| 1 | //# ProfileFit1D.h: Class to fit profiles to vectors
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| 2 | //# Copyright (C) 2004
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| 3 | //# Associated Universities, Inc. Washington DC, USA.
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| 4 | //#
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| 5 | //# This library is free software; you can redistribute it and/or modify it
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| 6 | //# under the terms of the GNU Library General Public License as published by
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| 7 | //# the Free Software Foundation; either version 2 of the License, or (at your
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| 8 | //# option) any later version.
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| 9 | //#
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| 10 | //# This library is distributed in the hope that it will be useful, but WITHOUT
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| 11 | //# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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| 12 | //# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public
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| 13 | //# License for more details.
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| 14 | //#
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| 15 | //# You should have received a copy of the GNU Library General Public License
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| 16 | //# along with this library; if not, write to the Free Software Foundation,
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| 17 | //# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
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| 18 | //#
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| 19 | //# Correspondence concerning AIPS++ should be addressed as follows:
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| 20 | //# Internet email: aips2-request@nrao.edu.
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| 21 | //# Postal address: AIPS++ Project Office
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| 22 | //# National Radio Astronomy Observatory
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| 23 | //# 520 Edgemont Road
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| 24 | //# Charlottesville, VA 22903-2475 USA
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| 25 | //#
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| 26 | //# $Id: ProfileFit1D.h 20299 2008-04-03 05:56:44Z gervandiepen $
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| 27 |
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| 28 | #ifndef COMPONENTS_PROFILEFIT1D_H
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| 29 | #define COMPONENTS_PROFILEFIT1D_H
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| 30 |
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| 31 | //# Includes
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| 32 | #include <casa/aips.h>
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| 33 | #include <casa/Arrays/Vector.h>
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| 34 |
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| 35 | #include <components/SpectralComponents/SpectralList.h>
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| 36 | #include <components/SpectralComponents/SpectralFit.h>
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| 37 |
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| 38 | namespace casa {
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| 39 |
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| 40 | class SpectralElement;
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| 41 |
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| 42 | // <summary>
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| 43 | // Fit spectral components to a Vector of data
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| 44 | // </summary>
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| 45 |
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| 46 | // <use visibility=export>
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| 47 |
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| 48 | // <reviewed reviewer="" date="" tests="tProfileFit1D.cc">
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| 49 | // </reviewed>
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| 50 |
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| 51 | // <prerequisite>
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| 52 | // <li> <linkto class="SpectralElement">SpectralElement</linkto>
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| 53 | // <li> <linkto class="SpectralList">SpectralList</linkto>
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| 54 | // <li> <linkto class="SpectralFit">SpectralFit</linkto>
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| 55 | // </prerequisite>
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| 56 |
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| 57 | // <synopsis>
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| 58 | // Fit lists (held in class SpectralList) of SpectralElements to a
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| 59 | // Vector of data. Each SpectralElement can be one from a variety
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| 60 | // of types. The values of the parameters for each SpectralElement
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| 61 | // provide the initial starting guesses for the fitting process.
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| 62 | // Also, a SpectralElement object holds a mask indicating whether
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| 63 | // a parameter should be held fixed or solved for. After the
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| 64 | // fitting is done, a new SpectralList holding SpectralElements with
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| 65 | // the fitted parameters is created.
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| 66 | //
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| 67 | // For all the functions that return a status Bool, True is good. If
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| 68 | // False is returned, an error message can be recovered with function
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| 69 | // <src>errorMessage</src>, You should not proceed if False is returned.
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| 70 | // </synopsis>
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| 71 |
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| 72 | // <example>
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| 73 | // <srcblock>
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| 74 | // const uInt n = 512;
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| 75 | // Vector<Double> x(n);
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| 76 | // Vector<Double> y(n);
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| 77 | // Vector<Bool> m(n);
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| 78 | //
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| 79 | // // Code to fill data vectors x,y,m
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| 80 | //
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| 81 | // ProfileFit1D<Float> fitter;
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| 82 | // Bool ok = fitter.setData (x, y, m);
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| 83 | // ok = fitter.setGaussianElements (2);
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| 84 | // ok = fitter.fit();
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| 85 | // const SpectralList& fitList = fitter.getList(True);
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| 86 | // </srcblock>
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| 87 | // </example>
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| 88 |
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| 89 | // <todo asof="2004/07/10">
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| 90 | // <li> Add constraints
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| 91 | // </todo>
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| 92 | //
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| 93 | //
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| 94 | // <note role=caution>
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| 95 | // At the moment, because of templating limitations of the underlying
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| 96 | // fitting classes, you must use template type Double. This restriction
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| 97 | // will be lifted in the future.
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| 98 | // </note>
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| 99 | //
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| 100 |
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| 101 | template <class T> class ProfileFit1D
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| 102 | {
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| 103 | public:
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| 104 | // Constructor
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| 105 | ProfileFit1D();
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| 106 |
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| 107 | // Destructor
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| 108 | ~ProfileFit1D();
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| 109 |
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| 110 | // Copy constructor. Uses copy semantics.
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| 111 | ProfileFit1D(const ProfileFit1D& other);
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| 112 |
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| 113 | // Assignment operator. Uses copy semantics.
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| 114 | ProfileFit1D& operator=(const ProfileFit1D& other);
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| 115 |
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| 116 | // Set abcissa, ordinate, mask and weights. A True mask value means the
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| 117 | // data are good. If you don't specify the weights vector, all weights
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| 118 | // are assumed to be unity. If you don't specify a mask it will be
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| 119 | // created as all good.
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| 120 | // Status is returned, if False, error message can be recovered with <src>errorMessage</src>
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| 121 | // <group>
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| 122 | Bool setData (const Vector<Double>& x, const Vector<T>& y, const Vector<Bool>& mask,
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| 123 | const Vector<Double>& weight);
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| 124 | Bool setData (const Vector<Double>& x, const Vector<T>& y, const Vector<Bool>& mask);
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| 125 | Bool setData (const Vector<Double>& x, const Vector<T>& y);
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| 126 | // </group>
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| 127 |
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| 128 | // Set a SpectralList of SpectralElements to fit for.
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| 129 | // The SpectralElements in the list hold the
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| 130 | // initial estimates and must reflect the abcissa and ordinate units.
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| 131 | // They also contain the information about whether
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| 132 | // specific parameters are to be held fixed or allowed to vary in
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| 133 | // the fitting process.
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| 134 | // You can recover the list of elements with function getList.
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| 135 | void setElements (const SpectralList& list);
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| 136 |
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| 137 | // Set a SpectralList of Gaussian SpectralElements to fit for.
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| 138 | // The initial estimates for the Gaussians will be automatically determined.
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| 139 | // All of the parameters created by this function will be solved for
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| 140 | // by default. You can recover the list of elements with function getList.
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| 141 | // Status is returned, if False, error message can be
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| 142 | // recovered with <src>errorMessage</src>
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| 143 | Bool setGaussianElements (uInt nGauss);
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| 144 |
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| 145 | // Add new SpectralElement(s) to the SpectralList (can be empty)
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| 146 | // of SpectralElements to be fit for.
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| 147 | //<group>
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| 148 | void addElement (const SpectralElement& el);
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| 149 | void addElements (const SpectralList& list);
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| 150 | // </group>
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| 151 |
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| 152 | // Clear the SpectralList of elements to be fit for
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| 153 | void clearList ();
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| 154 |
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| 155 | // Set range mask. You can specify a number of ranges
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| 156 | // via a vector of start indices (or X values) and a vector of end
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| 157 | // indices (or X values). When argument insideIsGood is True,
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| 158 | // a mask will be created which
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| 159 | // will be True (good) inside the ranges and bad (False)
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| 160 | // outside of those ranges. When argument insideIsGood is False,
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| 161 | // the mask will be False (bad) inside the ranges and
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| 162 | // True (good) outside of those ranges. When the data are fit, a total
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| 163 | // mask is formed combining (via a logical AND) the
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| 164 | // data mask (setData) and this range mask.
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| 165 | // Status is returned, if False, error message can be recovered with <src>errorMessage</src>
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| 166 | // <group>
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| 167 | Bool setRangeMask (const Vector<uInt>& startIndex,
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| 168 | const Vector<uInt>& endIndex,
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| 169 | Bool insideIsGood=True);
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| 170 | Bool setRangeMask (const Vector<T>& startIndex,
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| 171 | const Vector<T>& endIndex,
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| 172 | Bool insideIsGood=True);
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| 173 | // </group>
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| 174 |
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| 175 | // Recover masks. These are the data mask (setData) the range
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| 176 | // mask (setRangeMask may be length zero) and the total
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| 177 | // mask combining the two.
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| 178 | // <group>
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| 179 | Vector<Bool> getDataMask() const {return itsDataMask;};
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| 180 | Vector<Bool> getRangeMask() const {return itsRangeMask;}
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| 181 | Vector<Bool> getTotalMask() const {return makeTotalMask();};
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| 182 | // </group>
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| 183 |
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| 184 | // Do the fit and return status. Returns convergence status.
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| 185 | // Error conditions in the solution process will generate
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| 186 | // an AipsError exception and you should catch these yourself.
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| 187 | Bool fit ();
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| 188 |
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| 189 | // Get Chi Squared of fit
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| 190 | Double getChiSquared () const {return itsFitter.chiSq();}
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| 191 |
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| 192 | // Get number of iterations for last fit
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| 193 | Double getNumberIterations () const {return itsFitter.nIterations();}
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| 194 |
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| 195 | // Recover the list of elements. You can get the elements
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| 196 | // as initially estimated (fit=False), or after fitting
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| 197 | // (fit=True). In the latter case, the SpectralElements
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| 198 | // hold the parameters and errors of the fit.
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| 199 | const SpectralList& getList (Bool fit=True) const;
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| 200 |
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| 201 | // Recover vectors for the estimate, fit and residual.
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| 202 | // If you don't specify which element, all elements are included
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| 203 | // If the Vectors are returned with zero length, it means an error
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| 204 | // condition exists (e.g. asking for fit before you do one). In this
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| 205 | // case an error message can be recovered with function <src>errorMessage</src>.
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| 206 | //<group>
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| 207 | Vector<T> getEstimate (Int which=-1) const;
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| 208 | Vector<T> getFit (Int which=-1) const;
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| 209 | Vector<T> getResidual (Int which=-1, Bool fit=True) const;
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| 210 | //</group>
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| 211 |
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| 212 | // Recover the error message
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| 213 | String errorMessage () const {return itsError;};
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| 214 |
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| 215 | private:
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| 216 | Vector<Double> itsX; // Abcissa (really should not be type T)
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| 217 | Vector<T> itsY; // Ordinate
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| 218 | Vector<Double> itsWeight; // Weights
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| 219 | Vector<Bool> itsDataMask; // Data mask
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| 220 | Vector<Bool> itsRangeMask; // Mask associated with ranges
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| 221 | //
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| 222 | SpectralList itsList; // List of elements to fit for
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| 223 | //
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| 224 | SpectralFit itsFitter; // Fitter
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| 225 | mutable String itsError; // Error message
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| 226 |
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| 227 | // Functions
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| 228 | Vector<Bool> makeTotalMask() const;
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| 229 | SpectralList getSubsetList (const SpectralList& list, Int which) const;
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| 230 | void checkType() const;
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| 231 | void copy(const ProfileFit1D<T>& other);
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| 232 | };
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| 233 |
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| 234 | } //#End casa namespace
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| 235 | #ifndef CASACORE_NO_AUTO_TEMPLATES
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| 236 | #include <components/SpectralComponents/ProfileFit1D.tcc>
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| 237 | #endif //# CASACORE_NO_AUTO_TEMPLATES
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| 238 | #endif
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