[91] | 1 | //#---------------------------------------------------------------------------
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[890] | 2 | //# Fitter.cc: A Fitter class for spectra
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[91] | 3 | //#--------------------------------------------------------------------------
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| 4 | //# Copyright (C) 2004
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[125] | 5 | //# ATNF
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[91] | 6 | //#
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| 7 | //# This program is free software; you can redistribute it and/or modify it
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| 8 | //# under the terms of the GNU General Public License as published by the Free
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option)
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| 10 | //# any later version.
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| 11 | //#
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| 12 | //# This program is distributed in the hope that it will be useful, but
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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| 15 | //# Public License for more details.
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| 16 | //#
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| 17 | //# You should have received a copy of the GNU General Public License along
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc.,
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
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| 20 | //#
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| 21 | //# Correspondence concerning this software should be addressed as follows:
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| 22 | //# Internet email: Malte.Marquarding@csiro.au
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| 23 | //# Postal address: Malte Marquarding,
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| 24 | //# Australia Telescope National Facility,
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| 25 | //# P.O. Box 76,
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| 26 | //# Epping, NSW, 2121,
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| 27 | //# AUSTRALIA
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| 28 | //#
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[891] | 29 | //# $Id: STFitter.cpp 1387 2007-07-26 16:00:22Z TakTsutsumi $
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[91] | 30 | //#---------------------------------------------------------------------------
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[125] | 31 | #include <casa/aips.h>
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[91] | 32 | #include <casa/Arrays/ArrayMath.h>
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| 33 | #include <casa/Arrays/ArrayLogical.h>
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| 34 | #include <scimath/Fitting.h>
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| 35 | #include <scimath/Fitting/LinearFit.h>
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| 36 | #include <scimath/Functionals/CompiledFunction.h>
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| 37 | #include <scimath/Functionals/CompoundFunction.h>
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| 38 | #include <scimath/Functionals/Gaussian1D.h>
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| 39 | #include <scimath/Functionals/Polynomial.h>
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| 40 | #include <scimath/Mathematics/AutoDiff.h>
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| 41 | #include <scimath/Mathematics/AutoDiffMath.h>
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| 42 | #include <scimath/Fitting/NonLinearFitLM.h>
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| 43 | #include <components/SpectralComponents/SpectralEstimate.h>
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| 44 |
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[894] | 45 | #include "STFitter.h"
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| 46 |
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[91] | 47 | using namespace asap;
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[125] | 48 | using namespace casa;
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[91] | 49 |
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[890] | 50 | Fitter::Fitter()
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[91] | 51 | {
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| 52 | }
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| 53 |
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[890] | 54 | Fitter::~Fitter()
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[91] | 55 | {
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[517] | 56 | reset();
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[91] | 57 | }
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| 58 |
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[890] | 59 | void Fitter::clear()
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[91] | 60 | {
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[517] | 61 | for (uInt i=0;i< funcs_.nelements();++i) {
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| 62 | delete funcs_[i]; funcs_[i] = 0;
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| 63 | }
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[612] | 64 | funcs_.resize(0,True);
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[517] | 65 | parameters_.resize();
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[1232] | 66 | fixedpar_.resize();
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[517] | 67 | error_.resize();
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| 68 | thefit_.resize();
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| 69 | estimate_.resize();
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| 70 | chisquared_ = 0.0;
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[91] | 71 | }
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[517] | 72 |
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[890] | 73 | void Fitter::reset()
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[91] | 74 | {
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[517] | 75 | clear();
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| 76 | x_.resize();
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| 77 | y_.resize();
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| 78 | m_.resize();
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[91] | 79 | }
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| 80 |
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| 81 |
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[890] | 82 | bool Fitter::computeEstimate() {
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[517] | 83 | if (x_.nelements() == 0 || y_.nelements() == 0)
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| 84 | throw (AipsError("No x/y data specified."));
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[91] | 85 |
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[517] | 86 | if (dynamic_cast<Gaussian1D<Float>* >(funcs_[0]) == 0)
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| 87 | return false;
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| 88 | uInt n = funcs_.nelements();
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| 89 | SpectralEstimate estimator(n);
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| 90 | estimator.setQ(5);
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| 91 | Int mn,mx;
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| 92 | mn = 0;
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| 93 | mx = m_.nelements()-1;
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| 94 | for (uInt i=0; i<m_.nelements();++i) {
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| 95 | if (m_[i]) {
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| 96 | mn = i;
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| 97 | break;
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[108] | 98 | }
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[517] | 99 | }
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| 100 | for (uInt j=m_.nelements()-1; j>=0;--j) {
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| 101 | if (m_[j]) {
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| 102 | mx = j;
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| 103 | break;
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[108] | 104 | }
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[517] | 105 | }
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[1067] | 106 | //mn = 0+x_.nelements()/10;
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| 107 | //mx = x_.nelements()-x_.nelements()/10;
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[517] | 108 | estimator.setRegion(mn,mx);
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| 109 | //estimator.setWindowing(True);
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| 110 | SpectralList listGauss = estimator.estimate(x_, y_);
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| 111 | parameters_.resize(n*3);
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| 112 | Gaussian1D<Float>* g = 0;
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| 113 | for (uInt i=0; i<n;i++) {
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| 114 | g = dynamic_cast<Gaussian1D<Float>* >(funcs_[i]);
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| 115 | if (g) {
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| 116 | (*g)[0] = listGauss[i].getAmpl();
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| 117 | (*g)[1] = listGauss[i].getCenter();
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| 118 | (*g)[2] = listGauss[i].getFWHM();
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[91] | 119 | }
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[517] | 120 | }
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| 121 | estimate_.resize();
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| 122 | listGauss.evaluate(estimate_,x_);
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| 123 | return true;
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[91] | 124 | }
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| 125 |
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[890] | 126 | std::vector<float> Fitter::getEstimate() const
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[91] | 127 | {
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[517] | 128 | if (estimate_.nelements() == 0)
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| 129 | throw (AipsError("No estimate set."));
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| 130 | std::vector<float> stlout;
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| 131 | estimate_.tovector(stlout);
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| 132 | return stlout;
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[91] | 133 | }
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| 134 |
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| 135 |
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[890] | 136 | bool Fitter::setExpression(const std::string& expr, int ncomp)
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[91] | 137 | {
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[517] | 138 | clear();
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| 139 | if (expr == "gauss") {
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| 140 | if (ncomp < 1) throw (AipsError("Need at least one gaussian to fit."));
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| 141 | funcs_.resize(ncomp);
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| 142 | for (Int k=0; k<ncomp; ++k) {
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| 143 | funcs_[k] = new Gaussian1D<Float>();
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| 144 | }
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| 145 | } else if (expr == "poly") {
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| 146 | funcs_.resize(1);
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| 147 | funcs_[0] = new Polynomial<Float>(ncomp);
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| 148 | } else {
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| 149 | cerr << " compiled functions not yet implemented" << endl;
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| 150 | //funcs_.resize(1);
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| 151 | //funcs_[0] = new CompiledFunction<Float>();
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| 152 | //funcs_[0]->setFunction(String(expr));
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| 153 | return false;
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| 154 | }
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| 155 | return true;
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[91] | 156 | }
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| 157 |
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[890] | 158 | bool Fitter::setData(std::vector<float> absc, std::vector<float> spec,
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[91] | 159 | std::vector<bool> mask)
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| 160 | {
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| 161 | x_.resize();
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| 162 | y_.resize();
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| 163 | m_.resize();
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| 164 | // convert std::vector to casa Vector
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| 165 | Vector<Float> tmpx(absc);
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| 166 | Vector<Float> tmpy(spec);
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| 167 | Vector<Bool> tmpm(mask);
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| 168 | AlwaysAssert(tmpx.nelements() == tmpy.nelements(), AipsError);
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| 169 | x_ = tmpx;
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| 170 | y_ = tmpy;
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| 171 | m_ = tmpm;
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| 172 | return true;
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| 173 | }
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| 174 |
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[890] | 175 | std::vector<float> Fitter::getResidual() const
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[91] | 176 | {
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| 177 | if (residual_.nelements() == 0)
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| 178 | throw (AipsError("Function not yet fitted."));
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| 179 | std::vector<float> stlout;
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| 180 | residual_.tovector(stlout);
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| 181 | return stlout;
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| 182 | }
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| 183 |
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[890] | 184 | std::vector<float> Fitter::getFit() const
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[91] | 185 | {
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| 186 | Vector<Float> out = thefit_;
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| 187 | std::vector<float> stlout;
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| 188 | out.tovector(stlout);
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| 189 | return stlout;
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| 190 |
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| 191 | }
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| 192 |
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[890] | 193 | std::vector<float> Fitter::getErrors() const
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[91] | 194 | {
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| 195 | Vector<Float> out = error_;
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| 196 | std::vector<float> stlout;
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| 197 | out.tovector(stlout);
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| 198 | return stlout;
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| 199 | }
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| 200 |
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[890] | 201 | bool Fitter::setParameters(std::vector<float> params)
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[91] | 202 | {
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| 203 | Vector<Float> tmppar(params);
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| 204 | if (funcs_.nelements() == 0)
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| 205 | throw (AipsError("Function not yet set."));
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| 206 | if (parameters_.nelements() > 0 && tmppar.nelements() != parameters_.nelements())
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| 207 | throw (AipsError("Number of parameters inconsistent with function."));
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[1232] | 208 | if (parameters_.nelements() == 0) {
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[91] | 209 | parameters_.resize(tmppar.nelements());
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[1232] | 210 | if (tmppar.nelements() != fixedpar_.nelements()) {
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| 211 | fixedpar_.resize(tmppar.nelements());
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| 212 | fixedpar_ = False;
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| 213 | }
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| 214 | }
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[91] | 215 | if (dynamic_cast<Gaussian1D<Float>* >(funcs_[0]) != 0) {
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| 216 | uInt count = 0;
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| 217 | for (uInt j=0; j < funcs_.nelements(); ++j) {
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| 218 | for (uInt i=0; i < funcs_[j]->nparameters(); ++i) {
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| 219 | (funcs_[j]->parameters())[i] = tmppar[count];
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| 220 | parameters_[count] = tmppar[count];
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| 221 | ++count;
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| 222 | }
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| 223 | }
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| 224 | } else if (dynamic_cast<Polynomial<Float>* >(funcs_[0]) != 0) {
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| 225 | for (uInt i=0; i < funcs_[0]->nparameters(); ++i) {
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| 226 | parameters_[i] = tmppar[i];
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| 227 | (funcs_[0]->parameters())[i] = tmppar[i];
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| 228 | }
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| 229 | }
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[1232] | 230 | // reset
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| 231 | if (params.size() == 0) {
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| 232 | parameters_.resize();
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| 233 | fixedpar_.resize();
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| 234 | }
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[91] | 235 | return true;
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| 236 | }
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| 237 |
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[890] | 238 | bool Fitter::setFixedParameters(std::vector<bool> fixed)
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[91] | 239 | {
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| 240 | if (funcs_.nelements() == 0)
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| 241 | throw (AipsError("Function not yet set."));
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[1232] | 242 | if (fixedpar_.nelements() > 0 && fixed.size() != fixedpar_.nelements())
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[91] | 243 | throw (AipsError("Number of mask elements inconsistent with function."));
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[1232] | 244 | if (fixedpar_.nelements() == 0) {
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| 245 | fixedpar_.resize(parameters_.nelements());
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| 246 | fixedpar_ = False;
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| 247 | }
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[91] | 248 | if (dynamic_cast<Gaussian1D<Float>* >(funcs_[0]) != 0) {
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| 249 | uInt count = 0;
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| 250 | for (uInt j=0; j < funcs_.nelements(); ++j) {
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| 251 | for (uInt i=0; i < funcs_[j]->nparameters(); ++i) {
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[1232] | 252 | funcs_[j]->mask(i) = !fixed[count];
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| 253 | fixedpar_[count] = fixed[count];
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[91] | 254 | ++count;
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| 255 | }
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| 256 | }
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| 257 | } else if (dynamic_cast<Polynomial<Float>* >(funcs_[0]) != 0) {
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| 258 | for (uInt i=0; i < funcs_[0]->nparameters(); ++i) {
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[1232] | 259 | fixedpar_[i] = fixed[i];
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| 260 | funcs_[0]->mask(i) = !fixed[i];
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[91] | 261 | }
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| 262 | }
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| 263 | return true;
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| 264 | }
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| 265 |
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[890] | 266 | std::vector<float> Fitter::getParameters() const {
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[91] | 267 | Vector<Float> out = parameters_;
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| 268 | std::vector<float> stlout;
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| 269 | out.tovector(stlout);
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| 270 | return stlout;
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| 271 | }
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| 272 |
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[890] | 273 | std::vector<bool> Fitter::getFixedParameters() const {
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[108] | 274 | Vector<Bool> out(parameters_.nelements());
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| 275 | if (fixedpar_.nelements() == 0) {
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[1232] | 276 | return std::vector<bool>();
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[108] | 277 | //throw (AipsError("No parameter mask set."));
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| 278 | } else {
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| 279 | out = fixedpar_;
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| 280 | }
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| 281 | std::vector<bool> stlout;
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| 282 | out.tovector(stlout);
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| 283 | return stlout;
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[91] | 284 | }
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| 285 |
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[890] | 286 | float Fitter::getChisquared() const {
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[91] | 287 | return chisquared_;
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| 288 | }
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| 289 |
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[890] | 290 | bool Fitter::fit() {
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[517] | 291 | NonLinearFitLM<Float> fitter;
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| 292 | CompoundFunction<Float> func;
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[612] | 293 |
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| 294 | uInt n = funcs_.nelements();
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[517] | 295 | for (uInt i=0; i<n; ++i) {
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| 296 | func.addFunction(*funcs_[i]);
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| 297 | }
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[612] | 298 |
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[517] | 299 | fitter.setFunction(func);
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| 300 | fitter.setMaxIter(50+n*10);
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| 301 | // Convergence criterium
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| 302 | fitter.setCriteria(0.001);
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[612] | 303 |
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[517] | 304 | // Fit
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| 305 | Vector<Float> sigma(x_.nelements());
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| 306 | sigma = 1.0;
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[890] | 307 |
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[517] | 308 | parameters_.resize();
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| 309 | parameters_ = fitter.fit(x_, y_, sigma, &m_);
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[1067] | 310 | if ( !fitter.converged() ) {
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| 311 | return false;
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| 312 | }
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[517] | 313 | std::vector<float> ps;
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| 314 | parameters_.tovector(ps);
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| 315 | setParameters(ps);
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[612] | 316 |
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[517] | 317 | error_.resize();
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| 318 | error_ = fitter.errors();
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[612] | 319 |
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[517] | 320 | chisquared_ = fitter.getChi2();
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[890] | 321 |
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[517] | 322 | residual_.resize();
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| 323 | residual_ = y_;
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| 324 | fitter.residual(residual_,x_);
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| 325 | // use fitter.residual(model=True) to get the model
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| 326 | thefit_.resize(x_.nelements());
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| 327 | fitter.residual(thefit_,x_,True);
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| 328 | return true;
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| 329 | }
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[483] | 330 |
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[1387] | 331 | bool Fitter::lfit() {
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| 332 | LinearFit<Float> fitter;
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| 333 | CompoundFunction<Float> func;
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[483] | 334 |
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[1387] | 335 | uInt n = funcs_.nelements();
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| 336 | for (uInt i=0; i<n; ++i) {
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| 337 | func.addFunction(*funcs_[i]);
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| 338 | }
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| 339 |
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| 340 | fitter.setFunction(func);
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| 341 | //fitter.setMaxIter(50+n*10);
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| 342 | // Convergence criterium
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| 343 | //fitter.setCriteria(0.001);
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| 344 |
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| 345 | // Fit
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| 346 | Vector<Float> sigma(x_.nelements());
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| 347 | sigma = 1.0;
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| 348 |
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| 349 | parameters_.resize();
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| 350 | parameters_ = fitter.fit(x_, y_, sigma, &m_);
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| 351 | std::vector<float> ps;
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| 352 | parameters_.tovector(ps);
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| 353 | setParameters(ps);
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| 354 |
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| 355 | error_.resize();
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| 356 | error_ = fitter.errors();
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| 357 |
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| 358 | chisquared_ = fitter.getChi2();
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| 359 |
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| 360 | residual_.resize();
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| 361 | residual_ = y_;
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| 362 | fitter.residual(residual_,x_);
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| 363 | // use fitter.residual(model=True) to get the model
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| 364 | thefit_.resize(x_.nelements());
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| 365 | fitter.residual(thefit_,x_,True);
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| 366 | return true;
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| 367 | }
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| 368 |
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[890] | 369 | std::vector<float> Fitter::evaluate(int whichComp) const
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| 370 | {
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[517] | 371 | std::vector<float> stlout;
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[890] | 372 | uInt idx = uInt(whichComp);
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[517] | 373 | Float y;
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| 374 | if ( idx < funcs_.nelements() ) {
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| 375 | for (uInt i=0; i<x_.nelements(); ++i) {
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| 376 | y = (*funcs_[idx])(x_[i]);
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| 377 | stlout.push_back(float(y));
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| 378 | }
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| 379 | }
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| 380 | return stlout;
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| 381 | }
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[483] | 382 |
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