relationship(s) between the (i+1)th and the zeroth
// (reference) Gaussian. The first element of each row describes the ratio of
// amplitudes between the (i+1)th and reference Gaussian, the second element
// describes the difference between the center locations of the (i+1)th and
// reference Gaussian, and the third represents the ratio of the FWHM of the
// (i+1)th and reference Gaussian. A value of 0 for any of these indicates there
// is no fixed relationship for that parameter. At least one value must be non-zero
// for each row and any combination of elements (including all of them) can be
// non-zero for any row in this matrix. The values of parameters of non-reference
// lines in the input vector that are constrained to the reference line are
// implicitly ignored and set in the constructor according to the specified
// constraint. If any of the parameters of the reference line are specified as
// fixed, the corresponding parameters of any non-reference lines which have the
// corresponding parameters constrained to the reference line are also implicitly
// fixed. Fixing a parameter in a non-reference line that is constrained to the
// corresponding parameter of the reference line that is not fixed will cause an
// exception.
// </synopsis>
//
// <example>
// This is how to specify a doublet in which the only constraint is that the amplitudes
// between the lines must be fixed, the first Gaussian must have an ampliute of 0.6 times
// the zeroth (reference) Gaussian. Other than that, all other parameters can
// vary during the fit:

// GaussianSpectralElement reference(5, 25, 16);
// // The amplitude value of first is ignored because of the relationship to the
// // reference, but it still must be specified in the constructor and must be
// // non-zero or an exception will be thrown.
// GaussianSpectralElement first(1, 40, 17);
// Vector<GaussianSpectralElement> pair(2);
// pair[0] = reference;
// pair[1] = first;
// // initialize constraints matrix to have nothing constrained (all values 0)
// Matrix<Double> fixedRel(1, 3, 0);
// // Set the ratio of amplitudes between the first and reference (zeroth) line
// // to be 0.6.
// fixedRel[0][0] = 0.6
// GaussianMultipletSpectralElement doublet(pair,"",fixedRel);
// </example>
//
// <motivation>
// To allow specifying constraints between different Gaussian spectral
// lines for fitting, eg to support fitting of doublets.
// </motivation>

class GaussianMultipletSpectralElement: public CompiledSpectralElement {
public:

	// Construct a Gaussian multiplet. The values of non-reference (non-zeroth)
	// estimates will be automatically adjusted if there is a fixed relationship
	// between a non-reference Gaussian parameter and the corresponding reference
	// Gaussian parameter.
	GaussianMultipletSpectralElement(
		const vector<GaussianSpectralElement>& estimates,
		const Matrix<Double>& fixedRelationships
	);

	// copy semantics
	GaussianMultipletSpectralElement(
		const GaussianMultipletSpectralElement& other
	);

	~GaussianMultipletSpectralElement();

	SpectralElement* clone() const;

	// copy semantics
	GaussianMultipletSpectralElement &operator=(
		const GaussianMultipletSpectralElement& other
	);

	Bool operator==(
		const GaussianMultipletSpectralElement& other
	) const;

	// get the gaussians
	const vector<GaussianSpectralElement>& getGaussians() const;

	// get the constraints matrix
	const Matrix<Double>& getConstraints() const;

	//<group>
	// These methods must be public because the architecture of
	// the class hierarchy requires it and set() and setError()
	// must be accessible by fitters. However, it is strongly
	// recommended that other classes not call these methods for
	// object configuration but rather set them implicitly at
	// construction via the Vector<GaussianSpectralElement>
	// passed to the constructor.
	void set(const Vector<Double>& param);

	void setError(const Vector<Double> &err);

	void fix(const Vector<Bool>& fix);
	// </group>
	// Save to a record.
	Bool toRecord(RecordInterface& out) const;

private:
	vector<GaussianSpectralElement> _gaussians;
	Matrix<Double> _constraints;
	Matrix<uInt> _paramIndices;
};

ostream &operator<<(ostream &os, const GaussianMultipletSpectralElement &elem);

} //# NAMESPACE CASA - END

#endif